Optimal segmentation and packaging process

DOEpatents

Kostelnik, K.M.; Meservey, R.H.; Landon, M.D.

1999-08-10

A process for improving packaging efficiency uses three dimensional, computer simulated models with various optimization algorithms to determine the optimal segmentation process and packaging configurations based on constraints including container limitations. The present invention is applied to a process for decontaminating, decommissioning (D and D), and remediating a nuclear facility involving the segmentation and packaging of contaminated items in waste containers in order to minimize the number of cuts, maximize packaging density, and reduce worker radiation exposure. A three-dimensional, computer simulated, facility model of the contaminated items are created. The contaminated items are differentiated. The optimal location, orientation and sequence of the segmentation and packaging of the contaminated items is determined using the simulated model, the algorithms, and various constraints including container limitations. The cut locations and orientations are transposed to the simulated model. The contaminated items are actually segmented and packaged. The segmentation and packaging may be simulated beforehand. In addition, the contaminated items may be cataloged and recorded. 3 figs.

Development and Use of an Open-Source, User-Friendly Package to Simulate Voltammetry Experiments

ERIC Educational Resources Information Center

Wang, Shuo; Wang, Jing; Gao, Yanjing

2017-01-01

An open-source electrochemistry simulation package has been developed that simulates the electrode processes of four reaction mechanisms and two typical electroanalysis techniques: cyclic voltammetry and chronoamperometry. Unlike other open-source simulation software, this package balances the features with ease of learning and implementation and…

Kinematics Simulation Analysis of Packaging Robot with Joint Clearance

NASA Astrophysics Data System (ADS)

Zhang, Y. W.; Meng, W. J.; Wang, L. Q.; Cui, G. H.

2018-03-01

Considering the influence of joint clearance on the motion error, repeated positioning accuracy and overall position of the machine, this paper presents simulation analysis of a packaging robot — 2 degrees of freedom(DOF) planar parallel robot based on the characteristics of high precision and fast speed of packaging equipment. The motion constraint equation of the mechanism is established, and the analysis and simulation of the motion error are carried out in the case of turning the revolute clearance. The simulation results show that the size of the joint clearance will affect the movement accuracy and packaging efficiency of the packaging robot. The analysis provides a reference point of view for the packaging equipment design and selection criteria and has a great significance on the packaging industry automation.

Shifting Perspectives: Using Complexity Theory to Anticipate Strategic Surprise

DTIC Science & Technology

2015-08-08

Master’s Thesis 3. DATES COVERED (From - To) 21-07-2014 to 11-06-2015 4. TITLE AND SUBTITLE SHIFTING PERSPECTIVES: USING COMPLEXITY THEORY TO...SCA Socio-Cultural Analysis SNA Social Network Analysis TCO Transnational Criminal Organization U.S. United States WMD Weapons of Mass...the 2014 Russian invasion of Ukraine, and the rise of the Islamic State following the war in Iraq. Considering the amount of money , time, and emphasis

Phase III trial comparing 3-6 months of adjuvant FOLFOX4/XELOX in stage II-III colon cancer: safety and compliance in the TOSCA trial.

PubMed

Lonardi, S; Sobrero, A; Rosati, G; Di Bartolomeo, M; Ronzoni, M; Aprile, G; Massida, B; Scartozzi, M; Banzi, M; Zampino, M G; Pasini, F; Marchetti, P; Cantore, M; Zaniboni, A; Rimassa, L; Ciuffreda, L; Ferrari, D; Barni, S; Zagonel, V; Maiello, E; Rulli, E; Labianca, R

2016-11-01

Six months of oxaliplatin-based adjuvant chemotherapy is standard of care for radically resected stage III colon cancer and an accepted option for high-risk stage II. A shorter duration of therapy, if equally efficacious, would be advantageous for patients and Health-Care Systems. TOSCA ['Randomized trial investigating the role of FOLFOX-4 or XELOX (3 versus 6 months) regimen duration and bevacizumab as adjuvant therapy for patients with stage II/III colon cancer] is an open-label, phase III, multicenter, noninferiority trial randomizing patients with high-risk stage II or stage III radically resected colon cancer to receive 3 months (arm 3 m) versus 6 months (arm 6 m) of FOLFOX4/XELOX. Primary end-point was relapse-free survival. We present here safety and compliance data. From June 2007 to March 2013, 3759 patients were accrued from 130 Italian sites, 64% receiving FOLFOX4 and 36% XELOX in either arm. Treatment completion rate without any modification was 35% versus 12% and with delays or dose reduction 52% versus 44% in arm 3 and 6 m. Treatment was permanently discontinued in 8% (arm 3 m) and 33% (arm 6 m). In arm 6 m, 50% of patients discontinuing treatment did so after completing 80% of planned program. Grade 3+ toxicities were higher in arm 6 m than that in 3 m. Grade 2+ neuropathy was 31.2% versus 8.8% (P < 0.0001) while grade 3+ was 8.4 versus 1.3 (P < 0.0001), in arm 3 and 6 m. Seven deaths within 30 days from last treatment administration in arm 6 m and three deaths in arm 3 m were observed (0.3% versus 0.1%, P = 0.34). TOSCA is the first trial comparing 3 versus 6 months of adjuvant chemotherapy completing accrual within the international initiative of treatment duration evaluation (International Duration Evaluation of Adjuvant, IDEA). High compliance to treatment in control arm will allow a correct assessment of potential differences between the two treatment durations. NCT00646607. © The Author 2016. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Signalling product healthiness through symbolic package cues: Effects of package shape and goal congruence on consumer behaviour.

PubMed

van Ooijen, Iris; Fransen, Marieke L; Verlegh, Peeter W J; Smit, Edith G

2017-02-01

Three studies show that product packaging shape serves as a cue that communicates healthiness of food products. Inspired by embodiment accounts, we show that packaging that simulates a slim body shape acts as a symbolic cue for product healthiness (e.g., low in calories), as opposed to packaging that simulates a wide body shape. Furthermore, we show that the effect of slim package shape on consumer behaviour is goal dependent. Whereas simulation of a slim (vs. wide) body shape increases choice likelihood and product attitude when consumers have a health-relevant shopping goal, packaging shape does not affect these outcomes when consumers have a hedonic shopping goal. In Study 3, we adopt a realistic shopping paradigm using a shelf with authentic products, and find that a slim (as opposed to wide) package shape increases on-shelf product recognition and increases product attitude for healthy products. We discuss results and implications regarding product positioning and the packaging design process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Prone to feel guilty: Self-evaluative emotions in alcohol-dependence.

PubMed

Grynberg, Delphine; de Timary, Philippe; Van Heuverswijn, Aude; Maurage, Pierre

2017-10-01

Prior research has repeatedly shown that alcohol-dependence is associated with interpersonal difficulties. However, guilt and shame, two crucial self-evaluative emotions triggered by the transgression of social norms, have not been explored among alcohol-dependent individuals despite their important role in psychiatric disorders. The present study thus aimed to investigate whether alcohol-dependence is associated with greater proneness to negatively evaluate one's own behaviors (guilt) or the entire self (shame). 25 alcohol-dependent individuals (ADI) and 25 matched healthy individuals completed a scenario-based inventory (TOSCA-3), requiring from participants to rate the extent they will react to each scenario in terms of (contextualized) guilt and shame. Participants also completed a list of adjectives related to the frequency at which they generally experience (uncontextualized) guilt and shame (PFQ-2). When controlling for possible confounds (i.e., depression and anxiety), ADI reported greater proneness to experience guilt at the TOSCA-3 (η 2 =.22) compared to healthy individuals. This study is the first to show that alcohol-dependence is associated with greater contextualized guilt-proneness, i.e., negative evaluation of one's own behaviors that transgress social norms. Therefore, these results reinforce the relevance of social disorders in alcohol-dependence and indicate that ADI may benefit of therapeutic programs to avoid a generalization of guilt towards shame. Copyright © 2017 Elsevier B.V. All rights reserved.

Self-conscious affects: their adaptive Functions and relationship to depressive mood.

PubMed

Uji, Masayo; Kitamura, Toshinori; Nagata, Toshiaki

2011-01-01

This study used a structural equation model to examine the influence of resilience on the four self-conscious affects (guilt-proneness, shame-proneness, externalization, and detachment) assessed in the Test of Self-Conscious Affect-3 (TOSCA-3) and their impact on depressive mood. Our subject population consisted of 447 Japanese university students. The first analysis explored which TOSCA-3 affects help an individual adapt to stressful situations. The concept of "resilience" was used as an indicator to evaluate the adaptive functions. We based this on the assumption that an individual with higher resilience is able to use more adaptive affects. In the second analysis, taking the above relationship between resilience and the self-conscious affects into consideration, we examined how those variables as well as a negative life event are related to depressive mood. To assess the resilience level and depressive mood, we adopted the Resilience Scale (RS) and Self-rating Depressive Scale (SDS), respectively. The first analysis showed that the more resilient an individual was, the more prone they were to "detachment" and the less "shame" they experienced. The level of resilience did not have a significant effect on "guilt" or "externalization." In the second analysis we found that "resilience" had a direct inverse effect on depressive mood that was also mediated by "shame" and "detachment." We discuss how the particular self-conscious affects comprising each adaptive function are related to depressive mood.

Influence of different materials on the thermal behavior of a CDIP-8 ceramic package

NASA Astrophysics Data System (ADS)

Weide, Kirsten; Keck, Christian

1999-08-01

The temperature distribution inside a package is determined by the heat transfer from the package to the ambient, depending on the heat conductivities of the different used materials. With the help of finite element simulations the thermal behavior of the package can be characterized. In precise simulations convection and radiation effects have to be taken into account. In this paper the influence of different materials like the ceramic, the pin and die attach material and adhesive material between the chip and the die attach on the thermal resistance of the ceramic package will be investigated. A finite element model of the ceramic package including a voltage regulator on the chip was created. The simulations were carried out with the finite element program ANSYS. An easy way to take the radiation effect into account, which normally is difficult to handle in the simulation, will be shown. The results of the simulations are verified by infrared measurements. A comparison of the thermal resistance between the best case and worst case for different package materials was done. The thermal conductivity of the ceramic material shows the strongest influence on the thermal resistance.

pysimm: A Python Package for Simulation of Molecular Systems

NASA Astrophysics Data System (ADS)

Fortunato, Michael; Colina, Coray

pysimm, short for python simulation interface for molecular modeling, is a python package designed to facilitate the structure generation and simulation of molecular systems through convenient and programmatic access to object-oriented representations of molecular system data. This poster presents core features of pysimm and design philosophies that highlight a generalized methodology for incorporation of third-party software packages through API interfaces. The integration with the LAMMPS simulation package is explained to demonstrate this methodology. pysimm began as a back-end python library that powered a cloud-based application on nanohub.org for amorphous polymer simulation. The extension from a specific application library to general purpose simulation interface is explained. Additionally, this poster highlights the rapid development of new applications to construct polymer chains capable of controlling chain morphology such as molecular weight distribution and monomer composition.

INDOOR AIR QUALITY AND INHALATION EXPOSURE - SIMULATION TOOL KIT

EPA Science Inventory

A Microsoft Windows-based indoor air quality (IAQ) simulation software package is presented. Named Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short, this package complements and supplements existing IAQ simulation programs and is desi...

Clinical Relevance Versus Statistical Significance: Aman and Colleagues Respond to Editorial.

PubMed

Aman, Michael G; Arnold, L Eugene; Barterian, Justin A

2018-05-01

We would like to respond to the thought-provoking editorial by Dr. Jon McClellan 1 regarding our article "Clinical Implications from the Treatment of Severe Childhood Aggression (TOSCA) Study: A Re-Analysis and Integration of Findings," published in the December 2017 issue of JAACAP. 2 We address some issues on which we partially disagree, and comment on convergence of opinion. Copyright © 2018 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

Real time flight simulation methodology

NASA Technical Reports Server (NTRS)

Parrish, E. A.; Cook, G.; Mcvey, E. S.

1977-01-01

Substitutional methods for digitization, input signal-dependent integrator approximations, and digital autopilot design were developed. The software framework of a simulator design package is described. Included are subroutines for iterative designs of simulation models and a rudimentary graphics package.

A MODFLOW Infiltration Device Package for Simulating Storm Water Infiltration.

PubMed

Jeppesen, Jan; Christensen, Steen

2015-01-01

This article describes a MODFLOW Infiltration Device (INFD) Package that can simulate infiltration devices and their two-way interaction with groundwater. The INFD Package relies on a water balance including inflow of storm water, leakage-like seepage through the device faces, overflow, and change in storage. The water balance for the device can be simulated in multiple INFD time steps within a single MODFLOW time step, and infiltration from the device can be routed through the unsaturated zone to the groundwater table. A benchmark test shows that the INFD Package's analytical solution for stage computes exact results for transient behavior. To achieve similar accuracy by the numerical solution of the MODFLOW Surface-Water Routing (SWR1) Process requires many small time steps. Furthermore, the INFD Package includes an improved representation of flow through the INFD sides that results in lower infiltration rates than simulated by SWR1. The INFD Package is also demonstrated in a transient simulation of a hypothetical catchment where two devices interact differently with groundwater. This simulation demonstrates that device and groundwater interaction depends on the thickness of the unsaturated zone because a shallow groundwater table (a likely result from storm water infiltration itself) may occupy retention volume, whereas a thick unsaturated zone may cause a phase shift and a change of amplitude in groundwater table response to a change of infiltration. We thus find that the INFD Package accommodates the simulation of infiltration devices and groundwater in an integrated manner on small as well as large spatial and temporal scales. © 2014, National Ground Water Association.

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

NASA Astrophysics Data System (ADS)

Butterworth, J. M.; Butterworth, S.

2003-06-01

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.

GneimoSim: A Modular Internal Coordinates Molecular Dynamics Simulation Package

PubMed Central

Larsen, Adrien B.; Wagner, Jeffrey R.; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-01-01

The Generalized Newton Euler Inverse Mass Operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this paper we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. PMID:25263538

GneimoSim: a modular internal coordinates molecular dynamics simulation package.

PubMed

Larsen, Adrien B; Wagner, Jeffrey R; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-12-05

The generalized Newton-Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. © 2014 Wiley Periodicals, Inc.

GillesPy: A Python Package for Stochastic Model Building and Simulation.

PubMed

Abel, John H; Drawert, Brian; Hellander, Andreas; Petzold, Linda R

2016-09-01

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community.

GillesPy: A Python Package for Stochastic Model Building and Simulation

PubMed Central

Abel, John H.; Drawert, Brian; Hellander, Andreas; Petzold, Linda R.

2017-01-01

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community. PMID:28630888

Feelings of guilt and shame in patients with rheumatoid arthritis.

PubMed

Ten Klooster, Peter M; Christenhusz, Lieke C A; Taal, Erik; Eggelmeijer, Frank; van Woerkom, Jan-Maarten; Rasker, Johannes J

2014-07-01

This study aims to determine whether patients with rheumatoid arthritis (RA) experience more general feelings of guilt and shame than their peers without RA and to examine possible correlates of guilt and shame in RA. In a cross-sectional survey study, 85 out-patients with RA (77 % female; median disease duration, 11 years) and 59 peer controls completed the Experience of Shame Scale (ESS) and the Test of Self-Conscious Affect (TOSCA). Patients additionally completed measures of health status, self-efficacy, cognitive emotion regulation, and numerical rating scales for life satisfaction and happiness. Patients and peer controls were well matched for sociodemographic characteristics. No significant differences between patients and controls were found for guilt or different types of shame as measured with the TOSCA or ESS. In multivariate analyses, female patients reported more feelings of bodily shame and higher guilt proneness, while younger patients reported more character and bodily shame. Worse social functioning and more self-blaming coping strategies were the strongest independent correlates of shame. Shame proneness was only independently associated with more self-blame, whereas guilt proneness was only associated with female sex. None of the physical aspects of the disease, including pain and physical functioning, correlated with feelings of guilt and shame. Patients with longstanding RA do not experience more general feelings of shame or guilt than their peers without RA. Shame and guilt in RA is primarily associated with demographic and psychosocial characteristics and not with physical severity of the disease.

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

PubMed

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.

The effect of a simulation training package on skill acquisition for duplex arterial stenosis detection.

PubMed

Jaffer, Usman; Normahani, Pasha; Singh, Prashant; Aslam, Mohammed; Standfield, Nigel J

2015-01-01

In vascular surgery, duplex ultrasonography is a valuable diagnostic tool in patients with peripheral vascular disease, and there is increasing demand for vascular surgeons to be able to perform duplex scanning. This study evaluates the role of a novel simulation training package on vascular ultrasound (US) skill acquisition. A total of 19 novices measured predefined stenosis in a simulated pulsatile vessel using both peak systolic velocity ratio (PSVR) and diameter reduction (DR) methods before and after a short period of training using a simulated training package. The training package consisted of a simulated pulsatile vessel phantom, a set of instructional videos, duplex ultrasound objective structured assessment of technical skills (DUOSATS) tool, and a portable US scanner. Quantitative metrics (procedure time, percentage error using PSVR and DR methods, DUOSAT scores, and global rating scores) before and after training were compared. Subjects spent a median time of 144 mins (IQR: 60-195) training using the simulation package. Subjects exhibited statistically significant improvements when comparing pretraining and posttraining DUOSAT scores (pretraining = 17 [16-19.3] vs posttraining = 30 [27.8-31.8]; p < 0.01), global rating score (pretraining = 1 [1-2] vs posttraining = 4 [3.8-4]; p < 0.01), percentage error using both the DR (pretraining = 12.6% [9-29.6] vs posttraining = 10.3% [8.9-11.1]; p = 0.03) and PSVR (pretraining = 60% [40-60] vs posttraining = 20% [6.7-20]; p < 0.01) methods. In this study, subjects with no previous practical US experience developed the ability to both acquire and interpret arterial duplex images in a pulsatile simulated phantom following a short period of goal direct training using a simulation training package. A simulation training package may be a valuable tool for integration into a vascular training program. However, further work is needed to explore whether these newly attained skills are translated into clinical assessment. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

Validation of thermal effects of LED package by using Elmer finite element simulation method

NASA Astrophysics Data System (ADS)

Leng, Lai Siang; Retnasamy, Vithyacharan; Mohamad Shahimin, Mukhzeer; Sauli, Zaliman; Taniselass, Steven; Bin Ab Aziz, Muhamad Hafiz; Vairavan, Rajendaran; Kirtsaeng, Supap

2017-02-01

The overall performance of the Light-emitting diode, LED package is critically affected by the heat attribution. In this study, open source software - Elmer FEM has been utilized to study the thermal analysis of the LED package. In order to perform a complete simulation study, both Salome software and ParaView software were introduced as Pre and Postprocessor. The thermal effect of the LED package was evaluated by this software. The result has been validated with commercially licensed software based on previous work. The percentage difference from both simulation results is less than 5% which is tolerable and comparable.

Documentation of a computer program to simulate aquifer-system compaction using the modular finite-difference ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Prudic, David E.

1988-01-01

The process of permanent compaction is not routinely included in simulations of groundwater flow. To simulate storage changes from both elastic and inelastic compaction, a computer program was written for use with the U. S. Geological Survey modular finite-difference groundwater flow model. The new program is called the Interbed-Storage Package. In the Interbed-Storage Package, elastic compaction or expansion is assumed to be proportional to change in head. The constant of proportionality is the product of skeletal component of elastic specific storage and thickness of the sediments. Similarly, inelastic compaction is assumed to be proportional to decline in head. The constant of proportionality is the product of the skeletal component of inelastic specific storage and the thickness of the sediments. Storage changes are incorporated into the groundwater flow model by adding an additional term to the flow equation. Within a model time step, the package appropriately apportions storage changes between elastic and inelastic components on the basis of the relation of simulated head to the previous minimum head. Another package that allows for a time-varying specified-head boundary is also documented. This package was written to reduce the data requirements for test simulations of the Interbed-Storage Package. (USGS)

A user's guide to the ssWavelets package

Treesearch

J.H. ​Gove

2017-01-01

ssWavelets is an R package that is meant to be used in conjunction with the sampSurf package (Gove, 2012) to perform wavelet decomposition on the results of a sampling surface simulation. In general, the wavelet filter decomposes the sampSurf simulation results by scale (distance), with each scale corresponding to a different level of the...

Simulating the Effects of Financial Aid Packages on College Student Stopout, Reenrollment Spells, and Graduation Chances

ERIC Educational Resources Information Center

DesJardins, Stephen L.; McCall, Brian P.

2010-01-01

This study investigates the impact that different financial aid packages have on student stopout, reenrollment, and graduation probabilities. The authors simulate how various financial aid packaging regimes affect the occurrence and timing of these events. Their findings indicate that the number and duration of enrollment and stopout spells affect…

Migration and sorption phenomena in packaged foods.

PubMed

Gnanasekharan, V; Floros, J D

1997-10-01

Rapidly developing analytical capabilities and continuously evolving stringent regulations have made food/package interactions a subject of intense research. This article focuses on: (1) the migration of package components such as oligomers and monomers, processing aids, additives, and residual reactants in to packaged foods, and (2) sorption of food components such as flavors, lipids, and moisture into packages. Principles of diffusion and thermodynamics are utilized to describe the mathematics of migration and sorption. Mathematical models are developed from first principles, and their applicability is illustrated using numerical simulations and published data. Simulations indicate that available models are system (polymer-penetrant) specific. Furthermore, some models best describe the early stages of migration/sorption, whereas others should be used for the late stages of these phenomena. Migration- and/or sorption-related problems with respect to glass, metal, paper-based and polymeric packaging materials are discussed, and their importance is illustrated using published examples. The effects of migrating and absorbed components on food safety, quality, and the environment are presented for various foods and packaging materials. The impact of currently popular packaging techniques such as microwavable, ovenable, and retortable packaging on migration and sorption are discussed with examples. Analytical techniques for investigating migration and sorption phenomena in food packaging are critically reviewed, with special emphasis on the use and characteristics of food-simulating liquids (FSLs). Finally, domestic and international regulations concerning migration in packaged foods, and their impact on food packaging is briefly presented.

A User-Friendly Software Package for HIFU Simulation

NASA Astrophysics Data System (ADS)

Soneson, Joshua E.

2009-04-01

A freely-distributed, MATLAB (The Mathworks, Inc., Natick, MA)-based software package for simulating axisymmetric high-intensity focused ultrasound (HIFU) beams and their heating effects is discussed. The package (HIFU_Simulator) consists of a propagation module which solves the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation and a heating module which solves Pennes' bioheat transfer (BHT) equation. The pressure, intensity, heating rate, temperature, and thermal dose fields are computed, plotted, the output is released to the MATLAB workspace for further user analysis or postprocessing.

spMC: an R-package for 3D lithological reconstructions based on spatial Markov chains

NASA Astrophysics Data System (ADS)

Sartore, Luca; Fabbri, Paolo; Gaetan, Carlo

2016-09-01

The paper presents the spatial Markov Chains (spMC) R-package and a case study of subsoil simulation/prediction located in a plain site of Northeastern Italy. spMC is a quite complete collection of advanced methods for data inspection, besides spMC implements Markov Chain models to estimate experimental transition probabilities of categorical lithological data. Furthermore, simulation methods based on most known prediction methods (as indicator Kriging and CoKriging) were implemented in spMC package. Moreover, other more advanced methods are available for simulations, e.g. path methods and Bayesian procedures, that exploit the maximum entropy. Since the spMC package was developed for intensive geostatistical computations, part of the code is implemented for parallel computations via the OpenMP constructs. A final analysis of this computational efficiency compares the simulation/prediction algorithms by using different numbers of CPU cores, and considering the example data set of the case study included in the package.

Ohmic Heating of an Electrically Conductive Food Package.

PubMed

Kanogchaipramot, Kanyawee; Tongkhao, Kullanart; Sajjaanantakul, Tanaboon; Kamonpatana, Pitiya

2016-12-01

Ohmic heating through an electrically conductive food package is a new approach to heat the food and its package as a whole after packing to avoid post-process contamination and to serve consumer needs for convenience. This process has been successfully completed using polymer film integrated with an electrically conductive film to form a conductive package. Orange juice packed in the conductive package surrounded with a conductive medium was pasteurized in an ohmic heater. A mathematical model was developed to simulate the temperature distribution within the package and its surroundings. A 3-D thermal-electric model showed heating uniformity inside the food package while the hot zone appeared in the orange juice adjacent to the conductive film. The accuracy of the model was determined by comparing the experimental results with the simulated temperature and current drawn; the model showed good agreement between the actual and simulated results. An inoculated pack study using Escherichia coli O157:H7 indicated negative growth of viable microorganisms at the target and over target lethal process temperatures, whereas the microorganism was present in the under target temperature treatment. Consequently, our developed ohmic heating system with conductive packaging offers potential for producing safe food. © 2016 Institute of Food Technologists®.

DNA Packaging in Bacteriophage: Is Twist Important?

PubMed Central

Spakowitz, Andrew James; Wang, Zhen-Gang

2005-01-01

We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with rotation exhibits a spool-like character that is consistent with experimental and previous theoretical work, whereas feeding without rotation results in a folded conformation inconsistent with a spool conformation. The chain segment density shows a layered structure, which is more pronounced for packaging with rotation. However, in both cases, the conformation is marked by frequent jumps of the polymer chain from layer to layer, potentially influencing the ability to disentangle during subsequent ejection. Ejection simulations with and without Brownian forces show that Brownian forces are necessary to achieve complete ejection of the polymer chain in the absence of external forces. PMID:15805174

DNA packaging in bacteriophage: is twist important?

PubMed

Spakowitz, Andrew James; Wang, Zhen-Gang

2005-06-01

We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with rotation exhibits a spool-like character that is consistent with experimental and previous theoretical work, whereas feeding without rotation results in a folded conformation inconsistent with a spool conformation. The chain segment density shows a layered structure, which is more pronounced for packaging with rotation. However, in both cases, the conformation is marked by frequent jumps of the polymer chain from layer to layer, potentially influencing the ability to disentangle during subsequent ejection. Ejection simulations with and without Brownian forces show that Brownian forces are necessary to achieve complete ejection of the polymer chain in the absence of external forces.

Differential maneuvering simulator data reduction and analysis software

NASA Technical Reports Server (NTRS)

Beasley, G. P.; Sigman, R. S.

1972-01-01

A multielement data reduction and analysis software package has been developed for use with the Langley differential maneuvering simulator (DMS). This package, which has several independent elements, was developed to support all phases of DMS aircraft simulation studies with a variety of both graphical and tabular information. The overall software package is considered unique because of the number, diversity, and sophistication of the element programs available for use in a single study. The purpose of this paper is to discuss the overall DMS data reduction and analysis package by reviewing the development of the various elements of the software, showing typical results that can be obtained, and discussing how each element can be used.

Documentation of a computer program to simulate transient leakage from confining units using the modular finite-difference, ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Leahy, P.P.; Navoy, A.S.

1994-01-01

Transient leakage into or out of a compressible fine-grained confining unit results from ground- water storage changes within the unit. The computer program described in this report provides a new method of simulating transient leakage using the U.S. Geological Survey modular finite- difference ground-water flow model (MODFLOW). The new program is referred to as the Transient- Leakage Package. The Transient-Leakage Package solves integrodifferential equations that describe flow across the upper and lower boundaries of confining units. For each confining unit, vertical hydraulic conductivity, thickness, and specific storage are specified in input arrays. These properties can vary from cell to cell and the confining unit need not be present at all locations in the grid; however, the confining units must be bounded above and below by model layers in which head is calculated or specified. The package was used in an example problem to simulate drawdown around a pumping well in a system with two aquifers separated by a confining unit. For drawdown values in excess of 1 centimeter, the solution using the new package closely matched an exact analytical solution. The problem also was simulated without the new package by using a separate model layer to represent the confining unit. That simulation was refined by using two model layers to represent the confining unit. The simulation using the Transient-Leakage Package was faster and more accurate than either of the simulations using model layers to represent the confining unit.

Shipboard communications center modernization network simulation report

DOT National Transportation Integrated Search

1995-08-01

Commercially available simulation packages were investigated to determine their suitability for modeling the USCG Cutter Communications Center (CCC). The suitability of a candidate package was based upon it meeting the operational goals and hardware ...

Effectiveness of Simulation in a Hybrid and Online Networking Course.

ERIC Educational Resources Information Center

Cameron, Brian H.

2003-01-01

Reports on a study that compares the performance of students enrolled in two sections of a Web-based computer networking course: one utilizing a simulation package and the second utilizing a static, graphical software package. Analysis shows statistically significant improvements in performance in the simulation group compared to the…

User's guide to the Variably Saturated Flow (VSF) process to MODFLOW

USGS Publications Warehouse

Thoms, R. Brad; Johnson, Richard L.; Healy, Richard W.

2006-01-01

A new process for simulating three-dimensional (3-D) variably saturated flow (VSF) using Richards' equation has been added to the 3-D modular finite-difference ground-water model MODFLOW. Five new packages are presented here as part of the VSF Process--the Richards' Equation Flow (REF1) Package, the Seepage Face (SPF1) Package, the Surface Ponding (PND1) Package, the Surface Evaporation (SEV1) Package, and the Root Zone Evapotranspiration (RZE1) Package. Additionally, a new Adaptive Time-Stepping (ATS1) Package is presented for use by both the Ground-Water Flow (GWF) Process and VSF. The VSF Process allows simulation of flow in unsaturated media above the ground-water zone and facilitates modeling of ground-water/surface-water interactions. Model performance is evaluated by comparison to an analytical solution for one-dimensional (1-D) constant-head infiltration (Dirichlet boundary condition), field experimental data for a 1-D constant-head infiltration, laboratory experimental data for two-dimensional (2-D) constant-flux infiltration (Neumann boundary condition), laboratory experimental data for 2-D transient drainage through a seepage face, and numerical model results (VS2DT) of a 2-D flow-path simulation using realistic surface boundary conditions. A hypothetical 3-D example case also is presented to demonstrate the new capability using periodic boundary conditions (for example, daily precipitation) and varied surface topography over a larger spatial scale (0.133 square kilometer). The new model capabilities retain the modular structure of the MODFLOW code and preserve MODFLOW's existing capabilities as well as compatibility with commercial pre-/post-processors. The overall success of the VSF Process in simulating mixed boundary conditions and variable soil types demonstrates its utility for future hydrologic investigations. This report presents a new flow package implementing the governing equations for variably saturated ground-water flow, four new boundary condition packages unique to unsaturated flow, the Adaptive Time-Stepping Package for use with both the GWF Process and the new VSF Process, detailed descriptions of the input and output files for each package, and six simulation examples verifying model performance.

Halley's Comet and Beyond.

ERIC Educational Resources Information Center

Sneider, Cary; DeVore, Edna

1986-01-01

Reviews software packages under these headings: (1) simulations of experiments; (2) space flight simulators; (3) planetariums; (4) space adventure games; and (5) drill and practice packages (designed for testing purposes or for helping students learn basic astronomy vocabulary). (JN)

Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

PubMed

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2012-07-15

The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

MODFLOW-2000 Ground-Water Model?User Guide to the Subsidence and Aquifer-System Compaction (SUB) Package

USGS Publications Warehouse

Hoffmann, Jörn; Leake, S.A.; Galloway, D.L.; Wilson, Alicia M.

2003-01-01

This report documents a computer program, the Subsidence and Aquifer-System Compaction (SUB) Package, to simulate aquifer-system compaction and land subsidence using the U.S. Geological Survey modular finite-difference ground-water flow model, MODFLOW-2000. The SUB Package simulates elastic (recoverable) compaction and expansion, and inelastic (permanent) compaction of compressible fine-grained beds (interbeds) within the aquifers. The deformation of the interbeds is caused by head or pore-pressure changes, and thus by changes in effective stress, within the interbeds. If the stress is less than the preconsolidation stress of the sediments, the deformation is elastic; if the stress is greater than the preconsolidation stress, the deformation is inelastic. The propagation of head changes within the interbeds is defined by a transient, one-dimensional (vertical) diffusion equation. This equation accounts for delayed release of water from storage or uptake of water into storage in the interbeds. Properties that control the timing of the storage changes are vertical hydraulic diffusivity and interbed thickness. The SUB Package supersedes the Interbed Storage Package (IBS1) for MODFLOW, which assumes that water is released from or taken into storage with changes in head in the aquifer within a single model time step and, therefore, can be reasonably used to simulate only thin interbeds. The SUB Package relaxes this assumption and can be used to simulate time-dependent drainage and compaction of thick interbeds and confining units. The time-dependent drainage can be turned off, in which case the SUB Package gives results identical to those from IBS1. Three sample problems illustrate the usefulness of the SUB Package. One sample problem verifies that the package works correctly. This sample problem simulates the drainage of a thick interbed in response to a step change in head in the adjacent aquifer and closely matches the analytical solution. A second sample problem illustrates the effects of seasonally varying discharge and recharge to an aquifer system with a thick interbed. A third sample problem simulates a multilayered regional ground-water basin. Model input files for the third sample problem are included in the appendix.

Literacity: A multimedia adult literacy package combining NASA technology, recursive ID theory, and authentic instruction theory

NASA Technical Reports Server (NTRS)

Willis, Jerry; Willis, Dee Anna; Walsh, Clare; Stephens, Elizabeth; Murphy, Timothy; Price, Jerry; Stevens, William; Jackson, Kevin; Villareal, James A.; Way, Bob

1994-01-01

An important part of NASA's mission involves the secondary application of its technologies in the public and private sectors. One current application under development is LiteraCity, a simulation-based instructional package for adults who do not have functional reading skills. Using fuzzy logic routines and other technologies developed by NASA's Information Systems Directorate and hypermedia sound, graphics, and animation technologies the project attempts to overcome the limited impact of adult literacy assessment and instruction by involving the adult in an interactive simulation of real-life literacy activities. The project uses a recursive instructional development model and authentic instruction theory. This paper describes one component of a project to design, develop, and produce a series of computer-based, multimedia instructional packages. The packages are being developed for use in adult literacy programs, particularly in correctional education centers. They use the concepts of authentic instruction and authentic assessment to guide development. All the packages to be developed are instructional simulations. The first is a simulation of 'finding a friend a job.'

Three-Dimensional (3D) Nanometrology Based on Scanning Electron Microscope (SEM) Stereophotogrammetry.

PubMed

Tondare, Vipin N; Villarrubia, John S; Vlada R, András E

2017-10-01

Three-dimensional (3D) reconstruction of a sample surface from scanning electron microscope (SEM) images taken at two perspectives has been known for decades. Nowadays, there exist several commercially available stereophotogrammetry software packages. For testing these software packages, in this study we used Monte Carlo simulated SEM images of virtual samples. A virtual sample is a model in a computer, and its true dimensions are known exactly, which is impossible for real SEM samples due to measurement uncertainty. The simulated SEM images can be used for algorithm testing, development, and validation. We tested two stereophotogrammetry software packages and compared their reconstructed 3D models with the known geometry of the virtual samples used to create the simulated SEM images. Both packages performed relatively well with simulated SEM images of a sample with a rough surface. However, in a sample containing nearly uniform and therefore low-contrast zones, the height reconstruction error was ≈46%. The present stereophotogrammetry software packages need further improvement before they can be used reliably with SEM images with uniform zones.

Flight simulation software at NASA Dryden Flight Research Center

NASA Technical Reports Server (NTRS)

Norlin, Ken A.

1995-01-01

The NASA Dryden Flight Research Center has developed a versatile simulation software package that is applicable to a broad range of fixed-wing aircraft. This package has evolved in support of a variety of flight research programs. The structure is designed to be flexible enough for use in batch-mode, real-time pilot-in-the-loop, and flight hardware-in-the-loop simulation. Current simulations operate on UNIX-based platforms and are coded with a FORTRAN shell and C support routines. This paper discusses the features of the simulation software design and some basic model development techniques. The key capabilities that have been included in the simulation are described. The NASA Dryden simulation software is in use at other NASA centers, within industry, and at several universities. The straightforward but flexible design of this well-validated package makes it especially useful in an engineering environment.

An extension of the OpenModelica compiler for using Modelica models in a discrete event simulation

DOE PAGES

Nutaro, James

2014-11-03

In this article, a new back-end and run-time system is described for the OpenModelica compiler. This new back-end transforms a Modelica model into a module for the adevs discrete event simulation package, thereby extending adevs to encompass complex, hybrid dynamical systems. The new run-time system that has been built within the adevs simulation package supports models with state-events and time-events and that comprise differential-algebraic systems with high index. Finally, although the procedure for effecting this transformation is based on adevs and the Discrete Event System Specification, it can be adapted to any discrete event simulation package.

The Cloud Feedback Model Intercomparison Project Observational Simulator Package: Version 2

NASA Astrophysics Data System (ADS)

Swales, Dustin J.; Pincus, Robert; Bodas-Salcedo, Alejandro

2018-01-01

The Cloud Feedback Model Intercomparison Project Observational Simulator Package (COSP) gathers together a collection of observation proxies or satellite simulators that translate model-simulated cloud properties to synthetic observations as would be obtained by a range of satellite observing systems. This paper introduces COSP2, an evolution focusing on more explicit and consistent separation between host model, coupling infrastructure, and individual observing proxies. Revisions also enhance flexibility by allowing for model-specific representation of sub-grid-scale cloudiness, provide greater clarity by clearly separating tasks, support greater use of shared code and data including shared inputs across simulators, and follow more uniform software standards to simplify implementation across a wide range of platforms. The complete package including a testing suite is freely available.

ATTIRE (analytical tools for thermal infrared engineering): A sensor simulation and modeling package

NASA Astrophysics Data System (ADS)

Jaggi, S.

1993-02-01

The Advanced Sensor Development Laboratory (ASDL) at the Stennis Space Center develops, maintains and calibrates remote sensing instruments for the National Aeronautics & Space Administration (NASA). To perform system design trade-offs, analysis, and establish system parameters, ASDL has developed a software package for analytical simulation of sensor systems. This package called 'Analytical Tools for Thermal InfraRed Engineering' - ATTIRE, simulates the various components of a sensor system. The software allows each subsystem of the sensor to be analyzed independently for its performance. These performance parameters are then integrated to obtain system level information such as Signal-to-Noise Ratio (SNR), Noise Equivalent Radiance (NER), Noise Equivalent Temperature Difference (NETD) etc. This paper describes the uses of the package and the physics that were used to derive the performance parameters.

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

NASA Astrophysics Data System (ADS)

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.

Air-cooling characteristics of simulated grape packages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frederick, R.L.; Comunian, F.

Experimental simulation of the external forced convection on the outside of grape packages was performed. Average heat transfer coefficients for air flow around such containers were found to range from 8 to 13.4 W/(m[sup 2]K). A physical description of the convective process was formulated on the basis of data obtained in three types of experiment. Expressions for the average heat transfer coefficient from single packages in air flow were proposed.

A Tutorial on RxODE: Simulating Differential Equation Pharmacometric Models in R.

PubMed

Wang, W; Hallow, K M; James, D A

2016-01-01

This tutorial presents the application of an R package, RxODE, that facilitates quick, efficient simulations of ordinary differential equation models completely within R. Its application is illustrated through simulation of design decision effects on an adaptive dosing regimen. The package provides an efficient, versatile way to specify dosing scenarios and to perform simulation with variability with minimal custom coding. Models can be directly translated to Rshiny applications to facilitate interactive, real-time evaluation/iteration on simulation scenarios.

A Geant4 simulation of the depth dose percentage in brain tumors treatments using protons and carbon ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diaz, José A. M., E-mail: joadiazme@unal.edu.co; Torres, D. A., E-mail: datorresg@unal.edu.co

2016-07-07

The deposited energy and dose distribution of beams of protons and carbon over a head are simulated using the free tool package Geant4 and the data analysis package ROOT-C++. The present work shows a methodology to understand the microscopical process occurring in a session of hadron-therapy using advance simulation tools.

Increasing the Number of Replications in Item Response Theory Simulations: Automation through SAS and Disk Operating System

ERIC Educational Resources Information Center

Gagne, Phill; Furlow, Carolyn; Ross, Terris

2009-01-01

In item response theory (IRT) simulation research, it is often necessary to use one software package for data generation and a second software package to conduct the IRT analysis. Because this can substantially slow down the simulation process, it is sometimes offered as a justification for using very few replications. This article provides…

Constraint monitoring in TOSCA

NASA Technical Reports Server (NTRS)

Beck, Howard

1992-01-01

The Job-Shop Scheduling Problem (JSSP) deals with the allocation of resources over time to factory operations. Allocations are subject to various constraints (e.g., production precedence relationships, factory capacity constraints, and limits on the allowable number of machine setups) which must be satisfied for a schedule to be valid. The identification of constraint violations and the monitoring of constraint threats plays a vital role in schedule generation in terms of the following: (1) directing the scheduling process; and (2) informing scheduling decisions. This paper describes a general mechanism for identifying constraint violations and monitoring threats to the satisfaction of constraints throughout schedule generation.

On Fitting Generalized Linear Mixed-effects Models for Binary Responses using Different Statistical Packages

PubMed Central

Zhang, Hui; Lu, Naiji; Feng, Changyong; Thurston, Sally W.; Xia, Yinglin; Tu, Xin M.

2011-01-01

Summary The generalized linear mixed-effects model (GLMM) is a popular paradigm to extend models for cross-sectional data to a longitudinal setting. When applied to modeling binary responses, different software packages and even different procedures within a package may give quite different results. In this report, we describe the statistical approaches that underlie these different procedures and discuss their strengths and weaknesses when applied to fit correlated binary responses. We then illustrate these considerations by applying these procedures implemented in some popular software packages to simulated and real study data. Our simulation results indicate a lack of reliability for most of the procedures considered, which carries significant implications for applying such popular software packages in practice. PMID:21671252

Advances in HYDRA and its application to simulations of Inertial Confinement Fusion targets

NASA Astrophysics Data System (ADS)

Marinak, M. M.; Kerbel, G. D.; Koning, J. M.; Patel, M. V.; Sepke, S. M.; Brown, P. N.; Chang, B.; Procassini, R.; Veitzer, S. A.

2008-11-01

We will outline new capabilities added to the HYDRA 2D/3D multiphysics ICF simulation code. These include a new SN multigroup radiation transport package (1D), constitutive models for elastic-plastic (strength) effects, and a mix model. A Monte Carlo burn package is being incorporated to model diagnostic signatures of neutrons, gamma rays and charged particles. A 3D MHD package that treats resistive MHD is available. Improvements to HYDRA's implicit Monte Carlo photonics package, including the addition of angular biasing, now enable integrated hohlraum simulations to complete in substantially shorter time. The heavy ion beam deposition package now includes a new model for ion stopping power developed by the Tech-X Corporation, with improved accuracy below the Bragg peak. Examples will illustrate HYDRA's enhanced capabilities to simulate various aspects of inertial confinement fusion targets.This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344. The work of Tech-X personnel was funded by the Department of Energy under Small Business Innovation Research Contract No. DE-FG02-03ER83797.

Implementation of interconnect simulation tools in spice

NASA Technical Reports Server (NTRS)

Satsangi, H.; Schutt-Aine, J. E.

1993-01-01

Accurate computer simulation of high speed digital computer circuits and communication circuits requires a multimode approach to simulate both the devices and the interconnects between devices. Classical circuit analysis algorithms (lumped parameter) are needed for circuit devices and the network formed by the interconnected devices. The interconnects, however, have to be modeled as transmission lines which incorporate electromagnetic field analysis. An approach to writing a multimode simulator is to take an existing software package which performs either lumped parameter analysis or field analysis and add the missing type of analysis routines to the package. In this work a traditionally lumped parameter simulator, SPICE, is modified so that it will perform lossy transmission line analysis using a different model approach. Modifying SPICE3E2 or any other large software package is not a trivial task. An understanding of the programming conventions used, simulation software, and simulation algorithms is required. This thesis was written to clarify the procedure for installing a device into SPICE3E2. The installation of three devices is documented and the installations of the first two provide a foundation for installation of the lossy line which is the third device. The details of discussions are specific to SPICE, but the concepts will be helpful when performing installations into other circuit analysis packages.

Regional demand forecasting and simulation model: user's manual. Task 4, final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parhizgari, A M

1978-09-25

The Department of Energy's Regional Demand Forecasting Model (RDFOR) is an econometric and simulation system designed to estimate annual fuel-sector-region specific consumption of energy for the US. Its purposes are to (1) provide the demand side of the Project Independence Evaluation System (PIES), (2) enhance our empirical insights into the structure of US energy demand, and (3) assist policymakers in their decisions on and formulations of various energy policies and/or scenarios. This report provides a self-contained user's manual for interpreting, utilizing, and implementing RDFOR simulation software packages. Chapters I and II present the theoretical structure and the simulation of RDFOR,more » respectively. Chapter III describes several potential scenarios which are (or have been) utilized in the RDFOR simulations. Chapter IV presents an overview of the complete software package utilized in simulation. Chapter V provides the detailed explanation and documentation of this package. The last chapter describes step-by-step implementation of the simulation package using the two scenarios detailed in Chapter III. The RDFOR model contains 14 fuels: gasoline, electricity, natural gas, distillate and residual fuels, liquid gases, jet fuel, coal, oil, petroleum products, asphalt, petroleum coke, metallurgical coal, and total fuels, spread over residential, commercial, industrial, and transportation sectors.« less

Options for reducing food waste by quality-controlled logistics using intelligent packaging along the supply chain.

PubMed

Heising, Jenneke K; Claassen, G D H; Dekker, Matthijs

2017-10-01

Optimising supply chain management can help to reduce food waste. This paper describes how intelligent packaging can be used to reduce food waste when used in supply chain management based on quality-controlled logistics (QCL). Intelligent packaging senses compounds in the package that correlate with the critical quality attribute of a food product. The information on the quality of each individual packaged food item that is provided by the intelligent packaging can be used for QCL. In a conceptual approach it is explained that monitoring food quality by intelligent packaging sensors makes it possible to obtain information about the variation in the quality of foods and to use a dynamic expiration date (IP-DED) on a food package. The conceptual approach is supported by quantitative data from simulations on the effect of using the information of intelligent packaging in supply chain management with the goal to reduce food waste. This simulation shows that by using the information on the quality of products that is provided by intelligent packaging, QCL can substantially reduce food waste. When QCL is combined with dynamic pricing based on the predicted expiry dates, a further waste reduction is envisaged.

Implementation and use of direct-flow connections in a coupled ground-water and surface-water model

USGS Publications Warehouse

Swain, Eric D.

1994-01-01

The U.S. Geological Survey's MODFLOW finite-difference ground-water flow model has been coupled with three surface-water packages - the MODBRANCH, River, and Stream packages - to simulate surface water and its interaction with ground water. Prior to the development of the coupling packages, the only interaction between these modeling packages was that leakage values could be passed between MODFLOW and the three surface-water packages. To facilitate wider and more flexible uses of the models, a computer program was developed and added to MODFLOW to allow direct flows or stages to be passed between any of the packages and MODFLOW. The flows or stages calculated in one package can be set as boundary discharges or stages to be used in another package. Several modeling packages can be used in the same simulation depending upon the level of sophistication needed in the various reaches being modeled. This computer program is especially useful when any of the River, Stream, or MODBRANCH packages are used to model a river flowing directly into or out of wetlands in direct connection with the aquifer and represented in the model as an aquifer block. A field case study is shown to illustrate an application.

An electron-beam dose deposition experiment: TIGER 1-D simulation code versus thermoluminescent dosimetry

NASA Astrophysics Data System (ADS)

Murrill, Steven R.; Tipton, Charles W.; Self, Charles T.

1991-03-01

The dose absorbed in an integrated circuit (IC) die exposed to a pulse of low-energy electrons is a strong function of both electron energy and surrounding packaging materials. This report describes an experiment designed to measure how well the Integrated TIGER Series one-dimensional (1-D) electron transport simulation program predicts dose correction factors for a state-of-the-art IC package and package/printed circuit board (PCB) combination. These derived factors are compared with data obtained experimentally using thermoluminescent dosimeters (TLD's) and the FX-45 flash x-ray machine (operated in electron-beam (e-beam) mode). The results of this experiment show that the TIGER 1-D simulation code can be used to accurately predict FX-45 e-beam dose deposition correction factors for reasonably complex IC packaging configurations.

Documentation of a computer program to simulate aquifer-system compaction using the modular finite-difference ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Prudic, David E.

1991-01-01

Removal of ground water by pumping from aquifers may result in compaction of compressible fine-grained beds that are within or adjacent to the aquifers. Compaction of the sediments and resulting land subsidence may be permanent if the head declines result in vertical stresses beyond the previous maximum stress. The process of permanent compaction is not routinely included in simulations of ground-water flow. To simulate storage changes from both elastic and inelastic compaction, a computer program was written for use with the U.S. Geological Survey modular finite-difference ground- water flow model. The new program, the Interbed-Storage Package, is designed to be incorporated into this model. In the Interbed-Storage Package, elastic compaction or expansion is assumed to be proportional to change in head. The constant of proportionality is the product of the skeletal component of elastic specific storage and the thickness of the sediments. Similarly, inelastic compaction is assumed to be proportional to decline in head. The constant of proportionality is the product of the skeletal component of inelastic specific storage and the thickness of the sediments. Storage changes are incorporated into the ground-water flow model by adding an additional term to the right-hand side of the flow equation. Within a model time step, the package appropriately apportions storage changes between elastic and inelastic components on the basis of the relation of simulated head to the previous minimum (preconsolidation) head. Two tests were performed to verify that the package works correctly. The first test compared model-calculated storage and compaction changes to hand-calculated values for a three-dimensional simulation. Model and hand-calculated values were essentially equal. The second test was performed to compare the results of the Interbed-Storage Package with results of the one-dimensional Helm compaction model. This test problem simulated compaction in doubly draining confining beds stressed by head changes in adjacent aquifers. The Interbed-Storage Package and the Helm model computed essentially equal values of compaction. Documentation of the Interbed-Storage Package includes data input instructions, flow charts, narratives, and listings for each of the five modules included in the package. The documentation also includes an appendix describing input instructions and a listing of a computer program for time-variant specified-head boundaries. That package was developed to reduce the amount of data input and output associated with one of the Interbed-Storage Package test problems.

Teaching Science and Mathematics Subjects Using the Excel Spreadsheet Package

ERIC Educational Resources Information Center

Ibrahim, Dogan

2009-01-01

The teaching of scientific subjects usually require laboratories where students can put the theory they have learned into practice. Traditionally, electronic programmable calculators, dedicated software, or expensive software simulation packages, such as MATLAB have been used to simulate scientific experiments. Recently, spreadsheet programs have…

PLATSIM: A Simulation and Analysis Package for Large-Order Flexible Systems. Version 2.0

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Kenny, Sean P.; Giesy, Daniel P.

1997-01-01

The software package PLATSIM provides efficient time and frequency domain analysis of large-order generic space platforms. PLATSIM can perform open-loop analysis or closed-loop analysis with linear or nonlinear control system models. PLATSIM exploits the particular form of sparsity of the plant matrices for very efficient linear and nonlinear time domain analysis, as well as frequency domain analysis. A new, original algorithm for the efficient computation of open-loop and closed-loop frequency response functions for large-order systems has been developed and is implemented within the package. Furthermore, a novel and efficient jitter analysis routine which determines jitter and stability values from time simulations in a very efficient manner has been developed and is incorporated in the PLATSIM package. In the time domain analysis, PLATSIM simulates the response of the space platform to disturbances and calculates the jitter and stability values from the response time histories. In the frequency domain analysis, PLATSIM calculates frequency response function matrices and provides the corresponding Bode plots. The PLATSIM software package is written in MATLAB script language. A graphical user interface is developed in the package to provide convenient access to its various features.

Structural and thermodynamic principles of viral packaging.

PubMed

Petrov, Anton S; Harvey, Stephen C

2007-01-01

Packaging of genetic material inside a capsid is one of the major processes in the lifecycle of bacteriophages. To establish the basic principles of packing double-stranded DNA into a phage, we present a low-resolution model of bacteriophage varphi29 and report simulations of DNA packaging. The simulations show excellent agreement with available experimental data, including the forces of packaging and the average structures seen in cryo-electron microscopy. The conformation of DNA inside the bacteriophage is primarily determined by the shape of the capsid and the elastic properties of DNA, but the energetics of packaging are dominated by electrostatic repulsions and the large entropic penalty associated with DNA confinement. In this slightly elongated capsid, the DNA assumes a folded toroidal conformation, rather than a coaxial spool. The model can be used to study packaging of other bacteriophages with different shapes under a range of environmental conditions.

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

PubMed

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.

Thick photosensitive polyimide film side wall angle variability and scum improvement for IC packaging stress control

NASA Astrophysics Data System (ADS)

Mehta, Sohan Singh; Yeung, Marco; Mirza, Fahad; Raman, Thiagarajan; Longenbach, Travis; Morgan, Justin; Duggan, Mark; Soedibyo, Rio A.; Reidy, Sean; Rabie, Mohamed; Cho, Jae Kyu; Premachandran, C. S.; Faruqui, Danish

2018-03-01

In this paper, we demonstrate photosensitive polyimide (PSPI) profile optimization to effectively reduce stress concentrations and enable PSPI as protection package-induced stress. Through detailed package simulation, we demonstrate 45% reduction in stress as the sidewall angle (SWA) of PSPI is increased from 45 to 80 degrees in Cu pillar package types. Through modulation of coating and develop multi-step baking temperature and time, as well as dose energy and post litho surface treatments, we demonstrate a method for reliably obtaining PSPI sidewall angle >75 degree. Additionally, we experimentally validate the simulation findings that PSPI sidewall angle impacts chip package interaction (CPI). Finally, we conclude this paper with PSPI material and tool qualification requirements for future technology node based on current challenges.

On fitting generalized linear mixed-effects models for binary responses using different statistical packages.

PubMed

Zhang, Hui; Lu, Naiji; Feng, Changyong; Thurston, Sally W; Xia, Yinglin; Zhu, Liang; Tu, Xin M

2011-09-10

The generalized linear mixed-effects model (GLMM) is a popular paradigm to extend models for cross-sectional data to a longitudinal setting. When applied to modeling binary responses, different software packages and even different procedures within a package may give quite different results. In this report, we describe the statistical approaches that underlie these different procedures and discuss their strengths and weaknesses when applied to fit correlated binary responses. We then illustrate these considerations by applying these procedures implemented in some popular software packages to simulated and real study data. Our simulation results indicate a lack of reliability for most of the procedures considered, which carries significant implications for applying such popular software packages in practice. Copyright © 2011 John Wiley & Sons, Ltd.

Observational evidence of fire-driven changes to tropical cloudiness

NASA Astrophysics Data System (ADS)

Tosca, Michael; Diner, David; Garay, Michael; Kalashnikova, Olga

2014-05-01

Anthropogenic fires in the tropics emit smoke aerosols that affect cloud dynamics, meteorology and climate (Tosca et al., 2013). We developed a new technique to observationally quantify the cloud response to biomass burning aerosols using aerosol retrievals from the Multi-angle Imaging SpectroRadiometer (MISR) and non-coincident cloud retrievals from the MODerate resolution Imaging Spectroradiometer (MODIS) from collocated morning and afternoon overpasses. The Global Fire Emissions Database, version 3 and Level 2 data from scenes acquired between 2006 and 2010 were used to quantify changes in cloud fraction from morning (10:30am local time) to afternoon (1:30pm local time) in the presence of varying fire-aerosol burdens. This temporal offset allowed for analysis of the evolution of clouds in the presence of aerosols, something that previous methods using coincident observations could not produce. We controlled for large-scale meteorological differences between scenes using reanalysis data from the ERA-interim product and matching scenes with fire smoke to those with no smoke and similar initial (morning) meteorological conditions. Elevated aerosol optical depths (AODs) reduced cloud fraction from morning to afternoon in the Southeast Asia, Central America and northern Africa burning regions. In mostly cloudy conditions, aerosols significantly reduced cloud fraction, but in clear skies, cloud fraction increased. These results support the general hypothesis of a positive feedback loop between anthropogenic burning and cloudiness in tropical regions, and are consistent with previous studies linking smoke aerosols to convective cloud reduction. Tosca, M.G., J.T. Randerson and C.S. Zender (2013), Global impact of smoke aerosols from landscape fires on climate and the Hadley circulation, Atmos. Chem. Phys., 13, 5227-5241, doi: 10.5194/acp-13-5227-2013.

Influence of dietary fat and carbohydrates proportions on plasma lipids, glucose control and low-grade inflammation in patients with type 2 diabetes-The TOSCA.IT Study.

PubMed

Vitale, M; Masulli, M; Rivellese, A A; Babini, A C; Boemi, M; Bonora, E; Buzzetti, R; Ciano, O; Cignarelli, M; Cigolini, M; Clemente, G; Citro, G; Corsi, L; Dall'Aglio, E; Del Prato, S; Di Cianni, G; Dolci, M A; Giordano, C; Iannarelli, R; Iovine, C; Lapolla, A; Lauro, D; Leotta, S; Mazzucchelli, C; Montani, V; Perriello, G; Romano, G; Romeo, F; Santarelli, L; di Cola, R Schiano; Squatrito, S; Tonutti, L; Trevisan, R; Turco, A A; Zamboni, C; Riccardi, G; Vaccaro, O

2016-06-01

The optimal macronutrient composition of the diet for the management of type 2 diabetes is debated, particularly with regard to the ideal proportion of fat and carbohydrates. The aim of the study was to explore the association of different proportions of fat and carbohydrates of the diet-within the ranges recommended by different guidelines-with metabolic risk factors. We studied 1785 people with type 2 diabetes, aged 50-75, enrolled in the TOSCA.IT Study. Dietary habits were assessed using a validated food-frequency questionnaire (EPIC). Anthropometry, fasting lipids, HbA1c and C-reactive protein (CRP) were measured. Increasing fat intake from <25 to ≥35 % is associated with a significant increase in LDL-cholesterol, triglycerides, HbA1c and CRP (p < 0.05). Increasing carbohydrates intake from <45 to ≥60 % is associated with significantly lower triglycerides, HbA1c and CRP (p < 0.05). A fiber intake ≥15 g/1000 kcal is associated with a better plasma lipids profile and lower HbA1c and CRP than lower fiber consumption. A consumption of added sugars of ≥10 % of the energy intake is associated with a more adverse plasma lipids profile and higher CRP than lower intake. In people with type 2 diabetes, variations in the proportion of fat and carbohydrates of the diet, within the relatively narrow ranges recommended by different nutritional guidelines, significantly impact on the metabolic profile and markers of low-grade inflammation. The data support the potential for reducing the intake of fat and added sugars, preferring complex, slowly absorbable, carbohydrates.

Dihydropyrimidine dehydrogenase pharmacogenetics for predicting fluoropyrimidine-related toxicity in the randomised, phase III adjuvant TOSCA trial in high-risk colon cancer patients

PubMed Central

Ruzzo, A; Graziano, F; Galli, Fabio; Galli, Francesca; Rulli, E; Lonardi, S; Ronzoni, M; Massidda, B; Zagonel, V; Pella, N; Mucciarini, C; Labianca, R; Ionta, M T; Bagaloni, I; Veltri, E; Sozzi, P; Barni, S; Ricci, V; Foltran, L; Nicolini, M; Biondi, E; Bramati, A; Turci, D; Lazzarelli, S; Verusio, C; Bergamo, F; Sobrero, A; Frontini, L; Menghi, M; Magnani, M

2017-01-01

Background: Dihydropyrimidine dehydrogenase (DPD) catabolises ∼85% of the administered dose of fluoropyrimidines. Functional DPYD gene variants cause reduced/abrogated DPD activity. DPYD variants analysis may help for defining individual patients’ risk of fluoropyrimidine-related severe toxicity. Methods: The TOSCA Italian randomised trial enrolled colon cancer patients for 3 or 6 months of either FOLFOX-4 or XELOX adjuvant chemotherapy. In an ancillary pharmacogenetic study, 10 DPYD variants (*2A rs3918290 G>A, *13 rs55886062 T>G, rs67376798 A>T, *4 rs1801158 G>A, *5 rs1801159 A>G, *6 rs1801160 G>A, *9A rs1801265 T>C, rs2297595 A>G, rs17376848 T>C, and rs75017182 C>G), were retrospectively tested for associations with ⩾grade 3 fluoropyrimidine-related adverse events (FAEs). An association analysis and a time-to-toxicity (TTT) analysis were planned. To adjust for multiple testing, the Benjamini and Hochberg’s False Discovery Rate (FDR) procedure was used. Results: FAEs occurred in 194 out of 508 assessable patients (38.2%). In the association analysis, FAEs occurred more frequently in *6 rs1801160 A allele carriers (FDR=0.0083). At multivariate TTT analysis, significant associations were found for *6 rs1801160 A allele carriers (FDR<0.0001), *2A rs3918290 A allele carriers (FDR<0.0001), and rs2297595 GG genotype carriers (FDR=0.0014). Neutropenia was the most common FAEs (28.5%). *6 rs1801160 (FDR<0.0001), and *2A rs3918290 (FDR=0.0004) variant alleles were significantly associated with time to neutropenia. Conclusions: This study adds evidence on the role of DPYD pharmacogenetics for safety of patients undergoing fluoropyrimidine-based chemotherapy. PMID:29065426

Dihydropyrimidine dehydrogenase pharmacogenetics for predicting fluoropyrimidine-related toxicity in the randomised, phase III adjuvant TOSCA trial in high-risk colon cancer patients.

PubMed

Ruzzo, A; Graziano, F; Galli, Fabio; Galli, Francesca; Rulli, E; Lonardi, S; Ronzoni, M; Massidda, B; Zagonel, V; Pella, N; Mucciarini, C; Labianca, R; Ionta, M T; Bagaloni, I; Veltri, E; Sozzi, P; Barni, S; Ricci, V; Foltran, L; Nicolini, M; Biondi, E; Bramati, A; Turci, D; Lazzarelli, S; Verusio, C; Bergamo, F; Sobrero, A; Frontini, L; Menghi, M; Magnani, M

2017-10-24

Dihydropyrimidine dehydrogenase (DPD) catabolises ∼85% of the administered dose of fluoropyrimidines. Functional DPYD gene variants cause reduced/abrogated DPD activity. DPYD variants analysis may help for defining individual patients' risk of fluoropyrimidine-related severe toxicity. The TOSCA Italian randomised trial enrolled colon cancer patients for 3 or 6 months of either FOLFOX-4 or XELOX adjuvant chemotherapy. In an ancillary pharmacogenetic study, 10 DPYD variants (*2A rs3918290 G>A, *13 rs55886062 T>G, rs67376798 A>T, *4 rs1801158 G>A, *5 rs1801159 A>G, *6 rs1801160 G>A, *9A rs1801265 T>C, rs2297595 A>G, rs17376848 T>C, and rs75017182 C>G), were retrospectively tested for associations with ⩾grade 3 fluoropyrimidine-related adverse events (FAEs). An association analysis and a time-to-toxicity (TTT) analysis were planned. To adjust for multiple testing, the Benjamini and Hochberg's False Discovery Rate (FDR) procedure was used. FAEs occurred in 194 out of 508 assessable patients (38.2%). In the association analysis, FAEs occurred more frequently in *6 rs1801160 A allele carriers (FDR=0.0083). At multivariate TTT analysis, significant associations were found for *6 rs1801160 A allele carriers (FDR<0.0001), *2A rs3918290 A allele carriers (FDR<0.0001), and rs2297595 GG genotype carriers (FDR=0.0014). Neutropenia was the most common FAEs (28.5%). *6 rs1801160 (FDR<0.0001), and *2A rs3918290 (FDR=0.0004) variant alleles were significantly associated with time to neutropenia. This study adds evidence on the role of DPYD pharmacogenetics for safety of patients undergoing fluoropyrimidine-based chemotherapy.

A Turbine Based Combined Cycle Engine Inlet Model and Mode Transition Simulation Based on HiTECC Tool

NASA Technical Reports Server (NTRS)

Csank, Jeffrey; Stueber, Thomas

2012-01-01

An inlet system is being tested to evaluate methodologies for a turbine based combined cycle propulsion system to perform a controlled inlet mode transition. Prior to wind tunnel based hardware testing of controlled mode transitions, simulation models are used to test, debug, and validate potential control algorithms. One candidate simulation package for this purpose is the High Mach Transient Engine Cycle Code (HiTECC). The HiTECC simulation package models the inlet system, propulsion systems, thermal energy, geometry, nozzle, and fuel systems. This paper discusses the modification and redesign of the simulation package and control system to represent the NASA large-scale inlet model for Combined Cycle Engine mode transition studies, mounted in NASA Glenn s 10-foot by 10-foot Supersonic Wind Tunnel. This model will be used for designing and testing candidate control algorithms before implementation.

A Turbine Based Combined Cycle Engine Inlet Model and Mode Transition Simulation Based on HiTECC Tool

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Stueber, Thomas J.

2012-01-01

An inlet system is being tested to evaluate methodologies for a turbine based combined cycle propulsion system to perform a controlled inlet mode transition. Prior to wind tunnel based hardware testing of controlled mode transitions, simulation models are used to test, debug, and validate potential control algorithms. One candidate simulation package for this purpose is the High Mach Transient Engine Cycle Code (HiTECC). The HiTECC simulation package models the inlet system, propulsion systems, thermal energy, geometry, nozzle, and fuel systems. This paper discusses the modification and redesign of the simulation package and control system to represent the NASA large-scale inlet model for Combined Cycle Engine mode transition studies, mounted in NASA Glenn s 10- by 10-Foot Supersonic Wind Tunnel. This model will be used for designing and testing candidate control algorithms before implementation.

Faster than Real-Time Dynamic Simulation for Large-Size Power System with Detailed Dynamic Models using High-Performance Computing Platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Renke; Jin, Shuangshuang; Chen, Yousu

This paper presents a faster-than-real-time dynamic simulation software package that is designed for large-size power system dynamic simulation. It was developed on the GridPACKTM high-performance computing (HPC) framework. The key features of the developed software package include (1) faster-than-real-time dynamic simulation for a WECC system (17,000 buses) with different types of detailed generator, controller, and relay dynamic models, (2) a decoupled parallel dynamic simulation algorithm with optimized computation architecture to better leverage HPC resources and technologies, (3) options for HPC-based linear and iterative solvers, (4) hidden HPC details, such as data communication and distribution, to enable development centered on mathematicalmore » models and algorithms rather than on computational details for power system researchers, and (5) easy integration of new dynamic models and related algorithms into the software package.« less

Multi-dimensional simulation package for ultrashort pulse laser-matter interactions

NASA Astrophysics Data System (ADS)

Suslova, Anastassiya; Hassanein, Ahmed

2017-10-01

Advanced simulation models recently became a popular tool of investigation of ultrashort pulse lasers (USPLs) to enhance understanding of the physics and allow minimizing the experimental costs for optimization of laser and target parameters for various applications. Our research interest is focused on developing multi-dimensional simulation package FEMTO-2D to investigate the USPL-matter interactions and laser induced effects. The package is based on solution of two heat conduction equations for electron and lattice sub-systems - enhanced two temperature model (TTM). We have implemented theoretical approach based on the collision theory to define the thermal dependence of target material optical properties and thermodynamic parameters. Our approach allowed elimination of fitted parameters commonly used in TTM based simulations. FEMTO-2D is used to simulated the light absorption and interactions for several metallic targets as a function of wavelength and pulse duration for wide range of laser intensity. The package has capability to consider different angles of incidence and polarization. It has also been used to investigate the damage threshold of the gold coated optical components with the focus on the role of the film thickness and substrate heat sink effect. This work was supported by the NSF, PIRE project.

Unmanned Air Vehicle -Version 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fred Oppel, SNL 06134

2013-04-17

This package contains modules that model the mobility of systems such as helicopters and fixed wing flying in the air. This package currently models first order physics - basically a velocity integrator. UAV mobility uses an internal clock to maintain stable, high-fidelity simulations over large time steps This package depends on interface that reside in the Mobility package.

"FluSpec": A Simulated Experiment in Fluorescence Spectroscopy

ERIC Educational Resources Information Center

Bigger, Stephen W.; Bigger, Andrew S.; Ghiggino, Kenneth P.

2014-01-01

The "FluSpec" educational software package is a fully contained tutorial on the technique of fluorescence spectroscopy as well as a simulator on which experiments can be performed. The procedure for each of the experiments is also contained within the package along with example analyses of results that are obtained using the software.

Microwave heating causes rapid degradation of antioxidants in polypropylene packaging, leading to greatly increased specific migration to food simulants as shown by ESI-MS and GC-MS.

PubMed

Alin, Jonas; Hakkarainen, Minna

2011-05-25

Microwave heating of commercial microwavable polypropylene packaging in contact with fatty food simulants caused significant antioxidant degradation and increased specific migration as shown by electrospray ionization-mass spectrometry (ESI-MS) and gas chromatography-mass spectrometry (GC-MS). Degradation of the antioxidants Irgafos 168 and Irganox 1010 was not detected during conventional heating of polypropylene packaging at the same temperature. The migration into aqueous food simulants was primarily restricted by the water solubility of the migrants. Using isooctane as fatty food simulant caused significant swelling and greatly enhanced overall migration values compared to the other fatty food simulant, 99.9% ethanol, or the aqueous food simulants 10% ethanol, 3% acetic acid, or water. ESI-MS spectra clearly reflected the overall migration values, and the number and amount of compounds detected decreased as the hydrophilicity of the food simulant increased. ESI-MS was shown to be an excellent tool for the analysis of semivolatile migrants and a good complement to GC-MS analysis of volatile migrants.

Experimental Verification of the Use of Metal Filled Via Hole Fences for Crosstalk Control of Microstrip Lines in LTCC Packages

NASA Technical Reports Server (NTRS)

Ponchak, George E.; Chun, Donghoon; Katehi, Linda P. B.; Yook, Jong-Gwan

1999-01-01

Coupling between microstrip lines in dense RF packages is a common problem that degrades circuit performance. Prior 3D-FEM electromagnetic simulations have shown that metal filled via hole fences between two adjacent microstrip lines actually increases coupling between the lines; however, if the top of the via posts are connected by a metal Strip, coupling is reduced. In this paper, experimental verification of the 3D-FEM simulations Is demonstrated for commercially fabricated LTCC packages.

DNA packaging in viral capsids with peptide arms.

PubMed

Cao, Qianqian; Bachmann, Michael

2017-01-18

Strong chain rigidity and electrostatic self-repulsion of packed double-stranded DNA in viruses require a molecular motor to pull the DNA into the capsid. However, what is the role of electrostatic interactions between different charged components in the packaging process? Though various theories and computer simulation models were developed for the understanding of viral assembly and packaging dynamics of the genome, long-range electrostatic interactions and capsid structure have typically been neglected or oversimplified. By means of molecular dynamics simulations, we explore the effects of electrostatic interactions on the packaging dynamics of DNA based on a coarse-grained DNA and capsid model by explicitly including peptide arms (PAs), linked to the inner surface of the capsid, and counterions. Our results indicate that the electrostatic interactions between PAs, DNA, and counterions have a significant influence on the packaging dynamics. We also find that the packed DNA conformations are largely affected by the structure of the PA layer, but the packaging rate is insensitive to the layer structure.

Path selection system simulation and evaluation for a Martian roving vehicle

NASA Technical Reports Server (NTRS)

Boheim, S. L.; Prudon, W. C.

1972-01-01

The simulation and evaluation of proposed path selection systems for an autonomous Martian roving vehicle was developed. The package incorporates a number of realistic features, such as the simulation of random effects due to vehicle bounce and sensor-reading uncertainty, to increase the reliability of the results. Qualitative and quantitative evaluation criteria were established. The performance of three different path selection systems was evaluated to determine the effectiveness of the simulation package, and to form some preliminary conclusions regarding the tradeoffs involved in a path selection system design.

Python-based geometry preparation and simulation visualization toolkits for STEPS

PubMed Central

Chen, Weiliang; De Schutter, Erik

2014-01-01

STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations. PMID:24782754

McStas 1.7 - a new version of the flexible Monte Carlo neutron scattering package

NASA Astrophysics Data System (ADS)

Willendrup, Peter; Farhi, Emmanuel; Lefmann, Kim

2004-07-01

Current neutron instrumentation is both complex and expensive, and accurate simulation has become essential both for building new instruments and for using them effectively. The McStas neutron ray-trace simulation package is a versatile tool for producing such simulations, developed in collaboration between Risø and ILL. The new version (1.7) has many improvements, among these added support for the popular Microsoft Windows platform. This presentation will demonstrate a selection of the new features through a simulation of the ILL IN6 beamline.

[A research of letter color visibility in package insert information using simulator].

PubMed

Kamimura, Naoki; Kinoshita, Noriyuki; Onaga, Midori; Watanabe, Yurika; Ijuin, Kazushige; Shikamura, Yoshiaki; Negishi, Kenichi; Kaiho, Fusao; Ohta, Takafumi

2012-01-01

Package insert of pharmaceutical drug is one of the most prioritized information for pharmacists to secure safety of patients. However, the color of character, size, font and so on are various company by company product to product from a viewpoint of visibility. It may be cause a serious accident in case visibility is unclear, although it is the most important information. Moreover, package insert with high visibility is required for color vision defectives from a viewpoint of a universal design. Then, the authors selected the package insert which has the boxed warning in the ethical pharmaceutical currently stored mostly in the present health insurance pharmacy and quantified the red color using the color meter. We advocate the state of a suitable package insert from a viewpoint of a universal design, whether the red color is high visible or not for color vision defectives using simulator.

ProtSqueeze: simple and effective automated tool for setting up membrane protein simulations.

PubMed

Yesylevskyy, Semen O

2007-01-01

The major challenge in setting up membrane protein simulations is embedding the protein into the pre-equilibrated lipid bilayer. Several techniques were proposed to achieve optimal packing of the lipid molecules around the protein. However, all of them possess serious disadvantages, which limit their applicability and discourage the users of simulation packages from using them. In the present work, we analyzed existing approaches and proposed a new procedure of protein insertion into the lipid bilayer, which is implemented in the ProtSqueeze software. The advantages of ProtSqueeze are as follows: (1) the insertion algorithm is simple, understandable, and controllable; (2) the software can work with virtually any simulation package on virtually any platform; (3) no modification of the source code of the simulation package is needed; (4) the procedure of insertion is as automated as possible; (5) ProtSqueeze is distributed for free under a general public license. In this work, we present the architecture and the algorithm of ProtSqueeze and demonstrate its usage in case studies.

JGromacs: a Java package for analyzing protein simulations.

PubMed

Münz, Márton; Biggin, Philip C

2012-01-23

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

JGromacs: A Java Package for Analyzing Protein Simulations

PubMed Central

2011-01-01

In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license. PMID:22191855

VS2DI: Model use, calibration, and validation

USGS Publications Warehouse

Healy, Richard W.; Essaid, Hedeff I.

2012-01-01

VS2DI is a software package for simulating water, solute, and heat transport through soils or other porous media under conditions of variable saturation. The package contains a graphical preprocessor for constructing simulations, a postprocessor for displaying simulation results, and numerical models that solve for flow and solute transport (VS2DT) and flow and heat transport (VS2DH). Flow is described by the Richards equation, and solute and heat transport are described by advection-dispersion equations; the finite-difference method is used to solve these equations. Problems can be simulated in one, two, or three (assuming radial symmetry) dimensions. This article provides an overview of calibration techniques that have been used with VS2DI; included is a detailed description of calibration procedures used in simulating the interaction between groundwater and a stream fed by drainage from agricultural fields in central Indiana. Brief descriptions of VS2DI and the various types of problems that have been addressed with the software package are also presented.

Comment on "Evaluating interactions between groundwater and vadose zone using the HYDRUS-based flow package for MODFLOW" by Navin Kumar C. Twarakavi, Jirka Šimůnek and Sophia Seo

USGS Publications Warehouse

Niswonger, R.G.; Prudic, David E.

2009-01-01

Twarakavi et al (2008) compared four packages that can be used to estimate recharge for regional-scale groundwater flow simulations using MODFLOW (Harbaugh, 2005). This comment is focused on the comparisons made between two of these packages, namely, UZF1 (Niswonger et al., 2006) and a derivative of HYDRUS referred to herein as HYDRUS (Seo et al., 2007). In their paper, Twarakavi et al. (2008) stated that HYDRUS more accurately simulates unsaturated flow processes and groundwater recharge as compared to UZF1. However, Twarakavi et al. (2008) did not address several important differences between these models that undermine the advantages of HYDRUS as compared to UZF1 for simulating recharge. These differences were not revealed by the comparisons presented by Twarakavi et al. because the test simulations used to compare the models were too simple

Migration of perfluoroalkyl acids from food packaging to food simulants.

PubMed

Xu, Y; Noonan, G O; Begley, T H

2013-01-01

A broad range of fluorochemicals is used to impart oil and water barrier properties to paper and paperboard food packaging. Many of the fluorochemicals are applied to paper and paperboard as complex mixtures containing reaction products and by-products and unreacted starting materials. This work primarily focussed on the determination of seven perfluorocarboxylic acids (PFCAs) in two commercially available food contact papers: a di-perfluoro-alkyloxy-amino-acid and a perfluoroalkyl phosphate surfactant. In addition, the migration of the PFCAs into five food simulants from two commercial packages was evaluated. All seven PFCAs were detected in the range of 700-2220 µg kg⁻¹ of paper, while three perfluoroalkyl sulphonates were under the LOD. Results from migration tests showed that migration depends on paper characteristics, time and food simulant. The percentage of migration after 10 days at 40°C ranged from 4.8% to 100% for the two papers and different food simulants.

Getting started with package sampSurf

Treesearch

Jeffrey H. Gove

2014-01-01

The sampSurf package is designed to facilitate the comparison of new and existing areal sampling methods through simulation. The package is thoroughly documented in several vignettes as mentioned below. This document is meant to point you in the right direction in finding the needed information to get started using sampSurf.

A New Streamflow-Routing (SFR1) Package to Simulate Stream-Aquifer Interaction with MODFLOW-2000

USGS Publications Warehouse

Prudic, David E.; Konikow, Leonard F.; Banta, Edward R.

2004-01-01

The increasing concern for water and its quality require improved methods to evaluate the interaction between streams and aquifers and the strong influence that streams can have on the flow and transport of contaminants through many aquifers. For this reason, a new Streamflow-Routing (SFR1) Package was written for use with the U.S. Geological Survey's MODFLOW-2000 ground-water flow model. The SFR1 Package is linked to the Lake (LAK3) Package, and both have been integrated with the Ground-Water Transport (GWT) Process of MODFLOW-2000 (MODFLOW-GWT). SFR1 replaces the previous Stream (STR1) Package, with the most important difference being that stream depth is computed at the midpoint of each reach instead of at the beginning of each reach, as was done in the original Stream Package. This approach allows for the addition and subtraction of water from runoff, precipitation, and evapotranspiration within each reach. Because the SFR1 Package computes stream depth differently than that for the original package, a different name was used to distinguish it from the original Stream (STR1) Package. The SFR1 Package has five options for simulating stream depth and four options for computing diversions from a stream. The options for computing stream depth are: a specified value; Manning's equation (using a wide rectangular channel or an eight-point cross section); a power equation; or a table of values that relate flow to depth and width. Each stream segment can have a different option. Outflow from lakes can be computed using the same options. Because the wetted perimeter is computed for the eight-point cross section and width is computed for the power equation and table of values, the streambed conductance term no longer needs to be calculated externally whenever the area of streambed changes as a function of flow. The concentration of solute is computed in a stream network when MODFLOW-GWT is used in conjunction with the SFR1 Package. The concentration of a solute in a stream reach is based on a mass-balance approach and accounts for exchanges with (inputs from or losses to) ground-water systems. Two test examples are used to illustrate some of the capabilities of the SFR1 Package. The first test simulation was designed to illustrate how pumping of ground water from an aquifer connected to streams can affect streamflow, depth, width, and streambed conductance using the different options. The second test simulation was designed to illustrate solute transport through interconnected lakes, streams, and aquifers. Because of the need to examine time series results from the model simulations, the Gage Package first described in the LAK3 documentation was revised to include time series results of selected variables (streamflows, stream depth and width, streambed conductance, solute concentrations, and solute loads) for specified stream reaches. The mass-balance or continuity approach for routing flow and solutes through a stream network may not be applicable for all interactions between streams and aquifers. The SFR1 Package is best suited for modeling long-term changes (months to hundreds of years) in ground-water flow and solute concentrations using averaged flows in streams. The Package is not recommended for modeling the transient exchange of water between streams and aquifers when the objective is to examine short-term (minutes to days) effects caused by rapidly changing streamflows.

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

NASA Astrophysics Data System (ADS)

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 discharges, which are updated immediately (a calibration only needs a couple of seconds or less, a simulation is almost immediate). In addition, time series of internal variables, live-visualisation of internal variables evolution and performance statistics are provided. This interface allows for hands-on exercises that can include for instance the analysis by students of: - The effects of each parameter and model components on simulated discharge - The effects of objective functions based on high flows- or low flows-focused criteria on simulated discharge - The seasonality of the model components. References Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2016). shiny: Web Application Framework for R. R package version 0.13.2. https://CRAN.R-project.org/package=shiny Coron L., Thirel G., Perrin C., Delaigue O., Andréassian V., airGR: a suite of lumped hydrological models in an R-package, Environmental Modelling and software, 2017, submitted. Coron, L., Perrin, C. and Michel, C. (2016). airGR: Suite of GR hydrological models for precipitation-runoff modelling. R package version 1.0.3. https://webgr.irstea.fr/airGR/?lang=en. Olivier Delaigue and Laurent Coron (2016). airGRteaching: Tools to simplify the use of the airGR hydrological package by students. R package version 0.0.1. https://webgr.irstea.fr/airGR/?lang=en R Core Team (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Simple method for the selection of the appropriate food simulant for the evaluation of a specific food/packaging interaction.

PubMed

Hernández-Muñoz, P; Catalá, R; Gavara, R

2002-01-01

Knowledge of the extent of food/packaging interactions is essential to provide assurance of food quality and shelf life, especially in migration and sorption processes that commonly reach equilibrium during the lifetime of a commercial packaged foodstuff. The limits of sorption and migration must be measured in the presence of the specific food or an appropriate food simulant. The partition equilibrium of food aroma compounds between plastic films and foods or food simulants (K(A,P/L) has been characterized. Two polymers (LLDPE and PET), three organic compounds (ethyl caproate, hexanal and 2-phenylethanol), four food products with varying fat content (milk cream, mayonnaise, margarine and oil) and three simulants (ethanol 95%, n-heptane and isooctane) were selectedfor study. The results show the effect of the aroma compound volatility, and polarity, as well as its compatibility with the polymer and the food or food simulant. Equilibrium constants for the organic compound between the polymers and a gaseous phase (K(A,P/V)) as well as between the food (or food simulant) and a gaseous phase (K(A,L/V)) were also determined. An approach is presented to estimate K(A,P/V) from the binary equilibrium constants K(A,P/V) and K(A,L/V). Calculated results were shown to describe experimental data very well and indicated that compatibility between the aroma and the food or food simulant is the main contributing factor to the partition equilibrium describing the extent of food/packaging interactions. Therefore, the measurement of liquid/vapour equilibrium can be regarded as a powerful tool to compare the effectiveness of food simulants as substitutes of a particular food product and can be used as a guide for the selection of the appropriate simulant.

Maestro Workflow Conductor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Di Natale, Francesco

2017-06-01

MaestroWF is a Python tool and software package for loading YAML study specifications that represents a simulation campaign. The package is capable of parameterizing a study, pulling dependencies automatically, formatting output directories, and managing the flow and execution of the campaign. MaestroWF also provides a set of abstracted objects that can also be used to develop user specific scripts for launching simulation campaigns.

Temperature-package power correlations for open-mode geologic disposal concepts.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hardin, Ernest.

2013-02-01

Logistical simulation of spent nuclear fuel (SNF) management in the U.S. combines storage, transportation and disposal elements to evaluate schedule, cost and other resources needed for all major operations leading to final geologic disposal. Geologic repository reference options are associated with limits on waste package thermal power output at emplacement, in order to meet limits on peak temperature for certain key engineered and natural barriers. These package power limits are used in logistical simulation software such as CALVIN, as threshold requirements that must be met by means of decay storage or SNF blending in waste packages, before emplacement in amore » repository. Geologic repository reference options include enclosed modes developed for crystalline rock, clay or shale, and salt. In addition, a further need has been addressed for open modes in which SNF can be emplaced in a repository, then ventilated for decades or longer to remove heat, prior to permanent repository closure. For each open mode disposal concept there are specified durations for surface decay storage (prior to emplacement), repository ventilation, and repository closure operations. This study simulates those steps for several timing cases, and for SNF with three fuel-burnup characteristics, to develop package power limits at which waste packages can be emplaced without exceeding specified temperature limits many years later after permanent closure. The results are presented in the form of correlations that span a range of package power and peak postclosure temperature, for each open-mode disposal concept, and for each timing case. Given a particular temperature limit value, the corresponding package power limit for each case can be selected for use in CALVIN and similar tools.« less

Modeling hydraulic regenerative hybrid vehicles using AMESim and Matlab/Simulink

NASA Astrophysics Data System (ADS)

Lynn, Alfred; Smid, Edzko; Eshraghi, Moji; Caldwell, Niall; Woody, Dan

2005-05-01

This paper presents the overview of the simulation modeling of a hydraulic system with regenerative braking used to improve vehicle emissions and fuel economy. Two simulation software packages were used together to enhance the simulation capability for fuel economy results and development of vehicle and hybrid control strategy. AMESim, a hydraulic simulation software package modeled the complex hydraulic circuit and component hardware and was interlinked with a Matlab/Simulink model of the vehicle, engine and the control strategy required to operate the vehicle and the hydraulic hybrid system through various North American and European drive cycles.

IN-PACKAGE CHEMISTRY ABSTRACTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 EQ3/6more » 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.« less

NY TBO Research: Integrated Demand Management (IDM): IDM Concept, Tools, and Training Package

NASA Technical Reports Server (NTRS)

Smith, Nancy

2016-01-01

A series of human-in-the-loop simulation sessions were conducted in the Airspace Operations Laboratory (AOL) to evaluate a new traffic management concept called Integrated Demand Management (IDM). The simulation explored how to address chronic equity, throughput and delay issues associated with New Yorks high-volume airports by operationally integrating three current and NextGen capabilities the Collaborative Trajectory Options Program (CTOP), Time-Based Flow Management (TBFM) and Required Time of Arrival (RTA) in order to better manage traffic demand within the National Air Traffic System. A package of presentation slides was developed to describe the concept, tools, and training materials used in the simulation sessions. The package will be used to outbrief our stakeholders by both presenting orally and disseminating of the materials via email.

Sensitivity of a cloud parameterization package in the National Center for Atmospheric Research Community Climate Model

NASA Astrophysics Data System (ADS)

Kao, C.-Y. J.; Smith, W. S.

1999-05-01

A physically based cloud parameterization package, which includes the Arakawa-Schubert (AS) scheme for subgrid-scale convective clouds and the Sundqvist (SUN) scheme for nonconvective grid-scale layered clouds (hereafter referred to as the SUNAS cloud package), is incorporated into the National Center for Atmospheric Research (NCAR) Community Climate Model, Version 2 (CCM2). The AS scheme is used for a more reasonable heating distribution due to convective clouds and their associated precipitation. The SUN scheme allows for the prognostic computation of cloud water so that the cloud optical properties are more physically determined for shortwave and longwave radiation calculations. In addition, the formation of anvil-like clouds from deep convective systems is able to be simulated with the SUNAS package. A 10-year simulation spanning the period from 1980 to 1989 is conducted, and the effect of the cloud package on the January climate is assessed by comparing it with various available data sets and the National Center for Environmental Protection/NCAR reanalysis. Strengths and deficiencies of both the SUN and AS methods are identified and discussed. The AS scheme improves some aspects of the model dynamics and precipitation, especially with respect to the Pacific North America (PNA) pattern. CCM2's tendency to produce a westward bias of the 500 mbar stationary wave (time-averaged zonal anomalies) in the PNA sector is remedied apparently because of a less "locked-in" heating pattern in the tropics. The additional degree of freedom added by the prognostic calculation of cloud water in the SUN scheme produces interesting results in the modeled cloud and radiation fields compared with data. In general, too little cloud water forms in the tropics, while excessive cloud cover and cloud liquid water are simulated in midlatitudes. This results in a somewhat degraded simulation of the radiation budget. The overall simulated precipitation by the SUNAS package is, however, substantially improved over the original CCM2.

Column compression strength of tubular packaging forms made from paper

Treesearch

Thomas J. Urbanik; Sung K. Lee; Charles G. Johnson

2006-01-01

Tubular packaging forms fabricated and shaped from rolled paper are used as reinforcing corner posts for major appliances packaged in corrugated containers. Tests of column compression strength simulate the expected performance loads from appliances stacked in warehouses. Column strength depends on tube geometry, paper properties, basis weight, and number of...

GDINA and CDM Packages in R

ERIC Educational Resources Information Center

Rupp, André A.; van Rijn, Peter W.

2018-01-01

We review the GIDNA and CDM packages in R for fitting cognitive diagnosis/diagnostic classification models. We first provide a summary of their core capabilities and then use both simulated and real data to compare their functionalities in practice. We found that the most relevant routines in the two packages appear to be more similar than…

49 CFR 178.609 - Test requirements for packagings for infectious substances.

Code of Federal Regulations, 2012 CFR

2012-10-01

... solid infectious substance should be replaced by water or, where conditioning at −18 °C (0 °F) is specified, by water/antifreeze. Each primary receptacle must be filled to 98 percent capacity. Packagings... packaging. (e) The samples must be subjected to a water spray to simulate exposure to rainfall of...

49 CFR 178.609 - Test requirements for packagings for infectious substances.

Code of Federal Regulations, 2014 CFR

2014-10-01

... solid infectious substance should be replaced by water or, where conditioning at −18 °C (0 °F) is specified, by water/antifreeze. Each primary receptacle must be filled to 98 percent capacity. Packagings... packaging. (e) The samples must be subjected to a water spray to simulate exposure to rainfall of...

49 CFR 178.609 - Test requirements for packagings for infectious substances.

Code of Federal Regulations, 2013 CFR

2013-10-01

... solid infectious substance should be replaced by water or, where conditioning at −18 °C (0 °F) is specified, by water/antifreeze. Each primary receptacle must be filled to 98 percent capacity. Packagings... packaging. (e) The samples must be subjected to a water spray to simulate exposure to rainfall of...

Miniature stick-packaging--an industrial technology for pre-storage and release of reagents in lab-on-a-chip systems.

PubMed

van Oordt, Thomas; Barb, Yannick; Smetana, Jan; Zengerle, Roland; von Stetten, Felix

2013-08-07

Stick-packaging of goods in tubular-shaped composite-foil pouches has become a popular technology for food and drug packaging. We miniaturized stick-packaging for use in lab-on-a-chip (LOAC) systems to pre-store and on-demand release the liquid and dry reagents in a volume range of 80-500 μl. An integrated frangible seal enables the pressure-controlled release of reagents and simplifies the layout of LOAC systems, thereby making the package a functional microfluidic release unit. The frangible seal is adjusted to defined burst pressures ranging from 20 to 140 kPa. The applied ultrasonic welding process allows the packaging of temperature sensitive reagents. Stick-packs have been successfully tested applying recovery tests (where 99% (STDV = 1%) of 250 μl pre-stored liquid is released), long-term storage tests (where there is loss of only <0.5% for simulated 2 years) and air transport simulation tests. The developed technology enables the storage of a combination of liquid and dry reagents. It is a scalable technology suitable for rapid prototyping and low-cost mass production.

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules.

PubMed

Solernou, Albert; Hanson, Benjamin S; Richardson, Robin A; Welch, Robert; Read, Daniel J; Harlen, Oliver G; Harris, Sarah A

2018-03-01

Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package.

Reviews.

ERIC Educational Resources Information Center

Science Teacher, 1988

1988-01-01

Reviews four software packages available for IBM PC or Apple II. Includes "Graphical Analysis III"; "Space Max: Space Station Construction Simulation"; "Guesstimation"; and "Genetic Engineering Toolbox." Focuses on each packages' strengths in a high school context. (CW)

Romanian experience on packaging testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vieru, G.

2007-07-01

With more than twenty years ago, the Institute for Nuclear Research Pitesti (INR), through its Reliability and Testing Laboratory, was licensed by the Romanian Nuclear Regulatory Body- CNCAN and to carry out qualification tests [1] for packages intended to be used for the transport and storage of radioactive materials. Radioactive materials, generated by Romanian nuclear facilities [2] are packaged in accordance with national [3] and the IAEA's Regulations [1,6] for a safe transport to the disposal center. Subjecting these packages to the normal and simulating test conditions accomplish the evaluation and certification in order to prove the package technical performances.more » The paper describes the qualification tests for type A and B packages used for transport and storage of radioactive materials, during a period of 20 years of experience. Testing is used to substantiate assumption in analytical models and to demonstrate package structural response. The Romanian test facilities [1,3,6] are used to simulate the required qualification tests and have been developed at INR Pitesti, the main supplier of type A packages used for transport and storage of low radioactive wastes in Romania. The testing programme will continue to be a strong option to support future package development, to perform a broad range of verification and certification tests on radioactive material packages or component sections, such as packages used for transport of radioactive sources to be used for industrial or medical purposes [2,8]. The paper describes and contain illustrations showing some of the various tests packages which have been performed during certain periods and how they relate to normal conditions and minor mishaps during transport. Quality assurance and quality controls measures taken in order to meet technical specification provided by the design there are also presented and commented. (authors)« less

Results of intravehicular manned cargo-transfer studies in simulated weightlessness

NASA Technical Reports Server (NTRS)

Spady, A. A., Jr.; Beasley, G. P.; Yenni, K. R.; Eisele, D. F.

1972-01-01

A parametric investigation was conducted in a water immersion simulator to determine the effect of package mass, moment of inertia, and size on the ability of man to transfer cargo in simulated weightlessness. Results from this study indicate that packages with masses of at least 744 kg and moments of inertia of at least 386 kg-m2 can be manually handled and transferred satisfactorily under intravehicular conditions using either one- or two-rail motion aids. Data leading to the conclusions and discussions of test procedures and equipment are presented.

Item Response Data Analysis Using Stata Item Response Theory Package

ERIC Educational Resources Information Center

Yang, Ji Seung; Zheng, Xiaying

2018-01-01

The purpose of this article is to introduce and review the capability and performance of the Stata item response theory (IRT) package that is available from Stata v.14, 2015. Using a simulated data set and a publicly available item response data set extracted from Programme of International Student Assessment, we review the IRT package from…

Design and Evaluation of an Integrated Online Motion Control Training Package

ERIC Educational Resources Information Center

Buiu, C.

2009-01-01

The aim of this paper is to present an integrated Internet-based package for teaching the fundamentals of motion control by using a wide range of resources: theory, videos, simulators, games, quizzes, and a remote lab. The package is aimed at automation technicians, pupils at vocational schools and students taking an introductory course in…

The State System Exercise. Learning Packages in International Relations. Learning Package One.

ERIC Educational Resources Information Center

Coplin, William D.

Learning package 1, the first in a series of four, incorporates a simulation exercise designed to help students in higher education understand factors that affect the stability of the international relations system. Focus is on a "system" perspective in order to show the historical development and to point up the operation of various…

14 CFR Appendix E to Part 60 - Qualification Performance Standards for Quality Management Systems for Flight Simulation Training...

Code of Federal Regulations, 2014 CFR

2014-01-01

... data made available to the NSPM (the validation data package) includes the aircraft manufacturer's... longer in business), and if appropriate, with the person who supplied the aircraft data package for the FFS for the purposes of receiving notification of data package changes. E1.13. A policy, process, or...

14 CFR Appendix E to Part 60 - Qualification Performance Standards for Quality Management Systems for Flight Simulation Training...

Code of Federal Regulations, 2012 CFR

2012-01-01

... data made available to the NSPM (the validation data package) includes the aircraft manufacturer's... longer in business), and if appropriate, with the person who supplied the aircraft data package for the FFS for the purposes of receiving notification of data package changes. E1.13. A policy, process, or...

High Resolution Aerospace Applications using the NASA Columbia Supercomputer

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.; Aftosmis, Michael J.; Berger, Marsha

2005-01-01

This paper focuses on the parallel performance of two high-performance aerodynamic simulation packages on the newly installed NASA Columbia supercomputer. These packages include both a high-fidelity, unstructured, Reynolds-averaged Navier-Stokes solver, and a fully-automated inviscid flow package for cut-cell Cartesian grids. The complementary combination of these two simulation codes enables high-fidelity characterization of aerospace vehicle design performance over the entire flight envelope through extensive parametric analysis and detailed simulation of critical regions of the flight envelope. Both packages. are industrial-level codes designed for complex geometry and incorpor.ats. CuStomized multigrid solution algorithms. The performance of these codes on Columbia is examined using both MPI and OpenMP and using both the NUMAlink and InfiniBand interconnect fabrics. Numerical results demonstrate good scalability on up to 2016 CPUs using the NUMAIink4 interconnect, with measured computational rates in the vicinity of 3 TFLOP/s, while InfiniBand showed some performance degradation at high CPU counts, particularly with multigrid. Nonetheless, the results are encouraging enough to indicate that larger test cases using combined MPI/OpenMP communication should scale well on even more processors.

An Integrated Software Package to Enable Predictive Simulation Capabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Yousu; Fitzhenry, Erin B.; Jin, Shuangshuang

The power grid is increasing in complexity due to the deployment of smart grid technologies. Such technologies vastly increase the size and complexity of power grid systems for simulation and modeling. This increasing complexity necessitates not only the use of high-performance-computing (HPC) techniques, but a smooth, well-integrated interplay between HPC applications. This paper presents a new integrated software package that integrates HPC applications and a web-based visualization tool based on a middleware framework. This framework can support the data communication between different applications. Case studies with a large power system demonstrate the predictive capability brought by the integrated software package,more » as well as the better situational awareness provided by the web-based visualization tool in a live mode. Test results validate the effectiveness and usability of the integrated software package.« less

Wave Resource Characterization Using an Unstructured Grid Modeling Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wei-Cheng; Yang, Zhaoqing; Wang, Taiping

This paper presents a modeling study conducted on the central Oregon coast for wave resource characterization using the unstructured-grid SWAN model coupled with a nested-grid WWIII model. The flexibility of models of various spatial resolutions and the effects of open- boundary conditions simulated by a nested-grid WWIII model with different physics packages were evaluated. The model results demonstrate the advantage of the unstructured-grid modeling approach for flexible model resolution and good model skills in simulating the six wave resource parameters recommended by the International Electrotechnical Commission in comparison to the observed data in Year 2009 at National Data Buoy Centermore » Buoy 46050. Notably, spectral analysis indicates that the ST4 physics package improves upon the model skill of the ST2 physics package for predicting wave power density for large waves, which is important for wave resource assessment, device load calculation, and risk management. In addition, bivariate distributions show the simulated sea state of maximum occurrence with the ST4 physics package matched the observed data better than that with the ST2 physics package. This study demonstrated that the unstructured-grid wave modeling approach, driven by the nested-grid regional WWIII outputs with the ST4 physics package, can efficiently provide accurate wave hindcasts to support wave resource characterization. Our study also suggests that wind effects need to be considered if the dimension of the model domain is greater than approximately 100 km, or O (10^2 km).« less

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

DOE PAGES

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-10-25

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy.

PubMed

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-01-01

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic , using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic .

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pryor, Alan; Ophus, Colin; Miao, Jianwei

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations.

PubMed

Samoylova, Liubov; Buzmakov, Alexey; Chubar, Oleg; Sinn, Harald

2016-08-01

This article describes the WavePropaGator ( WPG ) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop ( SRW ) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.

ARM Data-Oriented Metrics and Diagnostics Package for Climate Model Evaluation Value-Added Product

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chengzhu; Xie, Shaocheng

A Python-based metrics and diagnostics package is currently being developed by the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Infrastructure Team at Lawrence Livermore National Laboratory (LLNL) to facilitate the use of long-term, high-frequency measurements from the ARM Facility in evaluating the regional climate simulation of clouds, radiation, and precipitation. This metrics and diagnostics package computes climatological means of targeted climate model simulation and generates tables and plots for comparing the model simulation with ARM observational data. The Coupled Model Intercomparison Project (CMIP) model data sets are also included in the package to enable model intercomparison as demonstratedmore » in Zhang et al. (2017). The mean of the CMIP model can serve as a reference for individual models. Basic performance metrics are computed to measure the accuracy of mean state and variability of climate models. The evaluated physical quantities include cloud fraction, temperature, relative humidity, cloud liquid water path, total column water vapor, precipitation, sensible and latent heat fluxes, and radiative fluxes, with plan to extend to more fields, such as aerosol and microphysics properties. Process-oriented diagnostics focusing on individual cloud- and precipitation-related phenomena are also being developed for the evaluation and development of specific model physical parameterizations. The version 1.0 package is designed based on data collected at ARM’s Southern Great Plains (SGP) Research Facility, with the plan to extend to other ARM sites. The metrics and diagnostics package is currently built upon standard Python libraries and additional Python packages developed by DOE (such as CDMS and CDAT). The ARM metrics and diagnostic package is available publicly with the hope that it can serve as an easy entry point for climate modelers to compare their models with ARM data. In this report, we first present the input data, which constitutes the core content of the metrics and diagnostics package in section 2, and a user's guide documenting the workflow/structure of the version 1.0 codes, and including step-by-step instruction for running the package in section 3.« less

Food choice: the battle between package, taste and consumption situation.

PubMed

Gutjar, Swetlana; de Graaf, Cees; Palascha, Aikaterini; Jager, Gerry

2014-09-01

The present study compared how intrinsic (sensory) and extrinsic (packaging) product properties influence actual food choice in combination with the concept of product appropriateness in a specific consumption context. Food choice of seven test products was measured in three breakfast sessions within a simulated cafeteria setting with subsequent product consumption. Test products were five breakfast drinks and two dessert products considered as inappropriate for breakfast. One hundred and three participants took part in a blind taste session, after which they chose one out of the seven foods to consume for breakfast. In a second session (familiar package session), the same participants based their choice on the package of the seven foods they tasted in the first session. An additional group of 65 participants took part in a third naïve package session, where they chose just on the basis of package without being previously exposed to the foods. Results showed that food choices in the naïve package session were guided by the package that labelled the products as "breakfast product". Food choices in the blind session were strongly correlated (r = 0.8) with the liking of the products. Food choice in the "familiar package session" lay between the blind and naïve package session. It is concluded that food choice in a simulated cafeteria setting is guided by extrinsic (package) as well as intrinsic (sensory) properties and both can act as a cue for product appropriateness given a specific consumption context. Depending on the salience of either intrinsic or extrinsic properties during the choice moment their impact on choice is stronger. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules

PubMed Central

Solernou, Albert

2018-01-01

Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package. PMID:29570700

Simulating reservoir leakage in ground-water models

USGS Publications Warehouse

Fenske, J.P.; Leake, S.A.; Prudic, David E.

1997-01-01

Leakage to ground water resulting from the expansion and contraction of reservoirs cannot be easily simulated by most ground-water flow models. An algorithm, entitled the Reservoir Package, was developed for the United States Geological Survey (USGS) three-dimensional finite-difference modular ground-water flow model MODFLOW. The Reservoir Package automates the process of specifying head-dependent boundary cells, eliminating the need to divide a simulation into many stress periods while improving accuracy in simulating changes in ground-water levels resulting from transient reservoir stage. Leakage between the reservoir and the underlying aquifer is simulated for each model cell corrresponding to the inundated area by multiplying the head difference between the reservoir and the aquifer with the hydraulic conductance of the reservoir-bed sediments.

Browndye: A Software Package for Brownian Dynamics

PubMed Central

McCammon, J. Andrew

2010-01-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. PMID:21132109

EQS Goes R: Simulations for SEM Using the Package REQS

ERIC Educational Resources Information Center

Mair, Patrick; Wu, Eric; Bentler, Peter M.

2010-01-01

The REQS package is an interface between the R environment of statistical computing and the EQS software for structural equation modeling. The package consists of 3 main functions that read EQS script files and import the results into R, call EQS script files from R, and run EQS script files from R and import the results after EQS computations.…

Renal angiomyolipoma in patients with tuberous sclerosis complex: findings from the TuberOus SClerosis registry to increase disease Awareness.

PubMed

Kingswood, J Chris; Belousova, Elena; Benedik, Mirjana P; Carter, Tom; Cottin, Vincent; Curatolo, Paolo; Dahlin, Maria; D' Amato, Lisa; d'Augères, Guillaume Beaure; de Vries, Petrus J; Ferreira, José C; Feucht, Martha; Fladrowski, Carla; Hertzberg, Christoph; Jozwiak, Sergiusz; Lawson, John A; Macaya, Alfons; Marques, Ruben; Nabbout, Rima; O'Callaghan, Finbar; Qin, Jiong; Sander, Valentin; Sauter, Matthias; Shah, Seema; Takahashi, Yukitoshi; Touraine, Renaud; Youroukos, Sotiris; Zonnenberg, Bernard; Jansen, Anna C

2018-04-25

Renal angiomyolipoma occurs at a high frequency in patients with tuberous sclerosis complex (TSC) and is associated with potentially life-threatening complications. Despite this frequency and severity, there are no large population-based cohort studies. Here we present baseline and follow-up data of the international TuberOus SClerosis registry to increase disease Awareness (TOSCA) with an aim to provide detailed clinical characteristics of renal angiomyolipoma among patients with TSC. Patients of any age with a documented clinic visit for TSC within 12 months or who were newly diagnosed with TSC before participation in the registry were eligible. Data specific to renal angiomyolipoma included physical tumour characteristics (multiple, bilateral, lesion size and growing lesions), clinical signs and symptoms, and management. The effects of age, gender and genotype on the prevalence of renal angiomyolipoma were also evaluated. Renal angiomyolipoma was reported in 51.8% of patients at baseline, with higher frequency in female patients (57.8% versus 42.2%). The median age at diagnosis was 12 years. Prevalence of angiomyolipoma was higher in patients with TSC2 compared with TSC1 mutations (59.2% versus 33.3%, P < 0.01). Of the 1031 patients with angiomyolipoma at baseline, multiple lesions were reported in 88.4% and bilateral in 83.9% of patients, while the size of angiomyolipoma was >3 cm in 34.3% of patients. Most patients were asymptomatic (82%). Frequently reported angiomyolipoma-related symptoms included bleeding, pain, elevated blood pressure and impaired renal function. Embolization and mammalian target of rapamycin inhibitors were the two most common treatment modalities. The TOSCA registry highlights the burden of renal angiomyolipoma in patients with TSC and shows that renal manifestations are initially asymptomatic and are influenced by gender and genotype. Furthermore, the occurrence of significant problems from angiomyolipoma in a minority of younger patients suggests that surveillance should begin in infancy or at initial diagnosis.

Simulating ground water-lake interactions: Approaches and insights

USGS Publications Warehouse

Hunt, R.J.; Haitjema, H.M.; Krohelski, J.T.; Feinstein, D.T.

2003-01-01

Approaches for modeling lake-ground water interactions have evolved significantly from early simulations that used fixed lake stages specified as constant head to sophisticated LAK packages for MODFLOW. Although model input can be complex, the LAK package capabilities and output are superior to methods that rely on a fixed lake stage and compare well to other simple methods where lake stage can be calculated. Regardless of the approach, guidelines presented here for model grid size, location of three-dimensional flow, and extent of vertical capture can facilitate the construction of appropriately detailed models that simulate important lake-ground water interactions without adding unnecessary complexity. In addition to MODFLOW approaches, lake simulation has been formulated in terms of analytic elements. The analytic element lake package had acceptable agreement with a published LAK1 problem, even though there were differences in the total lake conductance and number of layers used in the two models. The grid size used in the original LAK1 problem, however, violated a grid size guideline presented in this paper. Grid sensitivity analyses demonstrated that an appreciable discrepancy in the distribution of stream and lake flux was related to the large grid size used in the original LAK1 problem. This artifact is expected regardless of MODFLOW LAK package used. When the grid size was reduced, a finite-difference formulation approached the analytic element results. These insights and guidelines can help ensure that the proper lake simulation tool is being selected and applied.

Modelling robotic systems with DADS

NASA Technical Reports Server (NTRS)

Churchill, L. W.; Sharf, I.

1993-01-01

With the appearance of general off-the-shelf software packages for the simulation of mechanical systems, modelling and simulation of mechanisms has become an easier task. The authors have recently used one such package, DADS, to model the dynamics of rigid and flexible-link robotic manipulators. In this paper, we present this overview of our learning experiences with DADS, in the hope that it will shorten the learning process for others interested in this software.

Method to simulate and analyse induced stresses for laser crystal packaging technologies.

PubMed

Ribes-Pleguezuelo, Pol; Zhang, Site; Beckert, Erik; Eberhardt, Ramona; Wyrowski, Frank; Tünnermann, Andreas

2017-03-20

A method to simulate induced stresses for a laser crystal packaging technique and the consequent study of birefringent effects inside the laser cavities has been developed. The method has been implemented by thermo-mechanical simulations implemented with ANSYS 17.0. ANSYS results were later imported in VirtualLab Fusion software where input/output beams in terms of wavelengths and polarization were analysed. The study has been built in the context of a low-stress soldering technique implemented for glass or crystal optics packaging's called the solderjet bumping technique. The outcome of the analysis showed almost no difference between the input and output laser beams for the laser cavity constructed with an yttrium aluminum garnet active laser crystal, a second harmonic generator beta-barium borate, and the output laser mirror made of fused silica assembled by the low-stress solderjet bumping technique.

WebGL-enabled 3D visualization of a Solar Flare Simulation

NASA Astrophysics Data System (ADS)

Chen, A.; Cheung, C. M. M.; Chintzoglou, G.

2016-12-01

The visualization of magnetohydrodynamic (MHD) simulations of astrophysical systems such as solar flares often requires specialized software packages (e.g. Paraview and VAPOR). A shortcoming of using such software packages is the inability to share our findings with the public and scientific community in an interactive and engaging manner. By using the javascript-based WebGL application programming interface (API) and the three.js javascript package, we create an online in-browser experience for rendering solar flare simulations that will be interactive and accessible to the general public. The WebGL renderer displays objects such as vector flow fields, streamlines and textured isosurfaces. This allows the user to explore the spatial relation between the solar coronal magnetic field and the thermodynamic structure of the plasma in which the magnetic field is embedded. Plans for extending the features of the renderer will also be presented.

deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis.

PubMed

Low, Diana H P; Motakis, Efthymios

2013-10-01

Binding free energy calculations obtained through molecular dynamics simulations reflect intermolecular interaction states through a series of independent snapshots. Typically, the free energies of multiple simulated series (each with slightly different starting conditions) need to be estimated. Previous approaches carry out this task by moving averages at certain decorrelation times, assuming that the system comes from a single conformation description of binding events. Here, we discuss a more general approach that uses statistical modeling, wavelets denoising and hierarchical clustering to estimate the significance of multiple statistically distinct subpopulations, reflecting potential macrostates of the system. We present the deltaGseg R package that performs macrostate estimation from multiple replicated series and allows molecular biologists/chemists to gain physical insight into the molecular details that are not easily accessible by experimental techniques. deltaGseg is a Bioconductor R package available at http://bioconductor.org/packages/release/bioc/html/deltaGseg.html.

PlasmaPy: beginning a community developed Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas A.; Huang, Yi-Min; PlasmaPy Collaboration

2016-10-01

In recent years, researchers in several disciplines have collaborated on community-developed open source Python packages such as Astropy, SunPy, and SpacePy. These packages provide core functionality, common frameworks for data analysis and visualization, and educational tools. We propose that our community begins the development of PlasmaPy: a new open source core Python package for plasma physics. PlasmaPy could include commonly used functions in plasma physics, easy-to-use plasma simulation codes, Grad-Shafranov solvers, eigenmode solvers, and tools to analyze both simulations and experiments. The development will include modern programming practices such as version control, embedding documentation in the code, unit tests, and avoiding premature optimization. We will describe early code development on PlasmaPy, and discuss plans moving forward. The success of PlasmaPy depends on active community involvement and a welcoming and inclusive environment, so anyone interested in joining this collaboration should contact the authors.

An R package for simulating growth and organic wastage in aquaculture farms in response to environmental conditions and husbandry practices

PubMed Central

Baldan, Damiano; Porporato, Erika Maria Diletta; Pastres, Roberto

2018-01-01

A new R software package, RAC, is presented. RAC allows to simulate the rearing cycle of 4 species, finfish and shellfish, highly important in terms of production in the Mediterranean Sea. The package works both at the scale of the individual and of the farmed population. Mathematical models included in RAC were all validated in previous works, and account for growth and metabolism, based on input data characterizing the forcing functions—water temperature, and food quality/quantity. The package provides a demo dataset of forcings for each species, as well as a typical set of husbandry parameters for Mediterranean conditions. The present work illustrates RAC main features, and its current capabilities/limitations. Three test cases are presented as a proof of concept of RAC applicability, and to demonstrate its potential for integrating different open products nowadays provided by remote sensing and operational oceanography. PMID:29723208

NORTICA—a new code for cyclotron analysis

NASA Astrophysics Data System (ADS)

Gorelov, D.; Johnson, D.; Marti, F.

2001-12-01

The new package NORTICA (Numerical ORbit Tracking In Cyclotrons with Analysis) of computer codes for beam dynamics simulations is under development at NSCL. The package was started as a replacement for the code MONSTER [1] developed in the laboratory in the past. The new codes are capable of beam dynamics simulations in both CCF (Coupled Cyclotron Facility) accelerators, the K500 and K1200 superconducting cyclotrons. The general purpose of this package is assisting in setting and tuning the cyclotrons taking into account the main field and extraction channel imperfections. The computer platform for the package is Alpha Station with UNIX operating system and X-Windows graphic interface. A multiple programming language approach was used in order to combine the reliability of the numerical algorithms developed over the long period of time in the laboratory and the friendliness of modern style user interface. This paper describes the capability and features of the codes in the present state.

Behavior of Listeria monocytogenes at 7 degrees C in commercial turkey breast, with or without antimicrobials, after simulated contamination for manufacturing, retail and consumer settings.

PubMed

Lianou, Alexandra; Geornaras, Ifigenia; Kendall, Patricia A; Scanga, John A; Sofos, John N

2007-08-01

Uncured turkey breast, commercially available with or without a mixture of potassium lactate and sodium diacetate, was sliced, inoculated with a 10-strain composite of Listeria monocytogenes, vacuum-packaged, and stored at 4 degrees C, to simulate contamination after a lethal processing step at the plant. At 5, 15, 25 and 50 days of storage, packages were opened, slices were tested, and bags with remaining slices were reclosed with rubber bands; this simulated home use of plant-sliced and -packaged product. At the same above time intervals, portions of original product (stored at 4 degrees C in original processing bags) were sliced and inoculated as above, and packaged in delicatessen bags, simulating contamination during slicing/handling at retail or home. Both sets of bags were stored aerobically at 7 degrees C for 12 days to simulate home storage. L. monocytogenes populations were lower (P<0.05) during storage in turkey breast containing a combination of lactate and diacetate compared to product without antimicrobials under both contamination scenarios. Due to prolific growth of the pathogen under the plant-contamination scenario in product without lactate-diacetate during vacuum-packaged storage (4 degrees C), populations at 3 days of aerobic storage (7 degrees C) of such product ranged from 4.6 to 7.4 log cfu/cm(2). Under the retail/home-contamination scenario, mean growth rates (log cfu/cm(2)/day) of the organism during aerobic storage ranged from 0.14 to 0.16, and from 0.25 to 0.51, in product with and without lactate-diacetate, respectively; growth rates in turkey breast without antimicrobials decreased (P<0.05) with age of the product. Overall, product without antimicrobials inoculated to simulate plant-contamination and product with lactate-diacetate inoculated to simulate retail/home-contamination were associated with the highest and lowest pathogen levels during aerobic storage at 7 degrees C, respectively. However, 5- and 15-day-old turkey breast without lactate-diacetate stored aerobically for 12 days resulted in similar pathogen levels (7.3-7.7 log cfu/cm(2)), irrespective of contamination scenario.

High-Performance Computing for the Electromagnetic Modeling and Simulation of Interconnects

NASA Technical Reports Server (NTRS)

Schutt-Aine, Jose E.

1996-01-01

The electromagnetic modeling of packages and interconnects plays a very important role in the design of high-speed digital circuits, and is most efficiently performed by using computer-aided design algorithms. In recent years, packaging has become a critical area in the design of high-speed communication systems and fast computers, and the importance of the software support for their development has increased accordingly. Throughout this project, our efforts have focused on the development of modeling and simulation techniques and algorithms that permit the fast computation of the electrical parameters of interconnects and the efficient simulation of their electrical performance.

TESSIM: a simulator for the Athena-X-IFU

NASA Astrophysics Data System (ADS)

Wilms, J.; Smith, S. J.; Peille, P.; Ceballos, M. T.; Cobo, B.; Dauser, T.; Brand, T.; den Hartog, R. H.; Bandler, S. R.; de Plaa, J.; den Herder, J.-W. A.

2016-07-01

We present the design of tessim, a simulator for the physics of transition edge sensors developed in the framework of the Athena end to end simulation effort. Designed to represent the general behavior of transition edge sensors and to provide input for engineering and science studies for Athena, tessim implements a numerical solution of the linearized equations describing these devices. The simulation includes a model for the relevant noise sources and several implementations of possible trigger algorithms. Input and output of the software are standard FITS- files which can be visualized and processed using standard X-ray astronomical tool packages. Tessim is freely available as part of the SIXTE package (http://www.sternwarte.uni-erlangen.de/research/sixte/).

TESSIM: A Simulator for the Athena-X-IFU

NASA Technical Reports Server (NTRS)

Wilms, J.; Smith, S. J.; Peille, P.; Ceballos, M. T.; Cobo, B.; Dauser, T.; Brand, T.; Den Hartog, R. H.; Bandler, S. R.; De Plaa, J.;

Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

NASA Astrophysics Data System (ADS)

Dizkirici, Ayten; Tekpinar, Mustafa

2015-03-01

GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

In-Package Chemistry Abstraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

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, amore » 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 package has been breached but the drip shield remains intact, so all of the seepage flow is diverted from the waste package. The chemistry from the vapor influx case is used to determine the stability of colloids and the solubility of radionuclides available for transport by diffusion, and to determine the degradation rates for the waste forms. TSPA-LA uses the water influx case for the seismic scenario, where the waste package has been breached and the drip shield has been damaged such that seepage flow is actually directed into the waste package. The chemistry from the water influx case that is a function of the flow rate is used to determine the stability of colloids and the solubility of radionuclides available for transport by diffusion and advection, and to determine the degradation rates for the CSNF and HLW glass. TSPA-LA does not use this model for the igneous scenario. Outputs from the in-package chemistry model implemented inside TSPA-LA include pH, ionic strength, and total carbonate concentration. These inputs to TSPA-LA will be linked to the following principle factors: dissolution rates of the CSNF and HLWG, dissolved concentrations of radionuclides, and colloid generation.« less

Introducing Computer Simulation into the High School: An Applied Mathematics Curriculum.

ERIC Educational Resources Information Center

Roberts, Nancy

1981-01-01

A programing language called DYNAMO, developed especially for writing simulation models, is promoted. Details of six, self-teaching curriculum packages recently developed for simulation-oriented instruction are provided. (MP)

Use of computer modeling to investigate a dynamic interaction problem in the Skylab TACS quad-valve package

NASA Technical Reports Server (NTRS)

Hesser, R. J.; Gershman, R.

1975-01-01

A valve opening-response problem encountered during development of a control valve for the Skylab thruster attitude control system (TACS) is described. The problem involved effects of dynamic interaction among valves in the quad-redundant valve package. Also described is a detailed computer simulation of the quad-valve package which was helpful in resolving the problem.

MODFLOW-2005, The U.S. Geological Survey Modular Ground-Water Model - Documentation of the Multiple-Refined-Areas Capability of Local Grid Refinement (LGR) and the Boundary Flow and Head (BFH) Package

USGS Publications Warehouse

Mehl, Steffen W.; Hill, Mary C.

2007-01-01

This report documents the addition of the multiple-refined-areas capability to shared node Local Grid Refinement (LGR) and Boundary Flow and Head (BFH) Package of MODFLOW-2005, the U.S. Geological Survey modular, three-dimensional, finite-difference ground-water flow model. LGR now provides the capability to simulate ground-water flow by using one or more block-shaped, higher resolution local grids (child model) within a coarser grid (parent model). LGR accomplishes this by iteratively coupling separate MODFLOW-2005 models such that heads and fluxes are balanced across the shared interfacing boundaries. The ability to have multiple, nonoverlapping areas of refinement is important in situations where there is more than one area of concern within a regional model. In this circumstance, LGR can be used to simulate these distinct areas with higher resolution grids. LGR can be used in two-and three-dimensional, steady-state and transient simulations and for simulations of confined and unconfined ground-water systems. The BFH Package can be used to simulate these situations by using either the parent or child models independently.

An ARM data-oriented diagnostics package to evaluate the climate model simulation

NASA Astrophysics Data System (ADS)

Zhang, C.; Xie, S.

2016-12-01

A set of diagnostics that utilize long-term high frequency measurements from the DOE Atmospheric Radiation Measurement (ARM) program is developed for evaluating the regional simulation of clouds, radiation and precipitation in climate models. The diagnostics results are computed and visualized automatically in a python-based package that aims to serve as an easy entry point for evaluating climate simulations using the ARM data, as well as the CMIP5 multi-model simulations. Basic performance metrics are computed to measure the accuracy of mean state and variability of simulated regional climate. The evaluated physical quantities include vertical profiles of clouds, temperature, relative humidity, cloud liquid water path, total column water vapor, precipitation, sensible and latent heat fluxes, radiative fluxes, aerosol and cloud microphysical properties. Process-oriented diagnostics focusing on individual cloud and precipitation-related phenomena are developed for the evaluation and development of specific model physical parameterizations. Application of the ARM diagnostics package will be presented in the AGU session. This work is performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344, IM release number is: LLNL-ABS-698645.

Comprehensive testing to measure the response of butyl rubber to Hanford tank waste simulant

DOE Office of Scientific and Technical Information (OSTI.GOV)

NIGREY,PAUL J.

This report presents the findings of the Chemical Compatibility Program developed to evaluate plastic packaging components that may be incorporated in packaging mixed-waste forms for transportation. Consistent with the methodology outlined in this report, the authors performed the second phase of this experimental program to determine the effects of simulant Hanford tank mixed wastes on packaging seal materials. That effort involved the comprehensive testing of five plastic liner materials in an aqueous mixed-waste simulant. The testing protocol involved exposing the materials to {approximately}143, 286, 571, and 3,670 krad of gamma radiation and was followed by 7-, 14-, 28-, 180-day exposuresmore » to the waste simulant at 18, 50, and 60 C. Butyl rubber samples subjected to the same protocol were then evaluated by measuring seven material properties: specific gravity, dimensional changes, mass changes, hardness, compression set, vapor transport rates, and tensile properties. From the analyses, they determined that butyl rubber has relatively good resistance to radiation, this simulant, and a combination of these factors. These results suggest that butyl rubber is a relatively good seal material to withstand aqueous mixed wastes having similar composition to the one used in this study.« less

Response of ethylene propylene diene monomer rubber (EPDM) to simulant Hanford tank waste

DOE Office of Scientific and Technical Information (OSTI.GOV)

NIGREY,PAUL J.

2000-02-01

This report presents the findings of the Chemical Compatibility Program developed to evaluate plastic packaging components that may be incorporated in packaging mixed-waste forms for transportation. Consistent with the methodology outlined in this report, the author performed the second phase of this experimental program to determine the effects of simulant Hanford tank mixed wastes on packaging seal materials. That effort involved the comprehensive testing of five plastic liner materials in an aqueous mixed-waste simulant. The testing protocol involved exposing the materials to {approximately}143, 286, 571, and 3,670 krad of gamma radiation and was followed by 7-, 14-, 28-, 180-day exposuresmore » to the waste simulant at 18, 50, and 60 C. Ethylene propylene diene monomer (EPDM) rubber samples subjected to the same protocol were then evaluated by measuring seven material properties: specific gravity, dimensional changes, mass changes, hardness, compression set, vapor transport rates, and tensile properties. The author has determined that EPDM rubber has excellent resistance to radiation, this simulant, and a combination of these factors. These results suggest that EPDM is an excellent seal material to withstand aqueous mixed wastes having similar composition to the one used in this study.« less

PLATSIM: An efficient linear simulation and analysis package for large-order flexible systems

NASA Technical Reports Server (NTRS)

Maghami, Periman; Kenny, Sean P.; Giesy, Daniel P.

1995-01-01

PLATSIM is a software package designed to provide efficient time and frequency domain analysis of large-order generic space platforms implemented with any linear time-invariant control system. Time domain analysis provides simulations of the overall spacecraft response levels due to either onboard or external disturbances. The time domain results can then be processed by the jitter analysis module to assess the spacecraft's pointing performance in a computationally efficient manner. The resulting jitter analysis algorithms have produced an increase in speed of several orders of magnitude over the brute force approach of sweeping minima and maxima. Frequency domain analysis produces frequency response functions for uncontrolled and controlled platform configurations. The latter represents an enabling technology for large-order flexible systems. PLATSIM uses a sparse matrix formulation for the spacecraft dynamics model which makes both the time and frequency domain operations quite efficient, particularly when a large number of modes are required to capture the true dynamics of the spacecraft. The package is written in MATLAB script language. A graphical user interface (GUI) is included in the PLATSIM software package. This GUI uses MATLAB's Handle graphics to provide a convenient way for setting simulation and analysis parameters.

Logistic Regression with Multiple Random Effects: A Simulation Study of Estimation Methods and Statistical Packages.

PubMed

Kim, Yoonsang; Choi, Young-Ku; Emery, Sherry

2013-08-01

Several statistical packages are capable of estimating generalized linear mixed models and these packages provide one or more of three estimation methods: penalized quasi-likelihood, Laplace, and Gauss-Hermite. Many studies have investigated these methods' performance for the mixed-effects logistic regression model. However, the authors focused on models with one or two random effects and assumed a simple covariance structure between them, which may not be realistic. When there are multiple correlated random effects in a model, the computation becomes intensive, and often an algorithm fails to converge. Moreover, in our analysis of smoking status and exposure to anti-tobacco advertisements, we have observed that when a model included multiple random effects, parameter estimates varied considerably from one statistical package to another even when using the same estimation method. This article presents a comprehensive review of the advantages and disadvantages of each estimation method. In addition, we compare the performances of the three methods across statistical packages via simulation, which involves two- and three-level logistic regression models with at least three correlated random effects. We apply our findings to a real dataset. Our results suggest that two packages-SAS GLIMMIX Laplace and SuperMix Gaussian quadrature-perform well in terms of accuracy, precision, convergence rates, and computing speed. We also discuss the strengths and weaknesses of the two packages in regard to sample sizes.

Geant4 Modifications for Accurate Fission Simulations

NASA Astrophysics Data System (ADS)

Tan, Jiawei; Bendahan, Joseph

Monte Carlo is one of the methods to simulate the generation and transport of radiation through matter. The most widely used radiation simulation codes are MCNP and Geant4. The simulation of fission production and transport by MCNP has been thoroughly benchmarked. There is an increasing number of users that prefer using Geant4 due to the flexibility of adding features. However, it has been found that Geant4 does not have the proper fission-production cross sections and does not produce the correct fission products. To achieve accurate results for studies in fissionable material applications, Geant4 was modified to correct these inaccuracies and to add new capabilities. The fission model developed by the Lawrence Livermore National Laboratory was integrated into the neutron-fission modeling package. The photofission simulation capability was enabled using the same neutron-fission library under the assumption that nuclei fission in the same way, independent of the excitation source. The modified fission code provides the correct multiplicity of prompt neutrons and gamma rays, and produces delayed gamma rays and neutrons with time and energy dependencies that are consistent with ENDF/B-VII. The delayed neutrons are now directly produced by a custom package that bypasses the fragment cascade model. The modifications were made for U-235, U-238 and Pu-239 isotopes; however, the new framework allows adding new isotopes easily. The SLAC nuclear data library is used for simulation of isotopes with an atomic number above 92 because it is not available in Geant4. Results of the modified Geant4.10.1 package of neutron-fission and photofission for prompt and delayed radiation are compared with ENDFB-VII and with results produced with the original package.

Tests of potential functional barriers for laminated multilayer food packages. Part I: Low molecular weight permeants.

PubMed

Simal-Gándara, J; Sarria-Vidal, M; Koorevaar, A; Rijk, R

2000-08-01

The advent of the functional barrier concept in food packaging has brought with it a requirement for fast tests of permeation through potential barrier materials. In such tests it would be convenient for both foodstuffs and materials below the functional barrier (sub-barrier materials) to be represented by standard simulants. By means of inverse gas chromatography, liquid paraffin spiked with appropriate permeants was considered as a potential simulant of sub-barrier materials based on polypropylene (PP) or similar polyolefins. Experiments were performed to characterize the kinetics of the permeation of low molecular weight model permeants (octene, toluene and isopropanol) from liquid paraffin, through a surrogate potential functional barrier (25 microns-thick oriented PP) into the food stimulants olive oil and 3% (w/v) acetic acid. These permeation results were interpreted in terms of three permeation kinetic models regarding the solubility of a particular model permeant in the post-barrier medium (i.e. the food simulant). The results obtained justify the development and evaluation of liquid sub-barrier simulants that would allow flexible yet rigorous testing of new laminated multilayer packaging materials.

The R package 'RLumModel': Simulating charge transfer in quartz

NASA Astrophysics Data System (ADS)

Friedrich, Johannes; Kreutzer, Sebastian; Schmidt, Christoph

2017-04-01

Kinetic models of quartz luminescence have gained an important role for predicting experimental results and for understanding charge transfers in (natural) quartz as well as for other dosimetric materials, e.g., Al2O3:C. We present the R package 'RLumModel', offering an easy-to-use tool for simulating quartz luminescence signals (TL, OSL, LM-OSL and RF) based on five integrated and published parameter sets as well as the possibility to use own parameters. Simulation commands can be created (a) using the Risø Sequence Editor, (b) a built-in SAR sequence generator or (c) self-explanatory keywords for customised sequences. Results can be analysed seamlessly using the R package 'Luminescence' along with a visualisation of concentrations of electrons and holes in every trap/centre as well as in the valence and conduction band during all stages of the simulation. Modelling luminescence signals can help understanding charge transfer processes occurring in nature or during measurements in the laboratory. This will lead to a better understanding of several processes concerning geoscientific questions, because quartz is the second most abundant mineral in the Earth's continental crust.

Computer program for simulation of variable recharge with the U. S. Geological Survey modular finite-difference ground-water flow model (MODFLOW)

USGS Publications Warehouse

Kontis, A.L.

2001-01-01

The Variable-Recharge Package is a computerized method designed for use with the U.S. Geological Survey three-dimensional finitedifference ground-water flow model (MODFLOW-88) to simulate areal recharge to an aquifer. It is suitable for simulations of aquifers in which the relation between ground-water levels and land surface can affect the amount and distribution of recharge. The method is based on the premise that recharge to an aquifer cannot occur where the water level is at or above land surface. Consequently, recharge will vary spatially in simulations in which the Variable- Recharge Package is applied, if the water levels are sufficiently high. The input data required by the program for each model cell that can potentially receive recharge includes the average land-surface elevation and a quantity termed ?water available for recharge,? which is equal to precipitation minus evapotranspiration. The Variable-Recharge Package also can be used to simulate recharge to a valley-fill aquifer in which the valley fill and the adjoining uplands are explicitly simulated. Valley-fill aquifers, which are the most common type of aquifer in the glaciated northeastern United States, receive much of their recharge from upland sources as channeled and(or) unchanneled surface runoff and as lateral ground-water flow. Surface runoff in the uplands is generated in the model when the applied water available for recharge is rejected because simulated water levels are at or above land surface. The surface runoff can be distributed to other parts of the model by (1) applying the amount of the surface runoff that flows to upland streams (channeled runoff) to explicitly simulated streams that flow onto the valley floor, and(or) (2) applying the amount that flows downslope toward the valley- fill aquifer (unchanneled runoff) to specified model cells, typically those near the valley wall. An example model of an idealized valley- fill aquifer is presented to demonstrate application of the method and the type of information that can be derived from its use. Documentation of the Variable-Recharge Package is provided in the appendixes and includes listings of model code and of program variables. Comment statements in the program listings provide a narrative of the code. Input-data instructions and printed model output for the package are included.

Use of modflow drain package for simulating inter-basin transfer in abandoned coal mines

USGS Publications Warehouse

Kozar, Mark D.; McCoy, Kurt J.

2017-01-01

Simulation of groundwater flow in abandoned mines is difficult, especially where flux to and from mines is unknown or poorly quantified, and inter-basin transfer of groundwater occurs. A 3-year study was conducted in the Elkhorn area, West Virginia to better understand groundwater-flow processes and inter-basin transfer in above drainage abandoned coal mines. The study area was specifically selected, as all mines are located above the elevation of tributary receiving streams, to allow accurate measurements of discharge from mine portals and tributaries for groundwater model calibration. Abandoned mine workings were simulated in several ways, initially as a layer of high hydraulic conductivity bounded by lower permeability rock in adjacent strata, and secondly as rows of higher hydraulic conductivity embedded within a lower hydraulic conductivity coal aquifer matrix. Regardless of the hydraulic conductivity assigned to mine workings, neither approach to simulate mine workings could accurately reproduce the inter-basin transfer of groundwater from adjacent watersheds. To resolve the problem, a third approach was developed. The MODFLOW DRAIN package was used to simulate seepage into and through mine workings discharging water under unconfined conditions to Elkhorn Creek, North Fork, and tributaries of the Bluestone River. Drain nodes were embedded in a matrix of uniform hydraulic conductivity cells that represented the coal mine aquifer. Drain heads were empirically defined from well observations, and elevations were based on structure contours for the Pocahontas No. 3 mine workings. Use of the DRAIN package to simulate mine workings as an internal boundary condition resolved the inter-basin transfer problem, and effectively simulated a shift from a topographic- dominated to a dip-dominated flow system, by dewatering overlying unmined strata and shifting the groundwater drainage divide up dip within the Pocahontas No. 3 coal seam several kilometers into the adjacent Bluestone River Watershed. Model simulations prior to use of the DRAIN package for simulating mine workings produced estimated flows of 0.32 to 0.34 m3/s in each of the similar sized Elkhorn Creek and North Fork Watersheds, but failed to estimate inter-basin transfer of groundwater from the adjacent Bluestone River Watershed. The simulation of mine entries and discharge using the MODFLOW DRAIN package produced estimated flows of 0.46 and 0.26 m3/s for the Elkhorn Creek and North Fork watersheds respectively, which matched well measured flows for the respective watersheds of 0.47 and 0.26 m3/s.

Pressurized storm sewer simulation : model enhancement.

DOT National Transportation Integrated Search

1991-01-01

A modified Pressurized Flow Simulation Model, PFSM, was developed and attached to the Federal Highway Administration, FHWA, Pool Funded PFP-HYDRA Package. Four hydrograph options are available for simulating inflow to a sewer system under surcharge o...

Microcomputer Simulated CAD for Engineering Graphics.

ERIC Educational Resources Information Center

Huggins, David L.; Myers, Roy E.

1983-01-01

Describes a simulated computer-aided-graphics (CAD) program at The Pennsylvania State University. Rationale for the program, facilities, microcomputer equipment (Apple) used, and development of a software package for simulating applied engineering graphics are considered. (JN)

MODFLOW-2005 : the U.S. Geological Survey modular ground-water model--the ground-water flow process

USGS Publications Warehouse

Harbaugh, Arlen W.

2005-01-01

This report presents MODFLOW-2005, which is a new version of the finite-difference ground-water model commonly called MODFLOW. Ground-water flow is simulated using a block-centered finite-difference approach. Layers can be simulated as confined or unconfined. Flow associated with external stresses, such as wells, areal recharge, evapotranspiration, drains, and rivers, also can be simulated. The report includes detailed explanations of physical and mathematical concepts on which the model is based, an explanation of how those concepts are incorporated in the modular structure of the computer program, instructions for using the model, and details of the computer code. The modular structure consists of a MAIN Program and a series of highly independent subroutines. The subroutines are grouped into 'packages.' Each package deals with a specific feature of the hydrologic system that is to be simulated, such as flow from rivers or flow into drains, or with a specific method of solving the set of simultaneous equations resulting from the finite-difference method. Several solution methods are incorporated, including the Preconditioned Conjugate-Gradient method. The division of the program into packages permits the user to examine specific hydrologic features of the model independently. This also facilitates development of additional capabilities because new packages can be added to the program without modifying the existing packages. The input and output systems of the computer program also are designed to permit maximum flexibility. The program is designed to allow other capabilities, such as transport and optimization, to be incorporated, but this report is limited to describing the ground-water flow capability. The program is written in Fortran 90 and will run without modification on most computers that have a Fortran 90 compiler.

Documentation of a computer program to simulate stream-aquifer relations using a modular, finite-difference, ground-water flow model

USGS Publications Warehouse

Prudic, David E.

1989-01-01

Computer models are widely used to simulate groundwater flow for evaluating and managing the groundwater resource of many aquifers, but few are designed to also account for surface flow in streams. A computer program was written for use in the US Geological Survey modular finite difference groundwater flow model to account for the amount of flow in streams and to simulate the interaction between surface streams and groundwater. The new program is called the Streamflow-Routing Package. The Streamflow-Routing Package is not a true surface water flow model, but rather is an accounting program that tracks the flow in one or more streams which interact with groundwater. The program limits the amount of groundwater recharge to the available streamflow. It permits two or more streams to merge into one with flow in the merged stream equal to the sum of the tributary flows. The program also permits diversions from streams. The groundwater flow model with the Streamflow-Routing Package has an advantage over the analytical solution in simulating the interaction between aquifer and stream because it can be used to simulate complex systems that cannot be readily solved analytically. The Streamflow-Routing Package does not include a time function for streamflow but rather streamflow entering the modeled area is assumed to be instantly available to downstream reaches during each time period. This assumption is generally reasonable because of the relatively slow rate of groundwater flow. Another assumption is that leakage between streams and aquifers is instantaneous. This assumption may not be reasonable if the streams and aquifers are separated by a thick unsaturated zone. Documentation of the Streamflow-Routing Package includes data input instructions; flow charts, narratives, and listings of the computer program for each of four modules; and input data sets and printed results for two test problems, and one example problem. (Lantz-PTT)

Technical support package: Large, easily deployable structures. NASA Tech Briefs, Fall 1982, volume 7, no. 1

NASA Technical Reports Server (NTRS)

1982-01-01

Design and test data for packaging, deploying, and assembling structures for near term space platform systems, were provided by testing light type hardware in the Neutral Buoyancy Simulator. An optimum or near optimum structural configuration for varying degrees of deployment utilizing different levels of EVA and RMS was achieved. The design of joints and connectors and their lock/release mechanisms were refined to improve performance and operational convenience. The incorporation of utilities into structural modules to determine their effects on packaging and deployment was evaluated. By simulation tests, data was obtained for stowage, deployment, and assembly of the final structural system design to determine construction timelines, and evaluate system functioning and techniques.

Experimental Verification of the Use of Metal Filled Via Hole Fences for Crosstalk Control of Microstrip Lines in LTCC Packages

NASA Technical Reports Server (NTRS)

Ponchak, George E.; Chun, Donghoon; Yook, Jong-Gwan; Katehi, Linda P. B.

2001-01-01

Coupling between microstrip lines in dense RF packages is a common problem that degrades circuit performance. Prior three-dimensional-finite element method (3-D-FEM) electromagnetic simulations have shown that metal filled via hole fences between two adjacent microstrip lines actually Increases coupling between the lines: however, if the top of the via posts are connected by a metal strip, coupling is reduced. In this paper, experimental verification of the 3-D-FEM simulations is demonstrated for commercially fabricated low temperature cofired ceramic (LTCC) packages. In addition, measured attenuation of microstrip lines surrounded by the shielding structures is presented and shows that shielding structures do not change the attenuation characteristics of the line.

A graph-based computational framework for simulation and optimisation of coupled infrastructure networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jalving, Jordan; Abhyankar, Shrirang; Kim, Kibaek

Here, we present a computational framework that facilitates the construction, instantiation, and analysis of large-scale optimization and simulation applications of coupled energy networks. The framework integrates the optimization modeling package PLASMO and the simulation package DMNetwork (built around PETSc). These tools use a common graphbased abstraction that enables us to achieve compatibility between data structures and to build applications that use network models of different physical fidelity. We also describe how to embed these tools within complex computational workflows using SWIFT, which is a tool that facilitates parallel execution of multiple simulation runs and management of input and output data.more » We discuss how to use these capabilities to target coupled natural gas and electricity systems.« less

gadfly: A pandas-based Framework for Analyzing GADGET Simulation Data

NASA Astrophysics Data System (ADS)

Hummel, Jacob A.

2016-11-01

We present the first public release (v0.1) of the open-source gadget Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing simulation data from the astrophysical simulation codes gadget and gizmo using pandas, a thoroughly documented, open-source library providing high-performance, easy-to-use data structures that is quickly becoming the standard for data analysis in python. Gadfly is a framework for analyzing particle-based simulation data stored in the HDF5 format using pandas DataFrames. The package enables efficient memory management, includes utilities for unit handling, coordinate transformations, and parallel batch processing, and provides highly optimized routines for visualizing smoothed-particle hydrodynamics data sets.

A graph-based computational framework for simulation and optimisation of coupled infrastructure networks

DOE PAGES

Jalving, Jordan; Abhyankar, Shrirang; Kim, Kibaek; ...

2017-04-24

Here, we present a computational framework that facilitates the construction, instantiation, and analysis of large-scale optimization and simulation applications of coupled energy networks. The framework integrates the optimization modeling package PLASMO and the simulation package DMNetwork (built around PETSc). These tools use a common graphbased abstraction that enables us to achieve compatibility between data structures and to build applications that use network models of different physical fidelity. We also describe how to embed these tools within complex computational workflows using SWIFT, which is a tool that facilitates parallel execution of multiple simulation runs and management of input and output data.more » We discuss how to use these capabilities to target coupled natural gas and electricity systems.« less

Documentation of the Unsaturated-Zone Flow (UZF1) Package for modeling Unsaturated Flow Between the Land Surface and the Water Table with MODFLOW-2005

USGS Publications Warehouse

Niswonger, Richard G.; Prudic, David E.; Regan, R. Steven

2006-01-01

Percolation of precipitation through unsaturated zones is important for recharge of ground water. Rain and snowmelt at land surface are partitioned into different pathways including runoff, infiltration, evapotranspiration, unsaturated-zone storage, and recharge. A new package for MODFLOW-2005 called the Unsaturated-Zone Flow (UZF1) Package was developed to simulate water flow and storage in the unsaturated zone and to partition flow into evapotranspiration and recharge. The package also accounts for land surface runoff to streams and lakes. A kinematic wave approximation to Richards? equation is solved by the method of characteristics to simulate vertical unsaturated flow. The approach assumes that unsaturated flow occurs in response to gravity potential gradients only and ignores negative potential gradients; the approach further assumes uniform hydraulic properties in the unsaturated zone for each vertical column of model cells. The Brooks-Corey function is used to define the relation between unsaturated hydraulic conductivity and water content. Variables used by the UZF1 Package include initial and saturated water contents, saturated vertical hydraulic conductivity, and an exponent in the Brooks-Corey function. Residual water content is calculated internally by the UZF1 Package on the basis of the difference between saturated water content and specific yield. The UZF1 Package is a substitution for the Recharge and Evapotranspiration Packages of MODFLOW-2005. The UZF1 Package differs from the Recharge Package in that an infiltration rate is applied at land surface instead of a specified recharge rate directly to ground water. The applied infiltration rate is further limited by the saturated vertical hydraulic conductivity. The UZF1 Package differs from the Evapotranspiration Package in that evapotranspiration losses are first removed from the unsaturated zone above the evapotranspiration extinction depth, and if the demand is not met, water can be removed directly from ground water whenever the depth to ground water is less than the extinction depth. The UZF1 Package also differs from the Evapotranspiration Package in that water is discharged directly to land surface whenever the altitude of the water table exceeds land surface. Water that is discharged to land surface, as well as applied infiltration in excess of the saturated vertical hydraulic conductivity, may be routed directly as inflow to specified streams or lakes if these packages are active; otherwise, this water is removed from the model. The UZF1 Package was tested against the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model for a vertical unsaturated flow problem that includes evapotranspiration losses. This report also includes an example in which MODFLOW-2005 with the UZF1 Package was used to simulate a realistic surface-water/ground-water flow problem that includes time and space variable infiltration, evapotranspiration, runoff, and ground-water discharge to land surface and to streams. Another simpler problem is presented so that the user may use the input files as templates for new problems and to verify proper code installation.

POLLUTANT CONTROL TECHNIQUES FOR PACKAGE BOILERS: HARDWARE MODIFICATIONS AND ALTERNATE FUELS

EPA Science Inventory

The report gives results of investigations of four ways to control nitrogen oxide (NOx) emissions from package boilers (both field operating boilers and boiler simulators): (1) variations in combustor operating procedure; (2) combustion modification (flue gas recirculation and st...

TRANSIENT SUPPRESSION PACKAGING FOR REDUCED EMISSIONS FROM ROTARY KILN INCINERATORS

EPA Science Inventory

Experiments were performed on a 73 kW rotary kiln incinerator simulator to determine whether innovative waste packaging designs might reduce transient emissions of products of incomplete combustion due to batch charging of containerized liquid surrogate waste compounds bound on g...

Modelling of optoelectronic circuits based on resonant tunneling diodes

NASA Astrophysics Data System (ADS)

Rei, João. F. M.; Foot, James A.; Rodrigues, Gil C.; Figueiredo, José M. L.

2017-08-01

Resonant tunneling diodes (RTDs) are the fastest pure electronic semiconductor devices at room temperature. When integrated with optoelectronic devices they can give rise to new devices with novel functionalities due to their highly nonlinear properties and electrical gain, with potential applications in future ultra-wide-band communication systems (see e.g. EU H2020 iBROW Project). The recent coverage on these devices led to the need to have appropriated simulation tools. In this work, we present RTD based optoelectronic circuits simulation packages to provide circuit signal level analysis such as transient and frequency responses. We will present and discuss the models, and evaluate the simulation packages.

magnum.fe: A micromagnetic finite-element simulation code based on FEniCS

NASA Astrophysics Data System (ADS)

Abert, Claas; Exl, Lukas; Bruckner, Florian; Drews, André; Suess, Dieter

2013-11-01

We have developed a finite-element micromagnetic simulation code based on the FEniCS package called magnum.fe. Here we describe the numerical methods that are applied as well as their implementation with FEniCS. We apply a transformation method for the solution of the demagnetization-field problem. A semi-implicit weak formulation is used for the integration of the Landau-Lifshitz-Gilbert equation. Numerical experiments show the validity of simulation results. magnum.fe is open source and well documented. The broad feature range of the FEniCS package makes magnum.fe a good choice for the implementation of novel micromagnetic finite-element algorithms.

The General-Use Nodal Network Solver (GUNNS) Modeling Package for Space Vehicle Flow System Simulation

NASA Technical Reports Server (NTRS)

Harvey, Jason; Moore, Michael

2013-01-01

The General-Use Nodal Network Solver (GUNNS) is a modeling software package that combines nodal analysis and the hydraulic-electric analogy to simulate fluid, electrical, and thermal flow systems. GUNNS is developed by L-3 Communications under the TS21 (Training Systems for the 21st Century) project for NASA Johnson Space Center (JSC), primarily for use in space vehicle training simulators at JSC. It has sufficient compactness and fidelity to model the fluid, electrical, and thermal aspects of space vehicles in real-time simulations running on commodity workstations, for vehicle crew and flight controller training. It has a reusable and flexible component and system design, and a Graphical User Interface (GUI), providing capability for rapid GUI-based simulator development, ease of maintenance, and associated cost savings. GUNNS is optimized for NASA's Trick simulation environment, but can be run independently of Trick.

Improvements in simulation of multiple scattering effects in ATLAS fast simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basalaev, A. E., E-mail: artem.basalaev@cern.ch

Fast ATLAS Tracking Simulation (Fatras) package was verified on single layer geometry with respect to full simulation with GEANT4. Fatras hadronic interactions and multiple scattering simulation were studied in comparison with GEANT4. Disagreement was found in multiple scattering distributions of primary charged particles (μ, π, e). A new model for multiple scattering simulation was implemented in Fatras. The model was based on R. Frühwirth’s mixture models. New model was tested on single layer geometry and a good agreement with GEANT4 was achieved. Also a comparison of reconstructed tracks’ parameters was performed for Inner Detector geometry, and Fatras with new multiplemore » scattering model proved to have better agreement with GEANT4. New model of multiple scattering was added as a part of Fatras package in the development release of ATLAS software—ATHENA.« less

Effect of Initial Headspace O2 Level on the Growth and Volatile Metabolite Production of Leuconostoc Mesenteriodes and the Microbial and Sensorial Quality of Modified Atmosphere Packaged Par-Fried French Fries.

PubMed

Samapundo, Simbarashe; Mujuru, Felix Mugove; de Baenst, Ilse; Denon, Quenten; Devlieghere, Frank

2016-02-01

This study evaluated the effect of residual O2 level (0% to 5%) on microbial growth and volatile metabolite production on par-fried French fries packaged in a modified atmosphere with 60% CO2 (rest N2 ) at 4 °C. The results obtained showed that the initial headspace (IH) O2 level had an effect on growth of Leuconostoc mesenteroides on French fry simulation agar, whereby growth was slightly faster under 5% O2 . In terms of quantity, ethanol, 2-methyl-1-propanol, and dimethyl disulphide were the most significant volatile metabolites produced by L. mesenteroides. The production of ethanol by L. mesenteroides was highest on simulation agar packaged under low IH O2 levels (0% to 1%), indicating that the fermentative metabolism was induced under these conditions. In agreement with the results observed on the simulation medium, growth of native lactic acid bacteria was faster under an IH O2 level of 5%. In addition, ethanol, 2-methyl-1-propanol, and dimethyl disulphide were also quantitatively the most important volatile metabolites. However, in contrast, greater quantities of ethanol and dimethyl disulphide were produced on par-fried French fries packaged under 5% O2 . This was attributed to the limited growth of the native flora on the par-fried French fries under residual O2 levels of 0% and 1%. Although some significant differences (P < 0.05) occurred between the French fries packaged in 0%, 1%, and 5 % residual O2 during storage, all products were considered to be acceptable for consumption. The results of this study can be used to optimize the shelf-life of packaged chill stored potato products. © 2016 Institute of Food Technologists®

Dual Arm Work Package performance estimates and telerobot task network simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Draper, J.V.; Blair, L.M.

1997-02-01

This paper describes the methodology and results of a network simulation study of the Dual Arm Work Package (DAWP), to be employed for dismantling the Argonne National Laboratory CP-5 reactor. The development of the simulation model was based upon the results of a task analysis for the same system. This study was performed by the Oak Ridge National Laboratory (ORNL), in the Robotics and Process Systems Division. Funding was provided the US Department of Energy`s Office of Technology Development, Robotics Technology Development Program (RTDP). The RTDP is developing methods of computer simulation to estimate telerobotic system performance. Data were collectedmore » to provide point estimates to be used in a task network simulation model. Three skilled operators performed six repetitions of a pipe cutting task representative of typical teleoperation cutting operations.« less

Accelerated Monte Carlo Simulation on the Chemical Stage in Water Radiolysis using GPU

PubMed Central

Tian, Zhen; Jiang, Steve B.; Jia, Xun

2018-01-01

The accurate simulation of water radiolysis is an important step to understand the mechanisms of radiobiology and quantitatively test some hypotheses regarding radiobiological effects. However, the simulation of water radiolysis is highly time consuming, taking hours or even days to be completed by a conventional CPU processor. This time limitation hinders cell-level simulations for a number of research studies. We recently initiated efforts to develop gMicroMC, a GPU-based fast microscopic MC simulation package for water radiolysis. The first step of this project focused on accelerating the simulation of the chemical stage, the most time consuming stage in the entire water radiolysis process. A GPU-friendly parallelization strategy was designed to address the highly correlated many-body simulation problem caused by the mutual competitive chemical reactions between the radiolytic molecules. Two cases were tested, using a 750 keV electron and a 5 MeV proton incident in pure water, respectively. The time-dependent yields of all the radiolytic species during the chemical stage were used to evaluate the accuracy of the simulation. The relative differences between our simulation and the Geant4-DNA simulation were on average 5.3% and 4.4% for the two cases. Our package, executed on an Nvidia Titan black GPU card, successfully completed the chemical stage simulation of the two cases within 599.2 s and 489.0 s. As compared with Geant4-DNA that was executed on an Intel i7-5500U CPU processor and needed 28.6 h and 26.8 h for the two cases using a single CPU core, our package achieved a speed-up factor of 171.1-197.2. PMID:28323637

Accelerated Monte Carlo simulation on the chemical stage in water radiolysis using GPU

NASA Astrophysics Data System (ADS)

Tian, Zhen; Jiang, Steve B.; Jia, Xun

2017-04-01

The accurate simulation of water radiolysis is an important step to understand the mechanisms of radiobiology and quantitatively test some hypotheses regarding radiobiological effects. However, the simulation of water radiolysis is highly time consuming, taking hours or even days to be completed by a conventional CPU processor. This time limitation hinders cell-level simulations for a number of research studies. We recently initiated efforts to develop gMicroMC, a GPU-based fast microscopic MC simulation package for water radiolysis. The first step of this project focused on accelerating the simulation of the chemical stage, the most time consuming stage in the entire water radiolysis process. A GPU-friendly parallelization strategy was designed to address the highly correlated many-body simulation problem caused by the mutual competitive chemical reactions between the radiolytic molecules. Two cases were tested, using a 750 keV electron and a 5 MeV proton incident in pure water, respectively. The time-dependent yields of all the radiolytic species during the chemical stage were used to evaluate the accuracy of the simulation. The relative differences between our simulation and the Geant4-DNA simulation were on average 5.3% and 4.4% for the two cases. Our package, executed on an Nvidia Titan black GPU card, successfully completed the chemical stage simulation of the two cases within 599.2 s and 489.0 s. As compared with Geant4-DNA that was executed on an Intel i7-5500U CPU processor and needed 28.6 h and 26.8 h for the two cases using a single CPU core, our package achieved a speed-up factor of 171.1-197.2.

Accelerated Monte Carlo simulation on the chemical stage in water radiolysis using GPU.

PubMed

Tian, Zhen; Jiang, Steve B; Jia, Xun

2017-04-21

The accurate simulation of water radiolysis is an important step to understand the mechanisms of radiobiology and quantitatively test some hypotheses regarding radiobiological effects. However, the simulation of water radiolysis is highly time consuming, taking hours or even days to be completed by a conventional CPU processor. This time limitation hinders cell-level simulations for a number of research studies. We recently initiated efforts to develop gMicroMC, a GPU-based fast microscopic MC simulation package for water radiolysis. The first step of this project focused on accelerating the simulation of the chemical stage, the most time consuming stage in the entire water radiolysis process. A GPU-friendly parallelization strategy was designed to address the highly correlated many-body simulation problem caused by the mutual competitive chemical reactions between the radiolytic molecules. Two cases were tested, using a 750 keV electron and a 5 MeV proton incident in pure water, respectively. The time-dependent yields of all the radiolytic species during the chemical stage were used to evaluate the accuracy of the simulation. The relative differences between our simulation and the Geant4-DNA simulation were on average 5.3% and 4.4% for the two cases. Our package, executed on an Nvidia Titan black GPU card, successfully completed the chemical stage simulation of the two cases within 599.2 s and 489.0 s. As compared with Geant4-DNA that was executed on an Intel i7-5500U CPU processor and needed 28.6 h and 26.8 h for the two cases using a single CPU core, our package achieved a speed-up factor of 171.1-197.2.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

SU-E-T-558: Monte Carlo Photon Transport Simulations On GPU with Quadric Geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chi, Y; Tian, Z; Jiang, S

Purpose: Monte Carlo simulation on GPU has experienced rapid advancements over the past a few years and tremendous accelerations have been achieved. Yet existing packages were developed only in voxelized geometry. In some applications, e.g. radioactive seed modeling, simulations in more complicated geometry are needed. This abstract reports our initial efforts towards developing a quadric geometry module aiming at expanding the application scope of GPU-based MC simulations. Methods: We defined the simulation geometry consisting of a number of homogeneous bodies, each specified by its material composition and limiting surfaces characterized by quadric functions. A tree data structure was utilized tomore » define geometric relationship between different bodies. We modified our GPU-based photon MC transport package to incorporate this geometry. Specifically, geometry parameters were loaded into GPU’s shared memory for fast access. Geometry functions were rewritten to enable the identification of the body that contains the current particle location via a fast searching algorithm based on the tree data structure. Results: We tested our package in an example problem of HDR-brachytherapy dose calculation for shielded cylinder. The dose under the quadric geometry and that under the voxelized geometry agreed in 94.2% of total voxels within 20% isodose line based on a statistical t-test (95% confidence level), where the reference dose was defined to be the one at 0.5cm away from the cylinder surface. It took 243sec to transport 100million source photons under this quadric geometry on an NVidia Titan GPU card. Compared with simulation time of 99.6sec in the voxelized geometry, including quadric geometry reduced efficiency due to the complicated geometry-related computations. Conclusion: Our GPU-based MC package has been extended to support photon transport simulation in quadric geometry. Satisfactory accuracy was observed with a reduced efficiency. Developments for charged particle transport in this geometry are currently in progress.« less

Changes in the specific migration characteristics of packaging-food simulant combinations caused by ionizing radiation: Effect of food simulant

NASA Astrophysics Data System (ADS)

Zygoura, Panagiota D.; Paleologos, Evangelos K.; Kontominas, Michael G.

2011-08-01

The primary objective of the present study was to evaluate the extent to which the affinity of the surrounding medium for the migrant, as well as the packaging material, affects the specific migration characteristics of the latter. For this purpose, migration tests were conducted with vinylidene chloride copolymer (PVDC/PVC) in contact with the EU specified solvents simulating all food types: namely, distilled water, 3% w/v acetic acid, 10% v/v ethanol and isooctane. Migration testing was carried out at 40 °C for 10 days for the aqueous simulants, and at 20 °C for 2 days for the fatty food simulant (EC, 1997; EEC, 1993). In addition, food-grade saran film was subjected to ionizing radiation treatment with a [60Co] source at doses equal to 5, 15 and 25 kGy. Acetyl tributyl citrate (ATBC) plasticizer levels were monitored as a function of time for untreated, as well as gamma-irradiated packaging material, with a secondary objective to investigate the effect of ionizing radiation on polymer/migrant/surrounding medium interactions. Depending on the food simulant, determination of the analyte was performed by either direct gas chromatographic analysis, or surfactant (Triton X-114) mediated extraction followed by gas chromatographic-flame ionization detection (GC-FID). ATBC concentrations determined in aqueous and fatty food simulants were 0.216-0.497 and 5.0-5.9 mg/L, respectively. Therefore, the most efficient extracting medium of plasticizers in vinyl chloride copolymers is the non-polar isooctane. Moreover, an extremely high rate of ATBC migration into isooctane during the early stages of contact was observed. The above observation verifies the aggressiveness of isooctane towards plastic packaging materials. Amongst the aqueous food simulants tested, the 10% ethanol solution demonstrated the highest migration levels. Gamma-irradiation enhanced ATBC migration; specific migration levels increased with increasing contact time and radiation dose. This was expected, since ATBC did not undergo chemical decomposition upon irradiation up to 25 kGy. Finally, specific migration decreased proportionally with increasing polarity of the food-simulating solvent.

ANTS — a simulation package for secondary scintillation Anger-camera type detector in thermal neutron imaging

NASA Astrophysics Data System (ADS)

Morozov, A.; Defendi, I.; Engels, R.; Fraga, F. A. F.; Fraga, M. M. F. R.; Guerard, B.; Jurkovic, M.; Kemmerling, G.; Manzin, G.; Margato, L. M. S.; Niko, H.; Pereira, L.; Petrillo, C.; Peyaud, A.; Piscitelli, F.; Raspino, D.; Rhodes, N. J.; Sacchetti, F.; Schooneveld, E. M.; Van Esch, P.; Zeitelhack, K.

2012-08-01

A custom and fully interactive simulation package ANTS (Anger-camera type Neutron detector: Toolkit for Simulations) has been developed to optimize the design and operation conditions of secondary scintillation Anger-camera type gaseous detectors for thermal neutron imaging. The simulation code accounts for all physical processes related to the neutron capture, energy deposition pattern, drift of electrons of the primary ionization and secondary scintillation. The photons are traced considering the wavelength-resolved refraction and transmission of the output window. Photo-detection accounts for the wavelength-resolved quantum efficiency, angular response, area sensitivity, gain and single-photoelectron spectra of the photomultipliers (PMTs). The package allows for several geometrical shapes of the PMT photocathode (round, hexagonal and square) and offers a flexible PMT array configuration: up to 100 PMTs in a custom arrangement with the square or hexagonal packing. Several read-out patterns of the PMT array are implemented. Reconstruction of the neutron capture position (projection on the plane of the light emission) is performed using the center of gravity, maximum likelihood or weighted least squares algorithm. Simulation results reproduce well the preliminary results obtained with a small-scale detector prototype. ANTS executables can be downloaded from http://coimbra.lip.pt/~andrei/.

eSBMTools 1.0: enhanced native structure-based modeling tools.

PubMed

Lutz, Benjamin; Sinner, Claude; Heuermann, Geertje; Verma, Abhinav; Schug, Alexander

2013-11-01

Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints. We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2. http://sourceforge.net/projects/esbmtools/. alexander.schug@kit.edu. Supplementary data are available at Bioinformatics online.

LavaNet—Neural network development environment in a general mine planning package

NASA Astrophysics Data System (ADS)

Kapageridis, Ioannis Konstantinou; Triantafyllou, A. G.

2011-04-01

LavaNet is a series of scripts written in Perl that gives access to a neural network simulation environment inside a general mine planning package. A well known and a very popular neural network development environment, the Stuttgart Neural Network Simulator, is used as the base for the development of neural networks. LavaNet runs inside VULCAN™—a complete mine planning package with advanced database, modelling and visualisation capabilities. LavaNet is taking advantage of VULCAN's Perl based scripting environment, Lava, to bring all the benefits of neural network development and application to geologists, mining engineers and other users of the specific mine planning package. LavaNet enables easy development of neural network training data sets using information from any of the data and model structures available, such as block models and drillhole databases. Neural networks can be trained inside VULCAN™ and the results be used to generate new models that can be visualised in 3D. Direct comparison of developed neural network models with conventional and geostatistical techniques is now possible within the same mine planning software package. LavaNet supports Radial Basis Function networks, Multi-Layer Perceptrons and Self-Organised Maps.

Mechanical-Electrochemical-Thermal Simulation of Lithium-Ion Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santhanagopalan, Shriram; Zhang, Chao; Sprague, Michael A.

2016-06-01

Models capture the force response for single-cell and cell-string levels to within 15%-20% accuracy and predict the location for the origin of failure based on the deformation data from the experiments. At the module level, there is some discrepancy due to poor mechanical characterization of the packaging material between the cells. The thermal response (location and value of maximum temperature) agrees qualitatively with experimental data. In general, the X-plane results agree with model predictions to within 20% (pending faulty thermocouples, etc.); the Z-plane results show a bigger variability both between the models and test-results, as well as among multiple repeatsmore » of the tests. The models are able to capture the timing and sequence in voltage drop observed in the multi-cell experiments; the shapes of the current and temperature profiles need more work to better characterize propagation. The cells within packaging experience about 60% less force under identical impact test conditions, so the packaging on the test articles is robust. However, under slow-crush simulations, the maximum deformation of the cell strings with packaging is about twice that of cell strings without packaging.« less

Human exposure assessment of silver and copper migrating from an antimicrobial nanocoated packaging material into an acidic food simulant.

PubMed

Hannon, Joseph Christopher; Kerry, Joseph P; Cruz-Romero, Malco; Azlin-Hasim, Shafrina; Morris, Michael; Cummins, Enda

2016-09-01

To examine the human exposure to a novel silver and copper nanoparticle (AgNP and CuNP)/polystyrene-polyethylene oxide block copolymer (PS-b-PEO) food packaging coating, the migration of Ag and Cu into 3% acetic acid (3% HAc) food simulant was assessed at 60 °C for 10 days. Significantly lower migration was observed for Ag (0.46 mg/kg food) compared to Cu (0.82 mg/kg food) measured by inductively coupled plasma - atomic emission spectrometry (ICP-AES). In addition, no distinct population of AgNPs or CuNPs were observed in 3% HAc by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). The predicted human exposure to Ag and Cu was used to calculate a margin of exposure (MOE) for ionic species of Ag and Cu, which indicated the safe use of the food packaging in a hypothetical scenario (e.g. as fruit juice packaging). While migration exceeded regulatory limits, the calculated MOE suggests current migration limits may be conservative for specific nano-packaging applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

User’s guide for MapMark4GUI—A graphical user interface for the MapMark4 R package

USGS Publications Warehouse

Shapiro, Jason

2018-05-29

MapMark4GUI is an R graphical user interface (GUI) developed by the U.S. Geological Survey to support user implementation of the MapMark4 R statistical software package. MapMark4 was developed by the U.S. Geological Survey to implement probability calculations for simulating undiscovered mineral resources in quantitative mineral resource assessments. The GUI provides an easy-to-use tool to input data, run simulations, and format output results for the MapMark4 package. The GUI is written and accessed in the R statistical programming language. This user’s guide includes instructions on installing and running MapMark4GUI and descriptions of the statistical output processes, output files, and test data files.

Original Courseware for Introductory Psychology: Implementation and Evaluation.

ERIC Educational Resources Information Center

Slotnick, Robert S.

1988-01-01

Describes the implementation and field testing of PsychWare, a courseware package for introductory psychology developed and field tested at New York Institute of Technology. Highlights include the courseware package (10 software programs, a faculty manual, and a student workbook), and instructional design features (simulations, real-time…

Cleanup Verification Package for the 300 VTS Waste Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

S. W. Clark and T. H. Mitchell

2006-03-13

This cleanup verification package documents completion of remedial action for the 300 Area Vitrification Test Site, also known as the 300 VTS site. The site was used by Pacific Northwest National Laboratory as a field demonstration site for in situ vitrification of soils containing simulated waste.

ON UPGRADING THE NUMERICS IN COMBUSTION CHEMISTRY CODES. (R824970)

EPA Science Inventory

A method of updating and reusing legacy FORTRAN codes for combustion simulations is presented using the DAEPACK software package. The procedure is demonstrated on two codes that come with the CHEMKIN-II package, CONP and SENKIN, for the constant-pressure batch reactor simulati...

Fun!

ERIC Educational Resources Information Center

Horne, Thomas

1988-01-01

Describes four IBM compatible flight simulator software packages: (1) "Falcon," air to air combat in an F-16 fighter; (2) "Chuck Yeager's Advanced Flight Trainer," test flight 14 different aircraft; (3) "Jet," air to air combat; and (4) "Flight Simulator," a realistic PC flight simulator program. (MVL)

SIMULATION TOOL KIT FOR INDOOR AIR QUALITY AND INHALATION EXPOSURE (IAQX) VERSION 1.0 USER'S GUIDE

EPA Science Inventory

The User's Guide describes a Microsoft Windows-based indoor air quality (IAQ) simulation software package designed Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short. This software complements and supplements existing IAQ simulation programs and...

Update of global TC simulations using a variable resolution non-hydrostatic model

NASA Astrophysics Data System (ADS)

Park, S. H.

2017-12-01

Using in a variable resolution meshes in MPAS during 2017 summer., Tropical cyclone (TC) forecasts are simulated. Two physics suite are tested to explore performance and bias of each physics suite for TC forecasting. A WRF physics suite is selected from experience on weather forecasting and CAM (Community Atmosphere Model) physics is taken from a AMIP type climate simulation. Based on the last year results from CAM5 physical parameterization package and comparing with WRF physics, we investigated a issue with intensity bias using updated version of CAM physics (CAM6). We also compared these results with coupled version of TC simulations. During this talk, TC structure will be compared specially around of boundary layer and investigate their relationship between TC intensity and different physics package.

A generic multibody simulation

NASA Technical Reports Server (NTRS)

Hopping, K. A.; Kohn, W.

1986-01-01

Described is a dynamic simulation package which can be configured for orbital test scenarios involving multiple bodies. The rotational and translational state integration methods are selectable for each individual body and may be changed during a run if necessary. Characteristics of the bodies are determined by assigning components consisting of mass properties, forces, and moments, which are the outputs of user-defined environmental models. Generic model implementation is facilitated by a transformation processor which performs coordinate frame inversions. Transformations are defined in the initialization file as part of the simulation configuration. The simulation package includes an initialization processor, which consists of a command line preprocessor, a general purpose grammar, and a syntax scanner. These permit specifications of the bodies, their interrelationships, and their initial states in a format that is not dependent on a particular test scenario.

A Modular Three-Dimensional Finite-Difference Ground-Water Flow Model

USGS Publications Warehouse

McDonald, Michael G.; Harbaugh, Arlen W.; Guo, Weixing; Lu, Guoping

1988-01-01

This report presents a finite-difference model and its associated modular computer program. The model simulates flow in three dimensions. The report includes detailed explanations of physical and mathematical concepts on which the model is based and an explanation of how those concepts are incorporated in the modular structure of the computer program. The modular structure consists of a Main Program and a series of highly independent subroutines called 'modules.' The modules are grouped into 'packages.' Each package deals with a specific feature of the hydrologic system which is to be simulated, such as flow from rivers or flow into drains, or with a specific method of solving linear equations which describe the flow system, such as the Strongly Implicit Procedure or Slice-Successive Overrelaxation. The division of the program into modules permits the user to examine specific hydrologic features of the model independently. This also facilita development of additional capabilities because new packages can be added to the program without modifying the existing packages. The input and output systems of the computer program are also designed to permit maximum flexibility. Ground-water flow within the aquifer is simulated using a block-centered finite-difference approach. Layers can be simulated as confined, unconfined, or a combination of confined and unconfined. Flow associated with external stresses, such as wells, areal recharge, evapotranspiration, drains, and streams, can also be simulated. The finite-difference equations can be solved using either the Strongly Implicit Procedure or Slice-Successive Overrelaxation. The program is written in FORTRAN 77 and will run without modification on most computers that have a FORTRAN 77 compiler. For each program ,module, this report includes a narrative description, a flow chart, a list of variables, and a module listing.

NetMOD Version 2.0 Mathematical Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merchant, Bion J.; Young, Christopher J.; Chael, Eric P.

2015-08-01

NetMOD ( Net work M onitoring for O ptimal D etection) is a Java-based software package for conducting simulation of seismic, hydroacoustic and infrasonic networks. Network simulations have long been used to study network resilience to station outages and to determine where additional stations are needed to reduce monitoring thresholds. NetMOD makes use of geophysical models to determine the source characteristics, signal attenuation along the path between the source and station, and the performance and noise properties of the station. These geophysical models are combined to simulate the relative amplitudes of signal and noise that are observed at each ofmore » the stations. From these signal-to-noise ratios (SNR), the probabilities of signal detection at each station and event detection across the network of stations can be computed given a detection threshold. The purpose of this document is to clearly and comprehensively present the mathematical framework used by NetMOD, the software package developed by Sandia National Laboratories to assess the monitoring capability of ground-based sensor networks. Many of the NetMOD equations used for simulations are inherited from the NetSim network capability assessment package developed in the late 1980s by SAIC (Sereno et al., 1990).« less

Chemical compatibility screening results of plastic packaging to mixed waste simulants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nigrey, P.J.; Dickens, T.G.

1995-12-01

We have developed a chemical compatibility program for evaluating transportation packaging components for transporting mixed waste forms. We have performed the first phase of this experimental program to determine the effects of simulant mixed wastes on packaging materials. This effort involved the screening of 10 plastic materials in four liquid mixed waste simulants. The testing protocol involved exposing the respective materials to {approximately}3 kGy of gamma radiation followed by 14 day exposures to the waste simulants of 60 C. The seal materials or rubbers were tested using VTR (vapor transport rate) measurements while the liner materials were tested using specificmore » gravity as a metric. For these tests, a screening criteria of {approximately}1 g/m{sup 2}/hr for VTR and a specific gravity change of 10% was used. It was concluded that while all seal materials passed exposure to the aqueous simulant mixed waste, EPDM and SBR had the lowest VTRs. In the chlorinated hydrocarbon simulant mixed waste, only VITON passed the screening tests. In both the simulant scintillation fluid mixed waste and the ketone mixture simulant mixed waste, none of the seal materials met the screening criteria. It is anticipated that those materials with the lowest VTRs will be evaluated in the comprehensive phase of the program. For specific gravity testing of liner materials the data showed that while all materials with the exception of polypropylene passed the screening criteria, Kel-F, HDPE, and XLPE were found to offer the greatest resistance to the combination of radiation and chemicals.« less

XFEL OSCILLATOR SIMULATION INCLUDING ANGLE-DEPENDENT CRYSTAL REFLECTIVITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fawley, William; Lindberg, Ryan; Kim, K-J

The oscillator package within the GINGER FEL simulation code has now been extended to include angle-dependent reflectivity properties of Bragg crystals. Previously, the package was modified to include frequencydependent reflectivity in order to model x-ray FEL oscillators from start-up from shot noise through to saturation. We present a summary of the algorithms used for modeling the crystal reflectivity and radiation propagation outside the undulator, discussing various numerical issues relevant to the domain of high Fresnel number and efficient Hankel transforms. We give some sample XFEL-O simulation results obtained with the angle-dependent reflectivity model, with particular attention directed to the longitudinalmore » and transverse coherence of the radiation output.« less

Wavelet analysis to decompose a vibration simulation signal to improve pre-distribution testing of packaging

NASA Astrophysics Data System (ADS)

Griffiths, K. R.; Hicks, B. J.; Keogh, P. S.; Shires, D.

2016-08-01

In general, vehicle vibration is non-stationary and has a non-Gaussian probability distribution; yet existing testing methods for packaging design employ Gaussian distributions to represent vibration induced by road profiles. This frequently results in over-testing and/or over-design of the packaging to meet a specification and correspondingly leads to wasteful packaging and product waste, which represent 15bn per year in the USA and €3bn per year in the EU. The purpose of the paper is to enable a measured non-stationary acceleration signal to be replaced by a constructed signal that includes as far as possible any non-stationary characteristics from the original signal. The constructed signal consists of a concatenation of decomposed shorter duration signals, each having its own kurtosis level. Wavelet analysis is used for the decomposition process into inner and outlier signal components. The constructed signal has a similar PSD to the original signal, without incurring excessive acceleration levels. This allows an improved and more representative simulated input signal to be generated that can be used on the current generation of shaker tables. The wavelet decomposition method is also demonstrated experimentally through two correlation studies. It is shown that significant improvements over current international standards for packaging testing are achievable; hence the potential for more efficient packaging system design is possible.

Logistic Regression with Multiple Random Effects: A Simulation Study of Estimation Methods and Statistical Packages

PubMed Central

Kim, Yoonsang; Emery, Sherry

2013-01-01

Several statistical packages are capable of estimating generalized linear mixed models and these packages provide one or more of three estimation methods: penalized quasi-likelihood, Laplace, and Gauss-Hermite. Many studies have investigated these methods’ performance for the mixed-effects logistic regression model. However, the authors focused on models with one or two random effects and assumed a simple covariance structure between them, which may not be realistic. When there are multiple correlated random effects in a model, the computation becomes intensive, and often an algorithm fails to converge. Moreover, in our analysis of smoking status and exposure to anti-tobacco advertisements, we have observed that when a model included multiple random effects, parameter estimates varied considerably from one statistical package to another even when using the same estimation method. This article presents a comprehensive review of the advantages and disadvantages of each estimation method. In addition, we compare the performances of the three methods across statistical packages via simulation, which involves two- and three-level logistic regression models with at least three correlated random effects. We apply our findings to a real dataset. Our results suggest that two packages—SAS GLIMMIX Laplace and SuperMix Gaussian quadrature—perform well in terms of accuracy, precision, convergence rates, and computing speed. We also discuss the strengths and weaknesses of the two packages in regard to sample sizes. PMID:24288415

[Not Available].

PubMed

Pecevski, Dejan; Natschläger, Thomas; Schuch, Klaus

2009-01-01

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations.

Space Shuttle/TDRSS communication and tracking systems analysis

NASA Astrophysics Data System (ADS)

Lindsey, W. C.; Chie, C. M.; Cideciyan, R.; Dessouky, K.; Su, Y. T.; Tsang, C. S.

1986-04-01

In order to evaluate the technical and operational problem areas and provide a recommendation, the enhancements to the Tracking and Data Delay Satellite System (TDRSS) and Shuttle must be evaluated through simulation and analysis. These enhancement techniques must first be characterized, then modeled mathematically, and finally updated into LinCsim (analytical simulation package). The LinCsim package can then be used as an evaluation tool. Three areas of potential enhancements were identified: shuttle payload accommodations, TDRSS SSA and KSA services, and shuttle tracking system and navigation sensors. Recommendations for each area were discussed.

Space Shuttle/TDRSS communication and tracking systems analysis

NASA Technical Reports Server (NTRS)

Lindsey, W. C.; Chie, C. M.; Cideciyan, R.; Dessouky, K.; Su, Y. T.; Tsang, C. S.

1986-01-01

In order to evaluate the technical and operational problem areas and provide a recommendation, the enhancements to the Tracking and Data Delay Satellite System (TDRSS) and Shuttle must be evaluated through simulation and analysis. These enhancement techniques must first be characterized, then modeled mathematically, and finally updated into LinCsim (analytical simulation package). The LinCsim package can then be used as an evaluation tool. Three areas of potential enhancements were identified: shuttle payload accommodations, TDRSS SSA and KSA services, and shuttle tracking system and navigation sensors. Recommendations for each area were discussed.

Macromodels of digital integrated circuits for program packages of circuit engineering design

NASA Astrophysics Data System (ADS)

Petrenko, A. I.; Sliusar, P. B.; Timchenko, A. P.

1984-04-01

Various aspects of the generation of macromodels of digital integrated circuits are examined, and their effective application in program packages of circuit engineering design is considered. Three levels of macromodels are identified, and the application of such models to the simulation of circuit outputs is discussed.

Dynamic Modeling Using MCSim and R (SOT 2016 Biological Modeling Webinar Series)

EPA Science Inventory

MCSim is a stand-alone software package for simulating and analyzing dynamic models, with a focus on Bayesian analysis using Markov Chain Monte Carlo. While it is an extremely powerful package, it is somewhat inflexible, and offers only a limited range of analysis options, with n...

The Macro - Games Course Package.

ERIC Educational Resources Information Center

Heriot-Watt Univ., Edinburgh (Scotland). Esmee Fairbairn Economics Research Centre.

Part of an Economic Education Series, the course package is designed to teach basic concepts and fundamental principles of macroeconomics and how they can be applied to various world problems. For use with college students, learning is gained through lectures, discussion, simulation games, programmed learning, and text. Time allotment is a 15-week…

Spectral study and protein labeling of inclusion complex between dye and calixarene sulfonate.

PubMed

Fei, Xuening; Zhang, Yong; Zhu, Sen; Liu, Lijuan; Yu, Lu

2013-05-01

The host-guest inclusion complex of calix[6]arene sulfonate (SCA6) with thiazole orange (TO) formed in aqueous solution was studied. Absorption and fluorescence techniques were used for the analysis of this inclusion complex. The addition of calixarene sulfonate leads to a decrease in both absorption and fluorescence intensity of the dye, indicating that the inclusion complex was formed. Simultaneously, the inclusion phenomenon of another cyanine dye, Cy3, with calixarene sulfonate was investigated. The stability constant of the two complexes was determined, and the results were compared. The water solubility of TO dye was increased in the presence of calixarene sulfonate, and further protein labeling experiments suggested that this TO-SCA6 complex can act as a fluorescent probe for labeling of biomolecules.

Water Network Tool for Resilience v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-12-09

WNTR is a python package designed to simulate and analyze resilience of water distribution networks. The software includes: - Pressure driven and demand driven hydraulic simulation - Water quality simulation to track concentration, trace, and water age - Conditional controls to simulate power outages - Models to simulate pipe breaks - A wide range of resilience metrics - Analysis and visualization tools

Effect of packaging atmospheres on storage quality characteristics of heavily marbled beef longissimus steaks.

PubMed

Yang, Xiaoyin; Zhang, Yimin; Zhu, Lixian; Han, Mingshan; Gao, Shujuan; Luo, Xin

2016-07-01

The objective of this study was to investigate the effects of modified atmosphere packaging (MAP) systems on shelf-life and quality of beef steaks with high marbling. Four packaging types were used including 80% O2 MAP (80% O2+20% CO2), 50% O2 MAP (50% O2+30% CO2+20% N2), carbon monoxide MAP (0.4% CO+30% CO2+69.6% N2) and vacuum packaging (VP). Steaks were displayed under simulated retail conditions at 4°C for 12days. Purge loss, pH, color stability, oxidative stability and microbial counts were monitored. Aerobically packaged steaks exhibited a bright-red color at the first 4days. However, discoloration and oxidation became major factors limiting their shelf-life to 8days. Compared with aerobic packaging, anaerobic packaging extended shelf-life of heavily marbled beef steaks, due to better color stability, together with lower oxidation and microbial populations. Among all packaging methods, CO-MAP had the best preservation for steaks, with more red color than other packaging types. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessment of the migration potential of nanosilver from nanoparticle-coated low-density polyethylene food packaging into food simulants.

PubMed

Hannon, Joseph Christopher; Kerry, Joseph P; Cruz-Romero, Malco; Azlin-Hasim, Shafrina; Morris, Michael; Cummins, Enda

2016-01-01

An experimental nanosilver-coated low-density polyethylene (LDPE) food packaging was incubated with food simulants using a conventional oven and tested for migration according to European Commission Regulation No. 10/2011. The commercial LDPE films were coated using a layer-by-layer (LbL) technique and three levels of silver (Ag) precursor concentration (0.5%, 2% and 5% silver nitrate (AgNO3), respectively) were used to attach antimicrobial Ag. The experimental migration study conditions (time, temperature and food simulant) under conventional oven heating (10 days at 60°C, 2 h at 70°C, 2 h at 60°C or 10 days at 70°C) were chosen to simulate the worst-case storage period of over 6 months. In addition, migration was quantified under microwave heating. The total Ag migrant levels in the food simulants were quantified by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). Mean migration levels obtained by ICP-AES for oven heating were in the range 0.01-1.75 mg l(-1). Migration observed for microwave heating was found to be significantly higher when compared with oven heating for similar temperatures (100°C) and identical exposure times (2 min). In each of the packaging materials and food simulants tested, the presence of nanoparticles (NPs) was confirmed by scanning electron microscopy (SEM). On inspection of the migration observed under conventional oven heating, an important finding was the significant reduction in migration resulting from the increased Ag precursor concentration used to attach Ag on the LDPE LbL-coated films. This observation merits further investigation into the LbL coating process used, as it suggests potential for process modifications to reduce migration. In turn, any reduction in NP migration below regulatory limits could greatly support the antimicrobial silver nanoparticle (AgNP)-LDPE LbL-coated films being used as a food packaging material.

Modeling parameterized geometry in GPU-based Monte Carlo particle transport simulation for radiotherapy.

PubMed

Chi, Yujie; Tian, Zhen; Jia, Xun

2016-08-07

Monte Carlo (MC) particle transport simulation on a graphics-processing unit (GPU) platform has been extensively studied recently due to the efficiency advantage achieved via massive parallelization. Almost all of the existing GPU-based MC packages were developed for voxelized geometry. This limited application scope of these packages. The purpose of this paper is to develop a module to model parametric geometry and integrate it in GPU-based MC simulations. In our module, each continuous region was defined by its bounding surfaces that were parameterized by quadratic functions. Particle navigation functions in this geometry were developed. The module was incorporated to two previously developed GPU-based MC packages and was tested in two example problems: (1) low energy photon transport simulation in a brachytherapy case with a shielded cylinder applicator and (2) MeV coupled photon/electron transport simulation in a phantom containing several inserts of different shapes. In both cases, the calculated dose distributions agreed well with those calculated in the corresponding voxelized geometry. The averaged dose differences were 1.03% and 0.29%, respectively. We also used the developed package to perform simulations of a Varian VS 2000 brachytherapy source and generated a phase-space file. The computation time under the parameterized geometry depended on the memory location storing the geometry data. When the data was stored in GPU's shared memory, the highest computational speed was achieved. Incorporation of parameterized geometry yielded a computation time that was ~3 times of that in the corresponding voxelized geometry. We also developed a strategy to use an auxiliary index array to reduce frequency of geometry calculations and hence improve efficiency. With this strategy, the computational time ranged in 1.75-2.03 times of the voxelized geometry for coupled photon/electron transport depending on the voxel dimension of the auxiliary index array, and in 0.69-1.23 times for photon only transport.

Large-scale 3D simulations of ICF and HEDP targets

NASA Astrophysics Data System (ADS)

Marinak, Michael M.

2000-10-01

The radiation hydrodynamics code HYDRA continues to be developed and applied to 3D simulations of a variety of targets for both inertial confinement fusion (ICF) and high energy density physics. Several packages have been added enabling this code to perform ICF target simulations with similar accuracy as two-dimensional codes of long-time historical use. These include a laser ray trace and deposition package, a heavy ion deposition package, implicit Monte Carlo photonics, and non-LTE opacities, derived from XSN or the linearized response matrix approach.(R. More, T. Kato, Phys. Rev. Lett. 81, 814 (1998), S. Libby, F. Graziani, R. More, T. Kato, Proceedings of the 13th International Conference on Laser Interactions and Related Plasma Phenomena, (AIP, New York, 1997).) LTE opacities can also be calculated for arbitrary mixtures online by combining tabular values generated by different opacity codes. Thermonuclear burn, charged particle transport, neutron energy deposition, electron-ion coupling and conduction, and multigroup radiation diffusion packages are also installed. HYDRA can employ ALE hydrodynamics; a number of grid motion algorithms are available. Multi-material flows are resolved using material interface reconstruction. Results from large-scale simulations run on up to 1680 processors, using a combination of massively parallel processing and symmetric multiprocessing, will be described. A large solid angle simulation of Rayleigh-Taylor instability growth in a NIF ignition capsule has resolved simultaneously the full spectrum of the most dangerous modes that grow from surface roughness. Simulations of a NIF hohlraum illuminated with the initial 96 beam configuration have also been performed. The effect of the hohlraum’s 3D intrinsic drive asymmetry on the capsule implosion will be considered. We will also discuss results from a Nova experiment in which a copper sphere is crushed by a planar shock. Several interacting hydrodynamic instabilities, including the Widnall instability, cause breakup of the resulting vortex ring.

An epidemiological modeling and data integration framework.

PubMed

Pfeifer, B; Wurz, M; Hanser, F; Seger, M; Netzer, M; Osl, M; Modre-Osprian, R; Schreier, G; Baumgartner, C

2010-01-01

In this work, a cellular automaton software package for simulating different infectious diseases, storing the simulation results in a data warehouse system and analyzing the obtained results to generate prediction models as well as contingency plans, is proposed. The Brisbane H3N2 flu virus, which has been spreading during the winter season 2009, was used for simulation in the federal state of Tyrol, Austria. The simulation-modeling framework consists of an underlying cellular automaton. The cellular automaton model is parameterized by known disease parameters and geographical as well as demographical conditions are included for simulating the spreading. The data generated by simulation are stored in the back room of the data warehouse using the Talend Open Studio software package, and subsequent statistical and data mining tasks are performed using the tool, termed Knowledge Discovery in Database Designer (KD3). The obtained simulation results were used for generating prediction models for all nine federal states of Austria. The proposed framework provides a powerful and easy to handle interface for parameterizing and simulating different infectious diseases in order to generate prediction models and improve contingency plans for future events.

Using and Evaluating Resampling Simulations in SPSS and Excel.

ERIC Educational Resources Information Center

Smith, Brad

2003-01-01

Describes and evaluates three computer-assisted simulations used with Statistical Package for the Social Sciences (SPSS) and Microsoft Excel. Designed the simulations to reinforce and enhance student understanding of sampling distributions, confidence intervals, and significance tests. Reports evaluations revealed improved student comprehension of…

Buffer Management Simulation in ATM Networks

NASA Technical Reports Server (NTRS)

Yaprak, E.; Xiao, Y.; Chronopoulos, A.; Chow, E.; Anneberg, L.

1998-01-01

This paper presents a simulation of a new dynamic buffer allocation management scheme in ATM networks. To achieve this objective, an algorithm that detects congestion and updates the dynamic buffer allocation scheme was developed for the OPNET simulation package via the creation of a new ATM module.

Enhanced thermaly managed packaging for III-nitride light emitters

NASA Astrophysics Data System (ADS)

Kudsieh, Nicolas

In this Dissertation our work on `enhanced thermally managed packaging of high power semiconductor light sources for solid state lighting (SSL)' is presented. The motivation of this research and development is to design thermally high stable cost-efficient packaging of single and multi-chip arrays of III-nitrides wide bandgap semiconductor light sources through mathematical modeling and simulations. Major issues linked with this technology are device overheating which causes serious degradation in their illumination intensity and decrease in the lifetime. In the introduction the basics of III-nitrides WBG semiconductor light emitters are presented along with necessary thermal management of high power cingulated and multi-chip LEDs and laser diodes. This work starts at chip level followed by its extension to fully packaged lighting modules and devices. Different III-nitride structures of multi-quantum well InGaN/GaN and AlGaN/GaN based LEDs and LDs were analyzed using advanced modeling and simulation for different packaging designs and high thermal conductivity materials. Study started with basic surface mounted devices using conventional packaging strategies and was concluded with the latest thermal management of chip-on-plate (COP) method. Newly discovered high thermal conductivity materials have also been incorporated for this work. Our study also presents the new approach of 2D heat spreaders using such materials for SSL and micro LED array packaging. Most of the work has been presented in international conferences proceedings and peer review journals. Some of the latest work has also been submitted to well reputed international journals which are currently been reviewed for publication. .

PCSIM: A Parallel Simulation Environment for Neural Circuits Fully Integrated with Python

PubMed Central

Pecevski, Dejan; Natschläger, Thomas; Schuch, Klaus

2008-01-01

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations. PMID:19543450

KMgene: a unified R package for gene-based association analysis for complex traits.

PubMed

Yan, Qi; Fang, Zhou; Chen, Wei; Stegle, Oliver

2018-02-09

In this report, we introduce an R package KMgene for performing gene-based association tests for familial, multivariate or longitudinal traits using kernel machine (KM) regression under a generalized linear mixed model (GLMM) framework. Extensive simulations were performed to evaluate the validity of the approaches implemented in KMgene. http://cran.r-project.org/web/packages/KMgene. qi.yan@chp.edu or wei.chen@chp.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

Eddylicious: A Python package for turbulent inflow generation

NASA Astrophysics Data System (ADS)

Mukha, Timofey; Liefvendahl, Mattias

2018-01-01

A Python package for generating inflow for scale-resolving computer simulations of turbulent flow is presented. The purpose of the package is to unite existing inflow generation methods in a single code-base and make them accessible to users of various Computational Fluid Dynamics (CFD) solvers. The currently existing functionality consists of an accurate inflow generation method suitable for flows with a turbulent boundary layer inflow and input/output routines for coupling with the open-source CFD solver OpenFOAM.

Modelling groundwater seepage zones in an unconfined aquifer with MODFLOW: different approaches

NASA Astrophysics Data System (ADS)

Leterme, Bertrand; Gedeon, Matej

2014-05-01

In areas where groundwater level occurs close to surface topography, the discharge of groundwater flow to the ground surface (or seepage) can be an important aspect of catchment hydrological cycle. It is also associated with valuable zones from an ecological point of view, often having a permanent shallow water table and constant lithotrophic water quality (Batelaan et al., 2003). In the present study, we try to implement a correct representation of this seepage process in a MODFLOW-HYDRUS coupled model for a small catchment (18.6 km²) of north-east Belgium. We started from an exisiting transient groundwater model of the unconfined aquifer in the study area (Gedeon and Mallants, 2009) discretized in 50x50 m cells. As the model did not account for seepage, hydraulic heads were simulated above the surface topography in certain zones. In the coupled MODFLOW-HYDRUS setup, transient boundary conditions (potential evapotranspiration and precipitation) are used to calculate the recharge with the HYDRUS package (Seo et al., 2007) for MODFLOW-2000 (Harbaugh et al., 2000). Coupling HYDRUS to MODFLOW involves the definition of a number of zones based on similarity in estimated groundwater depth, soil type and land cover. Concerning simulation of seepage, several existing packages are tested, including the DRAIN package (as in Reeve et al., 2006), the SPF package (from VSF Process; Thoms et al., 2006) and the PBC package (Post, 2011). Alternatively to the HYDRUS package for MODFLOW, the UZF package (Niswonger et al., 2006) for the simulation of recharge (and seepage) is also tested. When applicable, the parameterization of drain conductance in the top layer is critical and is investigated in relation to the soil hydraulic conductivity values used for the unsaturated zone (HYDRUS). Furthermore, stability issues are discussed, and where successful model runs are obtained, simulation results are compared with observed groundwater levels from a piezometric network. Spatial and temporal variability of the seepage zones is obtained and can be compared against seepage indicators such as soil maps or types of plant habitat. References Batelaan, O., De Smedt, F., Triest, L., 2003. Regional groundwater discharge: phreatophyte mapping, groundwater modelling and impact analysis of land-use change. Journal of Hydrology 275, 86-108. Gedeon, M., Mallants, D., 2009. Local-scale transient groundwater flow calculations. Project near surface disposal of category A waste at Dessel, NIRAS/ONDRAF, 74 p. Harbaugh, A.W., Banta, E.R., Hill, M.C., McDonald, M.G., 2000. MODFLOW-2000, the U.S. Geological Survey modular ground-water model user guide to modularization concepts and the ground-water flow process. USGS, Denver, CO. Niswonger, R.G., Prudic, D.E., Regan, R.S., 2006. Documentation of the Unsaturated-Zone Flow (UZF1) package for modeling unsaturated flow between the land surface and the water table with MODFLOW-2005. Techniques and Methods 6-A19, USGS, Denver, CO. Post, V.E.A., 2011. A new package for simulating periodic boundary conditions in MODFLOW and SEAWAT. Computers & Geosciences 37, 1843-1849. Reeve, A.S., Evensen, R., Glaser, P.H., Siegel, D.I., Rosenberry, D., 2006. Flow path oscillations in transient ground-water simulations of large peatland systems. Journal of Hydrology 316, 313-324. Seo, H.S., Šimůnek, J., Poeter, E.P., 2007. Documentation of the HYDRUS Package for MODFLOW-2000, the U.S. Geological Survey Modular Ground-Water Model. Colorado School of Mines, Golden, CO. Thoms, R.B., Johnson, R.L., Healy, R.W., 2006. User's guide to the Variably Saturated Flow (VSF) Process for MODFLOW. U.S. Geological Survey Techniques and Methods 6-A18, p. 58.

Virtual Environment User Interfaces to Support RLV and Space Station Simulations in the ANVIL Virtual Reality Lab

NASA Technical Reports Server (NTRS)

Dumas, Joseph D., II

1998-01-01

Several virtual reality I/O peripherals were successfully configured and integrated as part of the author's 1997 Summer Faculty Fellowship work. These devices, which were not supported by the developers of VR software packages, use new software drivers and configuration files developed by the author to allow them to be used with simulations developed using those software packages. The successful integration of these devices has added significant capability to the ANVIL lab at MSFC. In addition, the author was able to complete the integration of a networked virtual reality simulation of the Space Shuttle Remote Manipulator System docking Space Station modules which was begun as part of his 1996 Fellowship. The successful integration of this simulation demonstrates the feasibility of using VR technology for ground-based training as well as on-orbit operations.

Transmission of ˜ 10 keV electron beams through thin ceramic foils: Measurements and Monte Carlo simulations of electron energy distribution functions

NASA Astrophysics Data System (ADS)

Morozov, A.; Heindl, T.; Skrobol, C.; Wieser, J.; Krücken, R.; Ulrich, A.

2008-07-01

Electron beams with particle energy of ~10 keV were sent through 300 nm thick ceramic (Si3N4 + SiO2) foils and the resulting electron energy distribution functions were recorded using a retarding grid technique. The results are compared with Monte Carlo simulations performed with two publicly available packages, Geant4 and Casino v2.42. It is demonstrated that Geant4, unlike Casino, provides electron energy distribution functions very similar to the experimental distributions. Both simulation packages provide a quite precise average energy of transmitted electrons: we demonstrate that the maximum uncertainty of the calculated values of the average energy is 6% for Geant4 and 8% for Casino, taking into account all systematic uncertainties and the discrepancies in the experimental and simulated data.

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

PubMed Central

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.

2015-01-01

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815

Development of a cross-section based stream package for MODFLOW

NASA Astrophysics Data System (ADS)

Ou, G.; Chen, X.; Irmak, A.

2012-12-01

Accurate simulation of stream-aquifer interactions for wide rivers using the streamflow routing package in MODFLOW is very challenging. To better represent a wide river spanning over multiple model grid cells, a Cross-Section based streamflow Routing (CSR) package is developed and incorporated into MODFLOW to simulate the interaction between streams and aquifers. In the CSR package, a stream segment is represented as a four-point polygon instead of a polyline which is traditionally used in streamflow routing simulation. Each stream segment is composed of upstream and downstream cross-sections. A cross-section consists of a number of streambed points possessing coordinates, streambed thicknesses and streambed hydraulic conductivities to describe the streambed geometry and hydraulic properties. The left and right end points are used to determine the locations of the stream segments. According to the cross-section geometry and hydraulic properties, CSR calculates the new stream stage at the cross-section using the Brent's method to solve the Manning's Equation. A module is developed to automatically compute the area of the stream segment polygon on each intersected MODFLOW grid cell as the upstream and downstream stages change. The stream stage and streambed hydraulic properties of model grids are interpolated based on the streambed points. Streambed leakage is computed as a function of streambed conductance and difference between the groundwater level and stream stage. The Muskingum-Cunge flow routing scheme with variable parameters is used to simulate the streamflow as the groundwater (discharge or recharge) contributes as lateral flows. An example is used to illustrate the capabilities of the CSR package. The result shows that the CSR is applicable to describing the spatial and temporal variation in the interaction between streams and aquifers. The input data become simple due to that the internal program automatically interpolates the cross-section data to each model grid cell.

High Energy Boundary Conditions for a Cartesian Mesh Euler Solver

NASA Technical Reports Server (NTRS)

Pandya, Shishir; Murman, Scott; Aftosmis, Michael

2003-01-01

Inlets and exhaust nozzles are common place in the world of flight. Yet, many aerodynamic simulation packages do not provide a method of modelling such high energy boundaries in the flow field. For the purposes of aerodynamic simulation, inlets and exhausts are often fared over and it is assumed that the flow differences resulting from this assumption are minimal. While this is an adequate assumption for the prediction of lift, the lack of a plume behind the aircraft creates an evacuated base region thus effecting both drag and pitching moment values. In addition, the flow in the base region is often mis-predicted resulting in incorrect base drag. In order to accurately predict these quantities, a method for specifying inlet and exhaust conditions needs to be available in aerodynamic simulation packages. A method for a first approximation of a plume without accounting for chemical reactions is added to the Cartesian mesh based aerodynamic simulation package CART3D. The method consists of 3 steps. In the first step, a components approach where each triangle is assigned a component number is used. Here, a method for marking the inlet or exhaust plane triangles as separate components is discussed. In step two, the flow solver is modified to accept a reference state for the components marked inlet or exhaust. In the third step, the flow solver uses these separated components and the reference state to compute the correct flow condition at that triangle. The present method is implemented in the CART3D package which consists of a set of tools for generating a Cartesian volume mesh from a set of component triangulations. The Euler equations are solved on the resulting unstructured Cartesian mesh. The present methods is implemented in this package and its usefulness is demonstrated with two validation cases. A generic missile body is also presented to show the usefulness of the method on a real world geometry.

Facilitating hydrological data analysis workflows in R: the RHydro package

NASA Astrophysics Data System (ADS)

Buytaert, Wouter; Moulds, Simon; Skoien, Jon; Pebesma, Edzer; Reusser, Dominik

2015-04-01

The advent of new technologies such as web-services and big data analytics holds great promise for hydrological data analysis and simulation. Driven by the need for better water management tools, it allows for the construction of much more complex workflows, that integrate more and potentially more heterogeneous data sources with longer tool chains of algorithms and models. With the scientific challenge of designing the most adequate processing workflow comes the technical challenge of implementing the workflow with a minimal risk for errors. A wide variety of new workbench technologies and other data handling systems are being developed. At the same time, the functionality of available data processing languages such as R and Python is increasing at an accelerating pace. Because of the large diversity of scientific questions and simulation needs in hydrology, it is unlikely that one single optimal method for constructing hydrological data analysis workflows will emerge. Nevertheless, languages such as R and Python are quickly gaining popularity because they combine a wide array of functionality with high flexibility and versatility. The object-oriented nature of high-level data processing languages makes them particularly suited for the handling of complex and potentially large datasets. In this paper, we explore how handling and processing of hydrological data in R can be facilitated further by designing and implementing a set of relevant classes and methods in the experimental R package RHydro. We build upon existing efforts such as the sp and raster packages for spatial data and the spacetime package for spatiotemporal data to define classes for hydrological data (HydroST). In order to handle simulation data from hydrological models conveniently, a HM class is defined. Relevant methods are implemented to allow for an optimal integration of the HM class with existing model fitting and simulation functionality in R. Lastly, we discuss some of the design challenges of the RHydro package, including integration with big data technologies, web technologies, and emerging data models in hydrology.

Software Comparison for Renewable Energy Deployment in a Distribution Network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, David Wenzhong; Muljadi, Eduard; Tian, Tian

The main objective of this report is to evaluate different software options for performing robust distributed generation (DG) power system modeling. The features and capabilities of four simulation tools, OpenDSS, GridLAB-D, CYMDIST, and PowerWorld Simulator, are compared to analyze their effectiveness in analyzing distribution networks with DG. OpenDSS and GridLAB-D, two open source software, have the capability to simulate networks with fluctuating data values. These packages allow the running of a simulation each time instant by iterating only the main script file. CYMDIST, a commercial software, allows for time-series simulation to study variations on network controls. PowerWorld Simulator, another commercialmore » tool, has a batch mode simulation function through the 'Time Step Simulation' tool, which obtains solutions for a list of specified time points. PowerWorld Simulator is intended for analysis of transmission-level systems, while the other three are designed for distribution systems. CYMDIST and PowerWorld Simulator feature easy-to-use graphical user interfaces (GUIs). OpenDSS and GridLAB-D, on the other hand, are based on command-line programs, which increase the time necessary to become familiar with the software packages.« less

Simulation studies on the effect of positioning tolerances on optical coupling efficiency

NASA Astrophysics Data System (ADS)

Pamidighantam, Ramana V.; Yeo, Yongkee; Sudharsanam, Krishnamachari; Lee, Sik Pong; Iyer, Mahadevan K.

2002-08-01

The development of Optoelectronic components for communications is converging towards access networks where device cost makes a significant impact on the market acceptance. Thus, the device design engineer needs to input assembly, fabrication and process constraints into the design at an early stage. The present study is part of a Project on Packaging of Optical Components that IME, Singapore has initiated as part of an ongoing Electronics Packaging Research Consortium with industry partnership. In the present study, the coupling of optical radiation from a laser diode to optical fiber is simulated for a fiber optic transmitter component development project. Different optical configurations based on direct coupling, spherical ball lenses, integral lensed fibers and thermally expanded fibers are created within the commercially available transmitter package space. The effect of optical element variables on the placement tolerance is analyzed and will be reported. The effect of alignment tolerances on the optical coupling is analyzed. Simulation results are presented recommending realizable alignment and placement tolerances to develop a low cost short range link distance transmitter.

COSMOG: Cosmology Oriented Sub-mm Modeling of Galactic Foregrounds

NASA Technical Reports Server (NTRS)

Kashlinsky, A.; Leisawitz, D.

2004-01-01

With upcoming missions in mid- and far-Infrared there is a need for software packages to reliably simulate the planned observations. This would help in both planning the observation and scanning strategy and in developing the concepts of the far-off missions. As this workshop demonstrated, many of the new missions are to be in the far-IR range of the electromagnetic spectrum and at the same time will map the sky with a sub-arcsec angular resolution. We present here a computer package for simulating foreground maps for the planned sub-mm and far-IR missions. such as SPECS. The package allows to study confusion limits and simulate cosmological observations for specified sky location interactively and in real time. Most of the emission at wavelengths long-ward of approximately 50 microns is dominated by Galactic cirrus and Zodiacal dust emission. Stellar emission at these wavelengths is weak and is for now neglected. Cosmological sources (distant and not-so-distant) galaxies for specified cosmologies will be added. Briefly, the steps that the algorithm goes through is described.

Space-Shuttle Emulator Software

NASA Technical Reports Server (NTRS)

Arnold, Scott; Askew, Bill; Barry, Matthew R.; Leigh, Agnes; Mermelstein, Scott; Owens, James; Payne, Dan; Pemble, Jim; Sollinger, John; Thompson, Hiram;

Ares I-X Range Safety Simulation Verification and Analysis Independent Validation and Verification

NASA Technical Reports Server (NTRS)

Merry, Carl M.; Tarpley, Ashley F.; Craig, A. Scott; Tartabini, Paul V.; Brewer, Joan D.; Davis, Jerel G.; Dulski, Matthew B.; Gimenez, Adrian; Barron, M. Kyle

2011-01-01

NASA s Ares I-X vehicle launched on a suborbital test flight from the Eastern Range in Florida on October 28, 2009. To obtain approval for launch, a range safety final flight data package was generated to meet the data requirements defined in the Air Force Space Command Manual 91-710 Volume 2. The delivery included products such as a nominal trajectory, trajectory envelopes, stage disposal data and footprints, and a malfunction turn analysis. The Air Force s 45th Space Wing uses these products to ensure public and launch area safety. Due to the criticality of these data, an independent validation and verification effort was undertaken to ensure data quality and adherence to requirements. As a result, the product package was delivered with the confidence that independent organizations using separate simulation software generated data to meet the range requirements and yielded consistent results. This document captures Ares I-X final flight data package verification and validation analysis, including the methodology used to validate and verify simulation inputs, execution, and results and presents lessons learned during the process

Community-based benchmarking of the CMIP DECK experiments

NASA Astrophysics Data System (ADS)

Gleckler, P. J.

2015-12-01

A diversity of community-based efforts are independently developing "diagnostic packages" with little or no coordination between them. A short list of examples include NCAR's Climate Variability Diagnostics Package (CVDP), ORNL's International Land Model Benchmarking (ILAMB), LBNL's Toolkit for Extreme Climate Analysis (TECA), PCMDI's Metrics Package (PMP), the EU EMBRACE ESMValTool, the WGNE MJO diagnostics package, and CFMIP diagnostics. The full value of these efforts cannot be realized without some coordination. As a first step, a WCRP effort has initiated a catalog to document candidate packages that could potentially be applied in a "repeat-use" fashion to all simulations contributed to the CMIP DECK (Diagnostic, Evaluation and Characterization of Klima) experiments. Some coordination of community-based diagnostics has the additional potential to improve how CMIP modeling groups analyze their simulations during model-development. The fact that most modeling groups now maintain a "CMIP compliant" data stream means that in principal without much effort they could readily adopt a set of well organized diagnostic capabilities specifically designed to operate on CMIP DECK experiments. Ultimately, a detailed listing of and access to analysis codes that are demonstrated to work "out of the box" with CMIP data could enable model developers (and others) to select those codes they wish to implement in-house, potentially enabling more systematic evaluation during the model development process.

Monte carlo study of MOSFET packaging, optimised for improved energy response: single MOSFET filtration.

PubMed

Othman, M A R; Cutajar, D L; Hardcastle, N; Guatelli, S; Rosenfeld, A B

2010-09-01

Monte Carlo simulations of the energy response of a conventionally packaged single metal-oxide field effect transistors (MOSFET) detector were performed with the goal of improving MOSFET energy dependence for personal accident or military dosimetry. The MOSFET detector packaging was optimised. Two different 'drop-in' design packages for a single MOSFET detector were modelled and optimised using the GEANT4 Monte Carlo toolkit. Absorbed photon dose simulations of the MOSFET dosemeter placed in free-air response, corresponding to the absorbed doses at depths of 0.07 mm (D(w)(0.07)) and 10 mm (D(w)(10)) in a water equivalent phantom of size 30 x 30 x 30 cm(3) for photon energies of 0.015-2 MeV were performed. Energy dependence was reduced to within + or - 60 % for photon energies 0.06-2 MeV for both D(w)(0.07) and D(w)(10). Variations in the response for photon energies of 15-60 keV were 200 and 330 % for D(w)(0.07) and D(w)(10), respectively. The obtained energy dependence was reduced compared with that for conventionally packaged MOSFET detectors, which usually exhibit a 500-700 % over-response when used in free-air geometry.

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications.

PubMed

Du, Likai; Lan, Zhenggang

2015-04-14

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

Computer Simulation in Social Science.

ERIC Educational Resources Information Center

Garson, G. David

From a base in military models, computer simulation has evolved to provide a wide variety of applications in social science. General purpose simulation packages and languages such as FIRM, DYNAMO, and others have made significant contributions toward policy discussion in the social sciences and have well-documented efficacy in instructional…

The Sunspot Number and beyond : reconstructing detailed solar information over centuries

NASA Astrophysics Data System (ADS)

Lefevre, L.

2014-12-01

With four centuries of solar evolution, the International Sunspot Number (SSN) forms the longest solar time series currently available. It provides an essential reference for understanding and quantifying how the solar output has varied over decades and centuries and thus for assessing the variations of the main natural forcing on the Earth climate. Because of its importance, this unique time-series must be closely monitored for any possible biases and drifts. Here, we report about recent disagreements between solar indices, for example the sunspot sumber and the 10.7cm radio flux. Recent analyses indicate that while part of this divergence may be due to a calibration drift in the SSN, it also results from an intrinsic change in the global magnetic parameters of sunspots and solar active regions, suggesting a possible transition to a new activity regime. Going beyond the SSN series, in the framework of the TOSCA (www.cost-tosca.eu/) and SOLID (projects.pmodwrc.ch/solid/) projects, we produced a survey of all existing catalogs providing detailed sunspot information (Lefevre & Clette, 2014:10.1007/s11207-012-0184-5) and we also located different primary solar images and drawing collections that can be exploitable to complement the existing catalogs. These are first steps towards the construction of a multi-parametric time series of multiple sunspot and sunspot group properties over more than a century, allowing to reconstruct and extend the current 1-D SSN series. By bringing new spatial, morphological and evolutionary information, such a data set should bring major advances for the modeling of the solar dynamo and solar irradiance. We will present here the current status of this work. The preliminary version catalog now extends over the last 150 years. It makes use of data from DPD (http://fenyi.solarobs.unideb.hu/DPD/index.html), from the Uccle Solar Equatorial Table (USET:http://sidc.oma.be/uset/) operated by the Royal Obeservatory of Belgium, the Greenwich Catalog (RGO:http://www.ngdc.noaa.gov/) as well as the Kodaikanal white light data.

Proneness to guilt, shame, and pride in children with Autism Spectrum Disorders and neurotypical children.

PubMed

Davidson, Denise; Hilvert, Elizabeth; Misiunaite, Ieva; Giordano, Michael

2018-06-01

Self-conscious emotions (e.g., guilt, shame, and pride) are complex emotions that require self-reflection and self-evaluation, and are thought to facilitate the maintenance of societal norms and personal standards. Despite the importance of self-conscious emotions, most research has focused on basic emotion processing in children with Autism Spectrum Disorders (ASD). Therefore, in the present study, we used the Test of Self-Conscious Affect for Children (TOSCA-C) to assess proneness to, or propensity to experience, the self-conscious emotions guilt, shame, and pride in children with ASD and neurotypical children. The TOSCA-C is designed to capture a child's natural tendency to experience a given emotion across a range of everyday situations [Tangney, Stuewig, & Mashek, 2007]. We also assessed how individual characteristics contribute to the development of proneness to self-conscious emotions, including theory of mind (ToM) and ASD symptomatology. In comparison to neurotypical children, children with ASD showed less proneness to guilt, although all children showed relatively high levels of proneness to guilt. Greater ToM ability was related to more proneness to guilt and authentic pride in children with ASD. Additionally, we found that children with ASD with more severe symptomatology were more prone to hubristic pride. Our results provide evidence of differences in proneness to self-conscious emotions in children with ASD, as well as highlight important mechanisms contributing to how children with ASD may experience self-conscious emotions. Autism Res 2018,11:883-892. ©2017 International Society for Autism Research, Wiley Periodicals, Inc. This research examined proneness to guilt, shame, and pride in children with Autism Spectrum Disorders (ASD) and neurotypical children. We found that children with ASD showed less proneness to guilt than neurotypical children. Better understanding of theory of mind was related to greater proneness to guilt and pride, but only for children with ASD. These findings are important because these complex emotions are linked with both positive and negative social behaviors towards others and oneself. © 2018 International Society for Autism Research, Wiley Periodicals, Inc.

Severely Aggressive Children Receiving Stimulant Medication Versus Stimulant and Risperidone: 12-Month Follow-Up of the TOSCA Trial.

PubMed

Gadow, Kenneth D; Brown, Nicole V; Arnold, L Eugene; Buchan-Page, Kristin A; Bukstein, Oscar G; Butter, Eric; Farmer, Cristan A; Findling, Robert L; Kolko, David J; Molina, Brooke S G; Rice, Robert R; Schneider, Jayne; Aman, Michael G

2016-06-01

The objective of this study was to evaluate 52-week clinical outcomes of children with co-occurring attention-deficit/hyperactivity disorder (ADHD), disruptive behavior disorder, and serious physical aggression who participated in a prospective, longitudinal study that began with a controlled, 9-week clinical trial comparing the relative efficacy of parent training + stimulant medication + placebo (Basic; n = 84) versus parent training + stimulant + risperidone (Augmented; n = 84). Almost two-thirds (n = 108; 64%) of families in the 9-week study participated in week 52 follow-ups (Basic, n = 55; Augmented, n = 53) and were representative of the initial study sample. The assessment battery included caregiver and clinician ratings and laboratory tests. Only 43% of participants in the Augmented group and 36% in the Basic group still adhered to their assigned regimen (not significant [NS]); 23% of those in the Augmented group and 11% in the Basic group were taking no medication (NS). Both randomized groups improved baseline to follow-up, but the 3 primary parent-reported behavioral outcomes showed no significant between-group differences. Exploratory analyses indicated that participants in the Augmented group (65%) were more likely (p = .02) to have a Clinical Global Impressions (CGI) severity score of 1 to 3 (i.e., normal to mildly ill) at follow-up than those in the Basic group (42%). Parents rated 45% of children as impaired often or very often from ADHD, noncompliant, or aggressive behavior. The Augmented group had elevated prolactin levels, and the Basic group had decreased weight over time. Findings were generally similar whether groups were defined by randomized assignment or follow-up treatment status. Both treatment strategies were associated with clinical improvement at follow-up, and primary behavioral outcomes did not differ significantly. Many children evidenced lingering mental health concerns, suggesting the need for additional research into more effective interventions. Clinical trial registration information-Treatment of Severe Childhood Aggression (the TOSCA Study); http://clinicaltrials.gov/; NCT00796302. Published by Elsevier Inc.

Superconductive ADC Project Fabrication Package. Final Design Review Package (Briefing Charts)

DTIC Science & Technology

2010-09-07

Simulation Results Iin 1.45mV 2.5Ω 1pH 4pH 100fF 310uA 1fΩ Ic = 300uA Rn = 0.8Ω Cs = 0.32pF Ic = 300uA Rn = 0.8Ω Cs = 0.32pF Iin Vout Vout Ic = 500uA Rn...0.55Ω Cs = 0.32pF ONR Superconductive ADC CLIN/SLIN 0001AD September 2010, Brad Perranoski Pg. 17 Modulator Design Documentation Comparator Design...Comparator Design - Cadence Schematic & Simulation Comparator Testbench Simulation Results 1.45mV 2.5Ω 1pH 4pH 100fF 310uA 1fΩSine wave 100uApk Iin Ic

Testing a structural model for viral DNA packaging motor function by optical tweezers measurements, site directed mutagenesis, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Keller, Nicholas A.; Migliori, Amy D.; Arya, Gaurav; Rao, Venigalla B.; Smith, Douglas E.

2013-09-01

Many double-stranded DNA viruses employ a molecular motor to package DNA into preformed capsid shells. Based on structures of phage T4 motor proteins determined by X-ray crystallography and cryo-electron microscopy, Rao, Rossmann and coworkers recently proposed a structural model for motor function. They proposed that DNA is ratcheted by a large conformational change driven by electrostatic interactions between charged residues at an interface between two globular domains of the motor protein. We have conducted experiments to test this model by studying the effect on packaging under applied load of site-directed changes altering these residues. We observe significant impairment of packaging activity including reductions in packaging rate, percent time packaging, and time active under high load. We show that these measured impairments correlate well with alterations in free energies associated with the conformational change predicted by molecular dynamics simulations.

Low-Cost High-Speed Techniques for Real-Time Simulation of Power Electronic Systems

DTIC Science & Technology

2007-06-01

first implemented on the RT-Lab using Simulink S- fuctions . An effort was then initiated to code at least part of the simulation on the available FPGA. It...time simulation, and the use of simulation packages such as Matlab and Spice. The primary purpose of these calculations was to confirm that the

ROMI-RIP: Rough Mill RIP-first simulator user's guide

Treesearch

R. Edward Thomas

1995-01-01

The ROugh Mill RIP-first simulator (ROMI-RIP) is a computer software package for IBM compatible personal computers that simulates current industrial practices for gang-ripping lumber. This guide shows the user how to set and examine the results of simulations regarding current or proposed mill practices. ROMI-RIP accepts cutting bills with up to 300 different part...

Finite element for rotor/stator interactive forces in general engine dynamic simulation. Part 1: Development of bearing damper element

NASA Technical Reports Server (NTRS)

Adams, M. L.; Padovan, J.; Fertis, D. G.

1980-01-01

A general purpose squeeze-film damper interactive force element was developed, coded into a software package (module) and debugged. This software package was applied to nonliner dynamic analyses of some simple rotor systems. Results for pressure distributions show that the long bearing (end sealed) is a stronger bearing as compared to the short bearing as expected. Results of the nonlinear dynamic analysis, using a four degree of freedom simulation model, showed that the orbit of the rotating shaft increases nonlinearity to fill the bearing clearance as the unbalanced weight increases.

Seismic waveform modeling over cloud

NASA Astrophysics Data System (ADS)

Luo, Cong; Friederich, Wolfgang

2016-04-01

With the fast growing computational technologies, numerical simulation of seismic wave propagation achieved huge successes. Obtaining the synthetic waveforms through numerical simulation receives an increasing amount of attention from seismologists. However, computational seismology is a data-intensive research field, and the numerical packages usually come with a steep learning curve. Users are expected to master considerable amount of computer knowledge and data processing skills. Training users to use the numerical packages, correctly access and utilize the computational resources is a troubled task. In addition to that, accessing to HPC is also a common difficulty for many users. To solve these problems, a cloud based solution dedicated on shallow seismic waveform modeling has been developed with the state-of-the-art web technologies. It is a web platform integrating both software and hardware with multilayer architecture: a well designed SQL database serves as the data layer, HPC and dedicated pipeline for it is the business layer. Through this platform, users will no longer need to compile and manipulate various packages on the local machine within local network to perform a simulation. By providing users professional access to the computational code through its interfaces and delivering our computational resources to the users over cloud, users can customize the simulation at expert-level, submit and run the job through it.

Computer Simulation of Laboratory Experiments: An Unrealized Potential.

ERIC Educational Resources Information Center

Magin, D. J.; Reizes, J. A.

1990-01-01

Discussion of the use of computer simulation for laboratory experiments in undergraduate engineering education focuses on work at the University of New South Wales in the instructional design and software development of a package simulating a heat exchange device. The importance of integrating theory, design, and experimentation is also discussed.…

The Effects of Time Advance Mechanism on Simple Agent Behaviors in Combat Simulations

DTIC Science & Technology

2011-12-01

modeling packages that illustrate the differences between discrete-time simulation (DTS) and discrete-event simulation ( DES ) methodologies. Many combat... DES ) models , often referred to as “next-event” (Law and Kelton 2000) or discrete time simulation (DTS), commonly referred to as “time-step.” DTS...discrete-time simulation (DTS) and discrete-event simulation ( DES ) methodologies. Many combat models use DTS as their simulation time advance mechanism

Documentation of the seawater intrusion (SWI2) package for MODFLOW

USGS Publications Warehouse

Bakker, Mark; Schaars, Frans; Hughes, Joseph D.; Langevin, Christian D.; Dausman, Alyssa M.

2013-01-01

The SWI2 Package is the latest release of the Seawater Intrusion (SWI) Package for MODFLOW. The SWI2 Package allows three-dimensional vertically integrated variable-density groundwater flow and seawater intrusion in coastal multiaquifer systems to be simulated using MODFLOW-2005. Vertically integrated variable-density groundwater flow is based on the Dupuit approximation in which an aquifer is vertically discretized into zones of differing densities, separated from each other by defined surfaces representing interfaces or density isosurfaces. The numerical approach used in the SWI2 Package does not account for diffusion and dispersion and should not be used where these processes are important. The resulting differential equations are equivalent in form to the groundwater flow equation for uniform-density flow. The approach implemented in the SWI2 Package allows density effects to be incorporated into MODFLOW-2005 through the addition of pseudo-source terms to the groundwater flow equation without the need to solve a separate advective-dispersive transport equation. Vertical and horizontal movement of defined density surfaces is calculated separately using a combination of fluxes calculated through solution of the groundwater flow equation and a simple tip and toe tracking algorithm. Use of the SWI2 Package in MODFLOW-2005 only requires the addition of a single additional input file and modification of boundary heads to freshwater heads referenced to the top of the aquifer. Fluid density within model layers can be represented using zones of constant density (stratified flow) or continuously varying density (piecewise linear in the vertical direction) in the SWI2 Package. The main advantage of using the SWI2 Package instead of variable-density groundwater flow and dispersive solute transport codes, such as SEAWAT and SUTRA, is that fewer model cells are required for simulations using the SWI2 Package because every aquifer can be represented by a single layer of cells. This reduction in number of required model cells and the elimination of the need to solve the advective-dispersive transport equation results in substantial model run-time savings, which can be large for regional aquifers. The accuracy and use of the SWI2 Package is demonstrated through comparison with existing exact solutions and numerical solutions with SEAWAT. Results for an unconfined aquifer are also presented to demonstrate application of the SWI2 Package to a large-scale regional problem.

MOlecular MAterials Property Prediction Package (MOMAP) 1.0: a software package for predicting the luminescent properties and mobility of organic functional materials

NASA Astrophysics Data System (ADS)

Niu, Yingli; Li, Wenqiang; Peng, Qian; Geng, Hua; Yi, Yuanping; Wang, Linjun; Nan, Guangjun; Wang, Dong; Shuai, Zhigang

2018-04-01

MOlecular MAterials Property Prediction Package (MOMAP) is a software toolkit for molecular materials property prediction. It focuses on luminescent properties and charge mobility properties. This article contains a brief descriptive introduction of key features, theoretical models and algorithms of the software, together with examples that illustrate the performance. First, we present the theoretical models and algorithms for molecular luminescent properties calculation, which includes the excited-state radiative/non-radiative decay rate constant and the optical spectra. Then, a multi-scale simulation approach and its algorithm for the molecular charge mobility are described. This approach is based on hopping model and combines with Kinetic Monte Carlo and molecular dynamics simulations, and it is especially applicable for describing a large category of organic semiconductors, whose inter-molecular electronic coupling is much smaller than intra-molecular charge reorganisation energy.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langer, Steven H.; Karlin, Ian; Marinak, Marty M.

HYDRA is used to simulate a variety of experiments carried out at the National Ignition Facility (NIF) [4] and other high energy density physics facilities. HYDRA has packages to simulate radiation transfer, atomic physics, hydrodynamics, laser propagation, and a number of other physics effects. HYDRA has over one million lines of code and includes both MPI and thread-level (OpenMP and pthreads) parallelism. This paper measures the performance characteristics of HYDRA using hardware counters on an IBM BlueGene/Q system. We report key ratios such as bytes/instruction and memory bandwidth for several different physics packages. The total number of bytes read andmore » written per time step is also reported. We show that none of the packages which use significant time are memory bandwidth limited on a Blue Gene/Q. HYDRA currently issues very few SIMD instructions. The pressure on memory bandwidth will increase if high levels of SIMD instructions can be achieved.« less

Active cooling of microvascular composites for battery packaging

NASA Astrophysics Data System (ADS)

Pety, Stephen J.; Chia, Patrick X. L.; Carrington, Stephen M.; White, Scott R.

2017-10-01

Batteries in electric vehicles (EVs) require a packaging system that provides both thermal regulation and crash protection. A novel packaging scheme is presented that uses active cooling of microvascular carbon fiber reinforced composites to accomplish this multifunctional objective. Microvascular carbon fiber/epoxy composite panels were fabricated and their cooling performance assessed over a range of thermal loads and experimental conditions. Tests were performed for different values of coolant flow rate, channel spacing, panel thermal conductivity, and applied heat flux. More efficient cooling occurs when the coolant flow rate is increased, channel spacing is reduced, and thermal conductivity of the host composite is increased. Computational fluid dynamics (CFD) simulations were also performed and correlate well with the experimental data. CFD simulations of a typical EV battery pack confirm that microvascular composite panels can adequately cool battery cells generating 500 W m-2 heat flux below 40 °C.

Use of optical technique for inspection of warpage of IC packages

NASA Astrophysics Data System (ADS)

Toh, Siew-Lok; Chau, Fook S.; Ong, Sim Heng

2001-06-01

The packaging of IC packages has changed over the years, form dual-in-line, wire-bond, and pin-through-hole in printed wiring board technologies in the 1970s to ball grid array, chip scale and surface mount technologies in the 1990s. Reliability has been a big problem for manufacturers for some moisture-sensitive packages. One of the potential problems in plastic IC packages is moisture-induced popcorn effect which can arise during the reflow process. Shearography is a non-destructive inspection technique that may be used to detect the delamination and warpage of IC packages. It is non-contacting and permits a full-field observation of surface displacement derivatives. Another advantage of this technique is that it is able to give the real-time formation of the fringes which indicate flaws in the IC package under real-time simulation condition of Surface Mount Technology (SMT) IR reflow profile. It is extremely fast and convenient to study the true behavior of the packaging deformation during the SMT process. It can be concluded that shearography has the potential for the real- time detection, in situ and non-destructive inspection of IC packages during the surface mount process.

SpectraPLOT, Visualization Package with a User-Friendly Graphical Interface

NASA Astrophysics Data System (ADS)

Sebald, James; Macfarlane, Joseph; Golovkin, Igor

2017-10-01

SPECT3D is a collisional-radiative spectral analysis package designed to compute detailed emission, absorption, or x-ray scattering spectra, filtered images, XRD signals, and other synthetic diagnostics. The spectra and images are computed for virtual detectors by post-processing the results of hydrodynamics simulations in 1D, 2D, and 3D geometries. SPECT3D can account for a variety of instrumental response effects so that direct comparisons between simulations and experimental measurements can be made. SpectraPLOT is a user-friendly graphical interface for viewing a wide variety of results from SPECT3D simulations, and applying various instrumental effects to the simulated images and spectra. We will present SpectraPLOT's ability to display a variety of data, including spectra, images, light curves, streaked spectra, space-resolved spectra, and drilldown plasma property plots, for an argon-doped capsule implosion experiment example. Future SpectraPLOT features and enhancements will also be discussed.

Fast emulation of track reconstruction in the CMS simulation

NASA Astrophysics Data System (ADS)

Komm, Matthias; CMS Collaboration

2017-10-01

Simulated samples of various physics processes are a key ingredient within analyses to unlock the physics behind LHC collision data. Samples with more and more statistics are required to keep up with the increasing amounts of recorded data. During sample generation, significant computing time is spent on the reconstruction of charged particle tracks from energy deposits which additionally scales with the pileup conditions. In CMS, the FastSimulation package is developed for providing a fast alternative to the standard simulation and reconstruction workflow. It employs various techniques to emulate track reconstruction effects in particle collision events. Several analysis groups in CMS are utilizing the package, in particular those requiring many samples to scan the parameter space of physics models (e.g. SUSY) or for the purpose of estimating systematic uncertainties. The strategies for and recent developments in this emulation are presented, including a novel, flexible implementation of tracking emulation while retaining a sufficient, tuneable accuracy.

Preliminary Dynamic Feasibility and Analysis of a Spherical, Wind-Driven (Tumbleweed), Martian Rover

NASA Technical Reports Server (NTRS)

Flick, John J.; Toniolo, Matthew D.

2005-01-01

The process and findings are presented from a preliminary feasibility study examining the dynamics characteristics of a spherical wind-driven (or Tumbleweed) rover, which is intended for exploration of the Martian surface. The results of an initial feasibility study involving several worst-case mobility situations that a Tumbleweed rover might encounter on the surface of Mars are discussed. Additional topics include the evaluation of several commercially available analysis software packages that were examined as possible platforms for the development of a Monte Carlo Tumbleweed mission simulation tool. This evaluation lead to the development of the Mars Tumbleweed Monte Carlo Simulator (or Tumbleweed Simulator) using the Vortex physics software package from CM-Labs, Inc. Discussions regarding the development and evaluation of the Tumbleweed Simulator, as well as the results of a preliminary analysis using the tool are also presented. Finally, a brief conclusions section is presented.

Adaptively restrained molecular dynamics in LAMMPS

NASA Astrophysics Data System (ADS)

Kant Singh, Krishna; Redon, Stephane

2017-07-01

Adaptively restrained molecular dynamics (ARMD) is a recently introduced particles simulation method that switches positional degrees of freedom on and off during simulation in order to speed up calculations. In the NVE ensemble, ARMD allows users to trade between precision and speed while, in the NVT ensemble, it makes it possible to compute statistical averages faster. Despite the conceptual simplicity of the approach, however, integrating it in existing molecular dynamics packages is non-trivial, in particular since implemented potentials should a priori be rewritten to take advantage of frozen particles and achieve a speed-up. In this paper, we present novel algorithms for integrating ARMD in LAMMPS, a popular multi-purpose molecular simulation package. In particular, we demonstrate how to enable ARMD in LAMMPS without having to re-implement all available force fields. The proposed algorithms are assessed on four different benchmarks, and show how they allow us to speed up simulations up to one order of magnitude.

A passive and active microwave-vector radiative transfer (PAM-VRT) model

NASA Astrophysics Data System (ADS)

Yang, Jun; Min, Qilong

2015-11-01

A passive and active microwave vector radiative transfer (PAM-VRT) package has been developed. This fast and accurate forward microwave model, with flexible and versatile input and output components, self-consistently and realistically simulates measurements/radiation of passive and active microwave sensors. The core PAM-VRT, microwave radiative transfer model, consists of five modules: gas absorption (two line-by-line databases and four fast models); hydrometeor property of water droplets and ice (spherical and nonspherical) particles; surface emissivity (from Community Radiative Transfer Model (CRTM)); vector radiative transfer of successive order of scattering (VSOS); and passive and active microwave simulation. The PAM-VRT package has been validated against other existing models, demonstrating good accuracy. The PAM-VRT not only can be used to simulate or assimilate measurements of existing microwave sensors, but also can be used to simulate observation results at some new microwave sensors.

Quality and physiological responses of two late-season sweet cherry cultivars 'Lapins' and 'Skeena' to modified atmosphere packaging (MAP) during simulated long distance ocean shipping

USDA-ARS?s Scientific Manuscript database

Flavor loss, skin darkening, pitting, splitting, pedicel browning, and decay are the major quality deteriorations in sweet cherries during storage/shipping. In this research, three modified atmosphere packaging (MAP) liners with varied gas permeability were evaluated for the effect on quality deteri...

BEARCLAW: Boundary Embedded Adaptive Refinement Conservation LAW package

NASA Astrophysics Data System (ADS)

Mitran, Sorin

2011-04-01

The BEARCLAW package is a multidimensional, Eulerian AMR-capable computational code written in Fortran to solve hyperbolic systems for astrophysical applications. It is part of AstroBEAR, a hydrodynamic & magnetohydrodynamic code environment designed for a variety of astrophysical applications which allows simulations in 2, 2.5 (i.e., cylindrical), and 3 dimensions, in either cartesian or curvilinear coordinates.

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

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

PubMed

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

2017-09-30

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

Benchmark tests for a Formula SAE Student car prototyping

NASA Astrophysics Data System (ADS)

Mariasiu, Florin

2011-12-01

Aerodynamic characteristics of a vehicle are important elements in its design and construction. A low drag coefficient brings significant fuel savings and increased engine power efficiency. In designing and developing vehicles trough computer simulation process to determine the vehicles aerodynamic characteristics are using dedicated CFD (Computer Fluid Dynamics) software packages. However, the results obtained by this faster and cheaper method, are validated by experiments in wind tunnels tests, which are expensive and were complex testing equipment are used in relatively high costs. Therefore, the emergence and development of new low-cost testing methods to validate CFD simulation results would bring great economic benefits for auto vehicles prototyping process. This paper presents the initial development process of a Formula SAE Student race-car prototype using CFD simulation and also present a measurement system based on low-cost sensors through which CFD simulation results were experimentally validated. CFD software package used for simulation was Solid Works with the FloXpress add-on and experimental measurement system was built using four piezoresistive force sensors FlexiForce type.

Food-packaging migration models: A critical discussion.

PubMed

Gavriil, Gavriil; Kanavouras, Antonis; Coutelieris, Frank A

2017-06-14

The widely accepted and used migration models that describe the mass transport from polymeric packaging material to food and food simulants are confirmed here. A critical review of the most accepted models is presented in detail. Their main advantages and weak points, regarding their predictive accuracy, are discussed and weighted toward their usage extensiveness. By identifying the specific areas where using such models may not provide a strong correlation between theoretical and actual results, this work also aims in outlining some particular directions regarding further research on food - packaging interactions.

Phi29 Connector-DNA Interactions Govern DNA Crunching and Rotation, Supporting the Check-Valve Model

PubMed Central

Kumar, Rajendra; Grubmüller, Helmut

2016-01-01

During replication of the ϕ29 bacteriophage inside a bacterial host cell, a DNA packaging motor transports the viral DNA into the procapsid against a pressure difference of up to 40 ± 20 atm. Several models have been proposed for the underlying molecular mechanism. Here we have used molecular dynamics simulations to examine the role of the connector part of the motor, and specifically the one-way revolution and the push-roll model. We have focused at the structure and intermolecular interactions between the DNA and the connector, for which a near-complete structure is available. The connector is found to induce considerable DNA deformations with respect to its canonical B-form. We further assessed by force-probe simulations to which extent the connector is able to prevent DNA leakage and found that the connector can act as a partial one-way valve by a check-valve mechanism via its mobile loops. Analysis of the geometry, flexibility, and energetics of channel lysine residues suggested that this arrangement of residues is incompatible with the observed DNA packaging step-size of ∼2.5 bp, such that the step-size is probably determined by the other components of the motor. Previously proposed DNA revolution and rolling motions inside the connector channel are both found implausible due to structural entanglement between the DNA and connector loops that have not been resolved in the crystal structure. Rather, in the simulations, the connector facilitates minor DNA rotation during the packaging process compatible with recent optical-tweezers experiments. Combined with the available experimental data, our simulation results suggest that the connector acts as a check-valve that prevents DNA leakage and induces DNA compression and rotation during DNA packaging. PMID:26789768

ROMI 4.0: Rough mill simulator 4.0 users manual

Treesearch

R. Edward Thomas; Timo Grueneberg; Urs Buehlmann

2015-01-01

The Rough MIll simulator (ROMI Version 4.0) is a computer software package for personal computers (PCs) that simulates current industrial practices for rip-first, chop-first, and rip and chop-first lumber processing. This guide shows how to set up the software; design, implement, and execute simulations; and examine the results. ROMI 4.0 accepts cutting bills with as...

MPPhys—A many-particle simulation package for computational physics education

NASA Astrophysics Data System (ADS)

Müller, Thomas

2014-03-01

In a first course to classical mechanics elementary physical processes like elastic two-body collisions, the mass-spring model, or the gravitational two-body problem are discussed in detail. The continuation to many-body systems, however, is deferred to graduate courses although the underlying equations of motion are essentially the same and although there is a strong motivation for high-school students in particular because of the use of particle systems in computer games. The missing link between the simple and the more complex problem is a basic introduction to solve the equations of motion numerically which could be illustrated, however, by means of the Euler method. The many-particle physics simulation package MPPhys offers a platform to experiment with simple particle simulations. The aim is to give a principle idea how to implement many-particle simulations and how simulation and visualization can be combined for interactive visual explorations. Catalogue identifier: AERR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERR_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 111327 No. of bytes in distributed program, including test data, etc.: 608411 Distribution format: tar.gz Programming language: C++, OpenGL, GLSL, OpenCL. Computer: Linux and Windows platforms with OpenGL support. Operating system: Linux and Windows. RAM: Source Code 4.5 MB Complete package 242 MB Classification: 14, 16.9. External routines: OpenGL, OpenCL Nature of problem: Integrate N-body simulations, mass-spring models Solution method: Numerical integration of N-body-simulations, 3D-Rendering via OpenGL. Running time: Problem dependent

Effects of simulant mixed waste on EPDM and butyl rubber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nigrey, P.J.; Dickens, T.G.

1997-11-01

The authors have developed a Chemical Compatibility Testing Program for the evaluation of plastic packaging components which may be used in transporting mixed waste forms. In this program, they have screened 10 plastic materials in four liquid mixed waste simulants. These plastics were butadiene-acrylonitrile copolymer (Nitrile) rubber, cross-linked polyethylene, epichlorohydrin rubber, ethylene-propylene (EPDM) rubber, fluorocarbons (Viton and Kel-F{trademark}), polytetrafluoro-ethylene (Teflon), high-density polyethylene, isobutylene-isoprene copolymer (Butyl) rubber, polypropylene, and styrene-butadiene (SBR) rubber. The selected simulant mixed wastes were (1) an aqueous alkaline mixture of sodium nitrate and sodium nitrite; (2) a chlorinated hydrocarbon mixture; (3) a simulant liquid scintillation fluid; andmore » (4) a mixture of ketones. The screening testing protocol involved exposing the respective materials to approximately 3 kGy of gamma radiation followed by 14-day exposures to the waste simulants at 60 C. The rubber materials or elastomers were tested using Vapor Transport Rate measurements while the liner materials were tested using specific gravity as a metric. The authors have developed a chemical compatibility program for the evaluation of plastic packaging components which may be incorporated in packaging for transporting mixed waste forms. From the data analyses performed to date, they have identified the thermoplastic, polychlorotrifluoroethylene, as having the greatest chemical compatibility after having been exposed to gamma radiation followed by exposure to the Hanford Tank simulant mixed waste. The most striking observation from this study was the poor performance of polytetrafluoroethylene under these conditions. In the evaluation of the two elastomeric materials they have concluded that while both materials exhibit remarkable resistance to these environmental conditions, EPDM has a greater resistance to this corrosive simulant mixed waste.« less

Computer Simulation Is an Undervalued Tool for Genetic Analysis: A Historical View and Presentation of SHIMSHON – A Web-Based Genetic Simulation Package

PubMed Central

Greenberg, David A.

2011-01-01

Computer simulation methods are under-used tools in genetic analysis because simulation approaches have been portrayed as inferior to analytic methods. Even when simulation is used, its advantages are not fully exploited. Here, I present SHIMSHON, our package of genetic simulation programs that have been developed, tested, used for research, and used to generated data for Genetic Analysis Workshops (GAW). These simulation programs, now web-accessible, can be used by anyone to answer questions about designing and analyzing genetic disease studies for locus identification. This work has three foci: (1) the historical context of SHIMSHON's development, suggesting why simulation has not been more widely used so far. (2) Advantages of simulation: computer simulation helps us to understand how genetic analysis methods work. It has advantages for understanding disease inheritance and methods for gene searches. Furthermore, simulation methods can be used to answer fundamental questions that either cannot be answered by analytical approaches or cannot even be defined until the problems are identified and studied, using simulation. (3) I argue that, because simulation was not accepted, there was a failure to grasp the meaning of some simulation-based studies of linkage. This may have contributed to perceived weaknesses in linkage analysis; weaknesses that did not, in fact, exist. PMID:22189467

ATK-ForceField: a new generation molecular dynamics software package

NASA Astrophysics Data System (ADS)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

Moving from Batch to Field Using the RT3D Reactive Transport Modeling System

NASA Astrophysics Data System (ADS)

Clement, T. P.; Gautam, T. R.

2002-12-01

The public domain reactive transport code RT3D (Clement, 1997) is a general-purpose numerical code for solving coupled, multi-species reactive transport in saturated groundwater systems. The code uses MODFLOW to simulate flow and several modules of MT3DMS to simulate the advection and dispersion processes. RT3D employs the operator-split strategy which allows the code solve the coupled reactive transport problem in a modular fashion. The coupling between reaction and transport is defined through a separate module where the reaction equations are specified. The code supports a versatile user-defined reaction option that allows users to define their own reaction system through a Fortran-90 subroutine, known as the RT3D-reaction package. Further a utility code, known as BATCHRXN, allows the users to independently test and debug their reaction package. To analyze a new reaction system at a batch scale, users should first run BATCHRXN to test the ability of their reaction package to model the batch data. After testing, the reaction package can simply be ported to the RT3D environment to study the model response under 1-, 2-, or 3-dimensional transport conditions. This paper presents example problems that demonstrate the methods for moving from batch to field-scale simulations using BATCHRXN and RT3D codes. The first example describes a simple first-order reaction system for simulating the sequential degradation of Tetrachloroethene (PCE) and its daughter products. The second example uses a relatively complex reaction system for describing the multiple degradation pathways of Tetrachloroethane (PCA) and its daughter products. References 1) Clement, T.P, RT3D - A modular computer code for simulating reactive multi-species transport in 3-Dimensional groundwater aquifers, Battelle Pacific Northwest National Laboratory Research Report, PNNL-SA-28967, September, 1997. Available at: http://bioprocess.pnl.gov/rt3d.htm.

Software Reviews.

ERIC Educational Resources Information Center

Bitter, Gary G., Ed.

1989-01-01

Reviews three software packages: (1) "Physics," tutorial, grades 11-12, Macintosh; (2) "Hands On Math: Volume I," interactive math exploration/simulation of manipulatives use, grades K-7, Apple II; and (3) "A.I.: An Experience with Artificial Intelligence," simulation, grades 5-12, Apple II. (MVL)

Computer Simulations: An Integrating Tool.

ERIC Educational Resources Information Center

Bilan, Bohdan J.

This introduction to computer simulations as an integrated learning experience reports on their use with students in grades 5 through 10 using commercial software packages such as SimCity, SimAnt, SimEarth, and Civilization. Students spent an average of 60 hours with the simulation games and reported their experiences each week in a personal log.…

Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator.

PubMed

Dequidt, Alain; Devémy, Julien; Pádua, Agílio A H

2016-01-25

LAMMPS is a very customizable molecular dynamics simulation software, which can be used to simulate a large diversity of systems. We introduce a new package for simulation of polarizable systems with LAMMPS using thermalized Drude oscillators. The implemented functionalities are described and are illustrated by examples. The implementation was validated by comparing simulation results with published data and using a reference software. Computational performance is also analyzed.

An assessment of the cloud signals simulated by NICAM using ISCCP, CALIPSO, and CloudSat satellite simulators

NASA Astrophysics Data System (ADS)

Kodama, C.; Noda, A. T.; Satoh, M.

2012-06-01

This study presents an assessment of three-dimensional structures of hydrometeors simulated by the NICAM, global nonhydrostatic atmospheric model without cumulus parameterization, using multiple satellite data sets. A satellite simulator package (COSP: the CFMIP Observation Simulator Package) is employed to consistently compare model output with ISCCP, CALIPSO, and CloudSat satellite observations. Special focus is placed on high thin clouds, which are not observable in the conventional ISCCP data set, but can be detected by the CALIPSO observations. For the control run, the NICAM simulation qualitatively captures the geographical distributions of the high, middle, and low clouds, even though the horizontal mesh spacing is as coarse as 14 km. The simulated low cloud is very close to that of the CALIPSO low cloud. Both the CloudSat observations and NICAM simulation show a boomerang-type pattern in the radar reflectivity-height histogram, suggesting that NICAM realistically simulates the deep cloud development process. A striking difference was found in the comparisons of high thin cirrus, showing overestimated cloud and higher cloud top in the model simulation. Several model sensitivity experiments are conducted with different cloud microphysical parameters to reduce the model-observation discrepancies in high thin cirrus. In addition, relationships among clouds, Hadley circulation, outgoing longwave radiation and precipitation are discussed through the sensitivity experiments.

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

USGS Publications Warehouse

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.

Integrated Nuclear and Conventional Theater Warfare Simulation (INWARS) Documentation. Part IV. User’s Manual Component. Volume III. EAD C2I Inputs.

DTIC Science & Technology

1980-02-08

hours 0 Input Format: Integer b. Creatina Rescource Allocation Blocks The creation of a specific resource allocation block as a directive component is...is directed. 0 Range: N/A . Input Format: INT/NUC/CHM b. Creatina Employment Packages An employment package block has the structure portrayed in Figure

Influence of Food with High Moisture Content on Oxygen Barrier Property of Polyvinyl Alcohol (PVA)/Vermiculite Nanocomposite Coated Multilayer Packaging Film.

PubMed

Kim, Jung Min; Lee, Min Hyeock; Ko, Jung A; Kang, Dong Ho; Bae, Hojae; Park, Hyun Jin

2018-02-01

This study investigates the potential complications in applying nanoclay-based waterborne coating to packaging films for food with high moisture content. Multilayer packaging films were prepared by dry laminating commercially available polyvinyl alcohol (PVA)/vermiculite nanocomposite coating films and linear low-density polyethylene film, and the changes in oxygen barrier properties were investigated according to different relative humidity using 3 types of food simulants. When the relative humidity was above 60%, the oxygen permeability increased sharply, but this was reversible. Deionized water and 3% acetic acid did not cause any large structural change in the PVA/vermiculite nanocomposite but caused a reversible deterioration of the oxygen barrier properties. In contrast, 50% ethanol, a simulant for the semifatty food, induced irreversible structural changes with deterioration of the oxygen barrier property. These changes are due to the characteristics of PVA rather than vermiculite. We believe this manuscript would be of interest to the wide group of researchers, organizations, and companies in the field of developing nanoclay-based gas barrier packaging for foods with high moisture content. Hence, we wish to diffuse our knowledge to the scientific community. © 2018 Institute of Food Technologists®.

Realistic Simulations of Coronagraphic Observations with WFIRST

NASA Astrophysics Data System (ADS)

Rizzo, Maxime; Zimmerman, Neil; Roberge, Aki; Lincowski, Andrew; Arney, Giada; Stark, Chris; Jansen, Tiffany; Turnbull, Margaret; WFIRST Science Investigation Team (Turnbull)

2018-01-01

We present a framework to simulate observing scenarios with the WFIRST Coronagraphic Instrument (CGI). The Coronagraph and Rapid Imaging Spectrograph in Python (crispy) is an open-source package that can be used to create CGI data products for analysis and development of post-processing routines. The software convolves time-varying coronagraphic PSFs with realistic astrophysical scenes which contain a planetary architecture, a consistent dust structure, and a background field composed of stars and galaxies. The focal plane can be read out by a WFIRST electron-multiplying CCD model directly, or passed through a WFIRST integral field spectrograph model first. Several elementary post-processing routines are provided as part of the package.

Use of the MATRIXx Integrated Toolkit on the Microwave Anisotropy Probe Attitude Control System

NASA Technical Reports Server (NTRS)

Ward, David K.; Andrews, Stephen F.; McComas, David C.; ODonnell, James R., Jr.

1999-01-01

Recent advances in analytical software tools allow the analysis, simulation, flight code, and documentation of an algorithm to be generated from a single source, all within one integrated analytical design package. NASA's Microwave Anisotropy Probe project has used one such package, Integrated Systems' MATRIXx suite, in the design of the spacecraft's Attitude Control System. The project's experience with the linear analysis, simulation, code generation, and documentation tools will be presented and compared with more traditional development tools. In particular, the quality of the flight software generated will be examined in detail. Finally, lessons learned on each of the tools will be shared.

Kassiopeia: a modern, extensible C++ particle tracking package

DOE Office of Scientific and Technical Information (OSTI.GOV)

Furse, Daniel; Groh, Stefan; Trost, Nikolaus

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease-of-use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur inmore » flight such as bulk scattering and decay, and stochastic surface processes occurring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopeia.« less

Migration of nanoparticles from plastic packaging materials containing carbon black into foodstuffs

PubMed Central

Bott, Johannes; Störmer, Angela; Franz, Roland

2014-01-01

Carbon black was investigated to assess and quantify the possibility that nanoparticles might migrate out of plastic materials used in the food packaging industry. Two types of carbon black were incorporated in low-density polyethylene (LDPE) and polystyrene (PS) at 2.5% and 5.0% loading (w/w), and then subjected to migration studies. The samples were exposed to different food simulants according to European Union Plastics Regulation 10/2011, simulating long-term storage with aqueous and fatty foodstuffs. Asymmetric flow field-flow fractionation (AF4) coupled to a multi-angle laser light-scattering (MALLS) detector was used to separate, characterise and quantify the potential release of nanoparticles. The AF4 method was successful in differentiating carbon black from other matrix components, such as extracted polymer chains, in the migration solution. At a detection limit of 12 µg kg−1, carbon black did not migrate from the packaging material into food simulants. The experimental findings are in agreement with theoretical considerations based on migration modelling. From both the experimental findings and theoretical considerations, it can be concluded that carbon black does not migrate into food once it is incorporated into a plastics food contact material. PMID:25105506

Migration of nanoparticles from plastic packaging materials containing carbon black into foodstuffs.

PubMed

Bott, Johannes; Störmer, Angela; Franz, Roland

2014-01-01

Carbon black was investigated to assess and quantify the possibility that nanoparticles might migrate out of plastic materials used in the food packaging industry. Two types of carbon black were incorporated in low-density polyethylene (LDPE) and polystyrene (PS) at 2.5% and 5.0% loading (w/w), and then subjected to migration studies. The samples were exposed to different food simulants according to European Union Plastics Regulation 10/2011, simulating long-term storage with aqueous and fatty foodstuffs. Asymmetric flow field-flow fractionation (AF4) coupled to a multi-angle laser light-scattering (MALLS) detector was used to separate, characterise and quantify the potential release of nanoparticles. The AF4 method was successful in differentiating carbon black from other matrix components, such as extracted polymer chains, in the migration solution. At a detection limit of 12 µg kg⁻¹, carbon black did not migrate from the packaging material into food simulants. The experimental findings are in agreement with theoretical considerations based on migration modelling. From both the experimental findings and theoretical considerations, it can be concluded that carbon black does not migrate into food once it is incorporated into a plastics food contact material.

Kassiopeia: a modern, extensible C++ particle tracking package

DOE PAGES

Furse, Daniel; Groh, Stefan; Trost, Nikolaus; ...

2017-05-16

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease-of-use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur inmore » flight such as bulk scattering and decay, and stochastic surface processes occurring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopeia.« less

Kassiopeia: a modern, extensible C++ particle tracking package

NASA Astrophysics Data System (ADS)

Furse, Daniel; Groh, Stefan; Trost, Nikolaus; Babutzka, Martin; Barrett, John P.; Behrens, Jan; Buzinsky, Nicholas; Corona, Thomas; Enomoto, Sanshiro; Erhard, Moritz; Formaggio, Joseph A.; Glück, Ferenc; Harms, Fabian; Heizmann, Florian; Hilk, Daniel; Käfer, Wolfgang; Kleesiek, Marco; Leiber, Benjamin; Mertens, Susanne; Oblath, Noah S.; Renschler, Pascal; Schwarz, Johannes; Slocum, Penny L.; Wandkowsky, Nancy; Wierman, Kevin; Zacher, Michael

2017-05-01

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease-of-use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur in flight such as bulk scattering and decay, and stochastic surface processes occurring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle’s state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopeia.

Simulation of interaction between ground water in an alluvial aquifer and surface water in a large braided river

USGS Publications Warehouse

Leake, S.A.; Lilly, M.R.

1995-01-01

The Fairbanks, Alaska, area has many contaminated sites in a shallow alluvial aquifer. A ground-water flow model is being developed using the MODFLOW finite-difference ground-water flow model program with the River Package. The modeled area is discretized in the horizontal dimensions into 118 rows and 158 columns of approximately 150-meter square cells. The fine grid spacing has the advantage of providing needed detail at the contaminated sites and surface-water features that bound the aquifer. However, the fine spacing of cells adds difficulty to simulating interaction between the aquifer and the large, braided Tanana River. In particular, the assignment of a river head is difficult if cells are much smaller than the river width. This was solved by developing a procedure for interpolating and extrapolating river head using a river distance function. Another problem is that future transient simulations would require excessive numbers of input records using the current version of the River Package. The proposed solution to this problem is to modify the River Package to linearly interpolate river head for time steps within each stress period, thereby reducing the number of stress periods required.

Monte Carlo Particle Lists: MCPL

NASA Astrophysics Data System (ADS)

Kittelmann, T.; Klinkby, E.; Knudsen, E. B.; Willendrup, P.; Cai, X. X.; Kanaki, K.

2017-09-01

A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community, along with converters and plugins for several popular simulation packages.

Effectiveness of some recent antimicrobial packaging concepts.

PubMed

Vermeiren, L; Devlieghere, F; Debevere, J

2002-01-01

A new type of active packaging is the combination of food-packaging materials with antimicrobial substances to control microbial surface contamination of foods. For both migrating and non-migrating antimicrobial materials, intensive contact between the food product and packaging material is required and therefore potential food applications include especially vacuum or skin-packaged products, e.g. vacuum-packaged meat, fish, poultry or cheese. Several antimicrobial compounds have been combined with different types of carriers (plastic and rubber articles, paper-based materials, textile fibrils and food-packaging materials). Until now, however, few antimicrobial concepts have found applications as a food-packaging material. Antimicrobial packaging materials cannot legally be used in the EU at the moment. The potential use would require amendments of several different legal texts involving areas such as food additives, food packaging, hygiene, etc. The main objective of this paper is to provide a state of the art about the different types of antimicrobial concepts, their experimental development and commercialization, and to present a case study summarizing the results of investigations on the feasibility of a low-density polyethylene (LDPE)-film containing triclosan to inhibit microbial growth on food surfaces and consequently prolong shelf-life or improve microbial food safety. In contrast with the strong antimicrobial effect in in-vitro simulated vacuum-packaged conditions against the psychrotrophic food pathogen L. monocytogenes, the 1000 mg kg(-1) containing triclosan film did not effectively reduce spoilage bacteria and growth of L. monocytogenes on refrigerated vacuum-packaged chicken breasts stored at 7 degrees C.

Complete indium-free CW 200W passively cooled high power diode laser array using double-side cooling technology

NASA Astrophysics Data System (ADS)

Wang, Jingwei; Zhu, Pengfei; Liu, Hui; Liang, Xuejie; Wu, Dihai; Liu, Yalong; Yu, Dongshan; Zah, Chung-en; Liu, Xingsheng

2017-02-01

High power diode lasers have been widely used in many fields. To meet the requirements of high power and high reliability, passively cooled single bar CS-packaged diode lasers must be robust to withstand thermal fatigue and operate long lifetime. In this work, a novel complete indium-free double-side cooling technology has been applied to package passively cooled high power diode lasers. Thermal behavior of hard solder CS-package diode lasers with different packaging structures was simulated and analyzed. Based on these results, the device structure and packaging process of double-side cooled CS-packaged diode lasers were optimized. A series of CW 200W 940nm high power diode lasers were developed and fabricated using hard solder bonding technology. The performance of the CW 200W 940nm high power diode lasers, such as output power, spectrum, thermal resistance, near field, far field, smile, lifetime, etc., is characterized and analyzed.

ROMI-3: Rough-Mill Simulator Version 3.0: User's Guide

Treesearch

Joel M. Weiss; R. Edward Thomas; R. Edward Thomas

2005-01-01

ROMI-3 Rough-Mill Simulator is a software package that simulates current industrial practices for rip-first and chop-first lumber processing. This guide shows the user how to set up and examine the results of simulations of current or proposed mill practices. ROMI-3 accepts cutting bills with as many as 600 combined solid and/or panel part sizes. Plots of processed...

You save money when you buy in bulk: does volume-based pricing cause people to buy more beer?

PubMed

Bray, Jeremy W; Loomis, Brett R; Engelen, Mark

2009-05-01

This paper uses supermarket scanner data to estimate brand- and packaging-specific own- and cross-price elasticities for beer. We find that brand- and packaging-specific beer sales are highly price elastic. Cross-price elasticity estimates suggest that individuals are more likely to buy a higher-volume package of the same brand of beer than they are to switch brands. Policy simulations suggest that regulation of volume-based price discounts is potentially more effective than a tax increase at reducing beer consumption. Our results suggest that volume-based price discounting induces people to buy larger-volume packages of beer and may lead to an increased overall beer consumption. (c) 2008 John Wiley & Sons, Ltd.

Numeric analysis of terahertz wave propagation in familiar packaging materials

NASA Astrophysics Data System (ADS)

Zhang, Lihong; Yang, Guang

2015-10-01

To assess the potential application of terahertz waves in security examination, the transmission characteristics of terahertz waves in packaging materials should be studied. This paper simulates the propagation of terahertz waves in cloth and paper, studies the changes of shape and position of crest of terahertz waves before and after these materials, and gets the law of these changes, which has potential applications in thickness measurement for the thin insulated materials; gives reflected and transmitted wave of terahertz waves, and computes reflected and transmitted coefficient, indicates the good transmission properties of these materials for terahertz waves, which provides the theoretical basis for the realization of contactless security examination of packaged post, package and people pass the important passageway (such as airport and station).

Python Open source Waveform ExtractoR (POWER): an open source, Python package to monitor and post-process numerical relativity simulations

NASA Astrophysics Data System (ADS)

Johnson, Daniel; Huerta, E. A.; Haas, Roland

2018-01-01

Numerical simulations of Einstein’s field equations provide unique insights into the physics of compact objects moving at relativistic speeds, and which are driven by strong gravitational interactions. Numerical relativity has played a key role to firmly establish gravitational wave astrophysics as a new field of research, and it is now paving the way to establish whether gravitational wave radiation emitted from compact binary mergers is accompanied by electromagnetic and astro-particle counterparts. As numerical relativity continues to blend in with routine gravitational wave data analyses to validate the discovery of gravitational wave events, it is essential to develop open source tools to streamline these studies. Motivated by our own experience as users and developers of the open source, community software, the Einstein Toolkit, we present an open source, Python package that is ideally suited to monitor and post-process the data products of numerical relativity simulations, and compute the gravitational wave strain at future null infinity in high performance environments. We showcase the application of this new package to post-process a large numerical relativity catalog and extract higher-order waveform modes from numerical relativity simulations of eccentric binary black hole mergers and neutron star mergers. This new software fills a critical void in the arsenal of tools provided by the Einstein Toolkit consortium to the numerical relativity community.

Probablistic Analyses of Waste Package Quantities Impacted by Potential Igneous Disruption at Yucca Mountain

NASA Astrophysics Data System (ADS)

Wallace, M. G.; Iuzzolina, H.

2005-12-01

A probabilistic analysis was conducted to estimate ranges for the numbers of waste packages that could be damaged in a potential future igneous event through a repository at Yucca Mountain. The analysis includes disruption from an intrusive igneous event and from an extrusive volcanic event. This analysis supports the evaluation of the potential consequences of future igneous activity as part of the total system performance assessment for the license application for the Yucca Mountain Project (YMP). The first scenario, igneous intrusion, investigated the case where one or more igneous dikes intersect the repository. A swarm of dikes was characterized by distributions of length, width, azimuth, and number of dikes and the spacings between them. Through the use in part of a latin hypercube simulator and a modified video game engine, mathematical relationships were built between those parameters and the number of waste packages hit. Corresponding cumulative distribution function curves (CDFs) for the number of waste packages hit under several different scenarios were calculated. Variations in dike thickness ranges, as well as in repository magma bulkhead positions were examined through sensitivity studies. It was assumed that all waste packages in an emplacement drift would be impacted if that drift was intersected by a dike. Over 10,000 individual simulations were performed. Based on these calculations, out of a total of over 11,000 planned waste packages distributed over an area of approximately 5.5 km2 , the median number of waste packages impacted was roughly 1/10 of the total. Individual cases ranged from 0 waste packages to the entire inventory being impacted. The igneous intrusion analysis involved an explicit characterization of dike-drift intersections, built upon various distributions that reflect the uncertainties associated with the inputs. The second igneous scenario, volcanic eruption (eruptive conduits), considered the effects of conduits formed in association with a volcanic eruption through the repository. Mathematical relations were built between the resulting conduit areas and the fraction of the repository area occupied by waste packages. This relation was used in conjunction with a joint distribution incorporating variability in eruptive conduit diameters and in the number of eruptive conduits that could intersect the repository.

Interoperable Open-Source Sensor-Net Frameworks with Sensor-Package Workbench Capabilities: Motivation, Survey of Resources, and Exploratory Results

DTIC Science & Technology

2010-06-01

Military Scenario Definition Language (MSDL) for Nontraditional Warfare Scenarios," Paper 09S- SIW -001, Proceedings of the Spring Simulation...Update to the M&S Community," Paper 09S- SIW -002, Proceedings of the Spring Simulation Interoperability Workshop, Simulation Interoperability...Multiple Simulations: An Application of the Military Scenario Definition Language (MSDL)," Paper 09S- SIW -003, Proc. of the Spring Simulation

Influence of factors on release of antimicrobials from antimicrobial packaging materials.

PubMed

Wu, Yu-Mei; Wang, Zhi-Wei; Hu, Chang-Ying; Nerín, Cristina

2018-05-03

Antimicrobial packaging materials (films or coatings) (APMs) have aroused great interest among the scientists or the experts specialized in material science, food science, packaging engineering, biology and chemistry. APMs have been used to package the food, such as dairy products, poultry, meat (e.g., beef), salmon muscle, pastry dough, fresh pasta, bakery products, fruits, vegetables and beverages. Some materials have been already commercialized. The ability of APMs to extend the shelf-life of the food depends on the release rate of the antimicrobials (AMs) from the materials to the food. The optimum rate is defined as target release rate (TRR). To achieve TRR, the influencing factors of the release rate should be considered. Herein we reviewed for the first time these factors and their influence on the release. These factors mainly include the AMs, food (or food simulant), packaging materials, the interactions among them, the temperature and environmental relative humidity (RH).

The Effect of Teacher Involvement on Student Performance in a Computer-Based Science Simulation.

ERIC Educational Resources Information Center

Waugh, Michael L.

Designed to investigate whether or not science teachers can positively influence student achievement in, and attitude toward, science, this study focused on a specific teaching strategy and utilization of a computer-based simulation. The software package used in the study was the simulation, Volcanoes, by Earthware Computer Services. The sample…

ROMI 4.0: Updated Rough Mill Simulator

Treesearch

Timo Grueneberg; R. Edward Thomas; Urs Buehlmann

2012-01-01

In the secondary hardwood industry, rough mills convert hardwood lumber into dimension parts for furniture, cabinets, and other wood products. ROMI 4.0, the US Department of Agriculture Forest Service's ROugh-MIll simulator, is a software package designed to simulate the cut-up of hardwood lumber in rough mills in such a way that a maximum possible component yield...

Improving the lean muscle color of dark-cutting beef by aging, antioxidant-enhancement, and modified atmospheric packaging.

PubMed

Wills, K M; Mitacek, R M; Mafi, G G; VanOverbeke, D L; Jaroni, D; Jadeja, R; Ramanathan, R

2017-12-01

The objective was to evaluate the effects of wet-aging, rosemary-enhancement, and modified atmospheric packaging on the color of dark-cutting beef during simulated retail display. No-roll dark-cutting strip loins ( = 12; pH > 6.0) were selected from a commercial packing plant within 3 d postharvest. Using a balanced incomplete block design, dark-cutting loins were sectioned in half, and assigned to 1 of 3 aging periods: 7, 14, or 21 d. After respective aging, each aged section was divided into 3 equal parts, and randomly assigned to 1 of 3 enhancement treatments: nonenhanced dark-cutting, dark-cutter enhanced with 0.1% rosemary, and dark-cutter enhanced with 0.2% rosemary. Following enhancement, steaks were randomly assigned to 1 of 3 packaging treatments: high-oxygen modified atmospheric packaging (HiOx-MAP; 80% O and 20% CO), carbon monoxide modified atmospheric packaging (CO-MAP; 0.4% CO, 69.6% N, and 30% CO), and polyvinyl chloride overwrap (PVC; 20% O). Instrumental and visual color measurements were recorded during 5 d simulated retail display. Lipid oxidation was determined utilizing the thiobarbituric acid reactive substances (TBARS) method. There was a significant packaging × enhancement × display time interaction for values and chroma ( 0.001). On d 0 of display, dark-cutting steaks enhanced with 0.1% and 0.2% rosemary and packaged in HiOx-MAP had greater ( 0.001) values and chroma than other dark-cutting packaging/enhancement treatments. A significant packaging × enhancement × display time interaction resulted for values ( 0.001). Dark-cutting steaks enhanced with 0.2% rosemary and packaged in HiOx-MAP was lighter ( 0.001; greater values) than other dark-cutting treatments on d 5 of display. There were no differences ( 0.34) in discoloration scores on d 5 among different dark-cutting treatments when steaks were packaged in HiOx- and CO-MAP. There was an aging period × enhancement × packaging interaction ( < 0.0033) for lipid oxidation. On d 0 of display, there were no differences ( 0.54) in TBARS values between different aging periods and enhancement treatments. Dark-cutting steaks enhanced with 0.2% rosemary had lower ( 0.001) TBARS values than 0.1% rosemary on d 5 when aged for 21 d and in HiOx-MAP. The results suggest that rosemary enhancement with CO- or HiOx-MAP has the potential to improve the surface color of dark-cutting beef.

pez: phylogenetics for the environmental sciences.

PubMed

Pearse, William D; Cadotte, Marc W; Cavender-Bares, Jeannine; Ives, Anthony R; Tucker, Caroline M; Walker, Steve C; Helmus, Matthew R

2015-09-01

pez is an R package that permits measurement, modelling and simulation of phylogenetic structure in ecological data. pez contains the first implementation of many methods in R, and aggregates existing data structures and methods into a single, coherent package. pez is released under the GPL v3 open-source license, available on the Internet from CRAN (http://cran.r-project.org). The package is under active development, and the authors welcome contributions (see http://github.com/willpearse/pez). will.pearse@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Simulations of neutron transport at low energy: a comparison between GEANT and MCNP.

PubMed

Colonna, N; Altieri, S

2002-06-01

The use of the simulation tool GEANT for neutron transport at energies below 20 MeV is discussed, in particular with regard to shielding and dose calculations. The reliability of the GEANT/MICAP package for neutron transport in a wide energy range has been verified by comparing the results of simulations performed with this package in a wide energy range with the prediction of MCNP-4B, a code commonly used for neutron transport at low energy. A reasonable agreement between the results of the two codes is found for the neutron flux through a slab of material (iron and ordinary concrete), as well as for the dose released in soft tissue by neutrons. These results justify the use of the GEANT/MICAP code for neutron transport in a wide range of applications, including health physics problems.

MODFLOW-LGR-Modifications to the streamflow-routing package (SFR2) to route streamflow through locally refined grids

USGS Publications Warehouse

Mehl, Steffen W.; Hill, Mary C.

2011-01-01

This report documents modifications to the Streamflow-Routing Package (SFR2) to route streamflow through grids constructed using the multiple-refined-areas capability of shared node Local Grid Refinement (LGR) of MODFLOW-2005. MODFLOW-2005 is the U.S. Geological Survey modular, three-dimensional, finite-difference groundwater-flow model. LGR provides the capability to simulate groundwater flow by using one or more block-shaped, higher resolution local grids (child model) within a coarser grid (parent model). LGR accomplishes this by iteratively coupling separate MODFLOW-2005 models such that heads and fluxes are balanced across the shared interfacing boundaries. Compatibility with SFR2 allows for streamflow routing across grids. LGR can be used in two- and three-dimensional, steady-state and transient simulations and for simulations of confined and unconfined groundwater systems.

SimulatorToFMU v0.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nouidui, Thierry; Wetter, Michael

SimulatorToFMU is a software package written in Python which allows users to export a memoryless Python-driven simulation program or script as a Functional Mock-up Unit (FMU) for model exchange or co-simulation.In CyDER (Cyber Physical Co-simulation Platform for Distributed Energy Resources in Smart Grids), SimulatorToFMU will allow exporting OPAL-RT as an FMU. This will enable OPAL-RT to be linked to CYMDIST and GridDyn FMUs through a standardized open source interface.

Knowledge-based simulation for aerospace systems

NASA Technical Reports Server (NTRS)

Will, Ralph W.; Sliwa, Nancy E.; Harrison, F. Wallace, Jr.

1988-01-01

Knowledge-based techniques, which offer many features that are desirable in the simulation and development of aerospace vehicle operations, exhibit many similarities to traditional simulation packages. The eventual solution of these systems' current symbolic processing/numeric processing interface problem will lead to continuous and discrete-event simulation capabilities in a single language, such as TS-PROLOG. Qualitative, totally-symbolic simulation methods are noted to possess several intrinsic characteristics that are especially revelatory of the system being simulated, and capable of insuring that all possible behaviors are considered.

Trick Simulation Environment 07

NASA Technical Reports Server (NTRS)

Lin, Alexander S.; Penn, John M.

2012-01-01

The Trick Simulation Environment is a generic simulation toolkit used for constructing and running simulations. This release includes a Monte Carlo analysis simulation framework and a data analysis package. It produces all auto documentation in XML. Also, the software is capable of inserting a malfunction at any point during the simulation. Trick 07 adds variable server output options and error messaging and is capable of using and manipulating wide characters for international support. Wide character strings are available as a fundamental type for variables processed by Trick. A Trick Monte Carlo simulation uses a statistically generated, or predetermined, set of inputs to iteratively drive the simulation. Also, there is a framework in place for optimization and solution finding where developers may iteratively modify the inputs per run based on some analysis of the outputs. The data analysis package is capable of reading data from external simulation packages such as MATLAB and Octave, as well as the common comma-separated values (CSV) format used by Excel, without the use of external converters. The file formats for MATLAB and Octave were obtained from their documentation sets, and Trick maintains generic file readers for each format. XML tags store the fields in the Trick header comments. For header files, XML tags for structures and enumerations, and the members within are stored in the auto documentation. For source code files, XML tags for each function and the calling arguments are stored in the auto documentation. When a simulation is built, a top level XML file, which includes all of the header and source code XML auto documentation files, is created in the simulation directory. Trick 07 provides an XML to TeX converter. The converter reads in header and source code XML documentation files and converts the data to TeX labels and tables suitable for inclusion in TeX documents. A malfunction insertion capability allows users to override the value of any simulation variable, or call a malfunction job, at any time during the simulation. Users may specify conditions, use the return value of a malfunction trigger job, or manually activate a malfunction. The malfunction action may consist of executing a block of input file statements in an action block, setting simulation variable values, call a malfunction job, or turn on/off simulation jobs.

Validation of a Laser-Ray Package in an Eulerian Code

NASA Astrophysics Data System (ADS)

Bradley, Paul; Hall, Mike; McKenty, Patrick; Collins, Tim; Keller, David

2014-10-01

A laser-ray absorption package was recently installed in the RAGE code by the Laboratory for Laser Energetics (LLE). In this presentation, we describe our use of this package to implode Omega 60 beam symmetric direct drive capsules. The capsules have outer diameters of about 860 microns, CH plastic shell thicknesses between 8 and 32 microns, DD or DT gas fills between 5 and 20 atmospheres, and a 1 ns square pulse of 23 to 27 kJ. These capsule implosions were previously modeled with a calibrated energy source in the outer layer of the capsule, where we matched bang time and burn ion temperature well, but the simulated yields were two to three times higher than the data. We will run simulations with laser ray energy deposition to the experiments and the results to the yield and spectroscopic data. Work performed by Los Alamos National Laboratory under Contract DE-AC52-06NA25396 for the National Nuclear Security Administration of the U.S. Department of Energy.

Plasticized poly(lactic acid)-poly(hydroxybutyrate) (PLA-PHB) blends incorporated with catechin intended for active food-packaging applications.

PubMed

Arrieta, Marina Patricia; Castro-López, María del Mar; Rayón, Emilio; Barral-Losada, Luis Fernando; López-Vilariño, José Manuel; López, Juan; González-Rodríguez, María Victoria

2014-10-15

Active biobased packaging materials based on poly(lactic acid)-poly(hydroxybutyrate) (PLA-PHB) blends were prepared by melt blending and fully characterized. Catechin incorporation, as antioxidant compound, enhanced the thermal stability, whereas its release was improved by the addition of acetyl(tributyl citrate) (ATBC) as plasticizer. Whereas the incorporation of ATBC resulted in a reduction of elastic modulus and hardness, catechin addition produced more rigid materials due to hydrogen-bonding interactions between catechin hydroxyl groups and carbonyl groups of PLA and PHB. The quantification of catechin released into a fatty food simulant and the antioxidant effectiveness after the release process were demonstrated. The effect of the materials' exposure to a food simulant was also investigated. PHB-added materials maintained their structural and mechanical properties after 10 days in a test medium that represents the worst foreseeable conditions of the intended use. Thus, plasticized PLA-PHB blends with catechin show their potential as biobased active packaging for fatty food.

Update 0.2 to "pysimm: A python package for simulation of molecular systems"

NASA Astrophysics Data System (ADS)

Demidov, Alexander G.; Fortunato, Michael E.; Colina, Coray M.

2018-01-01

An update to the pysimm Python molecular simulation API is presented. A major part of the update is the implementation of a new interface with CASSANDRA - a modern, versatile Monte Carlo molecular simulation program. Several significant improvements in the LAMMPS communication module that allow better and more versatile simulation setup are reported as well. An example of an application implementing iterative CASSANDRA-LAMMPS interaction is illustrated.

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

Interactive visualization of numerical simulation results: A tool for mission planning and data analysis

NASA Technical Reports Server (NTRS)

Berchem, J.; Raeder, J.; Walker, R. J.; Ashour-Abdalla, M.

1995-01-01

We report on the development of an interactive system for visualizing and analyzing numerical simulation results. This system is based on visualization modules which use the Application Visualization System (AVS) and the NCAR graphics packages. Examples from recent simulations are presented to illustrate how these modules can be used for displaying and manipulating simulation results to facilitate their comparison with phenomenological model results and observations.

MODFLOW-2000 : the U.S. Geological Survey modular ground-water model--documentation of the Advective-Transport Observation (ADV2) Package

USGS Publications Warehouse

Anderman, Evan R.; Hill, Mary Catherine

2001-01-01

Observations of the advective component of contaminant transport in steady-state flow fields can provide important information for the calibration of ground-water flow models. This report documents the Advective-Transport Observation (ADV2) Package, version 2, which allows advective-transport observations to be used in the three-dimensional ground-water flow parameter-estimation model MODFLOW-2000. The ADV2 Package is compatible with some of the features in the Layer-Property Flow and Hydrogeologic-Unit Flow Packages, but is not compatible with the Block-Centered Flow or Generalized Finite-Difference Packages. The particle-tracking routine used in the ADV2 Package duplicates the semi-analytical method of MODPATH, as shown in a sample problem. Particles can be tracked in a forward or backward direction, and effects such as retardation can be simulated through manipulation of the effective-porosity value used to calculate velocity. Particles can be discharged at cells that are considered to be weak sinks, in which the sink applied does not capture all the water flowing into the cell, using one of two criteria: (1) if there is any outflow to a boundary condition such as a well or surface-water feature, or (2) if the outflow exceeds a user specified fraction of the cell budget. Although effective porosity could be included as a parameter in the regression, this capability is not included in this package. The weighted sum-of-squares objective function, which is minimized in the Parameter-Estimation Process, was augmented to include the square of the weighted x-, y-, and z-components of the differences between the simulated and observed advective-front locations at defined times, thereby including the direction of travel as well as the overall travel distance in the calibration process. The sensitivities of the particle movement to the parameters needed to minimize the objective function are calculated for any particle location using the exact sensitivity-equation approach; the equations are derived by taking the partial derivatives of the semi-analytical particle-tracking equation with respect to the parameters. The ADV2 Package is verified by showing that parameter estimation using advective-transport observations produces the true parameter values in a small but complicated test case when exact observations are used. To demonstrate how the ADV2 Package can be used in practice, a field application is presented. In this application, the ADV2 Package is used first in the Sensitivity-Analysis mode of MODFLOW-2000 to calculate measures of the importance of advective-transport observations relative to head-dependent flow observations when either or both are used in conjunction with hydraulic-head observations in a simulation of the sewage-discharge plume at Cape Cod, Massachusetts. The ADV2 Package is then used in the Parameter-Estimation mode of MODFLOW-2000 to determine best-fit parameter values. It is concluded that, for this problem, advective-transport observations improved the calibration of the model and the estimation of ground-water flow parameters, and the use of formal parameter-estimation methods and related techniques produced significant insight into the physical system.

Can we teach core clinical obstetrics and gynaecology skills using low fidelity simulation in an interprofessional setting?

PubMed

Kumar, Arunaz; Gilmour, Carole; Nestel, Debra; Aldridge, Robyn; McLelland, Gayle; Wallace, Euan

2014-12-01

Core clinical skills acquisition is an essential component of undergraduate medical and midwifery education. Although interprofessional education is an increasingly common format for learning efficient teamwork in clinical medicine, its value in undergraduate education is less clear. We present a collaborative effort from the medical and midwifery schools of Monash University, Melbourne, towards the development of an educational package centred around a core skills-based workshop using low fidelity simulation models in an interprofessional setting. Detailed feedback on the package was positive with respect to the relevance of the teaching content, whether the topic was well taught by task trainers and simulation models used, pitch of level of teaching and perception of confidence gained in performing the skill on a real patient after attending the workshop. Overall, interprofessional core skills training using low fidelity simulation models introduced at an undergraduate level in medicine and midwifery had a good acceptance. © 2014 The Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

Analysis of Plane-Parallel Electron Beam Propagation in Different Media by Numerical Simulation Methods

NASA Astrophysics Data System (ADS)

Miloichikova, I. A.; Bespalov, V. I.; Krasnykh, A. A.; Stuchebrov, S. G.; Cherepennikov, Yu. M.; Dusaev, R. R.

2018-04-01

Simulation by the Monte Carlo method is widely used to calculate the character of ionizing radiation interaction with substance. A wide variety of programs based on the given method allows users to choose the most suitable package for solving computational problems. In turn, it is important to know exactly restrictions of numerical systems to avoid gross errors. Results of estimation of the feasibility of application of the program PCLab (Computer Laboratory, version 9.9) for numerical simulation of the electron energy distribution absorbed in beryllium, aluminum, gold, and water for industrial, research, and clinical beams are presented. The data obtained using programs ITS and Geant4 being the most popular software packages for solving the given problems and the program PCLab are presented in the graphic form. A comparison and an analysis of the results obtained demonstrate the feasibility of application of the program PCLab for simulation of the absorbed energy distribution and dose of electrons in various materials for energies in the range 1-20 MeV.

SimVascular: An Open Source Pipeline for Cardiovascular Simulation.

PubMed

Updegrove, Adam; Wilson, Nathan M; Merkow, Jameson; Lan, Hongzhi; Marsden, Alison L; Shadden, Shawn C

2017-03-01

Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.

GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics.

PubMed

Blumers, Ansel L; Tang, Yu-Hang; Li, Zhen; Li, Xuejin; Karniadakis, George E

2017-08-01

Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

Ion Beam Neutralization Using FEAs and Mirror Magnetic Fields

NASA Astrophysics Data System (ADS)

Nicolaescu, Dan; Sakai, Shigeki; Gotoh, Yasuhito; Ishikawa, Junzo

2011-01-01

Advanced implantation systems used for semiconductor processing require transportation of ion beams which are quasi-parallel and have low energy, such as (11B+,31P+,75As+) with energy in the range Eion = 200-1000 eV. Compensation of ion beam divergence may be obtained through electron injection and confinement in regions of non-uniform magnetic fields. Field emitter arrays with special properties are used as electron sources. The present study shows that electron confinement takes place in regions of gradient magnetic field, such as nearby analyzing, collimator and final energy magnets of the ion beam line. Modeling results have been obtained using Opera3D/Tosca/Scala. In regions of gradient magnetic field, electrons have helical trajectories which are confined like a cloud inside curved "magnetic bottles". An optimal range of positions with respect to the magnet for placing electron sources in gradient magnetic field has been shown to exist.

Narcissism: its function in modulating self-conscious emotions.

PubMed

Uji, Masayo; Nagata, Toshiaki; Kitamura, Toshinori

2012-01-01

This study focused on the functional aspects of narcissism in regulating self-conscious emotions (guilt, shame, hubristic pride, and achievement-oriented pride) as well as two other attribution styles (externalization and detachment). The authors investigated Japanese university students (N = 452) with regard to their self-conscious emotions using the Test of Self-Conscious Affect-3 (TOSCA-3) and their narcissistic personality using the short version of Narcissistic Personality Inventory (NPI-S). Structural equation modeling was used for the analysis. The authors found that narcissism led individuals to feel achievement-oriented pride, hubristic pride, externalization, and detachment, but inhibited feelings of shame. It did not have a significant effect on guilt. Shame-proneness prompted hubristic pride and externalization. Guilt-proneness inclined an individual toward achievement-oriented pride, but deterred externalization. In this article, the authors present and interpret these results in detail and then discuss how they can be utilized in psychotherapy.

Instrumental resolution of the chopper spectrometer 4SEASONS evaluated by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Kajimoto, Ryoichi; Sato, Kentaro; Inamura, Yasuhiro; Fujita, Masaki

2018-05-01

We performed simulations of the resolution function of the 4SEASONS spectrometer at J-PARC by using the Monte Carlo simulation package McStas. The simulations showed reasonably good agreement with analytical calculations of energy and momentum resolutions by using a simplified description. We implemented new functionalities in Utsusemi, the standard data analysis tool used in 4SEASONS, to enable visualization of the simulated resolution function and predict its shape for specific experimental configurations.

Excore Modeling with VERAShift

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandya, Tara M.; Evans, Thomas M.

It is important to be able to accurately predict the neutron flux outside the immediate reactor core for a variety of safety and material analyses. Monte Carlo radiation transport calculations are required to produce the high fidelity excore responses. Under this milestone VERA (specifically the VERAShift package) has been extended to perform excore calculations by running radiation transport calculations with Shift. This package couples VERA-CS with Shift to perform excore tallies for multiple state points concurrently, with each component capable of parallel execution on independent domains. Specifically, this package performs fluence calculations in the core barrel and vessel, or, performsmore » the requested tallies in any user-defined excore regions. VERAShift takes advantage of the general geometry package in Shift. This gives VERAShift the flexibility to explicitly model features outside the core barrel, including detailed vessel models, detectors, and power plant details. A very limited set of experimental and numerical benchmarks is available for excore simulation comparison. The Consortium for the Advanced Simulation of Light Water Reactors (CASL) has developed a set of excore benchmark problems to include as part of the VERA-CS verification and validation (V&V) problems. The excore capability in VERAShift has been tested on small representative assembly problems, multiassembly problems, and quarter-core problems. VERAView has also been extended to visualize these vessel fluence results from VERAShift. Preliminary vessel fluence results for quarter-core multistate calculations look very promising. Further development is needed to determine the details relevant to excore simulations. Validation of VERA for fluence and excore detectors still needs to be performed against experimental and numerical results.« less

CoFFEE: Corrections For Formation Energy and Eigenvalues for charged defect simulations

NASA Astrophysics Data System (ADS)

Naik, Mit H.; Jain, Manish

2018-05-01

Charged point defects in materials are widely studied using Density Functional Theory (DFT) packages with periodic boundary conditions. The formation energy and defect level computed from these simulations need to be corrected to remove the contributions from the spurious long-range interaction between the defect and its periodic images. To this effect, the CoFFEE code implements the Freysoldt-Neugebauer-Van de Walle (FNV) correction scheme. The corrections can be applied to charged defects in a complete range of material shapes and size: bulk, slab (or two-dimensional), wires and nanoribbons. The code is written in Python and features MPI parallelization and optimizations using the Cython package for slow steps.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks.

PubMed

Jenness, Samuel M; Goodreau, Steven M; Morris, Martina

2018-04-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel , designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel , designed to facilitate the exploration of novel research questions for advanced modelers.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks

PubMed Central

Jenness, Samuel M.; Goodreau, Steven M.; Morris, Martina

2018-01-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel, designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel, designed to facilitate the exploration of novel research questions for advanced modelers. PMID:29731699

tsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics.

PubMed

Becker, Alexander D; Grenfell, Bryan T

2017-01-01

tsiR is an open source software package implemented in the R programming language designed to analyze infectious disease time-series data. The software extends a well-studied and widely-applied algorithm, the time-series Susceptible-Infected-Recovered (TSIR) model, to infer parameters from incidence data, such as contact seasonality, and to forward simulate the underlying mechanistic model. The tsiR package aggregates a number of different fitting features previously described in the literature in a user-friendly way, providing support for their broader adoption in infectious disease research. Also included in tsiR are a number of diagnostic tools to assess the fit of the TSIR model. This package should be useful for researchers analyzing incidence data for fully-immunizing infectious diseases.

Monte Carlo reference data sets for imaging research: Executive summary of the report of AAPM Research Committee Task Group 195.

PubMed

Sechopoulos, Ioannis; Ali, Elsayed S M; Badal, Andreu; Badano, Aldo; Boone, John M; Kyprianou, Iacovos S; Mainegra-Hing, Ernesto; McMillan, Kyle L; McNitt-Gray, Michael F; Rogers, D W O; Samei, Ehsan; Turner, Adam C

2015-10-01

The use of Monte Carlo simulations in diagnostic medical imaging research is widespread due to its flexibility and ability to estimate quantities that are challenging to measure empirically. However, any new Monte Carlo simulation code needs to be validated before it can be used reliably. The type and degree of validation required depends on the goals of the research project, but, typically, such validation involves either comparison of simulation results to physical measurements or to previously published results obtained with established Monte Carlo codes. The former is complicated due to nuances of experimental conditions and uncertainty, while the latter is challenging due to typical graphical presentation and lack of simulation details in previous publications. In addition, entering the field of Monte Carlo simulations in general involves a steep learning curve. It is not a simple task to learn how to program and interpret a Monte Carlo simulation, even when using one of the publicly available code packages. This Task Group report provides a common reference for benchmarking Monte Carlo simulations across a range of Monte Carlo codes and simulation scenarios. In the report, all simulation conditions are provided for six different Monte Carlo simulation cases that involve common x-ray based imaging research areas. The results obtained for the six cases using four publicly available Monte Carlo software packages are included in tabular form. In addition to a full description of all simulation conditions and results, a discussion and comparison of results among the Monte Carlo packages and the lessons learned during the compilation of these results are included. This abridged version of the report includes only an introductory description of the six cases and a brief example of the results of one of the cases. This work provides an investigator the necessary information to benchmark his/her Monte Carlo simulation software against the reference cases included here before performing his/her own novel research. In addition, an investigator entering the field of Monte Carlo simulations can use these descriptions and results as a self-teaching tool to ensure that he/she is able to perform a specific simulation correctly. Finally, educators can assign these cases as learning projects as part of course objectives or training programs.

Onboard utilization of ground control points for image correction. Volume 3: Ground control point simulation software design

NASA Technical Reports Server (NTRS)

1981-01-01

The software developed to simulate the ground control point navigation system is described. The Ground Control Point Simulation Program (GCPSIM) is designed as an analysis tool to predict the performance of the navigation system. The system consists of two star trackers, a global positioning system receiver, a gyro package, and a landmark tracker.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yuying; Xie, Shaocheng

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 outputmore » 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 wherever possible. The ARM simulator is written in Fortran 90, just as is the COSP. It is incorporated into COSP to facilitate use by the climate modeling community. In order to evaluate simulator output, the observational counterpart of the simulator output, radar reflectivity-height histograms (CFAD) is also generated from the ARM observations. This report includes an overview of the ARM cloud radar simulator VAP and the required simulator-oriented ARM radar data product (radarCFAD) for validating simulator output, as well as a user guide for operating the ARM radar simulator VAP.« less

An Assessment of the Influence of the Industry Distribution Chain on the Oxygen Levels in Commercial Modified Atmosphere Packaged Cheddar Cheese Using Non-Destructive Oxygen Sensor Technology.

PubMed

O' Callaghan, Karen A M; Papkovsky, Dmitri B; Kerry, Joseph P

2016-06-20

The establishment and control of oxygen levels in packs of oxygen-sensitive food products such as cheese is imperative in order to maintain product quality over a determined shelf life. Oxygen sensors quantify oxygen concentrations within packaging using a reversible optical measurement process, and this non-destructive nature ensures the entire supply chain can be monitored and can assist in pinpointing negative issues pertaining to product packaging. This study was carried out in a commercial cheese packaging plant and involved the insertion of 768 sensors into 384 flow-wrapped cheese packs (two sensors per pack) that were flushed with 100% carbon dioxide prior to sealing. The cheese blocks were randomly assigned to two different storage groups to assess the effects of package quality, packaging process efficiency, and handling and distribution on package containment. Results demonstrated that oxygen levels increased in both experimental groups examined over the 30-day assessment period. The group subjected to a simulated industrial distribution route and handling procedures of commercial retailed cheese exhibited the highest level of oxygen detected on every day examined and experienced the highest rate of package failure. The study concluded that fluctuating storage conditions, product movement associated with distribution activities, and the possible presence of cheese-derived contaminants such as calcium lactate crystals were chief contributors to package failure.

An Assessment of the Influence of the Industry Distribution Chain on the Oxygen Levels in Commercial Modified Atmosphere Packaged Cheddar Cheese Using Non-Destructive Oxygen Sensor Technology

PubMed Central

O’ Callaghan, Karen A.M.; Papkovsky, Dmitri B.; Kerry, Joseph P.

2016-01-01

The establishment and control of oxygen levels in packs of oxygen-sensitive food products such as cheese is imperative in order to maintain product quality over a determined shelf life. Oxygen sensors quantify oxygen concentrations within packaging using a reversible optical measurement process, and this non-destructive nature ensures the entire supply chain can be monitored and can assist in pinpointing negative issues pertaining to product packaging. This study was carried out in a commercial cheese packaging plant and involved the insertion of 768 sensors into 384 flow-wrapped cheese packs (two sensors per pack) that were flushed with 100% carbon dioxide prior to sealing. The cheese blocks were randomly assigned to two different storage groups to assess the effects of package quality, packaging process efficiency, and handling and distribution on package containment. Results demonstrated that oxygen levels increased in both experimental groups examined over the 30-day assessment period. The group subjected to a simulated industrial distribution route and handling procedures of commercial retailed cheese exhibited the highest level of oxygen detected on every day examined and experienced the highest rate of package failure. The study concluded that fluctuating storage conditions, product movement associated with distribution activities, and the possible presence of cheese-derived contaminants such as calcium lactate crystals were chief contributors to package failure. PMID:27331815

Learning from concurrent Lightning Imaging Sensor and Lightning Mapping Array observations in preparation for the MTG-LI mission

NASA Astrophysics Data System (ADS)

Defer, Eric; Bovalo, Christophe; Coquillat, Sylvain; Pinty, Jean-Pierre; Farges, Thomas; Krehbiel, Paul; Rison, William

2016-04-01

The upcoming decade will see the deployment and the operation of French, European and American space-based missions dedicated to the detection and the characterization of the lightning activity on Earth. For instance the Tool for the Analysis of Radiation from lightNIng and Sprites (TARANIS) mission, with an expected launch in 2018, is a CNES mission dedicated to the study of impulsive energy transfers between the atmosphere of the Earth and the space environment. It will carry a package of Micro Cameras and Photometers (MCP) to detect and locate lightning flashes and triggered Transient Luminous Events (TLEs). At the European level, the Meteosat Third Generation Imager (MTG-I) satellites will carry in 2019 the Lightning Imager (LI) aimed at detecting and locating the lightning activity over almost the full disk of Earth as usually observed with Meteosat geostationary infrared/visible imagers. The American community plans to operate a similar instrument on the GOES-R mission for an effective operation in early 2016. In addition NASA will install in 2016 on the International Space Station the spare version of the Lightning Imaging Sensor (LIS) that has proved its capability to optically detect the tropical lightning activity from the Tropical Rainfall Measuring Mission (TRMM) spacecraft. We will present concurrent observations recorded by the optical space-borne Lightning Imaging Sensor (LIS) and the ground-based Very High Frequency (VHF) Lightning Mapping Array (LMA) for different types of lightning flashes. The properties of the cloud environment will also be considered in the analysis thanks to coincident observations of the different TRMM cloud sensors. The characteristics of the optical signal will be discussed according to the nature of the parent flash components and the cloud properties. This study should provide some insights not only on the expected optical signal that will be recorded by LI, but also on the definition of the validation strategy of LI, and on the synergetic use of LI and ground-based VHF mappers like the SAETTA LMA network in Corsica for operational and research activities. Acknowledgements: this study is part of the SOLID-PREVALS project and is supported by CNES-TOSCA.

The Amber Biomolecular Simulation Programs

PubMed Central

CASE, DAVID A.; CHEATHAM, THOMAS E.; DARDEN, TOM; GOHLKE, HOLGER; LUO, RAY; MERZ, KENNETH M.; ONUFRIEV, ALEXEY; SIMMERLING, CARLOS; WANG, BING; WOODS, ROBERT J.

2006-01-01

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. PMID:16200636

Advanced Simulation in Undergraduate Pilot Training: Automatic Instructional System

DTIC Science & Technology

1975-10-01

an addressable reel-to--reel audio tape recorder, a random access audio memory drum , and an interactive software package which permits the user to...audio memory drum , and an interactive software package which permits the user to develop preptogtahmed exercises. Figure 2 illustrates overall...Data Recprding System consists of two elements; an overlay program which performs the real-time sampling of specified variables and stores data to disc

Astronaut Stafford and Cosmonaut Leonov examines food packages for ASTP

NASA Technical Reports Server (NTRS)

1975-01-01

Two Apollo Soyuz Test Project (ASTP) crewmen look over food cans and packages in the Soyuz Orbital Module trainer in bldg 35 during ASTP joint crew training at JSC. They are Astronaut Thomas P. Stafford (left), commander of the American ASTP prime crew; and Cosmonaut Aleksey A. Leonov, commander of the Soviet ASTP first (prime) crew. The training session simulated activity on the second day in Earth orbit.

DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

NASA Astrophysics Data System (ADS)

Wang, Han; Zhang, Linfeng; Han, Jiequn; E, Weinan

2018-07-01

Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in Python/C++ that has been designed to minimize the effort required to build deep learning based representation of potential energy and force field and to perform molecular dynamics. Potential applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. DeePMD-kit is interfaced with TensorFlow, one of the most popular deep learning frameworks, making the training process highly automatic and efficient. On the other end, DeePMD-kit is interfaced with high-performance classical molecular dynamics and quantum (path-integral) molecular dynamics packages, i.e., LAMMPS and the i-PI, respectively. Thus, upon training, the potential energy and force field models can be used to perform efficient molecular simulations for different purposes. As an example of the many potential applications of the package, we use DeePMD-kit to learn the interatomic potential energy and forces of a water model using data obtained from density functional theory. We demonstrate that the resulted molecular dynamics model reproduces accurately the structural information contained in the original model.

Electrostatic plasma simulation by Particle-In-Cell method using ANACONDA package

NASA Astrophysics Data System (ADS)

Blandón, J. S.; Grisales, J. P.; Riascos, H.

2017-06-01

Electrostatic plasma is the most representative and basic case in plasma physics field. One of its main characteristics is its ideal behavior, since it is assumed be in thermal equilibrium state. Through this assumption, it is possible to study various complex phenomena such as plasma oscillations, waves, instabilities or damping. Likewise, computational simulation of this specific plasma is the first step to analyze physics mechanisms on plasmas, which are not at equilibrium state, and hence plasma is not ideal. Particle-In-Cell (PIC) method is widely used because of its precision for this kind of cases. This work, presents PIC method implementation to simulate electrostatic plasma by Python, using ANACONDA packages. The code has been corroborated comparing previous theoretical results for three specific phenomena in cold plasmas: oscillations, Two-Stream instability (TSI) and Landau Damping(LD). Finally, parameters and results are discussed.

Adaptive algorithms of position and energy reconstruction in Anger-camera type detectors: experimental data processing in ANTS

NASA Astrophysics Data System (ADS)

Morozov, A.; Defendi, I.; Engels, R.; Fraga, F. A. F.; Fraga, M. M. F. R.; Gongadze, A.; Guerard, B.; Jurkovic, M.; Kemmerling, G.; Manzin, G.; Margato, L. M. S.; Niko, H.; Pereira, L.; Petrillo, C.; Peyaud, A.; Piscitelli, F.; Raspino, D.; Rhodes, N. J.; Sacchetti, F.; Schooneveld, E. M.; Solovov, V.; Van Esch, P.; Zeitelhack, K.

2013-05-01

The software package ANTS (Anger-camera type Neutron detector: Toolkit for Simulations), developed for simulation of Anger-type gaseous detectors for thermal neutron imaging was extended to include a module for experimental data processing. Data recorded with a sensor array containing up to 100 photomultiplier tubes (PMT) or silicon photomultipliers (SiPM) in a custom configuration can be loaded and the positions and energies of the events can be reconstructed using the Center-of-Gravity, Maximum Likelihood or Least Squares algorithm. A particular strength of the new module is the ability to reconstruct the light response functions and relative gains of the photomultipliers from flood field illumination data using adaptive algorithms. The performance of the module is demonstrated with simulated data generated in ANTS and experimental data recorded with a 19 PMT neutron detector. The package executables are publicly available at http://coimbra.lip.pt/~andrei/

Development of biodegradable materials; balancing degradability and performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayer, J.M.; Allen, A.L.; Dell, P.A.

1993-12-31

The development of biodegradable materials suitable for packaging must take into consideration various performance criteria such as mechanical and barrier properties, as well as rate of biodegradability in given environments. Individual or blended biopolymer films were obtained commercially or blown into film in the laboratory and tested for tensile strength, ultimate elongation and oxygen barrier. These films were then subjected to accelerated marine biodegradation tests as well as simulated marine respirometry. Starch/ethylene vinyl alcohol films exhibited good mechanical and excellent oxygen barrier properties, but were very slow to biodegrade in the simulated and excellent oxygen barrier properties, but were verymore » slow to biodegrade in the simulated marine environment. Polyhydroxyalkanoates had good mechanical properties, average oxygen barrier and good biodegradability. Data indicate that performance and biodegradability of packaging can be tailored to needs by combining individual biopolymers in different proportions in blends and laminates.« less

Investigation of different modeling approaches for computational fluid dynamics simulation of high-pressure rocket combustors

NASA Astrophysics Data System (ADS)

Ivancic, B.; Riedmann, H.; Frey, M.; Knab, O.; Karl, S.; Hannemann, K.

2016-07-01

The paper summarizes technical results and first highlights of the cooperation between DLR and Airbus Defence and Space (DS) within the work package "CFD Modeling of Combustion Chamber Processes" conducted in the frame of the Propulsion 2020 Project. Within the addressed work package, DLR Göttingen and Airbus DS Ottobrunn have identified several test cases where adequate test data are available and which can be used for proper validation of the computational fluid dynamics (CFD) tools. In this paper, the first test case, the Penn State chamber (RCM1), is discussed. Presenting the simulation results from three different tools, it is shown that the test case can be computed properly with steady-state Reynolds-averaged Navier-Stokes (RANS) approaches. The achieved simulation results reproduce the measured wall heat flux as an important validation parameter very well but also reveal some inconsistencies in the test data which are addressed in this paper.

Direct Method Transcription for a Human-Class Translunar Injection Trajectory Optimization

NASA Technical Reports Server (NTRS)

Witzberger, Kevin E.; Zeiler, Tom

2012-01-01

This paper presents a new trajectory optimization software package developed in the framework of a low-to-high fidelity 3 degrees-of-freedom (DOF)/6-DOF vehicle simulation program named Mission Analysis Simulation Tool in Fortran (MASTIF) and its application to a translunar trajectory optimization problem. The functionality of the developed optimization package is implemented as a new "mode" in generalized settings to make it applicable for a general trajectory optimization problem. In doing so, a direct optimization method using collocation is employed for solving the problem. Trajectory optimization problems in MASTIF are transcribed to a constrained nonlinear programming (NLP) problem and solved with SNOPT, a commercially available NLP solver. A detailed description of the optimization software developed is provided as well as the transcription specifics for the translunar injection (TLI) problem. The analysis includes a 3-DOF trajectory TLI optimization and a 3-DOF vehicle TLI simulation using closed-loop guidance.

Engaging Undergraduate Math Majors in Geoscience Research using Interactive Simulations and Computer Art

NASA Astrophysics Data System (ADS)

Matott, L. S.; Hymiak, B.; Reslink, C. F.; Baxter, C.; Aziz, S.

2012-12-01

As part of the NSF-sponsored 'URGE (Undergraduate Research Group Experiences) to Compute' program, Dr. Matott has been collaborating with talented Math majors to explore the design of cost-effective systems to safeguard groundwater supplies from contaminated sites. Such activity is aided by a combination of groundwater modeling, simulation-based optimization, and high-performance computing - disciplines largely unfamiliar to the students at the outset of the program. To help train and engage the students, a number of interactive and graphical software packages were utilized. Examples include: (1) a tutorial for exploring the behavior of evolutionary algorithms and other heuristic optimizers commonly used in simulation-based optimization; (2) an interactive groundwater modeling package for exploring alternative pump-and-treat containment scenarios at a contaminated site in Billings, Montana; (3) the R software package for visualizing various concepts related to subsurface hydrology; and (4) a job visualization tool for exploring the behavior of numerical experiments run on a large distributed computing cluster. Further engagement and excitement in the program was fostered by entering (and winning) a computer art competition run by the Coalition for Academic Scientific Computation (CASC). The winning submission visualizes an exhaustively mapped optimization cost surface and dramatically illustrates the phenomena of artificial minima - valley locations that correspond to designs whose costs are only partially optimal.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loftin, B.; Abramczyk, G.; Koenig, R.

Radioactive materials are stored in a variety of locations throughout the DOE complex. At the Savannah River Site (SRS), materials are stored within dedicated facilities. Each of those facilities has a documented safety analysis (DSA) that describes accidents that the facility and the materials within it may encounter. Facilities at the SRS are planning on utilizing the certified Model 9977 Shipping Package as a long term storage package and one of these facilities required ballistics testing. Specifically, in order to meet the facility DSA, the radioactive materials (RAM) must be contained within the storage package after impact by a .223more » caliber round. In order to qualify the Model 9977 Shipping Package for storage in this location, the package had to be tested under these conditions. Over the past two years, the Model 9977 Shipping Package has been subjected to a series of ballistics tests. The purpose of the testing was to determine if the 9977 would be suitable for use as a storage package at a Savannah River Site facility. The facility requirements are that the package must not release any of its contents following the impact in its most vulnerable location by a .223 caliber round. A package, assembled to meet all of the design requirements for a certified 9977 shipping configuration and using simulated contents, was tested at the Savannah River Site in March of 2011. The testing was completed and the package was examined. The results of the testing and examination are presented in this paper.« less

Retail colour stability of lamb meat is influenced by breed type, muscle, packaging and iron concentration.

PubMed

Warner, R D; Kearney, G; Hopkins, D L; Jacob, R H

2017-07-01

The longissmus lumborum (LL) and semimembranosus (SM) muscles from 391 lamb carcasses, derived from various breed types, were used to investigate the effect of animal/muscle factors, packaging type [over-wrap (OW) or high oxygen modified atmosphere packaging (MAP O2 )] and duration of display on redness of meat during simulated retail display. Using statistical models the time required (in days) for redness to reach a threshold value of 3.5 (below this is unacceptable) was predicted. High levels of iron in the SM, but not LL, reduced the time for redness to reach 3.5 by 2-2.6days in MAP O2 and 0.5-0.8days in OW. The greater the proportion of Merino breed type, the shorter was the time for redness to reach the value of 3.5, an effect consistent across muscles and packaging types. In summary, breed type, packaging format, muscle and muscle iron levels had a significant impact on colour stability of sheep meat in oxygen-available packaging systems. Copyright © 2017. Published by Elsevier Ltd.

Stability of flavoured phytosterol-enriched drinking yogurts during storage as affected by different packaging materials.

PubMed

Semeniuc, Cristina Anamaria; Cardenia, Vladimiro; Mandrioli, Mara; Muste, Sevastiţa; Borsari, Andrea; Rodriguez-Estrada, Maria Teresa

2016-06-01

The aim of this study was to investigate the influence of different packaging materials on storage stability of flavoured phytosterol-enriched drinking yogurts. White vanilla (WV) and blood orange (BO) phytosterol-enriched drinking yogurts conditioned in mono-layer and triple-layer co-extruded plastic bottles were stored at +6 ± 1 °C for 35 days (under alternating 12 h light and 12 h darkness) to simulate shelf-life conditions. Samples were collected at three different storage times and subjected to determination of total sterol content (TSC), peroxide value (PV) and thiobarbituric acid reactive substances (TBARs). TSC was not significantly affected by packaging material or storage time and met the quantity declared on the label. PV was significantly influenced by yogurt type × packaging material × storage time interaction and TBARs by packaging material × storage time interaction. Between the two packaging materials, the triple-layer plastic mini bottle with black coloured and completely opaque intermediate layer offered the best protection against lipid oxidation. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Comparison of effects of copropagated and precomputed atmosphere profiles on Monte Carlo trajectory simulation

NASA Technical Reports Server (NTRS)

Queen, Eric M.; Omara, Thomas M.

1990-01-01

A realization of a stochastic atmosphere model for use in simulations is presented. The model provides pressure, density, temperature, and wind velocity as a function of latitude, longitude, and altitude, and is implemented in a three degree of freedom simulation package. This implementation is used in the Monte Carlo simulation of an aeroassisted orbital transfer maneuver and results are compared to those of a more traditional approach.

Modeling unsaturated zone flow and runoff processes by integrating MODFLOW-LGR and VSF, and creating the new CFL package

USGS Publications Warehouse

Borsia, I.; Rossetto, R.; Schifani, C.; Hill, Mary C.

2013-01-01

In this paper two modifications to the MODFLOW code are presented. One concerns an extension of Local Grid Refinement (LGR) to Variable Saturated Flow process (VSF) capability. This modification allows the user to solve the 3D Richards’ equation only in selected parts of the model domain. The second modification introduces a new package, named CFL (Cascading Flow), which improves the computation of overland flow when ground surface saturation is simulated using either VSF or the Unsaturated Zone Flow (UZF) package. The modeling concepts are presented and demonstrated. Programmer documentation is included in appendices.

User's Guide for Flight Simulation Data Visualization Workstation

NASA Technical Reports Server (NTRS)

Kaplan, Joseph A.; Chen, Ronnie; Kenney, Patrick S.; Koval, Christopher M.; Hutchinson, Brian K.

1996-01-01

Today's modern flight simulation research produces vast amounts of time sensitive data. The meaning of this data can be difficult to assess while in its raw format. Therefore, a method of breaking the data down and presenting it to the user in a graphical format is necessary. Simulation Graphics (SimGraph) is intended as a data visualization software package that will incorporate simulation data into a variety of animated graphical displays for easy interpretation by the simulation researcher. This document is intended as an end user's guide.

THE MARK I BUSINESS SYSTEM SIMULATION MODEL

DTIC Science & Technology

of a large-scale business simulation model as a vehicle for doing research in management controls. The major results of the program were the...development of the Mark I business simulation model and the Simulation Package (SIMPAC). SIMPAC is a method and set of programs facilitating the construction...of large simulation models. The object of this document is to describe the Mark I Corporation model, state why parts of the business were modeled as they were, and indicate the research applications of the model. (Author)

PENGEOM-A general-purpose geometry package for Monte Carlo simulation of radiation transport in material systems defined by quadric surfaces

NASA Astrophysics Data System (ADS)

Almansa, Julio; Salvat-Pujol, Francesc; Díaz-Londoño, Gloria; Carnicer, Artur; Lallena, Antonio M.; Salvat, Francesc

2016-02-01

The Fortran subroutine package PENGEOM provides a complete set of tools to handle quadric geometries in Monte Carlo simulations of radiation transport. The material structure where radiation propagates is assumed to consist of homogeneous bodies limited by quadric surfaces. The PENGEOM subroutines (a subset of the PENELOPE code) track particles through the material structure, independently of the details of the physics models adopted to describe the interactions. Although these subroutines are designed for detailed simulations of photon and electron transport, where all individual interactions are simulated sequentially, they can also be used in mixed (class II) schemes for simulating the transport of high-energy charged particles, where the effect of soft interactions is described by the random-hinge method. The definition of the geometry and the details of the tracking algorithm are tailored to optimize simulation speed. The use of fuzzy quadric surfaces minimizes the impact of round-off errors. The provided software includes a Java graphical user interface for editing and debugging the geometry definition file and for visualizing the material structure. Images of the structure are generated by using the tracking subroutines and, hence, they describe the geometry actually passed to the simulation code.

GIS-based channel flow and sediment transport simulation using CCHE1D coupled with AnnAGNPS

USDA-ARS?s Scientific Manuscript database

CCHE1D (Center for Computational Hydroscience and Engineering 1-Dimensional model) simulates unsteady free-surface flows with nonequilibrium, nonuniform sediment transport in dendritic channel networks. Since early 1990’s, the model and its software packages have been developed and continuously main...

College Students' Misconceptions about Evolutionary Trees

ERIC Educational Resources Information Center

Meir, Eli; Perry, Judy; Herron, Jon C.; Kingsolver, Joel

2007-01-01

Evolution is at the center of the biological sciences and is therefore a required topic for virtually every college biology student. Over the past year, the authors have been building a new simulation software package called EvoBeaker to teach college-level evolutionary biology through simulated experiments. They have built both micro and…

A Novel Use of Computer Simulation in an Applied Pharmacokinetics Course.

ERIC Educational Resources Information Center

Sullivan, Timothy J.

1982-01-01

The use of a package of interactive computer programs designed to simulate pharmacokinetic monitoring of drug therapy in a required undergraduate applied pharmacokinetics course is described. Students were assigned the problem of maintaining therapeutic drug concentrations in a computer generated "patient" as an adjunct to classroom instruction.…

Simulation Based Evaluation of Integrated Adaptive Control and Flight Planning Technologies

NASA Technical Reports Server (NTRS)

Campbell, Stefan Forrest; Kaneshige, John T.

2008-01-01

The objective of this work is to leverage NASA resources to enable effective evaluation of resilient aircraft technologies through simulation. This includes examining strengths and weaknesses of adaptive controllers, emergency flight planning algorithms, and flight envelope determination algorithms both individually and as an integrated package.

Discrete Event Simulation of a Suppression of Enemy Air Defenses (SEAD) Mission

DTIC Science & Technology

2008-03-01

component-based DES developed in Java® using the Simkit simulation package. Analysis of ship self air defense system selection ( Turan , 1999) is another...Institute of Technology, Wright-Patterson AFB OH, March 2003 (ADA445279 ) Turan , Bulent. A Comparative Analysis of Ship Self Air Defense (SSAD) Systems

Computer Simulation of Classic Studies in Psychology.

ERIC Educational Resources Information Center

Bradley, Drake R.

This paper describes DATASIM, a comprehensive software package which generates simulated data for actual or hypothetical research designs. DATASIM is primarily intended for use in statistics and research methods courses, where it is used to generate "individualized" datasets for students to analyze, and later to correct their answers.…

Play It Again: Teaching Statistics with Monte Carlo Simulation

ERIC Educational Resources Information Center

Sigal, Matthew J.; Chalmers, R. Philip

2016-01-01

Monte Carlo simulations (MCSs) provide important information about statistical phenomena that would be impossible to assess otherwise. This article introduces MCS methods and their applications to research and statistical pedagogy using a novel software package for the R Project for Statistical Computing constructed to lessen the often steep…

SEAWAT Version 4: A Computer Program for Simulation of Multi-Species Solute and Heat Transport

USGS Publications Warehouse

Langevin, Christian D.; Thorne, Daniel T.; Dausman, Alyssa M.; Sukop, Michael C.; Guo, Weixing

2008-01-01

The SEAWAT program is a coupled version of MODFLOW and MT3DMS designed to simulate three-dimensional, variable-density, saturated ground-water flow. Flexible equations were added to the program to allow fluid density to be calculated as a function of one or more MT3DMS species. Fluid density may also be calculated as a function of fluid pressure. The effect of fluid viscosity variations on ground-water flow was included as an option. Fluid viscosity can be calculated as a function of one or more MT3DMS species, and the program includes additional functions for representing the dependence on temperature. Although MT3DMS and SEAWAT are not explicitly designed to simulate heat transport, temperature can be simulated as one of the species by entering appropriate transport coefficients. For example, the process of heat conduction is mathematically analogous to Fickian diffusion. Heat conduction can be represented in SEAWAT by assigning a thermal diffusivity for the temperature species (instead of a molecular diffusion coefficient for a solute species). Heat exchange with the solid matrix can be treated in a similar manner by using the mathematically equivalent process of solute sorption. By combining flexible equations for fluid density and viscosity with multi-species transport, SEAWAT Version 4 represents variable-density ground-water flow coupled with multi-species solute and heat transport. SEAWAT Version 4 is based on MODFLOW-2000 and MT3DMS and retains all of the functionality of SEAWAT-2000. SEAWAT Version 4 also supports new simulation options for coupling flow and transport, and for representing constant-head boundaries. In previous versions of SEAWAT, the flow equation was solved for every transport timestep, regardless of whether or not there was a large change in fluid density. A new option was implemented in SEAWAT Version 4 that allows users to control how often the flow field is updated. New options were also implemented for representing constant-head boundaries with the Time-Variant Constant-Head (CHD) Package. These options allow for increased flexibility when using CHD flow boundaries with the zero-dispersive flux solute boundaries implemented by MT3DMS at constant-head cells. This report contains revised input instructions for the MT3DMS Dispersion (DSP) Package, Variable-Density Flow (VDF) Package, Viscosity (VSC) Package, and CHD Package. The report concludes with seven cases of an example problem designed to highlight many of the new features.

Migration and sensory properties of plastics-based nets used as food-contacting materials under ambient and high temperature heating conditions.

PubMed

Kontominas, M G; Goulas, A E; Badeka, A V; Nerantzaki, A

2006-06-01

Overall migration from a wide range of commercial plastics-based netting materials destined to be used as either meat or vegetable packaging materials into the fatty food simulant isooctane or the aqueous simulant distilled water, respectively, was studied. In addition, sensory tests of representative netting materials were carried out in bottled water in order to investigate possible development of off-odour/taste and discoloration in this food simulant as a result of migration from the netting material. Sensory tests were supplemented by determination of the volatile compounds' profile in table water exposed to the netting materials using SPME-GC/MS. Test conditions for packaging material/food simulant contact and method of overall migration analysis were according to European Union Directives 90/128 (EEC, 1990) and 2002/72 (EEC, 2002). The results showed that for both PET and polyethylene-based netting materials, overall migration values into distilled water ranged between 11.5 and 48.5 mg l(-1), well below the upper limit (60 mg l(-1)) for overall migration values from plastics-packaging materials set by the European Union. The overall migration values from netting materials into isooctane ranged between 38.0 and 624.0 mg l(-1), both below and above the European Union upper limit for migration. Sensory tests involving contact of representative samples with table water under refluxing (100 degrees C/4 h) conditions showed a number of the netting materials produced both off-odour and/or taste as well as discoloration of the food simulant rendering such materials unfit for the packaging of foodstuffs in applications involving heating at elevated temperatures. GC/MS analysis showed the presence of numerous volatile compounds being produced after netting materials/water contact under refluxing conditions. Although it is extremely difficult to establish a clear correlation between sensory off-odour development and GC/MS volatile compounds' profile, it may be postulated that plastics oxidation products such as hexanal, heptanal, octanal and 2,6 di-tert-butylquinone may contribute to off-odour development using commercially bottled table water as a food simulant. Likewise, compounds such as carbon disulfide, [1,1'-biphenyl]-2-ol and propanoic acid, 2 methyl 1-(1,1-dimethyl)-2-methyl-1,3-propanediyl ester probably originating from cotton and rubber components of netting materials may also contribute to off-odour/taste development.

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

PubMed

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

2018-01-09

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

Trends in the use of natural antioxidants in active food packaging: a review.

PubMed

Sanches-Silva, Ana; Costa, Denise; Albuquerque, Tânia G; Buonocore, Giovanna Giuliana; Ramos, Fernando; Castilho, Maria Conceição; Machado, Ana Vera; Costa, Helena S

2014-01-01

The demand for natural antioxidant active packaging is increasing due to its unquestionable advantages compared with the addition of antioxidants directly to the food. Therefore, the search for antioxidants perceived as natural, namely those that naturally occur in herbs and spices, is a field attracting great interest. In line with this, in the last few years, natural antioxidants such as α-tocopherol, caffeic acid, catechin, quercetin, carvacrol and plant extracts (e.g. rosemary extract) have been incorporated into food packaging. On the other hand, consumers and the food industry are also interested in active biodegradable/compostable packaging and edible films to reduce environmental impact, minimise food loss and minimise contaminants from industrial production and reutilisation by-products. The present review focuses on the natural antioxidants already applied in active food packaging, and it reviews the methods used to determine the oxidation protection effect of antioxidant active films and the methods used to quantify natural antioxidants in food matrices or food simulants. Lastly consumers' demands and industry trends are also addressed.

QFASAR: Quantitative fatty acid signature analysis with R

USGS Publications Warehouse

Bromaghin, Jeffrey F.

2017-01-01

Knowledge of predator diets provides essential insights into their ecology, yet diet estimation is challenging and remains an active area of research.Quantitative fatty acid signature analysis (QFASA) is a popular method of estimating diet composition that continues to be investigated and extended. However, software to implement QFASA has only recently become publicly available.I summarize a new R package, qfasar, for diet estimation using QFASA methods. The package also provides functionality to evaluate and potentially improve the performance of a library of prey signature data, compute goodness-of-fit diagnostics, and support simulation-based research. Several procedures in the package have not previously been published.qfasar makes traditional and recently published QFASA diet estimation methods accessible to ecologists for the first time. Use of the package is illustrated with signature data from Chukchi Sea polar bears and potential prey species.

Mass decomposition of galaxies using DECA software package

NASA Astrophysics Data System (ADS)

Mosenkov, A. V.

2014-01-01

The new DECA software package, which is designed to perform photometric analysis of the images of disk and elliptical galaxies having a regular structure, is presented. DECA is written in Python interpreted language and combines the capabilities of several widely used packages for astronomical data processing such as IRAF, SExtractor, and the GALFIT code used to perform two-dimensional decomposition of galaxy images into several photometric components (bulge+disk). DECA has the advantage that it can be applied to large samples of galaxies with different orientations with respect to the line of sight (including edge-on galaxies) and requires minimum human intervention. Examples of using the package to study a sample of simulated galaxy images and a sample of real objects are shown to demonstrate that DECA can be a reliable tool for the study of the structure of galaxies.

Fuzzy based attitude controller for flexible spacecraft with on/off thrusters

NASA Astrophysics Data System (ADS)

Knapp, Roger G.; Adams, Neil J.

A fuzzy-based attitude controller is designed for attitude control of a generic spacecraft with on/off thrusters. The controller is comprised of packages of rules dedicated to addressing different objectives (e.g., disturbance rejection, low fuel consumption, avoiding the excitation of flexible appendages, etc.). These rule packages can be inserted or removed depending on the requirements of the particular spacecraft and are parameterized based on vehicle parameters such as inertia or operational parameters such as the maneuvering rate. Individual rule packages can be 'weighted' relative to each other to emphasize the importance of one objective relative to another. Finally, the fuzzy controller and rule packages are demonstrated using the high-fidelity Space Shuttle Interactive On-Orbit Simulator (IOS) while performing typical on-orbit operations and are subsequently compared with the existing shuttle flight control system performance.

Fuzzy based attitude controller for flexible spacecraft with on/off thrusters

NASA Astrophysics Data System (ADS)

Knapp, Roger Glenn

1993-05-01

A fuzzy-based attitude controller is designed for attitude control of a generic spacecraft with on/off thrusters. The controller is comprised of packages of rules dedicated to addressing different objectives (e.g., disturbance rejection, low fuel consumption, avoiding the excitation of flexible appendages, etc.). These rule packages can be inserted or removed depending on the requirements of the particular spacecraft and are parameterized based on vehicle parameters such as inertia or operational parameters such as the maneuvering rate. Individual rule packages can be 'weighted' relative to each other to emphasize the importance of one objective relative to another. Finally, the fuzzy controller and rule packages are demonstrated using the high-fidelity Space Shuttle Interactive On-Orbit Simulator (IOS) while performing typical on-orbit operations and are subsequently compared with the existing shuttle flight control system performance.

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

PubMed Central

Alerstam, Erik; Lo, William Chun Yip; Han, Tianyi David; Rose, Jonathan; Andersson-Engels, Stefan; Lilge, Lothar

2010-01-01

A highly optimized Monte Carlo (MC) code package for simulating light transport is developed on the latest graphics processing unit (GPU) built for general-purpose computing from NVIDIA - the Fermi GPU. In biomedical optics, the MC method is the gold standard approach for simulating light transport in biological tissue, both due to its accuracy and its flexibility in modelling realistic, heterogeneous tissue geometry in 3-D. However, the widespread use of MC simulations in inverse problems, such as treatment planning for PDT, is limited by their long computation time. Despite its parallel nature, optimizing MC code on the GPU has been shown to be a challenge, particularly when the sharing of simulation result matrices among many parallel threads demands the frequent use of atomic instructions to access the slow GPU global memory. This paper proposes an optimization scheme that utilizes the fast shared memory to resolve the performance bottleneck caused by atomic access, and discusses numerous other optimization techniques needed to harness the full potential of the GPU. Using these techniques, a widely accepted MC code package in biophotonics, called MCML, was successfully accelerated on a Fermi GPU by approximately 600x compared to a state-of-the-art Intel Core i7 CPU. A skin model consisting of 7 layers was used as the standard simulation geometry. To demonstrate the possibility of GPU cluster computing, the same GPU code was executed on four GPUs, showing a linear improvement in performance with an increasing number of GPUs. The GPU-based MCML code package, named GPU-MCML, is compatible with a wide range of graphics cards and is released as an open-source software in two versions: an optimized version tuned for high performance and a simplified version for beginners (http://code.google.com/p/gpumcml). PMID:21258498

MT3D-USGS version 1: A U.S. Geological Survey release of MT3DMS updated with new and expanded transport capabilities for use with MODFLOW

USGS Publications Warehouse

Bedekar, Vivek; Morway, Eric D.; Langevin, Christian D.; Tonkin, Matthew J.

2016-09-30

MT3D-USGS, a U.S. Geological Survey updated release of the groundwater solute transport code MT3DMS, includes new transport modeling capabilities to accommodate flow terms calculated by MODFLOW packages that were previously unsupported by MT3DMS and to provide greater flexibility in the simulation of solute transport and reactive solute transport. Unsaturated-zone transport and transport within streams and lakes, including solute exchange with connected groundwater, are among the new capabilities included in the MT3D-USGS code. MT3D-USGS also includes the capability to route a solute through dry cells that may occur in the Newton-Raphson formulation of MODFLOW (that is, MODFLOW-NWT). New chemical reaction Package options include the ability to simulate inter-species reactions and parent-daughter chain reactions. A new pump-and-treat recirculation package enables the simulation of dynamic recirculation with or without treatment for combinations of wells that are represented in the flow model, mimicking the above-ground treatment of extracted water. A reformulation of the treatment of transient mass storage improves conservation of mass and yields solutions for better agreement with analytical benchmarks. Several additional features of MT3D-USGS are (1) the separate specification of the partitioning coefficient (Kd) within mobile and immobile domains; (2) the capability to assign prescribed concentrations to the top-most active layer; (3) the change in mass storage owing to the change in water volume now appears as its own budget item in the global mass balance summary; (4) the ability to ignore cross-dispersion terms; (5) the definition of Hydrocarbon Spill-Source Package (HSS) mass loading zones using regular and irregular polygons, in addition to the currently supported circular zones; and (6) the ability to specify an absolute minimum thickness rather than the default percent minimum thickness in dry-cell circumstances.Benchmark problems that implement the new features and packages test the accuracy of new code through comparison to analytical benchmarks, as well as to solutions from other published codes. The input file structure for MT3D-USGS adheres to MT3DMS conventions for backward compatibility: the new capabilities and packages described herein are readily invoked by adding three-letter package name acronyms to the name file or by setting input flags as needed. Memory is managed in MT3D-USGS using FORTRAN modules in order to simplify code development and expansion.

Preparing the nursing student for internship in a pre-registration nursing program: developing a problem based approach with the use of high fidelity simulation equipment.

PubMed

Nevin, M; Neill, F; Mulkerrins, J

2014-03-01

This paper aims to explore the development and evaluation results of a simulated skills package designed using a problem based learning approach with general nursing students. Internationally, the use of high fidelity simulated learning environments has escalated. This has occurred as a result of growing concerns relating to patient safety, patient litigation, lack of clinical opportunities for student nurses to gain experience and integration of new teaching methods into nursing curricula. There are however both proponents and opponents to the value of simulation and high fidelity simulation within nursing education. This study was conducted in an Irish school of nursing. A simulated learning support package was developed by nurse educators and piloted with 134 third year nursing students. This was evaluated using a questionnaire in which 87 students responded. Students generally found the simulation sessions realistic and useful in developing clinical skills, knowledge and confidence for clinical practice. However student issues regarding support with preparation for the session were highlighted. Also, the need for a more formalised structure for debriefing following the simulation sessions were identified. It is hoped that this paper will provide nurse educators with some guidance to aid future development of innovative and interactive teaching and learning strategies. Copyright © 2013 Elsevier Ltd. All rights reserved.

Using virtualization to protect the proprietary material science applications in volunteer computing

NASA Astrophysics Data System (ADS)

Khrapov, Nikolay P.; Rozen, Valery V.; Samtsevich, Artem I.; Posypkin, Mikhail A.; Sukhomlin, Vladimir A.; Oganov, Artem R.

2018-04-01

USPEX is a world-leading software for computational material design. In essence, USPEX splits simulation into a large number of workunits that can be processed independently. This scheme ideally fits the desktop grid architecture. Workunit processing is done by a simulation package aimed at energy minimization. Many of such packages are proprietary and should be protected from unauthorized access when running on a volunteer PC. In this paper we present an original approach based on virtualization. In a nutshell, the proprietary code and input files are stored in an encrypted folder and run inside a virtual machine image that is also password protected. The paper describes this approach in detail and discusses its application in USPEX@home volunteer project.

Automated Sequence Processor: Something Old, Something New

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Schrock, Mitchell; Fisher, Forest; Himes, Terry

2012-01-01

High productivity required for operations teams to meet schedules Risk must be minimized. Scripting used to automate processes. Scripts perform essential operations functions. Automated Sequence Processor (ASP) was a grass-roots task built to automate the command uplink process System engineering task for ASP revitalization organized. ASP is a set of approximately 200 scripts written in Perl, C Shell, AWK and other scripting languages.. ASP processes/checks/packages non-interactive commands automatically.. Non-interactive commands are guaranteed to be safe and have been checked by hardware or software simulators.. ASP checks that commands are non-interactive.. ASP processes the commands through a command. simulator and then packages them if there are no errors.. ASP must be active 24 hours/day, 7 days/week..

Use of advanced modeling techniques to optimize thermal packaging designs.

PubMed

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 during its validation. Thermal packaging is routinely used by the pharmaceutical industry to provide passive and active temperature control of their thermally sensitive products from manufacture through end use (termed the cold chain). In this study, the authors focus on passive temperature control (passive control does not require any external energy source and is entirely based on specific and/or latent heat of shipper components). As temperature-sensitive pharmaceuticals are being transported over longer distances, cold chain reliability is essential. To achieve reliability, a significant amount of time and resources must be invested in design, test, and production of optimized temperature-controlled packaging solutions. To shorten the cumbersome trial and error approach (design/test/design/test …), computer simulation (virtual prototyping and testing of thermal shippers) is a promising method. Although several companies have attempted to develop such a tool, there has been limited success to date. 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 coupled conductive/convective-based thermal shipper. A modeling technique capable of correctly capturing shipper thermal behavior can be used to develop packaging designs more quickly, reducing up-front costs while also improving shipper performance.

Efficient parallel simulation of CO2 geologic sequestration insaline aquifers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Keni; Doughty, Christine; Wu, Yu-Shu

2007-01-01

An efficient parallel simulator for large-scale, long-termCO2 geologic sequestration in saline aquifers has been developed. Theparallel simulator is a three-dimensional, fully implicit model thatsolves large, sparse linear systems arising from discretization of thepartial differential equations for mass and energy balance in porous andfractured media. The simulator is based on the ECO2N module of the TOUGH2code and inherits all the process capabilities of the single-CPU TOUGH2code, including a comprehensive description of the thermodynamics andthermophysical properties of H2O-NaCl- CO2 mixtures, modeling singleand/or two-phase isothermal or non-isothermal flow processes, two-phasemixtures, fluid phases appearing or disappearing, as well as saltprecipitation or dissolution. The newmore » parallel simulator uses MPI forparallel implementation, the METIS software package for simulation domainpartitioning, and the iterative parallel linear solver package Aztec forsolving linear equations by multiple processors. In addition, theparallel simulator has been implemented with an efficient communicationscheme. Test examples show that a linear or super-linear speedup can beobtained on Linux clusters as well as on supercomputers. Because of thesignificant improvement in both simulation time and memory requirement,the new simulator provides a powerful tool for tackling larger scale andmore complex problems than can be solved by single-CPU codes. Ahigh-resolution simulation example is presented that models buoyantconvection, induced by a small increase in brine density caused bydissolution of CO2.« less

PAINeT: An object-oriented software package for simulations of flow-field, transport coefficients and flux terms in non-equilibrium gas mixture flows

NASA Astrophysics Data System (ADS)

Istomin, V. A.

2018-05-01

The software package Planet Atmosphere Investigator of Non-equilibrium Thermodynamics (PAINeT) has been devel-oped for studying the non-equilibrium effects associated with electronic excitation, chemical reactions and ionization. These studies are necessary for modeling process in shock tubes, in high enthalpy flows, in nozzles or jet engines, in combustion and explosion processes, in modern plasma-chemical and laser technologies. The advantages and possibilities of the package implementation are stated. Within the framework of the package implementation, based on kinetic theory approximations (one-temperature and state-to-state approaches), calculations are carried out, and the limits of applicability of a simplified description of shock-heated air flows and any other mixtures chosen by the user are given. Using kinetic theory algorithms, a numerical calculation of the heat fluxes and relaxation terms can be performed, which is necessary for further comparison of engineering simulation with experi-mental data. The influence of state-to-state distributions over electronic energy levels on the coefficients of thermal conductivity, diffusion, heat fluxes and diffusion velocities of the components of various gas mixtures behind shock waves is studied. Using the software package the accuracy of different approximations of the kinetic theory of gases is estimated. As an example state-resolved atomic ionized mixture of N/N+/O/O+/e- is considered. It is shown that state-resolved diffusion coefficients of neutral and ionized species vary from level to level. Comparing results of engineering applications with those given by PAINeT, recommendations for adequate models selection are proposed.

Towards a Comprehensive Dynamic-chemistry Assimilation for Eos-Chem: Plans and Status in NASA's Data Assimilation Office

NASA Technical Reports Server (NTRS)

Pawson, Steven; Lin, Shian-Jiann; Rood, Richard B.; Stajner, Ivanka; Nebuda, Sharon; Nielsen, J. Eric; Douglass, Anne R.

2000-01-01

In order to support the EOS-Chem project, a comprehensive assimilation package for the coupled chemical-dynamical system is being developed by the Data Assimilation Office at NASA GSFC. This involves development of a coupled chemistry/meteorology model and of data assimilation techniques for trace species and meteorology. The model is being developed using the flux-form semi-Lagrangian dynamical core of Lin and Rood, the physical parameterizations from the NCAR Community Climate Model, and atmospheric chemistry modules from the Atmospheric Chemistry and Dynamics branch at NASA GSFC. To date the following results have been obtained: (i) multi-annual simulations with the dynamics-radiation model show the credibility of the package for atmospheric simulations; (ii) initial simulations including a limited number of middle atmospheric trace gases reveal the realistic nature of transport mechanisms, although there is still a need for some improvements. Samples of these results will be shown. A meteorological assimilation system is currently being constructed using the model; this will form the basis for the proposed meteorological/chemical assimilation package. The latter part of the presentation will focus on areas targeted for development in the near and far terms, with the objective of Providing a comprehensive assimilation package for the EOS-Chem science experiment. The first stage will target ozone assimilation. The plans also encompass a reanalysis (ReSTS) for the 1991-1995 period, which includes the Mt. Pinatubo eruption and the time when a large number of UARS observations were available. One of the most challenging aspects of future developments will be to couple theoretical advances in tracer assimilation with the practical considerations of a real environment and eventually a near-real-time assimilation system.

`spup' - An R Package for Analysis of Spatial Uncertainty Propagation and Application to Trace Gas Emission Simulations

NASA Astrophysics Data System (ADS)

Sawicka, K.; Breuer, L.; Houska, T.; Santabarbara Ruiz, I.; Heuvelink, G. B. M.

2016-12-01

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. Advances in uncertainty propagation analysis 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 techniques, as well as several uncertainty visualization functions. Here we will demonstrate that the 'spup' package is an effective and easy-to-use tool to be applied even in a very complex study case, and that it can be used in multi-disciplinary research and model-based decision support. As an example, we use the ecological LandscapeDNDC model to analyse propagation of uncertainties associated with spatial variability of the model driving forces such as rainfall, nitrogen deposition and fertilizer inputs. The uncertainty propagation is analysed for the prediction of emissions of N2O and CO2 for a German low mountainous, agriculturally developed catchment. The study tests the effect of spatial correlations on spatially aggregated model outputs, and could serve as an advice for developing best management practices and model improvement strategies.

Time And Temperature Dependent Micromechanical Properties Of Solder Joints For 3D-Package Integration

NASA Astrophysics Data System (ADS)

Roellig, Mike; Meier, Karsten; Metasch, Rene

2010-11-01

The recent development of 3D-integrated electronic packages is characterized by the need to increase the diversity of functions and to miniaturize. Currently many 3D-integration concepts are being developed and all of them demand new materials, new designs and new processing technologies. The combination of simulation and experimental investigation becomes increasingly accepted since simulations help to shorten the R&D cycle time and reduce costs. Numerical calculations like the Finite-Element-Method are strong tools to calculate stress conditions in electronic packages resulting from thermal strains due to the manufacturing process and environmental loads. It is essential for the application of numerical calculations that the material data is accurate and describes sufficiently the physical behaviour. The developed machine allows the measurement of time and temperature dependent micromechanical properties of solder joints. Solder joints, which are used to mechanically and electrically connect different packages, are physically measured as they leave the process. This allows accounting for process influences, which may change material properties. Additionally, joint sizes and metallurgical interactions between solder and under bump metallization can be respected by this particular measurement. The measurement allows the determination of material properties within a temperature range of 20° C-200° C. Further, the time dependent creep deformation can be measured within a strain-rate range of 10-31/s-10-81/s. Solder alloys based on Sn-Ag/Sn-Ag-Cu with additionally impurities and joint sizes down to O/ 200 μm were investigated. To finish the material characterization process the material model coefficient were extracted by FEM-Simulation to increase the accuracy of data.

Ceramic ball grid array package stress analysis

NASA Astrophysics Data System (ADS)

Badri, S. H. B. S.; Aziz, M. H. A.; Ong, N. R.; Sauli, Z.; Alcain, J. B.; Retnasamy, V.

2017-09-01

The ball grid array (BGA), a form of chip scale package (CSP), was developed as one of the most advanced surface mount devices, which may be assembled by an ordinary surface ball bumps are used instead of plated nickel and gold (Ni/Au) bumps. Assembly and reliability of the BGA's printed circuit board (PCB), which is soldered by conventional surface mount technology is considered in this study. The Ceramic Ball Grid Array (CBGA) is a rectangular ceramic package or square-shaped that will use the solder ball for external electrical connections instead of leads or wire for connections. The solder balls will be arranged in an array or grid at the bottom of the ceramic package body. In this study, ANSYS software is used to investigate the stress on the package for 2 balls and 4 balls of the CBGA package with the various force range of 1-3 Newton applied to the top of the die, top of the substrate and side of the substrate. The highest maximum stress was analyzed and the maximum equivalent stress was observed on the solder ball and the die. From the simulation result, the CBGA package with less solder balls experience higher stress compared to the package with many solder balls. Therefore, less number of solder ball on the CBGA package results higher stress and critically affect the reliability of the solder balls itself, substrate and die which can lead to the solder crack and also die crack.

A comparison of six software packages for evaluation of solid lung nodules using semi-automated volumetry: what is the minimum increase in size to detect growth in repeated CT examinations.

PubMed

de Hoop, Bartjan; Gietema, Hester; van Ginneken, Bram; Zanen, Pieter; Groenewegen, Gerard; Prokop, Mathias

2009-04-01

We compared interexamination variability of CT lung nodule volumetry with six currently available semi-automated software packages to determine the minimum change needed to detect the growth of solid lung nodules. We had ethics committee approval. To simulate a follow-up examination with zero growth, we performed two low-dose unenhanced CT scans in 20 patients referred for pulmonary metastases. Between examinations, patients got off and on the table. Volumes of all pulmonary nodules were determined on both examinations using six nodule evaluation software packages. Variability (upper limit of the 95% confidence interval of the Bland-Altman plot) was calculated for nodules for which segmentation was visually rated as adequate. We evaluated 214 nodules (mean diameter 10.9 mm, range 3.3 mm-30.0 mm). Software packages provided adequate segmentation in 71% to 86% of nodules (p < 0.001). In case of adequate segmentation, variability in volumetry between scans ranged from 16.4% to 22.3% for the various software packages. Variability with five to six software packages was significantly less for nodules >or=8 mm in diameter (range 12.9%-17.1%) than for nodules <8 mm (range 18.5%-25.6%). Segmented volumes of each package were compared to each of the other packages. Systematic volume differences were detected in 11/15 comparisons. This hampers comparison of nodule volumes between software packages.

Extended asymmetric hot region formation due to shockwave interactions following void collapse in shocked high explosive

NASA Astrophysics Data System (ADS)

Shan, Tzu-Ray; Wixom, Ryan R.; Thompson, Aidan P.

2016-08-01

In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed by coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. The formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.

STOCK: Structure mapper and online coarse-graining kit for molecular simulations

DOE PAGES

Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

2015-03-15

We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be providedmore » by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.« less

WinTRAX: A raytracing software package for the design of multipole focusing systems

NASA Astrophysics Data System (ADS)

Grime, G. W.

2013-07-01

The software package TRAX was a simulation tool for modelling the path of charged particles through linear cylindrical multipole fields described by analytical expressions and was a development of the earlier OXRAY program (Grime and Watt, 1983; Grime et al., 1982) [1,2]. In a 2005 comparison of raytracing software packages (Incerti et al., 2005) [3], TRAX/OXRAY was compared with Geant4 and Zgoubi and was found to give close agreement with the more modern codes. TRAX was a text-based program which was only available for operation in a now rare VMS workstation environment, so a new program, WinTRAX, has been developed for the Windows operating system. This implements the same basic computing strategy as TRAX, and key sections of the code are direct translations from FORTRAN to C++, but the Windows environment is exploited to make an intuitive graphical user interface which simplifies and enhances many operations including system definition and storage, optimisation, beam simulation (including with misaligned elements) and aberration coefficient determination. This paper describes the program and presents comparisons with other software and real installations.

ICEG2D: An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils with Ice Accretion

NASA Technical Reports Server (NTRS)

Thompson, David S.; Soni, Bharat K.

2000-01-01

An integrated software package, ICEG2D, was developed to automate computational fluid dynamics (CFD) simulations for single-element airfoils with ice accretion. ICEG2D is designed to automatically perform three primary functions: (1) generating a grid-ready, surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generating a high-quality grid using the generated surface point distribution, and (3) generating the input and restart files needed to run the general purpose CFD solver NPARC. ICEG2D can be executed in batch mode using a script file or in an interactive mode by entering directives from a command line. This report summarizes activities completed in the first year of a three-year research and development program to address issues related to CFD simulations for aircraft components with ice accretion. Specifically, this document describes the technology employed in the software, the installation procedure, and a description of the operation of the software package. Validation of the geometry and grid generation modules of ICEG2D is also discussed.

MEANS: python package for Moment Expansion Approximation, iNference and Simulation

PubMed Central

Fan, Sisi; Geissmann, Quentin; Lakatos, Eszter; Lukauskas, Saulius; Ale, Angelique; Babtie, Ann C.; Kirk, Paul D. W.; Stumpf, Michael P. H.

2016-01-01

Motivation: Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system’s moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems. Results: We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis. Availability and implementation: https://github.com/theosysbio/means Contacts: m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153663

MEANS: python package for Moment Expansion Approximation, iNference and Simulation.

PubMed

Fan, Sisi; Geissmann, Quentin; Lakatos, Eszter; Lukauskas, Saulius; Ale, Angelique; Babtie, Ann C; Kirk, Paul D W; Stumpf, Michael P H

2016-09-15

Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system's moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems. We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis. https://github.com/theosysbio/means m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Study of solvent sublation for concentration of trace phthalate esters in plastic beverage packaging and analysis by gas chromatography-mass spectrometry.

PubMed

Chang, Lin; Bi, Pengyu; Li, Xiaochen; Wei, Yun

2015-06-15

A novel trace analytical method based on solvent sublation (SS) and gas chromatography-mass spectrometry (GC-MS) was developed for the trace determination of twenty-two phthalate esters (PAEs) from plastic beverage packaging. In the solvent sublation section, the effects of solution pH, NaCl concentration, nitrogen flow rate, and sublation time on the sublation efficiency were investigated in detail, and the optimal conditions were obtained. The trace PAEs migrated from plastic beverage packaging to food simulants were separated and concentrated by solvent sublation, and then the trace target compounds in the concentrated solution were analyzed by GC-MS. According to the European Union Regulation, the food simulants including distilled water for the normal beverages and acetic acid solution (3%) for the acetic beverage of yogurt were prepared for migration tests. The trace analysis method showed good linearity, low limits of detection (LODs) of 1.6-183.5 ng/L, and satisfied recoveries (67.3-113.7%). Copyright © 2015 Elsevier Ltd. All rights reserved.

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees.

PubMed

Bennett, Dominic J; Sutton, Mark D; Turvey, Samuel T

2017-01-07

Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks. We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes. We present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.

Nanogranular soft magnetic material and on-package integrated inductors

NASA Astrophysics Data System (ADS)

Li, Liangliang

2007-12-01

Integrated inductors used in electronic circuits are mainly spiral-shaped aluminum devices fabricated on Si chip. They have several disadvantages---large silicon area consumption, high DC resistance and high cost. An attractive approach to address these issues is directly integrating inductors into package substrates, which provide plenty of usage area, low resistance and low cost. The goals of this dissertation are designing and fabricating magnetic and air-core inductors with characteristic low resistance and high quality factor on package substrates. The research work includes three parts which are summarized below. First, the CoFeHfO nanogranular magnetic material developed on Si wafers and package substrates by pulsed DC reactive sputtering were investigated. On Si wafers, the optimized CoFeHfO film has soft magnetic properties. On printed circuit board (PCB) substrates, these magnetic properties degrade due to the rough surface. Surface planarization such as chemical-mechanical polishing can be applied on PCB substrates to reduce the surface roughness and hence improve these properties. Second, on-package inductors with small resistances and high quality factors were designed, fabricated, measured and analyzed. Air-core and magnetic inductors (20 design variations) were built on 8-inch PCB substrates. The DC resistances of these inductors are less than 12 mO, one of the lowest values ever reported. The maximum quality factors can be as large as ˜80 at around 1 GHz for the air-core inductors and ˜25 at 200 MHz for the magnetic inductors. Third, inductor simulation was carried out to study the effects of magnetic materials on the properties of inductors using the Ansoft HFSS software package. The measurement data for the permeability spectra of the CoFeHfO film and the tensor nature of the permeability were taken into account in the simulation. The simulation results matched the experimental data for the inductances, resistances and quality factors. This established an accurate method for modeling high-frequency magnetic devices. Using this method, an inductor with a closed magnetic core was studied by varying the geometry of the core and copper coil. It has been found that the inductance of this inductor depends strongly on whether the permeability of the magnetic core is isotropic or anisotropic.

Psychology on Computers: Simulations, Experiments and Projects.

ERIC Educational Resources Information Center

Belcher, Duane M.; Smith, Stephen D.

PSYCOM is a unique mixed media package which combines high interest projects on the computer with a written text of expository material. It goes beyond most computer-assisted instruction which emphasizes drill and practice and testing of knowledge. A project might consist of a simulation or an actual experiment, or it might be a demonstration, a…

Optimal Living Environments for the Elderly: A Design Simulation Approach.

ERIC Educational Resources Information Center

Hoffman, Stephanie B.; And Others

PLANNED AGE (Planned Alternatives for Gerontological Environments) is a consumer/advocate-oriented design simulation package that provides: (a) a medium for user-planner interaction in the design of living and service environments for the aged; (b) an educational, planning, design, and evaluation tool that can be used by the elderly, their…

CPU SIM: A Computer Simulator for Use in an Introductory Computer Organization-Architecture Class.

ERIC Educational Resources Information Center

Skrein, Dale

1994-01-01

CPU SIM, an interactive low-level computer simulation package that runs on the Macintosh computer, is described. The program is designed for instructional use in the first or second year of undergraduate computer science, to teach various features of typical computer organization through hands-on exercises. (MSE)

A Computer-Based Simulation for Teaching Heat Transfer across a Woody Stem

ERIC Educational Resources Information Center

Maixner, Michael R.; Noyd, Robert K.; Krueger, Jerome A.

2010-01-01

To assist student understanding of heat transfer through woody stems, we developed an instructional package that included an Excel-based, one-dimensional simulation model and a companion instructional worksheet. Guiding undergraduate botany students to applying principles of thermodynamics to plants in nature is fraught with two main obstacles:…

Computer simulation of a space SAR using a range-sequential processor for soil moisture mapping

NASA Technical Reports Server (NTRS)

Fujita, M.; Ulaby, F. (Principal Investigator)

1982-01-01

The ability of a spaceborne synthetic aperture radar (SAR) to detect soil moisture was evaluated by means of a computer simulation technique. The computer simulation package includes coherent processing of the SAR data using a range-sequential processor, which can be set up through hardware implementations, thereby reducing the amount of telemetry involved. With such a processing approach, it is possible to monitor the earth's surface on a continuous basis, since data storage requirements can be easily met through the use of currently available technology. The Development of the simulation package is described, followed by an examination of the application of the technique to actual environments. The results indicate that in estimating soil moisture content with a four-look processor, the difference between the assumed and estimated values of soil moisture is within + or - 20% of field capacity for 62% of the pixels for agricultural terrain and for 53% of the pixels for hilly terrain. The estimation accuracy for soil moisture may be improved by reducing the effect of fading through non-coherent averaging.

Development of JSTAMP-Works/NV and HYSTAMP for Multipurpose Multistage Sheet Metal Forming Simulation

NASA Astrophysics Data System (ADS)

Umezu, Yasuyoshi; Watanabe, Yuko; Ma, Ninshu

2005-08-01

Since 1996, Japan Research Institute Limited (JRI) has been providing a sheet metal forming simulation system called JSTAMP-Works packaged the FEM solvers of LS-DYNA and JOH/NIKE, which might be the first multistage system at that time and has been enjoying good reputation among users in Japan. To match the recent needs, "faster, more accurate and easier", of process designers and CAE engineers, a new metal forming simulation system JSTAMP-Works/NV is developed. The JSTAMP-Works/NV packaged the automatic healing function of CAD and had much more new capabilities such as prediction of 3D trimming lines for flanging or hemming, remote control of solver execution for multi-stage forming processes and shape evaluation between FEM and CAD. On the other way, a multi-stage multi-purpose inverse FEM solver HYSTAMP is developed and will be soon put into market, which is approved to be very fast, quite accurate and robust. Lastly, authors will give some application examples of user defined ductile damage subroutine in LS-DYNA for the estimation of material failure and springback in metal forming simulation.

Progress on 3-D ICF simulations and Ray-Traced Power Deposition Method

NASA Astrophysics Data System (ADS)

Schmitt, Andrew J.; Fyfe, David E.

2016-10-01

We have performed 3D simulations of Omega-scale and NIF-scale spherical direct-drive targets with the massively parallel fastrad3d code. Of particular interest is the robustness of the targets to the low mode perturbations impressed on the target by the laser system and how it compares to the influence of the perturbations produced by laser imprinting. As part of this simulation capability, we have upgraded our smoothed 3D raytrace package to run in spherical geometry. This package, which connects rays to form bundles and performs power deposition calculations on the bundles, can decrease laser absorption noise while using fewer rays and less message passing. This model produces both the imprint and the low-mode asymmetry drive that we are interested in here. We show recent simulation results of directly-driven targets using conventional ignition drive, and report on the influences of the two sources - low mode asymmetry and laser imprint - as the pellet conditions (e.g. adiabat) are varied. Work supported by DoE/NNSA.

On Parallelizing Single Dynamic Simulation Using HPC Techniques and APIs of Commercial Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diao, Ruisheng; Jin, Shuangshuang; Howell, Frederic

Time-domain simulations are heavily used in today’s planning and operation practices to assess power system transient stability and post-transient voltage/frequency profiles following severe contingencies to comply with industry standards. Because of the increased modeling complexity, it is several times slower than real time for state-of-the-art commercial packages to complete a dynamic simulation for a large-scale model. With the growing stochastic behavior introduced by emerging technologies, power industry has seen a growing need for performing security assessment in real time. This paper presents a parallel implementation framework to speed up a single dynamic simulation by leveraging the existing stability model librarymore » in commercial tools through their application programming interfaces (APIs). Several high performance computing (HPC) techniques are explored such as parallelizing the calculation of generator current injection, identifying fast linear solvers for network solution, and parallelizing data outputs when interacting with APIs in the commercial package, TSAT. The proposed method has been tested on a WECC planning base case with detailed synchronous generator models and exhibits outstanding scalable performance with sufficient accuracy.« less

Time- and temperature-dependent migration studies of Irganox 1076 from plastics into foods and food simulants.

PubMed

Beldì, G; Pastorelli, S; Franchini, F; Simoneau, C

2012-01-01

The study provides an exhaustive set of migration data for octadecyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate (Irganox 1076) from low-density polyethylene (LDPE) in several food matrices. Irganox 1076 was used as a model migrant because it represents one of the typical substances used as an antioxidant in food packaging polymers. Kinetic (time-dependent) migration studies of Irganox 1076 were performed for selected foodstuffs chosen with different physical-chemical properties and in relation to the actual European food consumption market. The effect of fat content and of the temperature of storage on the migration from plastic packaging was evaluated. The results show that migration increased with fat content and storage temperature. All data obtained from real foods were also compared with data obtained from simulants tested in the same conditions. In all studied cases, the kinetics in simulants were higher than those in foodstuffs. The work provides data valuable for the extension of the validation of migration model developed on simulants to foodstuffs themselves.

Numerical simulation of a flow past a triangular sail-type blade of a wind generator using the ANSYS FLUENT software package

NASA Astrophysics Data System (ADS)

Kusaiynov, K.; Tanasheva, N. K.; Min'kov, L. L.; Nusupbekov, B. R.; Stepanova, Yu. O.; Rozhkova, A. V.

2016-02-01

An air flow past a single triangular sail-type blade of a wind turbine is analyzed by numerical simulation for low velocities of the incoming flow. The results of numerical simulation indicate a monotonic increase in the drag force and the lift force as functions of the incoming flow; empirical dependences of these quantities are obtained.

Step 1: Human System Integration Simulation and Flight Test Progress Report

NASA Technical Reports Server (NTRS)

2005-01-01

The Access 5 Human Systems Integration Work Package produced simulation and flight demonstration planning products for use throughout the program. These included: Test Objectives for Command, Control, Communications; Pilot Questionnaire for Command, Control, Communications; Air Traffic Controller Questionnaire for Command, Control, Communications; Test Objectives for Collision Avoidance; Pilot Questionnaire for Collision Avoidance; Plans for Unmanned Aircraft Systems Control Station Simulations Flight Requirements for the Airspace Operations Demonstration

DNA packaging and ejection forces in bacteriophage

PubMed Central

Kindt, James; Tzlil, Shelly; Ben-Shaul, Avinoam; Gelbart, William M.

2001-01-01

We calculate the forces required to package (or, equivalently, acting to eject) DNA into (from) a bacteriophage capsid, as a function of the loaded (ejected) length, under conditions for which the DNA is either self-repelling or self-attracting. Through computer simulation and analytical theory, we find the loading force to increase more than 10-fold (to tens of piconewtons) during the final third of the loading process; correspondingly, the internal pressure drops 10-fold to a few atmospheres (matching the osmotic pressure in the cell) upon ejection of just a small fraction of the phage genome. We also determine an evolution of the arrangement of packaged DNA from toroidal to spool-like structures. PMID:11707588

Software Reviews.

ERIC Educational Resources Information Center

Kimball, Jeffrey P.; And Others

1987-01-01

Describes a variety of computer software. The packages reviewed include a variety of simulations, a spread sheet, a printer driver and an alternative operating system for DBM.PCs and compatible programs. (BSR)

Modeling and Simulation of III-Nitride-Based Solar Cells using NextnanoRTM

NASA Astrophysics Data System (ADS)

Refaei, Malak

Nextnano3 software is a well-known package for simulating semiconductor band-structures at the nanoscale and predicting the general electronic structure. In this work, it is further demonstrated as a viable tool for the simulation of III-nitride solar cells. In order to prove this feasibility, the generally accepted solar cell simulation package, PC1D, was chosen for comparison. To critique the results from both PC1D and Nextnano3, the fundamental drift-diffusion equations were used to calculate the performance of a simple p-n homojunction solar cell device analytically. Silicon was picked as the material for this comparison between the outputs of the two simulators as well as the results of the drift-diffusion equations because it is a well-known material in both software tools. After substantiating the capabilities of Nextnano3 for the simulation solar cells, an InGaN single-junction solar cell was simulated. The effects of various indium compositions and device structures on the performance of this InGaN p-n homojunction solar cell was then investigated using Nextnano 3 as a simulation tool. For single-junction devices with varying bandgap, an In0.6Ga0.4N device with a bandgap of 1.44 eV was found to be the optimum. The results of this research demonstrate that the Nextnano3 software can be used to usefully simulate solar cells in general, and III-nitride solar cells specifically, for future study of nanoscale structured devices.

An Algorithm and R Program for Fitting and Simulation of Pharmacokinetic and Pharmacodynamic Data.

PubMed

Li, Jijie; Yan, Kewei; Hou, Lisha; Du, Xudong; Zhu, Ping; Zheng, Li; Zhu, Cairong

2017-06-01

Pharmacokinetic/pharmacodynamic link models are widely used in dose-finding studies. By applying such models, the results of initial pharmacokinetic/pharmacodynamic studies can be used to predict the potential therapeutic dose range. This knowledge can improve the design of later comparative large-scale clinical trials by reducing the number of participants and saving time and resources. However, the modeling process can be challenging, time consuming, and costly, even when using cutting-edge, powerful pharmacological software. Here, we provide a freely available R program for expediently analyzing pharmacokinetic/pharmacodynamic data, including data importation, parameter estimation, simulation, and model diagnostics. First, we explain the theory related to the establishment of the pharmacokinetic/pharmacodynamic link model. Subsequently, we present the algorithms used for parameter estimation and potential therapeutic dose computation. The implementation of the R program is illustrated by a clinical example. The software package is then validated by comparing the model parameters and the goodness-of-fit statistics generated by our R package with those generated by the widely used pharmacological software WinNonlin. The pharmacokinetic and pharmacodynamic parameters as well as the potential recommended therapeutic dose can be acquired with the R package. The validation process shows that the parameters estimated using our package are satisfactory. The R program developed and presented here provides pharmacokinetic researchers with a simple and easy-to-access tool for pharmacokinetic/pharmacodynamic analysis on personal computers.

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

NASA Astrophysics Data System (ADS)

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.

Muon simulation codes MUSIC and MUSUN for underground physics

NASA Astrophysics Data System (ADS)

Kudryavtsev, V. A.

2009-03-01

The paper describes two Monte Carlo codes dedicated to muon simulations: MUSIC (MUon SImulation Code) and MUSUN (MUon Simulations UNderground). MUSIC is a package for muon transport through matter. It is particularly useful for propagating muons through large thickness of rock or water, for instance from the surface down to underground/underwater laboratory. MUSUN is designed to use the results of muon transport through rock/water to generate muons in or around underground laboratory taking into account their energy spectrum and angular distribution.

Fuzzy simulation in concurrent engineering

NASA Technical Reports Server (NTRS)

Kraslawski, A.; Nystrom, L.

1992-01-01

Concurrent engineering is becoming a very important practice in manufacturing. A problem in concurrent engineering is the uncertainty associated with the values of the input variables and operating conditions. The problem discussed in this paper concerns the simulation of processes where the raw materials and the operational parameters possess fuzzy characteristics. The processing of fuzzy input information is performed by the vertex method and the commercial simulation packages POLYMATH and GEMS. The examples are presented to illustrate the usefulness of the method in the simulation of chemical engineering processes.

Investigation of the quality of stored red blood cells after simulated air drop in the maritime environment.

PubMed

Meli, Athinoula; Hancock, Vicky; Doughty, Heidi; Smedley, Steve; Cardigan, Rebecca; Wiltshire, Michael

2018-02-01

Maritime medical capability may be compromised by blood resupply. Air-dropped red blood cells (RBCs) is a possible mitigation factor. This study set out to evaluate RBC storage variables after a simulated parachute air drop into the sea, as limited data exist. The air load construction for the air drop of blood was subject to static drop assessment to simulate a worst-case parachute drop scenario. One control and two test Golden Hour shipping containers were each packaged with 10 RBC units. The control box was not dropped; Test Boxes 1 and 2 were further reinforced with waterproof boxes and underwent a simulated air drop on Day 7 or Day 8 postdonation, respectively. One day after the drop and once a week thereafter until Day 43 of storage, RBCs from each box were sampled and tested for full blood counts, hemolysis, adenosine triphosphate, 2,3-diphosphoglycerate, pH, extracellular potassium, glucose, lactate, deformability, and RBC microvesicles. The packaging configuration completed the air drop with no water ingress or physical damage. All units met UK specifications for volume, hemoglobin, and hemolysis. There were no significant differences for any of the variables studied between RBCs in the control box compared to RBCs in Test Boxes 1 and 2 combined over storage. The test proved that the packaging solution and the impact of a maritime air drop as performed in this study, on Day 7 or Day 8 postdonation, did not affect the in vitro quality of RBCs in SAGM over storage for 35 days. © 2017 AABB.

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

PubMed

Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F; Harger, Matthew; Torabifard, Hedieh; Cisneros, G Andrés; Schnieders, Michael J; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y; Ponder, Jay W; Piquemal, Jean-Philip

2018-01-28

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.

SU-C-BRC-06: OpenCL-Based Cross-Platform Monte Carlo Simulation Package for Carbon Ion Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, N; Tian, Z; Pompos, A

2016-06-15

Purpose: Monte Carlo (MC) simulation is considered to be the most accurate method for calculation of absorbed dose and fundamental physical quantities related to biological effects in carbon ion therapy. Its long computation time impedes clinical and research applications. We have developed an MC package, goCMC, on parallel processing platforms, aiming at achieving accurate and efficient simulations for carbon therapy. Methods: goCMC was developed under OpenCL framework. It supported transport simulation in voxelized geometry with kinetic energy up to 450 MeV/u. Class II condensed history algorithm was employed for charged particle transport with stopping power computed via Bethe-Bloch equation. Secondarymore » electrons were not transported with their energy locally deposited. Energy straggling and multiple scattering were modeled. Production of secondary charged particles from nuclear interactions was implemented based on cross section and yield data from Geant4. They were transported via the condensed history scheme. goCMC supported scoring various quantities of interest e.g. physical dose, particle fluence, spectrum, linear energy transfer, and positron emitting nuclei. Results: goCMC has been benchmarked against Geant4 with different phantoms and beam energies. For 100 MeV/u, 250 MeV/u and 400 MeV/u beams impinging to a water phantom, range difference was 0.03 mm, 0.20 mm and 0.53 mm, and mean dose difference was 0.47%, 0.72% and 0.79%, respectively. goCMC can run on various computing devices. Depending on the beam energy and voxel size, it took 20∼100 seconds to simulate 10{sup 7} carbons on an AMD Radeon GPU card. The corresponding CPU time for Geant4 with the same setup was 60∼100 hours. Conclusion: We have developed an OpenCL-based cross-platform carbon MC simulation package, goCMC. Its accuracy, efficiency and portability make goCMC attractive for research and clinical applications in carbon therapy.« less

Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kee, R.J.; Rupley, F.M.; Miller, J.A.

1989-09-01

This document is the user's manual for the second-generation Chemkin package. Chemkin is a software package for whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides an especially flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutinemore » Library. This library is a collection of about 100 highly modular Fortran subroutines that may be called to return information on equation of state, thermodynamic properties, and chemical production rates.« less

Molded underfill (MUF) encapsulation for flip-chip package: A numerical investigation

NASA Astrophysics Data System (ADS)

Azmi, M. A.; Abdullah, M. K.; Abdullah, M. Z.; Ariff, Z. M.; Saad, Abdullah Aziz; Hamid, M. F.; Ismail, M. A.

2017-07-01

This paper presents the numerical simulation of epoxy molding compound (EMC) filling in multi flip-chip packages during encapsulation process. The empty and a group flip chip packages were considered in the mold cavity in order to study the flow profile of the EMC. SOLIDWORKS software was used for three-dimensional modeling and it was incorporated into fluid analysis software namely as ANSYS FLUENT. The volume of fluid (VOF) technique was used for capturing the flow front profiles and Power Law model was applied for its rheology model. The numerical result are compared and discussed with previous experimental and it was shown a good conformity for model validation. The prediction of flow front was observed and analyzed at different filling time. The possibility and visual of void formation in the package is captured and the number of flip-chip is one factor that contributed to the void formation.

Evaluation Framework and Analyses for Thermal Energy Storage Integrated with Packaged Air Conditioning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kung, F.; Deru, M.; Bonnema, E.

2013-10-01

Few third-party guidance documents or tools are available for evaluating thermal energy storage (TES) integrated with packaged air conditioning (AC), as this type of TES is relatively new compared to TES integrated with chillers or hot water systems. To address this gap, researchers at the National Renewable Energy Laboratory conducted a project to improve the ability of potential technology adopters to evaluate TES technologies. Major project outcomes included: development of an evaluation framework to describe key metrics, methodologies, and issues to consider when assessing the performance of TES systems integrated with packaged AC; application of multiple concepts from the evaluationmore » framework to analyze performance data from four demonstration sites; and production of a new simulation capability that enables modeling of TES integrated with packaged AC in EnergyPlus. This report includes the evaluation framework and analysis results from the project.« less

Fuzzy based attitude controller for flexible spacecraft with on/off thrusters. M.S. Thesis - M.I.T., 1993

NASA Technical Reports Server (NTRS)

Knapp, Roger Glenn

1993-01-01

A fuzzy-based attitude controller is designed for attitude control of a generic spacecraft with on/off thrusters. The controller is comprised of packages of rules dedicated to addressing different objectives (e.g., disturbance rejection, low fuel consumption, avoiding the excitation of flexible appendages, etc.). These rule packages can be inserted or removed depending on the requirements of the particular spacecraft and are parameterized based on vehicle parameters such as inertia or operational parameters such as the maneuvering rate. Individual rule packages can be 'weighted' relative to each other to emphasize the importance of one objective relative to another. Finally, the fuzzy controller and rule packages are demonstrated using the high-fidelity Space Shuttle Interactive On-Orbit Simulator (IOS) while performing typical on-orbit operations and are subsequently compared with the existing shuttle flight control system performance.

A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package.

PubMed

Lan, Hongzhi; Updegrove, Adam; Wilson, Nathan M; Maher, Gabriel D; Shadden, Shawn C; Marsden, Alison L

2018-02-01

Patient-specific simulation plays an important role in cardiovascular disease research, diagnosis, surgical planning and medical device design, as well as education in cardiovascular biomechanics. simvascular is an open-source software package encompassing an entire cardiovascular modeling and simulation pipeline from image segmentation, three-dimensional (3D) solid modeling, and mesh generation, to patient-specific simulation and analysis. SimVascular is widely used for cardiovascular basic science and clinical research as well as education, following increased adoption by users and development of a GATEWAY web portal to facilitate educational access. Initial efforts of the project focused on replacing commercial packages with open-source alternatives and adding increased functionality for multiscale modeling, fluid-structure interaction (FSI), and solid modeling operations. In this paper, we introduce a major SimVascular (SV) release that includes a new graphical user interface (GUI) designed to improve user experience. Additional improvements include enhanced data/project management, interactive tools to facilitate user interaction, new boundary condition (BC) functionality, plug-in mechanism to increase modularity, a new 3D segmentation tool, and new computer-aided design (CAD)-based solid modeling capabilities. Here, we focus on major changes to the software platform and outline features added in this new release. We also briefly describe our recent experiences using SimVascular in the classroom for bioengineering education.

Modeling ICF With RAGE, BHR, And The New Laser Package

NASA Astrophysics Data System (ADS)

Cliche, Dylan; Welser-Sherrill, Leslie; Haines, Brian; Mancini, Roberto

2017-10-01

Inertial Confinement Fusion (ICF) is one method used to obtain thermonuclear burn through the either direct or indirect ablation of a millimeter-scale capsule with several lasers. Although progress has been made in theory, experiment, and diagnostics, the community has yet to reach ignition. A way of investigating this is through the use of high performance computer simulations of the implosion. RAGE is an advanced 1D, 2D, and 3D radiation adaptive grid Eulerian code used to simulate hydrodynamics of a system. Due to the unstable nature of two unequal densities accelerating into one another, it is important to include a turbulence model. BHR is a turbulence model which uses Reynolds-averaged Navier-Stokes (RANS) equations to model the mixing that occurs between the shell and fusion fuel material. Until recently, it was still difficult to model direct drive experiments because there was no laser energy deposition model in RAGE. Recently, a new laser energy deposition model has been implemented using the same ray tracing method as the Mazinisin laser package used at the OMEGA laser facility at the Laboratory for Laser Energetics (LLE) in Rochester, New York. Using the new laser package along with BHR for mixing allows us to more accurately simulate ICF implosions and obtain spatially and temporally resolved information (e.g. position, temperature, density, and mix concentrations) to give insight into what is happening inside the implosion.

The ARM Cloud Radar Simulator for Global Climate Models: A New Tool for Bridging Field Data and Climate Models

DOE PAGES

Zhang, Yuying; Xie, Shaocheng; Klein, Stephen A.; ...

2017-08-11

Clouds play an important role in Earth’s radiation budget and hydrological cycle. However, current global climate models (GCMs) have difficulties in accurately simulating clouds and precipitation. To improve the representation of clouds in climate models, it is crucial to identify where simulated clouds differ from real world observations of them. This can be difficult, since significant differences exist between how a climate model represents clouds and what instruments observe, both in terms of spatial scale and the properties of the hydrometeors which are either modeled or observed. To address these issues and minimize impacts of instrument limitations, the concept ofmore » instrument “simulators”, which convert model variables into pseudo-instrument observations, has evolved with the goal to facilitate and to improve the comparison of modeled clouds with observations. Many simulators have been (and continue to be) developed for a variety of instruments and purposes. Finally, a community satellite simulator package, the Cloud Feedback Model Intercomparison Project (CFMIP) Observation Simulator Package (COSP; Bodas-Salcedo et al. 2011), contains several independent satellite simulators and is being widely used in the global climate modeling community to exploit satellite observations for model cloud evaluation (e.g., Kay et al. 2012; Klein et al. 2013; Suzuki et al. 2013; Zhang et al. 2010).« less

The ARM Cloud Radar Simulator for Global Climate Models: A New Tool for Bridging Field Data and Climate Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yuying; Xie, Shaocheng; Klein, Stephen A.

Clouds play an important role in Earth’s radiation budget and hydrological cycle. However, current global climate models (GCMs) have difficulties in accurately simulating clouds and precipitation. To improve the representation of clouds in climate models, it is crucial to identify where simulated clouds differ from real world observations of them. This can be difficult, since significant differences exist between how a climate model represents clouds and what instruments observe, both in terms of spatial scale and the properties of the hydrometeors which are either modeled or observed. To address these issues and minimize impacts of instrument limitations, the concept ofmore » instrument “simulators”, which convert model variables into pseudo-instrument observations, has evolved with the goal to facilitate and to improve the comparison of modeled clouds with observations. Many simulators have been (and continue to be) developed for a variety of instruments and purposes. Finally, a community satellite simulator package, the Cloud Feedback Model Intercomparison Project (CFMIP) Observation Simulator Package (COSP; Bodas-Salcedo et al. 2011), contains several independent satellite simulators and is being widely used in the global climate modeling community to exploit satellite observations for model cloud evaluation (e.g., Kay et al. 2012; Klein et al. 2013; Suzuki et al. 2013; Zhang et al. 2010).« less

Capable Copper Electrodeposition Process for Integrated Circuit - substrate Packaging Manufacturing

NASA Astrophysics Data System (ADS)

Ghanbari, Nasrin

This work demonstrates a capable reverse pulse deposition methodology to influence gap fill behavior inside microvia along with a uniform deposit in the fine line patterned regions for substrate packaging applications. Interconnect circuitry in IC substrate packages comprises of stacked microvia that varies in depth from 20microm to 100microm with an aspect ratio of 0.5 to 1.5 and fine line patterns defined by photolithography. Photolithography defined pattern regions incorporate a wide variety of feature sizes including large circular pad structures with diameter of 20microm - 200microm, fine traces with varying widths of 3microm - 30microm and additional planar regions to define a IC substrate package. Electrodeposition of copper is performed to establish the desired circuit. Electrodeposition of copper in IC substrate applications holds certain unique challenges in that they require a low cost manufacturing process that enables a void-free gap fill inside the microvia along with uniform deposition of copper on exposed patterned regions. Deposition time scales to establish the desired metal thickness for such packages could range from several minutes to few hours. This work showcases a reverse pulse electrodeposition methodology that achieves void-free gap fill inside the microvia and uniform plating in FLS (Fine Lines and Spaces) regions with significantly higher deposition rates than traditional approaches. In order to achieve this capability, systematic experimental and simulation studies were performed. A strong correlation of independent parameters that govern the electrodeposition process such as bath temperature, reverse pulse plating parameters and the ratio of electrolyte concentrations is shown to the deposition kinetics and deposition uniformity in fine patterned regions and gap fill rate inside the microvia. Additionally, insight into the physics of via fill process is presented with secondary and tertiary current simulation efforts. Such efforts lead to show "smart" control of deposition rate at the top and bottom of via to avoid void formation. Finally, a parametric effect on grain size and the ensuing copper metallurgical characteristics of bulk copper is also shown to enable high reliability substrate packages for the IC packaging industry.

QDENSITY—A Mathematica quantum computer simulation

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Burdis, Joseph M.; Tabakin, Frank

2009-03-01

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. New version program summaryProgram title: QDENSITY 2.0 Catalogue identifier: ADXH_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 26 055 No. of bytes in distributed program, including test data, etc.: 227 540 Distribution format: tar.gz Programming language: Mathematica 6.0 Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4 Catalogue identifier of previous version: ADXH_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914 Classification: 4.15 Does the new version supersede the previous version?: Offers an alternative, more up to date, implementation Nature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters. Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed. Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0 Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0 Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.

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

NASA Astrophysics Data System (ADS)

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 statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

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

NASA Astrophysics Data System (ADS)

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 statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems.

PubMed

Mcclenny, Levi D; Imani, Mahdi; Braga-Neto, Ulisses M

2017-11-25

Gene regulatory networks govern the function of key cellular processes, such as control of the cell cycle, response to stress, DNA repair mechanisms, and more. Boolean networks have been used successfully in modeling gene regulatory networks. In the Boolean network model, the transcriptional state of each gene is represented by 0 (inactive) or 1 (active), and the relationship among genes is represented by logical gates updated at discrete time points. However, the Boolean gene states are never observed directly, but only indirectly and incompletely through noisy measurements based on expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays. The Partially-Observed Boolean Dynamical System (POBDS) signal model is distinct from other deterministic and stochastic Boolean network models in removing the requirement of a directly observable Boolean state vector and allowing uncertainty in the measurement process, addressing the scenario encountered in practice in transcriptomic analysis. BoolFilter is an R package that implements the POBDS model and associated algorithms for state and parameter estimation. It allows the user to estimate the Boolean states, network topology, and measurement parameters from time series of transcriptomic data using exact and approximated (particle) filters, as well as simulate the transcriptomic data for a given Boolean network model. Some of its infrastructure, such as the network interface, is the same as in the previously published R package for Boolean Networks BoolNet, which enhances compatibility and user accessibility to the new package. We introduce the R package BoolFilter for Partially-Observed Boolean Dynamical Systems (POBDS). The BoolFilter package provides a useful toolbox for the bioinformatics community, with state-of-the-art algorithms for simulation of time series transcriptomic data as well as the inverse process of system identification from data obtained with various expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays.

QDENSITY—A Mathematica Quantum Computer simulation

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Burdis, Joseph M.; Tabakin, Frank

2006-06-01

This Mathematica 5.2 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. Selected examples of the basic commands are presented here and a tutorial notebook, Tutorial.nb is provided with the package (available on our website) that serves as a full guide to the package. Finally, application is made to a variety of relevant cases, including Teleportation, Quantum Fourier transform, Grover's search and Shor's algorithm, in separate notebooks: QFT.nb, Teleportation.nb, Grover.nb and Shor.nb where each algorithm is explained in detail. Finally, two examples of the construction and manipulation of cluster states, which are part of "one way computing" ideas, are included as an additional tool in the notebook Cluster.nb. A Mathematica palette containing most commands in QDENSITY is also included: QDENSpalette.nb. Program summaryTitle of program: QDENSITY Catalogue identifier: ADXH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v1_0 Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Operating systems: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4 Programming language used: Mathematica 5.2 No. of bytes in distributed program, including test data, etc.: 180 581 No. of lines in distributed program, including test data, etc.: 19 382 Distribution format: tar.gz Method of solution: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed. QDENSITY is available at http://www.pitt.edu/~tabakin/QDENSITY.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lanier, Nicholas Edward

We have completed implementation of a laser package in LANL's principal AGEX design code, Cassio. Although we have greatly improved our target characterization and uncertainty quantification, we remain unable to satisfactorily simulate the NIF Pleiades data.

Athena X-IFU event reconstruction software: SIRENA

NASA Astrophysics Data System (ADS)

Ceballos, Maria Teresa; Cobo, Beatriz; Peille, Philippe; Wilms, Joern; Brand, Thorsten; Dauser, Thomas; Bandler, Simon; Smith, Stephen

2015-09-01

This contribution describes the status and technical details of the SIRENA package, the software currently in development to perform the on board event energy reconstruction for the Athena calorimeter X-IFU. This on board processing will be done in the X-IFU DRE unit and it will consist in an initial triggering of event pulses followed by an analysis (with the SIRENA package) to determine the energy content of such events.The current algorithm used by SIRENA is the optimal filtering technique (also used by ASTRO-H processor) although some other algorithms are also being tested.Here we present these studies and some preliminary results about the energy resolution of the instrument based on simulations done with the SIXTE simulator (http://www.sternwarte.uni-erlangen.de/research/sixte/) in which SIRENA is integrated.

Strehl-constrained reconstruction of post-adaptive optics data and the Software Package AIRY, v. 6.1

NASA Astrophysics Data System (ADS)

Carbillet, Marcel; La Camera, Andrea; Deguignet, Jérémy; Prato, Marco; Bertero, Mario; Aristidi, Éric; Boccacci, Patrizia

2014-08-01

We first briefly present the last version of the Software Package AIRY, version 6.1, a CAOS-based tool which includes various deconvolution methods, accelerations, regularizations, super-resolution, boundary effects reduction, point-spread function extraction/extrapolation, stopping rules, and constraints in the case of iterative blind deconvolution (IBD). Then, we focus on a new formulation of our Strehl-constrained IBD, here quantitatively compared to the original formulation for simulated near-infrared data of an 8-m class telescope equipped with adaptive optics (AO), showing their equivalence. Next, we extend the application of the original method to the visible domain with simulated data of an AO-equipped 1.5-m telescope, testing also the robustness of the method with respect to the Strehl ratio estimation.

User's manual for Interactive Data Display System (IDDS)

NASA Technical Reports Server (NTRS)

Stegeman, James D.

1992-01-01

A computer graphics package for the visualization of three-dimensional flow in turbomachinery has been developed and tested. This graphics package, called IDDS (Interactive Data Display System), is able to 'unwrap' the volumetric data cone associated with a centrifugal compressor and display the results in an easy to understand two-dimensional manner. IDDS will provide the majority of the visualization and analysis capability for the ICE (Integrated CFD and Experiment) system. This document is intended to serve as a user's manual for IDDS in a stand-alone mode. Currently, IDDS is capable of plotting two- or three-dimensional simulation data, but work is under way to expand IDDS so that experimental data can be accepted, plotted, and compared with a simulation dataset of the actual hardware being tested.

Simulating the dynamics of complex plasmas.

PubMed

Schwabe, M; Graves, D B

2013-08-01

Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively coupled plasma with a fluid code written for the commercial package comsol. The output of this model is used to calculate forces on microparticles. The microparticles are modeled using the molecular dynamics package lammps, which we extended to include the forces from the plasma. Using this method, we are able to reproduce void formation, the separation of particles of different sizes into layers, lane formation, vortex formation, and other effects.

MODFLOW Ground-Water Model - User Guide to the Subsidence and Aquifer-System Compaction Package (SUB-WT) for Water-Table Aquifers

USGS Publications Warehouse

Leake, S.A.; Galloway, D.L.

2007-01-01

A new computer program was developed to simulate vertical compaction in models of regional ground-water flow. The program simulates ground-water storage changes and compaction in discontinuous interbeds or in extensive confining units, accounting for stress-dependent changes in storage properties. The new program is a package for MODFLOW, the U.S. Geological Survey modular finite-difference ground-water flow model. Several features of the program make it useful for application in shallow, unconfined flow systems. Geostatic stress can be treated as a function of water-table elevation, and compaction is a function of computed changes in effective stress at the bottom of a model layer. Thickness of compressible sediments in an unconfined model layer can vary in proportion to saturated thickness.

Implementation of Solute Transport in the Vadose Zone into the `HYDRUS Package for MODFLOW'

NASA Astrophysics Data System (ADS)

Simunek, J.; Beegum, S.; Szymkiewicz, A.; Sudheer, K. P.

2017-12-01

The 'HYDRUS package for MODFLOW' was developed by Seo et al. (2007) and Twarakavi et al. (2008) to simultaneously evaluate transient water flow in both unsaturated and saturated zones. The package, which is based on the HYDRUS-1D model (Šimůnek et al., 2016) simulating unsaturated water flow in the vadose zone, was incorporated into MODFLOW (Harbaugh et al., 2000) simulating saturated groundwater flow. The HYDRUS package in the coupled model can be used to represent the effects of various unsaturated zone processes, including infiltration, evaporation, root water uptake, capillary rise, and recharge in homogeneous or layered soil profiles. The coupled model is effective in addressing spatially-variable saturated-unsaturated hydrological processes at the regional scale, allowing for complex layering in the unsaturated zone, spatially and temporarily variable water fluxes at the soil surface and in the root zone, and with alternating recharge and discharge fluxes (Twarakavi et al., 2008). One of the major limitations of the coupled model was that it could not be used to simulate at the same time solute transport. However, solute transport is highly dependent on water table fluctuations due to temporal and spatial variations in groundwater recharge. This is an important concern when the coupled model is used for analyzing groundwater contamination due to transport through the unsaturated zone. The objective of this study is to integrate the solute transport model (the solute transport part of HYDRUS-1D for the unsaturated zone and MT3DMS (Zheng and Wang, 1999; Zheng, 2009) for the saturated zone) into an existing coupled water flow model. The unsaturated zone component of the coupled model can consider solute transport involving many biogeochemical processes and reactions, including first-order degradation, volatilization, linear or nonlinear sorption, one-site kinetic sorption, two-site sorption, and two-kinetic sites sorption (Šimůnek and van Genuchten, 2008). Due to complex interactions at the groundwater table, certain modifications of the pressure head (compared to the original coupling) and solute concentration profiles were incorporated into the HYDRUS package. The developed integrated model is verified using HYDRUS-2D and analyzed for its computational time requirements.

The FluxCompensator: Making Radiative Transfer Models of Hydrodynamical Simulations Directly Comparable to Real Observations

NASA Astrophysics Data System (ADS)

Koepferl, Christine M.; Robitaille, Thomas P.

2017-11-01

When modeling astronomical objects throughout the universe, it is important to correctly treat the limitations of the data, for instance finite resolution and sensitivity. In order to simulate these effects, and to make radiative transfer models directly comparable to real observations, we have developed an open-source Python package called the FluxCompensator that enables the post-processing of the output of 3D Monte Carlo radiative transfer codes, such as Hyperion. With the FluxCompensator, realistic synthetic observations can be generated by modeling the effects of convolution with arbitrary point-spread functions, transmission curves, finite pixel resolution, noise, and reddening. Pipelines can be applied to compute synthetic observations that simulate observatories, such as the Spitzer Space Telescope or the Herschel Space Observatory. Additionally, this tool can read in existing observations (e.g., FITS format) and use the same settings for the synthetic observations. In this paper, we describe the package as well as present examples of such synthetic observations.

Tough2{_}MP: A parallel version of TOUGH2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Keni; Wu, Yu-Shu; Ding, Chris

2003-04-09

TOUGH2{_}MP is a massively parallel version of TOUGH2. It was developed for running on distributed-memory parallel computers to simulate large simulation problems that may not be solved by the standard, single-CPU TOUGH2 code. The new code implements an efficient massively parallel scheme, while preserving the full capacity and flexibility of the original TOUGH2 code. The new software uses the METIS software package for grid partitioning and AZTEC software package for linear-equation solving. The standard message-passing interface is adopted for communication among processors. Numerical performance of the current version code has been tested on CRAY-T3E and IBM RS/6000 SP platforms. Inmore » addition, the parallel code has been successfully applied to real field problems of multi-million-cell simulations for three-dimensional multiphase and multicomponent fluid and heat flow, as well as solute transport. In this paper, we will review the development of the TOUGH2{_}MP, and discuss the basic features, modules, and their applications.« less

Advanced simulation of mixed-material erosion/evolution and application to low and high-Z containing plasma facing components

NASA Astrophysics Data System (ADS)

Brooks, J. N.; Hassanein, A.; Sizyuk, T.

2013-07-01

Plasma interactions with mixed-material surfaces are being analyzed using advanced modeling of time-dependent surface evolution/erosion. Simulations use the REDEP/WBC erosion/redeposition code package coupled to the HEIGHTS package ITMC-DYN mixed-material formation/response code, with plasma parameter input from codes and data. We report here on analysis for a DIII-D Mo/C containing tokamak divertor. A DIII-D/DiMES probe experiment simulation predicts that sputtered molybdenum from a 1 cm diameter central spot quickly saturates (˜4 s) in the 5 cm diameter surrounding carbon probe surface, with subsequent re-sputtering and transport to off-probe divertor regions, and with high (˜50%) redeposition on the Mo spot. Predicted Mo content in the carbon agrees well with post-exposure probe data. We discuss implications and mixed-material analysis issues for Be/W mixing at the ITER outer divertor, and Li, C, Mo mixing at an NSTX divertor.

Migration of fluorochemical paper additives from food-contact paper into foods and food simulants.

PubMed

Begley, T H; Hsu, W; Noonan, G; Diachenko, G

2008-03-01

Fluorochemical-treated paper was tested to determine the amount of migration that occurs into foods and food-simulating liquids and the characteristics of the migration. Migration characteristics of fluorochemicals from paper were examined in Miglyol, butter, water, vinegar, water-ethanol solutions, emulsions and pure oil containing small amounts of emulsifiers. Additionally, microwave popcorn and chocolate spread were used to investigate migration. Results indicate that fluorochemicals paper additives do migrate to food during actual package use. For example, we found that microwave popcorn contained 3.2 fluorochemical mg kg(-1) popcorn after popping and butter contained 0.1 mg kg(-1) after 40 days at 4 degrees C. Tests also indicate that common food-simulating liquids for migration testing and package material evaluation might not provide an accurate indication of the amount of fluorochemical that actually migrates to food. Tests show that oil containing small amounts of an emulsifier can significantly enhance migration of a fluorochemical from paper.

Efficient Calculation of Exact Exchange Within the Quantum Espresso Software Package

NASA Astrophysics Data System (ADS)

Barnes, Taylor; Kurth, Thorsten; Carrier, Pierre; Wichmann, Nathan; Prendergast, David; Kent, Paul; Deslippe, Jack

Accurate simulation of condensed matter at the nanoscale requires careful treatment of the exchange interaction between electrons. In the context of plane-wave DFT, these interactions are typically represented through the use of approximate functionals. Greater accuracy can often be obtained through the use of functionals that incorporate some fraction of exact exchange; however, evaluation of the exact exchange potential is often prohibitively expensive. We present an improved algorithm for the parallel computation of exact exchange in Quantum Espresso, an open-source software package for plane-wave DFT simulation. Through the use of aggressive load balancing and on-the-fly transformation of internal data structures, our code exhibits speedups of approximately an order of magnitude for practical calculations. Additional optimizations are presented targeting the many-core Intel Xeon-Phi ``Knights Landing'' architecture, which largely powers NERSC's new Cori system. We demonstrate the successful application of the code to difficult problems, including simulation of water at a platinum interface and computation of the X-ray absorption spectra of transition metal oxides.

ProtPOS: a python package for the prediction of protein preferred orientation on a surface.

PubMed

Ngai, Jimmy C F; Mak, Pui-In; Siu, Shirley W I

2016-08-15

Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein-surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined. Here, we present ProtPOS which is a lightweight and easy-to-use python package that can predict low-energy protein orientations on a surface of interest. It combines a fast conformational sampling algorithm with the energy calculation of GROMACS. The advantage of ProtPOS is it allows users to select any force fields suitable for the system at hand and provide structural output readily available for further simulation studies. ProtPOS is freely available for academic and non-profit uses at http://cbbio.cis.umac.mo/software/protpos Supplementary data are available at Bioinformatics online. shirleysiu@umac.mo. © The Author 2016. Published by Oxford University Press.

The FluxCompensator: Making Radiative Transfer Models of Hydrodynamical Simulations Directly Comparable to Real Observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koepferl, Christine M.; Robitaille, Thomas P., E-mail: koepferl@usm.lmu.de

When modeling astronomical objects throughout the universe, it is important to correctly treat the limitations of the data, for instance finite resolution and sensitivity. In order to simulate these effects, and to make radiative transfer models directly comparable to real observations, we have developed an open-source Python package called the FluxCompensator that enables the post-processing of the output of 3D Monte Carlo radiative transfer codes, such as Hyperion. With the FluxCompensator, realistic synthetic observations can be generated by modeling the effects of convolution with arbitrary point-spread functions, transmission curves, finite pixel resolution, noise, and reddening. Pipelines can be applied tomore » compute synthetic observations that simulate observatories, such as the Spitzer Space Telescope or the Herschel Space Observatory . Additionally, this tool can read in existing observations (e.g., FITS format) and use the same settings for the synthetic observations. In this paper, we describe the package as well as present examples of such synthetic observations.« less

Evaluation of Endocrine Disrupting Compounds Migration in Household Food Containers under Domestic Use Conditions.

PubMed

Sáiz, Jorge; Gómara, Belén

2017-08-09

Plasticizers and plastic monomers are commonly used in packaging. Most of them act as endocrine disrupters and are susceptible to migrate from the packaging to the food. We evaluated the migration of endocrine disrupting compounds from three different household food containers to four food simulants under different domestic treatments and for different periods of time, with the aim of reproducing real domestic conditions. The results showed that the migration to the simulants increased with the storage time, up to more than 50 times in certain cases. The heating power seemed to increase the migration processes (up to more than 30 times), and reusing containers produced an increase or decrease of the concentrations depending on the container type and the simulant. The concentrations found were lower than other concentrations reported (always less than 4000 pg/mL, down to less than 20 pg/mL), which might be a consequence of the domestic conditions used.

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

PubMed

Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

2011-07-30

MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

ProtPOS: a python package for the prediction of protein preferred orientation on a surface

PubMed Central

Ngai, Jimmy C. F.; Mak, Pui-In; Siu, Shirley W. I.

2016-01-01

Summary: Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein–surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined. Here, we present ProtPOS which is a lightweight and easy-to-use python package that can predict low-energy protein orientations on a surface of interest. It combines a fast conformational sampling algorithm with the energy calculation of GROMACS. The advantage of ProtPOS is it allows users to select any force fields suitable for the system at hand and provide structural output readily available for further simulation studies. Availability and Implementation: ProtPOS is freely available for academic and non-profit uses at http://cbbio.cis.umac.mo/software/protpos Supplementary information: Supplementary data are available at Bioinformatics online. Contact: shirleysiu@umac.mo PMID:27153619

The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory

NASA Astrophysics Data System (ADS)

Lourderaj, Upakarasamy; Sun, Rui; Kohale, Swapnil C.; Barnes, George L.; de Jong, Wibe A.; Windus, Theresa L.; Hase, William L.

2014-03-01

The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling since the two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface that accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized.

OWL: A scalable Monte Carlo simulation suite for finite-temperature study of materials

NASA Astrophysics Data System (ADS)

Li, Ying Wai; Yuk, Simuck F.; Cooper, Valentino R.; Eisenbach, Markus; Odbadrakh, Khorgolkhuu

The OWL suite is a simulation package for performing large-scale Monte Carlo simulations. Its object-oriented, modular design enables it to interface with various external packages for energy evaluations. It is therefore applicable to study the finite-temperature properties for a wide range of systems: from simple classical spin models to materials where the energy is evaluated by ab initio methods. This scheme not only allows for the study of thermodynamic properties based on first-principles statistical mechanics, it also provides a means for massive, multi-level parallelism to fully exploit the capacity of modern heterogeneous computer architectures. We will demonstrate how improved strong and weak scaling is achieved by employing novel, parallel and scalable Monte Carlo algorithms, as well as the applications of OWL to a few selected frontier materials research problems. This research was supported by the Office of Science of the Department of Energy under contract DE-AC05-00OR22725.

Active food packaging based on molecularly imprinted polymers: study of the release kinetics of ferulic acid.

PubMed

Otero-Pazos, Pablo; Rodríguez-Bernaldo de Quirós, Ana; Sendón, Raquel; Benito-Peña, Elena; González-Vallejo, Victoria; Moreno-Bondi, M Cruz; Angulo, Immaculada; Paseiro-Losada, Perfecto

2014-11-19

A novel active packaging based on molecularly imprinted polymer (MIP) was developed for the controlled release of ferulic acid. The release kinetics of ferulic acid from the active system to food simulants (10, 20, and 50% ethanol (v/v), 3% acetic acid (w/v), and vegetable oil), substitutes (95% ethanol (v/v) and isooctane), and real food samples at different temperatures were studied. The key parameters of the diffusion process were calculated by using a mathematical modeling based on Fick's second law. The ferulic acid release was affected by the temperature as well as the percentage of ethanol of the simulant. The fastest release occurred in 95% ethanol (v/v) at 20 °C. The diffusion coefficients (D) obtained ranged between 1.8 × 10(-11) and 4.2 × 10(-9) cm(2)/s. A very good correlation between experimental and estimated data was obtained, and consequently the model could be used to predict the release of ferulic acid into food simulants and real food samples.

MySSP: Non-stationary evolutionary sequence simulation, including indels

PubMed Central

Rosenberg, Michael S.

2007-01-01

MySSP is a new program for the simulation of DNA sequence evolution across a phylogenetic tree. Although many programs are available for sequence simulation, MySSP is unique in its inclusion of indels, flexibility in allowing for non-stationary patterns, and output of ancestral sequences. Some of these features can individually be found in existing programs, but have not all have been previously available in a single package. PMID:19325855

Simulation-based intelligent robotic agent for Space Station Freedom

NASA Technical Reports Server (NTRS)

Biegl, Csaba A.; Springfield, James F.; Cook, George E.; Fernandez, Kenneth R.

1990-01-01

A robot control package is described which utilizes on-line structural simulation of robot manipulators and objects in their workspace. The model-based controller is interfaced with a high level agent-independent planner, which is responsible for the task-level planning of the robot's actions. Commands received from the agent-independent planner are refined and executed in the simulated workspace, and upon successful completion, they are transferred to the real manipulators.

Spontaneous Buckling of Lipid Bilayer and Vesicle Budding Induced by Antimicrobial Peptide Magainin 2: A Coarse-Grained Simulation Study

DTIC Science & Technology

2011-05-30

were added to neutralize each system. The GROMACS software package39 was used for simulations. The molecules in this paper refer to the CGMARTINI...accelerated.19 Most of the peptides on the surfaces ended up in clusters containing transmembrane pores, which appeared to perturb the bilayers significantly

Multidimensional computer simulation of Stirling cycle engines

NASA Technical Reports Server (NTRS)

Hall, Charles A.; Porsching, Thomas A.

1992-01-01

This report summarizes the activities performed under NASA-Grant NAG3-1097 during 1991. During that period, work centered on the following tasks: (1) to investigate more effective solvers for ALGAE; (2) to modify the plotting package for ALGAE; and (3) to validate ALGAE by simulating oscillating flow problems similar to those studied by Kurzweg and Ibrahim.

Employ Simulation Techniques. Second Edition. Module C-5 of Category C--Instructional Execution. Professional Teacher Education Module Series.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus. National Center for Research in Vocational Education.

One of a series of performance-based teacher education learning packages focusing upon specific professional competencies of vocational teachers, this learning module deals with employing simulation techniques. It consists of an introduction and four learning experiences. Covered in the first learning experience are various types of simulation…

Aerodynamic improvement of the assembly through which gas conduits are taken into a smoke stack by simulating gas flow on a computer

NASA Astrophysics Data System (ADS)

Prokhorov, V. B.; Fomenko, M. V.; Grigor'ev, I. V.

2012-06-01

Results from computer simulation of gas flow motion for gas conduits taken on one and two sides into the gas-removal shaft of a smoke stack with a constant cross section carried out using the SolidWorks and FlowVision application software packages are presented.

Simulation: The Effects of Simulation on High Stakes Testing in Undergradute Nursing Education

ERIC Educational Resources Information Center

Walters, Linda

2014-01-01

Many nursing programs use standardized testing packages in order to evaluate students' content mastery as well as predict probability of passing the National Council Licensure for Registered Nurses (NCLEX-RN). Instead of a diagnosis for weak content areas, programs implement testing policies in the belief that such policies ensure student success…

Documentation of a computer program to simulate lake-aquifer interaction using the MODFLOW ground water flow model and the MOC3D solute-transport model

USGS Publications Warehouse

Merritt, Michael L.; Konikow, Leonard F.

2000-01-01

Heads and flow patterns in surficial aquifers can be strongly influenced by the presence of stationary surface-water bodies (lakes) that are in direct contact, vertically and laterally, with the aquifer. Conversely, lake stages can be significantly affected by the volume of water that seeps through the lakebed that separates the lake from the aquifer. For these reasons, a set of computer subroutines called the Lake Package (LAK3) was developed to represent lake/aquifer interaction in numerical simulations using the U.S. Geological Survey three-dimensional, finite-difference, modular ground-water flow model MODFLOW and the U.S. Geological Survey three-dimensional method-of-characteristics solute-transport model MOC3D. In the Lake Package described in this report, a lake is represented as a volume of space within the model grid which consists of inactive cells extending downward from the upper surface of the grid. Active model grid cells bordering this space, representing the adjacent aquifer, exchange water with the lake at a rate determined by the relative heads and by conductances that are based on grid cell dimensions, hydraulic conductivities of the aquifer material, and user-specified leakance distributions that represent the resistance to flow through the material of the lakebed. Parts of the lake may become ?dry? as upper layers of the model are dewatered, with a concomitant reduction in lake surface area, and may subsequently rewet when aquifer heads rise. An empirical approximation has been encoded to simulate the rewetting of a lake that becomes completely dry. The variations of lake stages are determined by independent water budgets computed for each lake in the model grid. This lake budget process makes the package a simulator of the response of lake stage to hydraulic stresses applied to the aquifer. Implementation of a lake water budget requires input of parameters including those representing the rate of lake atmospheric recharge and evaporation, overland runoff, and the rate of any direct withdrawal from, or augmentation of, the lake volume. The lake/aquifer interaction may be simulated in both transient and steady-state flow conditions, and the user may specify that lake stages be computed explicitly, semi-implicitly, or fully-implicitly in transient simulations. The lakes, and all sources of water entering the lakes, may have solute concentrations associated with them for use in solute-transport simulations using MOC3D. The Stream Package of MODFLOW-2000 and MOC3D represents stream connections to lakes, either as inflows or outflows. Because lakes with irregular bathymetry can exist as separate pools of water at lower stages, that coalesce to become a single body of water at higher stages, logic was added to the Lake Package to allow the representation of this process as a user option. If this option is selected, a system of linked pools (sublakes) is identified in each time step and stages are equalized based on current relative sublake surface areas.

Dr.LiTHO: a development and research lithography simulator

NASA Astrophysics Data System (ADS)

Fühner, Tim; Schnattinger, Thomas; Ardelean, Gheorghe; Erdmann, Andreas

2007-03-01

This paper introduces Dr.LiTHO, a research and development oriented lithography simulation environment developed at Fraunhofer IISB to flexibly integrate our simulation models into one coherent platform. We propose a light-weight approach to a lithography simulation environment: The use of a scripting (batch) language as an integration platform. Out of the great variety of different scripting languages, Python proved superior in many ways: It exhibits a good-natured learning-curve, it is efficient, available on virtually any platform, and provides sophisticated integration mechanisms for existing programs. In this paper, we will describe the steps, required to provide Python bindings for existing programs and to finally generate an integrated simulation environment. In addition, we will give a short introduction into selected software design demands associated with the development of such a framework. We will especially focus on testing and (both technical and user-oriented) documentation issues. Dr.LiTHO Python files contain not only all simulation parameter settings but also the simulation flow, providing maximum flexibility. In addition to relatively simple batch jobs, repetitive tasks can be pooled in libraries. And as Python is a full-blown programming language, users can add virtually any functionality, which is especially useful in the scope of simulation studies or optimization tasks, that often require masses of evaluations. Furthermore, we will give a short overview of the numerous existing Python packages. Several examples demonstrate the feasibility and productiveness of integrating Python packages into custom Dr.LiTHO scripts.

HydroApps: An R package for statistical simulation to use in regional analysis

NASA Astrophysics Data System (ADS)

Ganora, D.

2013-12-01

The HydroApps package is a newborn R extension initially developed to support the use of a recent model for flood frequency estimation developed for applications in Northwestern Italy; it also contains some general tools for regional analyses and can be easily extended to include other statistical models. The package is currently at an experimental level of development. The HydroApps is a corollary of the SSEM project for regional flood frequency analysis, although it was developed independently to support various instances of regional analyses. Its aim is to provide a basis for interplay between statistical simulation and practical operational use. In particular, the main module of the package deals with the building of the confidence bands of flood frequency curves expressed by means of their L-moments. Other functions include pre-processing and visualization of hydrologic time series, analysis of the optimal design-flood under uncertainty, but also tools useful in water resources management for the estimation of flow duration curves and their sensitivity to water withdrawals. Particular attention is devoted to the code granularity, i.e. the level of detail and aggregation of the code: a greater detail means more low-level functions, which entails more flexibility but reduces the ease of use for practical use. A balance between detail and simplicity is necessary and can be resolved with appropriate wrapping functions and specific help pages for each working block. From a more general viewpoint, the package has not really and user-friendly interface, but runs on multiple operating systems and it's easy to update, as many other open-source projects., The HydroApps functions and their features are reported in order to share ideas and materials to improve the ';technological' and information transfer between scientist communities and final users like policy makers.

Program Package for 3d PIC Model of Plasma Fiber

NASA Astrophysics Data System (ADS)

Kulhánek, Petr; Břeň, David

2007-08-01

A fully three dimensional Particle in Cell model of the plasma fiber had been developed. The code is written in FORTRAN 95, implementation CVF (Compaq Visual Fortran) under Microsoft Visual Studio user interface. Five particle solvers and two field solvers are included in the model. The solvers have relativistic and non-relativistic variants. The model can deal both with periodical and non-periodical boundary conditions. The mechanism of the surface turbulences generation in the plasma fiber was successfully simulated with the PIC program package.

User's manual for the two-dimensional transputer graphics toolkit

NASA Technical Reports Server (NTRS)

Ellis, Graham K.

1988-01-01

The user manual for the 2-D graphics toolkit for a transputer based parallel processor is presented. The toolkit consists of a package of 2-D display routines that can be used for the simulation visualizations. It supports multiple windows, double buffered screens for animations, and simple graphics transformations such as translation, rotation, and scaling. The display routines are written in occam to take advantage of the multiprocessing features available on transputers. The package is designed to run on a transputer separate from the graphics board.

Modeling Impact-induced Failure of Polysilicon MEMS: A Multi-scale Approach.

PubMed

Mariani, Stefano; Ghisi, Aldo; Corigliano, Alberto; Zerbini, Sarah

2009-01-01

Failure of packaged polysilicon micro-electro-mechanical systems (MEMS) subjected to impacts involves phenomena occurring at several length-scales. In this paper we present a multi-scale finite element approach to properly allow for: (i) the propagation of stress waves inside the package; (ii) the dynamics of the whole MEMS; (iii) the spreading of micro-cracking in the failing part(s) of the sensor. Through Monte Carlo simulations, some effects of polysilicon micro-structure on the failure mode are elucidated.

A CAD approach to magnetic bearing design

NASA Technical Reports Server (NTRS)

Jeyaseelan, M.; Anand, D. K.; Kirk, J. A.

1988-01-01

A design methodology has been developed at the Magnetic Bearing Research Laboratory for designing magnetic bearings using a CAD approach. This is used in the algorithm of an interactive design software package. The package is a design tool developed to enable the designer to simulate the entire process of design and analysis of the system. Its capabilities include interactive input/modification of geometry, finding any possible saturation at critical sections of the system, and the design and analysis of a control system that stabilizes and maintains magnetic suspension.

SIMULATED COAL GAS MCFC POWER PLANT SYSTEM VERIFICATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

J.A. Scroppo

1998-07-01

This is the Technical Progress Report covering June 1998. All tasks have been completed, except for those discussed on the following pages. Unocal estimated the costs of dismantling and packaging the test facility for storage and shipment. The scope of work for the contract has been modified to accommodate the dismantling and packaging of the plant. An amendment to Sub-Contract No. MCP-9-UNO between M-C Power and Unocal has been executed which includes the Scope of Work in Unocal's cost estimate.

SIMULATED COAL GAS MCFC POWER PLANT SYSTEM VERIFICATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-10-31

This is the Technical Progress Report covering October 1998. All tasks have been completed, except for those discussed on the following pages. Unocal estimated the costs of dismantling and packaging the test facility for storage and shipment. The scope of work for the contract has been modified to accommodate the dismantling and packaging of the plant. An amendment to Sub-Contract No. MCP-9-UNO between M-C Power and Unocal has been executed which includes the Scope of Work in Unocal's cost estimate.

A comprehensive approach for the determination of extractable and leachable metals in pharmaceutical products by inductively-coupled plasma.

PubMed

Zuccarello, Daniel J; Murphy, Michael P; Meyer, Richard F; Winslow, Paul A

2009-01-01

A comprehensive digestive approach for determining the extractable and leachable metals in pharmaceutical products by inductively-coupled plasma is investigated. This study examines several acid digestion strategies for packaging materials, containers, and formulated products for complete trace metals analysis. Packaging materials, a food product, and a simulated drug product are evaluated for leachable metals by stressing the materials under accelerated stability conditions. Trace metal profiles of 64 elements for these materials are reported.

Phosphor chessboard packaging for white LEDs in high efficiency and high color performance

NASA Astrophysics Data System (ADS)

Nguyen, Quang-Khoi; Chang, Yu-Yu; Lu, Chun-Yan; Yang, Tsung-Hsun; Chung, Te-Yuan; Sun, Ching-Cherng

2016-09-01

We performed the simulation of white LEDs packaging with different chessboard structures of white light converting phosphor layer covered on GaN die chip. Three different types of chessboard structures are called type 1, type 2 and type 3, respectively. The result of investigation according to the phosphor thickness show the increasing of thickness of phosphor layer are, the decreasing of output blue light power are. Meanwhile, the changes of yellow light are neglect. Type 3 shows highest packaging efficiency of 74.3 % compares with packaging efficiency of type 2 and type 1 (72.5 % and 71.3 %, respectively). Type 3 also shows the most effect of forward light. Attention that the type 3 chessboard structure gets packaging efficiency of 74.3 % at color temperature of daylight as well as high saving of phosphor amount. The color temperatures of three types of chessboard structure are higher than 5000 K, so they are suitable for lighting purpose. The angular correlate color temperature deviation (ACCTD) of type 1, type 2 and type 3 are 6500K, 11500K and 17000K, respectively.

Documentation for the State Variables Package for the Groundwater-Management Process of MODFLOW-2005 (GWM-2005)

USGS Publications Warehouse

Ahlfeld, David P.; Barlow, Paul M.; Baker, Kristine M.

2011-01-01

Many groundwater-management problems are concerned with the control of one or more variables that reflect the state of a groundwater-flow system or a coupled groundwater/surface-water system. These system state variables include the distribution of heads within an aquifer, streamflow rates within a hydraulically connected stream, and flow rates into or out of aquifer storage. This report documents the new State Variables Package for the Groundwater-Management Process of MODFLOW-2005 (GWM-2005). The new package provides a means to explicitly represent heads, streamflows, and changes in aquifer storage as state variables in a GWM-2005 simulation. The availability of these state variables makes it possible to include system state in the objective function and enhances existing capabilities for constructing constraint sets for a groundwater-management formulation. The new package can be used to address groundwater-management problems such as the determination of withdrawal strategies that meet water-supply demands while simultaneously maximizing heads or streamflows, or minimizing changes in aquifer storage. Four sample problems are provided to demonstrate use of the new package for typical groundwater-management applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Edwin S.

Under the CRADA, NREL will provide assistance to NRGsim to debug and convert the EnergyPlus Hysteresis Phase Change Material ('PCM') model to C++ for adoption into the main code package of the EnergyPlus simulation engine.

Detailed design package for design of a video system providing optimal visual information for controlling payload and experiment operations with television

NASA Technical Reports Server (NTRS)

1975-01-01

A detailed description of a video system for controlling space shuttle payloads and experiments is presented in the preliminary design review and critical design review, first and second engineering design reports respectively, and in the final report submitted jointly with the design package. The material contained in the four subsequent sections of the package contains system descriptions, design data, and specifications for the recommended 2-view system. Section 2 contains diagrams relating to the simulation test configuration of the 2-view system. Section 3 contains descriptions and drawings of the deliverable breadboard equipment. A description of the recommended system is contained in Section 4 with equipment specifications in Section 5.

Polymeric Packaging for Fully Implantable Wireless Neural Microsensors

PubMed Central

Aceros, Juan; Yin, Ming; Borton, David A.; Patterson, William R.; Bull, Christopher; Nurmikko, Arto V.

2014-01-01

We present polymeric packaging methods used for subcutaneous, fully implantable, broadband, and wireless neurosensors. A new tool for accelerated testing and characterization of biocompatible polymeric packaging materials and processes is described along with specialized test units to simulate our fully implantable neurosensor components, materials and fabrication processes. A brief description of the implantable systems is presented along with their current encapsulation methods based on polydimethylsiloxane (PDMS). Results from in-vivo testing of multiple implanted neurosensors in swine and non-human primates are presented. Finally, a novel augmenting polymer thin film material to complement the currently employed PDMS is introduced. This thin layer coating material is based on the Plasma Enhanced Chemical Vapor Deposition (PECVD) process of Hexamethyldisiloxane (HMDSO) and Oxygen (O2). PMID:23365999

Satellite Data Simulator Unit: A Multisensor, Multispectral Satellite Simulator Package

NASA Technical Reports Server (NTRS)

Masunaga, Hirohiko; Matsui, Toshihisa; Tao, Wei-Kuo; Hou, Arthur Y.; Kummerow, Christian D.; Nakajima, Teruyuki; Bauer, Peter; Olson, William S.; Sekiguchi, Miho; Nakajima, Teruyuki

2010-01-01

Several multisensor simulator packages are being developed by different research groups across the world. Such simulator packages [e.g., COSP , CRTM, ECSIM, RTTO, ISSARS (under development), and SDSU (this article), among others] share overall aims, although some are targeted more on particular satellite programs or specific applications (for research purposes or for operational use) than others. The SDSU or Satellite Data Simulator Unit is a general-purpose simulator composed of Fortran 90 codes and applicable to spaceborne microwave radiometer, radar, and visible/infrared imagers including, but not limited to, the sensors listed in a table. That shows satellite programs particularly suitable for multisensor data analysis: some are single satellite missions carrying two or more instruments, while others are constellations of satellites flying in formation. The TRMM and A-Train are ongoing satellite missions carrying diverse sensors that observe clouds and precipitation, and will be continued or augmented within the decade to come by future multisensor missions such as the GPM and Earth-CARE. The ultimate goals of these present and proposed satellite programs are not restricted to clouds and precipitation but are to better understand their interactions with atmospheric dynamics/chemistry and feedback to climate. The SDSU's applicability is not technically limited to hydrometeor measurements either, but may be extended to air temperature and humidity observations by tuning the SDSU to sounding channels. As such, the SDSU and other multisensor simulators would potentially contribute to a broad area of climate and atmospheric sciences. The SDSU is not optimized to any particular orbital geometry of satellites. The SDSU is applicable not only to low-Earth orbiting platforms as listed in Table 1, but also to geostationary meteorological satellites. Although no geosynchronous satellite carries microwave instruments at present or in the near future, the SDSU would be useful for future geostationary satellites with a microwave radiometer and/or a radar aboard, which could become more feasible as engineering challenges are met. In this short article, the SDSU algorithm architecture and potential applications are reviewed in brief.

Evaluating variability and uncertainty separately in microbial quantitative risk assessment using two R packages.

PubMed

Pouillot, Régis; Delignette-Muller, Marie Laure

2010-09-01

Quantitative risk assessment has emerged as a valuable tool to enhance the scientific basis of regulatory decisions in the food safety domain. This article introduces the use of two new computing resources (R packages) specifically developed to help risk assessors in their projects. The first package, "fitdistrplus", gathers tools for choosing and fitting a parametric univariate distribution to a given dataset. The data may be continuous or discrete. Continuous data may be right-, left- or interval-censored as is frequently obtained with analytical methods, with the possibility of various censoring thresholds within the dataset. Bootstrap procedures then allow the assessor to evaluate and model the uncertainty around the parameters and to transfer this information into a quantitative risk assessment model. The second package, "mc2d", helps to build and study two dimensional (or second-order) Monte-Carlo simulations in which the estimation of variability and uncertainty in the risk estimates is separated. This package easily allows the transfer of separated variability and uncertainty along a chain of conditional mathematical and probabilistic models. The usefulness of these packages is illustrated through a risk assessment of hemolytic and uremic syndrome in children linked to the presence of Escherichia coli O157:H7 in ground beef. These R packages are freely available at the Comprehensive R Archive Network (cran.r-project.org). Copyright 2010 Elsevier B.V. All rights reserved.

Automated simulation as part of a design workstation

NASA Technical Reports Server (NTRS)

Cantwell, E.; Shenk, T.; Robinson, P.; Upadhye, R.

1990-01-01

A development project for a design workstation for advanced life-support systems incorporating qualitative simulation, required the implementation of a useful qualitative simulation capability and the integration of qualitative and quantitative simulations, such that simulation capabilities are maximized without duplication. The reason is that to produce design solutions to a system goal, the behavior of the system in both a steady and perturbed state must be represented. The paper reports on the Qualitative Simulation Tool (QST), on an expert-system-like model building and simulation interface toll called ScratchPad (SP), and on the integration of QST and SP with more conventional, commercially available simulation packages now being applied in the evaluation of life-support system processes and components.

The ATLAS Simulation Infrastructure

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2010-09-25

The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, andmore » the validation of the simulated output against known physics processes.« less

Fast parametric relationships for the large-scale reservoir simulation of mixed CH 4-CO 2 gas hydrate systems

DOE PAGES

Reagan, Matthew T.; Moridis, George J.; Seim, Katie S.

2017-03-27

A recent Department of Energy field test on the Alaska North Slope has increased interest in the ability to simulate systems of mixed CO 2-CH 4 hydrates. However, the physically realistic simulation of mixed-hydrate simulation is not yet a fully solved problem. Limited quantitative laboratory data leads to the use of various ab initio, statistical mechanical, or other mathematic representations of mixed-hydrate phase behavior. Few of these methods are suitable for inclusion in reservoir simulations, particularly for systems with large number of grid elements, 3D systems, or systems with complex geometric configurations. In this paper, we present a set ofmore » fast parametric relationships describing the thermodynamic properties and phase behavior of a mixed methane-carbon dioxide hydrate system. We use well-known, off-the-shelf hydrate physical properties packages to generate a sufficiently large dataset, select the most convenient and efficient mathematical forms, and fit the data to those forms to create a physical properties package suitable for inclusion in the TOUGH+ family of codes. Finally, the mapping of the phase and thermodynamic space reveals the complexity of the mixed-hydrate system and allows understanding of the thermodynamics at a level beyond what much of the existing laboratory data and literature currently offer.« less

Fast parametric relationships for the large-scale reservoir simulation of mixed CH4-CO2 gas hydrate systems

NASA Astrophysics Data System (ADS)

Reagan, Matthew T.; Moridis, George J.; Seim, Katie S.

2017-06-01

A recent Department of Energy field test on the Alaska North Slope has increased interest in the ability to simulate systems of mixed CO2-CH4 hydrates. However, the physically realistic simulation of mixed-hydrate simulation is not yet a fully solved problem. Limited quantitative laboratory data leads to the use of various ab initio, statistical mechanical, or other mathematic representations of mixed-hydrate phase behavior. Few of these methods are suitable for inclusion in reservoir simulations, particularly for systems with large number of grid elements, 3D systems, or systems with complex geometric configurations. In this work, we present a set of fast parametric relationships describing the thermodynamic properties and phase behavior of a mixed methane-carbon dioxide hydrate system. We use well-known, off-the-shelf hydrate physical properties packages to generate a sufficiently large dataset, select the most convenient and efficient mathematical forms, and fit the data to those forms to create a physical properties package suitable for inclusion in the TOUGH+ family of codes. The mapping of the phase and thermodynamic space reveals the complexity of the mixed-hydrate system and allows understanding of the thermodynamics at a level beyond what much of the existing laboratory data and literature currently offer.

Extended asymmetric hot region formation due to shockwave interactions following void collapse in shocked high explosive

DOE PAGES

Shan, Tzu -Ray; Wixom, Ryan R.; Thompson, Aidan P.

2016-08-01

In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed bymore » coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. Furthermore, the formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.« less

MASTOS: Mammography Simulation Tool for design Optimization Studies.

PubMed

Spyrou, G; Panayiotakis, G; Tzanakos, G

2000-01-01

Mammography is a high quality imaging technique for the detection of breast lesions, which requires dedicated equipment and optimum operation. The design parameters of a mammography unit have to be decided and evaluated before the construction of such a high cost of apparatus. The optimum operational parameters also must be defined well before the real breast examination. MASTOS is a software package, based on Monte Carlo methods, that is designed to be used as a simulation tool in mammography. The input consists of the parameters that have to be specified when using a mammography unit, and also the parameters specifying the shape and composition of the breast phantom. In addition, the input may specify parameters needed in the design of a new mammographic apparatus. The main output of the simulation is a mammographic image and calculations of various factors that describe the image quality. The Monte Carlo simulation code is PC-based and is driven by an outer shell of a graphical user interface. The entire software package is a simulation tool for mammography and can be applied in basic research and/or in training in the fields of medical physics and biomedical engineering as well as in the performance evaluation of new designs of mammography units and in the determination of optimum standards for the operational parameters of a mammography unit.

Extended asymmetric hot region formation due to shockwave interactions following void collapse in shocked high explosive

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shan, Tzu -Ray; Wixom, Ryan R.; Thompson, Aidan P.

In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed bymore » coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. Furthermore, the formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.« less

Fast parametric relationships for the large-scale reservoir simulation of mixed CH 4-CO 2 gas hydrate systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reagan, Matthew T.; Moridis, George J.; Seim, Katie S.

A recent Department of Energy field test on the Alaska North Slope has increased interest in the ability to simulate systems of mixed CO 2-CH 4 hydrates. However, the physically realistic simulation of mixed-hydrate simulation is not yet a fully solved problem. Limited quantitative laboratory data leads to the use of various ab initio, statistical mechanical, or other mathematic representations of mixed-hydrate phase behavior. Few of these methods are suitable for inclusion in reservoir simulations, particularly for systems with large number of grid elements, 3D systems, or systems with complex geometric configurations. In this paper, we present a set ofmore » fast parametric relationships describing the thermodynamic properties and phase behavior of a mixed methane-carbon dioxide hydrate system. We use well-known, off-the-shelf hydrate physical properties packages to generate a sufficiently large dataset, select the most convenient and efficient mathematical forms, and fit the data to those forms to create a physical properties package suitable for inclusion in the TOUGH+ family of codes. Finally, the mapping of the phase and thermodynamic space reveals the complexity of the mixed-hydrate system and allows understanding of the thermodynamics at a level beyond what much of the existing laboratory data and literature currently offer.« less

Reverse logistics system planning for recycling computers hardware: A case study

NASA Astrophysics Data System (ADS)

Januri, Siti Sarah; Zulkipli, Faridah; Zahari, Siti Meriam; Shamsuri, Siti Hajar

2014-09-01

This paper describes modeling and simulation of reverse logistics networks for collection of used computers in one of the company in Selangor. The study focuses on design of reverse logistics network for used computers recycling operation. Simulation modeling, presented in this work allows the user to analyze the future performance of the network and to understand the complex relationship between the parties involved. The findings from the simulation suggest that the model calculates processing time and resource utilization in a predictable manner. In this study, the simulation model was developed by using Arena simulation package.

Assessing Jail Inmates’ Proneness to Shame and Guilt: Feeling Bad About the Behavior or the Self?

PubMed Central

Tangney, June P.; Stuewig, Jeffrey; Mashek, Debra; Hastings, Mark

2011-01-01

This study of 550 jail inmates (379 male and 171 female) held on felony charges examines the reliability and validity of the Test of Self Conscious Affect –Socially Deviant Version (TOSCA-SD; Hanson & Tangney, 1996) as a measure of offenders’ proneness to shame and proneness to guilt. Discriminant validity (e.g., vis-à-vis self-esteem, negative affect, social desirability/impression management) and convergent validity (e.g., vis-à-vis correlations with empathy, externalization of blame, anger, psychological symptoms, and substance use problems) was supported, paralleling results from community samples. Further, proneness to shame and guilt were differentially related to widely used risk measures from the field of criminal justice (e.g., criminal history, psychopathy, violence risk, antisocial personality). Guilt-proneness appears to be a protective factor, whereas there was no evidence that shame-proneness serves an inhibitory function. Subsequent analyses indicate these findings generalize quite well across gender and race. Implications for intervention and sentencing practices are discussed. PMID:21743757

Measurement of the para-hydrogen concentration in the ISIS moderators using neutron transmission and thermal conductivity

NASA Astrophysics Data System (ADS)

Romanelli, Giovanni; Rudić, Svemir; Zanetti, Matteo; Andreani, Carla; Fernandez-Alonso, Felix; Gorini, Giuseppe; Krzystyniak, Maciej; Škoro, Goran

2018-04-01

We present an experimental study to determine the para-hydrogen concentration in the hydrogen moderators at the ISIS pulsed neutron and muon source. The experimental characterisation is based on neutron transmission experiments performed on the VESUVIO spectrometer, and thermal conductivity measurements using the TOSCA para-hydrogen rig. A reliable estimation of the level of para-hydrogen concentration in the hydrogen moderators is of crucial importance in the framework of a current project to completely refurbish the first target station at ISIS. Moreover, we report a new measurement of the total neutron cross section for normal hydrogen at 15 K on the broad energy range 3 meV -10 eV suggesting a revision of the most recent nuclear libraries for incident neutron energies lower than 10 meV. Finally, we characterise systematic errors affecting the para-hydrogen level estimation due to conversion from para to ortho hydrogen, as a function of the time a batch of gas spends in every component of our gas panel and apparatus.

Dakota Uncertainty Quantification Methods Applied to the CFD code Nek5000

DOE Office of Scientific and Technical Information (OSTI.GOV)

Delchini, Marc-Olivier; Popov, Emilian L.; Pointer, William David

This report presents the state of advancement of a Nuclear Energy Advanced Modeling and Simulation (NEAMS) project to characterize the uncertainty of the computational fluid dynamics (CFD) code Nek5000 using the Dakota package for flows encountered in the nuclear engineering industry. Nek5000 is a high-order spectral element CFD code developed at Argonne National Laboratory for high-resolution spectral-filtered large eddy simulations (LESs) and unsteady Reynolds-averaged Navier-Stokes (URANS) simulations.

Monte Carlo Simulations for VLBI2010

NASA Astrophysics Data System (ADS)

Wresnik, J.; Böhm, J.; Schuh, H.

2007-07-01

Monte Carlo simulations are carried out at the Institute of Geodesy and Geophysics (IGG), Vienna, and at Goddard Space Flight Center (GSFC), Greenbelt (USA), with the goal to design a new geodetic Very Long Baseline Interferometry (VLBI) system. Influences of the schedule, the network geometry and the main stochastic processes on the geodetic results are investigated. Therefore schedules are prepared with the software package SKED (Vandenberg 1999), and different strategies are applied to produce temporally very dense schedules which are compared in terms of baseline length repeatabilities. For the simulation of VLBI observations a Monte Carlo Simulator was set up which creates artificial observations by randomly simulating wet zenith delay and clock values as well as additive white noise representing the antenna errors. For the simulation at IGG the VLBI analysis software OCCAM (Titov et al. 2004) was adapted. Random walk processes with power spectrum densities of 0.7 and 0.1 psec2/sec are used for the simulation of wet zenith delays. The clocks are simulated with Allan Standard Deviations of 1*10^-14 @ 50 min and 2*10^-15 @ 15 min and three levels of white noise, 4 psec, 8 psec and, 16 psec, are added to the artificial observations. The variations of the power spectrum densities of the clocks and wet zenith delays, and the application of different white noise levels show clearly that the wet delay is the critical factor for the improvement of the geodetic VLBI system. At GSFC the software CalcSolve is used for the VLBI analysis, therefore a comparison between the software packages OCCAM and CalcSolve was done with simulated data. For further simulations the wet zenith delay was modeled by a turbulence model. This data was provided by Nilsson T. and was added to the simulation work. Different schedules have been run.

Numerical simulation of infiltration and groundwater recharge using the Hydrus for Modflow package and the BEST model of soil hydraulic properties

NASA Astrophysics Data System (ADS)

Gumuła-Kawęcka, Anna; Szymkiewicz, Adam; Angulo-Jaramillo, Rafael; Šimůnek, Jirka; Jaworska-Szulc, Beata; Pruszkowska-Caceres, Małgorzata; Gorczewska-Langner, Wioletta; Leterme, Bertrand; Jacques, Diederik

2017-04-01

ABSTRACT Groundwater recharge is a complex process, which depends on several factors, including the hydraulic properties of soils in the vadose zone. On the other hand, the rate of recharge is one of the main input data in hydrogeological models for saturated groundwater flow. Thus, there is an increasing understanding of the need for more complete representation of vadose zone processes in groundwater modeling. One of the possible approaches is to use a 1D model of water flow in the unsaturated zone coupled with 3D groundwater model for the saturated zone. Such an approach was implemented in the Hydrus for Modflow package (Seo et al. 2007), which combines two well-known and thoroughly tested modeling tools: groundwater flow simulator MODFLOW (Harbaugh 2005) and one-dimensional vadose zone simulator HYDRUS 1D (Šimůnek et al. 2016), based on the Richards equation. The Hydrus for Modflow package has been recently enhanced by implementing the BEST model of soil hydraulic properties (Lassabatere et al. 2006), which is a combination of van Genuchten - type retention function with Brooks-Corey type hydraulic conductivity function. The parameters of these functions can be divided into texture-related and structure-related and can be obtained from relatively simple lab and field tests. The method appears a promising tool for obtaining input data for vadose zone flow models. The main objective of this work is to evaluate the sensitivity of the recharge rates to the values of various parameters of the BEST model. Simulations are performed for a range of soil textural classes and plant covers, using meteorological data typical for northern Poland. ACKNOWLEDGEMENTS This work has been supported by National Science Centre, Poland in the framework of the project 2015/17/B/ST10/03233 "Groundwater recharge on outwash plain". REFERENCES [1]Harbaugh, A.W. (2005) MODFLOW-2005, the US Geological Survey modular ground-water model: the ground-water flow process. Reston, VA, USA. [2]Lassabatere L. et al. (2006) Beerkan estimation of soil transfer parameters through infiltration experiments—BEST. Soil Science Society of America Journal 70.2: 521-532. [3]Seo, H.S., Šimůnek J., Poeter E.P. (2007) Documentation of the Hydrus package for Modflow-2000, the US Geological Survey modular ground-water model. [4]Šimůnek, J., van Genuchten, M.Th., and Šejna, M. (2016) Recent developments and applications of the HYDRUS computer software packages, Vadose Zone Journal, 15(7), pp. 25, doi: 10.2136/vzj2016.04.0033.

AceCloud: Molecular Dynamics Simulations in the Cloud.

PubMed

Harvey, M J; De Fabritiis, G

2015-05-26

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

Two applications of the Recently Developed UZF-MT3DMS Model for Evaluating Nonpoint-Source Fluxes (Invited)

NASA Astrophysics Data System (ADS)

Morway, E. D.; Niswonger, R. G.; Nishikawa, T.

2013-12-01

The solute-transport model MT3DMS was modified to simulate transport in the unsaturated-zone by incorporating the additional flow terms calculated by the Unsaturated-Zone Flow (UZF) package developed for MODFLOW. Referred to as UZF-MT3DMS, the model simulates advection and dispersion of conservative and reactive solutes in unsaturated and saturated porous media. Significant time savings are realized owing to the efficiency of the kinematic -wave approximation used by the UZF1 package relative to Richards' equation-based approaches, facilitating the use of automated parameter-estimation routines wherein thousands of model runs may be required. Currently, UZF-MT3DMS is applied to two real-world applications of existing MODFLOW and MT3DMS models retro-fitted to use the UZF1 package for simulating the unsaturated component of the sub-surface system. In the first application, two regional-scale investigations located in Colorado's Lower Arkansas River Valley (LARV) are developed to evaluate the extent and severity of unsaturated-zone salinization contributing to crop yield loss. Preliminary results indicate root zone concentrations over both regions are at or above salinity-thresholds of most crop types grown in the LARV. Regional-scale modeling investigations of salinization found in the literature commonly use lumped-parameter models rather than physically-based distributed-parameter models. In the second application, located near Joshua Tree, CA, nitrate loading to the underlying unconfined aquifer from domestic septic systems is evaluated. Due to the region's thick unsaturated-zone and correspondingly long unsaturated-zone residence times (multi-decade), UZF-MT3DMS enabled direct simulation of spatially-varying concentration break-through curves at the water table.

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

PubMed

Adalsteinsson, David; McMillen, David; Elston, Timothy C

2004-03-08

Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

MODFLOW-OWHM v2: The next generation of fully integrated hydrologic simulation software

NASA Astrophysics Data System (ADS)

Boyce, S. E.; Hanson, R. T.; Ferguson, I. M.; Reimann, T.; Henson, W.; Mehl, S.; Leake, S.; Maddock, T.

2016-12-01

The One-Water Hydrologic Flow Model (One-Water) is a MODFLOW-based integrated hydrologic flow model designed for the analysis of a broad range of conjunctive-use and climate-related issues. One-Water fully links the movement and use of groundwater, surface water, and imported water for consumption by agriculture and natural vegetation on the landscape, and for potable and other uses within a supply-and-demand framework. One-Water includes linkages for deformation-, flow-, and head-dependent flows; additional observation and parameter options for higher-order calibrations; and redesigned code for facilitation of self-updating models and faster simulation run times. The next version of One-Water, currently under development, will include a new surface-water operations module that simulates dynamic reservoir operations, a new sustainability analysis package that facilitates the estimation and simulation of reduced storage depletion and captured discharge, a conduit-flow process for karst aquifers and leaky pipe networks, a soil zone process that adds an enhanced infiltration process, interflow, deep percolation and soil moisture, and a new subsidence and aquifer compaction package. It will also include enhancements to local grid refinement, and additional features to facilitate easier model updates, faster execution, better error messages, and more integration/cross communication between the traditional MODFLOW packages. By retaining and tracking the water within the hydrosphere, One-Water accounts for "all of the water everywhere and all of the time." This philosophy provides more confidence in the water accounting by the scientific community and provides the public a foundation needed to address wider classes of problems. Ultimately, more complex questions are being asked about water resources, so they require a more complete answer about conjunctive-use and climate-related issues.

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package.

PubMed

Kaus, Joseph W; Pierce, Levi T; Walker, Ross C; McCammont, J Andrew

2013-09-10

Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license.

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

PubMed Central

Pierce, Levi T.; Walker, Ross C.; McCammont, J. Andrew

2013-01-01

Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license. PMID:24185531