Performance of bias corrected MPEG rainfall estimate for rainfall-runoff simulation in the upper Blue Nile Basin, Ethiopia

NASA Astrophysics Data System (ADS)

Worqlul, Abeyou W.; Ayana, Essayas K.; Maathuis, Ben H. P.; MacAlister, Charlotte; Philpot, William D.; Osorio Leyton, Javier M.; Steenhuis, Tammo S.

2018-01-01

In many developing countries and remote areas of important ecosystems, good quality precipitation data are neither available nor readily accessible. Satellite observations and processing algorithms are being extensively used to produce satellite rainfall products (SREs). Nevertheless, these products are prone to systematic errors and need extensive validation before to be usable for streamflow simulations. In this study, we investigated and corrected the bias of Multi-Sensor Precipitation Estimate-Geostationary (MPEG) data. The corrected MPEG dataset was used as input to a semi-distributed hydrological model Hydrologiska Byråns Vattenbalansavdelning (HBV) for simulation of discharge of the Gilgel Abay and Gumara watersheds in the Upper Blue Nile basin, Ethiopia. The result indicated that the MPEG satellite rainfall captured 81% and 78% of the gauged rainfall variability with a consistent bias of underestimating the gauged rainfall by 60%. A linear bias correction applied significantly reduced the bias while maintaining the coefficient of correlation. The simulated flow using bias corrected MPEG SRE resulted in a simulated flow comparable to the gauge rainfall for both watersheds. The study indicated the potential of MPEG SRE in water budget studies after applying a linear bias correction.

NASA Constellation Distributed Simulation Middleware Trade Study

NASA Technical Reports Server (NTRS)

Hasan, David; Bowman, James D.; Fisher, Nancy; Cutts, Dannie; Cures, Edwin Z.

2008-01-01

This paper presents the results of a trade study designed to assess three distributed simulation middleware technologies for support of the NASA Constellation Distributed Space Exploration Simulation (DSES) project and Test and Verification Distributed System Integration Laboratory (DSIL). The technologies are the High Level Architecture (HLA), the Test and Training Enabling Architecture (TENA), and an XML-based variant of Distributed Interactive Simulation (DIS-XML) coupled with the Extensible Messaging and Presence Protocol (XMPP). According to the criteria and weights determined in this study, HLA scores better than the other two for DSES as well as the DSIL.

A Collaborative Extensible User Environment for Simulation and Knowledge Management

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

Freedman, Vicky L.; Lansing, Carina S.; Porter, Ellen A.

2015-06-01

In scientific simulation, scientists use measured data to create numerical models, execute simulations and analyze results from advanced simulators executing on high performance computing platforms. This process usually requires a team of scientists collaborating on data collection, model creation and analysis, and on authorship of publications and data. This paper shows that scientific teams can benefit from a user environment called Akuna that permits subsurface scientists in disparate locations to collaborate on numerical modeling and analysis projects. The Akuna user environment is built on the Velo framework that provides both a rich client environment for conducting and analyzing simulations andmore » a Web environment for data sharing and annotation. Akuna is an extensible toolset that integrates with Velo, and is designed to support any type of simulator. This is achieved through data-driven user interface generation, use of a customizable knowledge management platform, and an extensible framework for simulation execution, monitoring and analysis. This paper describes how the customized Velo content management system and the Akuna toolset are used to integrate and enhance an effective collaborative research and application environment. The extensible architecture of Akuna is also described and demonstrates its usage for creation and execution of a 3D subsurface simulation.« less

Building the ECON extension: Functionality and lessons learned

Treesearch

Fred C. Martin

2008-01-01

The functionality of the ECON extension to FVS is described with emphasis on the ability to dynamically interact with all elements of the FVS simulation process. Like other extensions, ECON is fully integrated within FVS. This integration allows: (1) analysis of multiple alternative tree-removal actions within a single simulation without altering “normal” stand...

Chapter 2: Fire and Fuels Extension: Model description

Treesearch

Sarah J. Beukema; Elizabeth D. Reinhardt; Julee A. Greenough; Donald C. E. Robinson; Werner A. Kurz

2003-01-01

The Fire and Fuels Extension to the Forest Vegetation Simulator is a model that simulates fuel dynamics and potential fire behavior over time, in the context of stand development and management. Existing models are used to represent forest stand development (the Forest Vegetation Simulator, Wykoff and others 1982), fire behavior (Rothermel 1972, Van Wagner 1977, and...

Urbanization and watershed sustainability: Collaborative simulation modeling of future development states

NASA Astrophysics Data System (ADS)

Randhir, Timothy O.; Raposa, Sarah

2014-11-01

Urbanization has a significant impact on water resources and requires a watershed-based approach to evaluate impacts of land use and urban development on watershed processes. This study uses a simulation with urban policy scenarios to model and strategize transferable recommendations for municipalities and cities to guide urban decisions using watershed ecohydrologic principles. The watershed simulation model is used to evaluation intensive (policy in existing built regions) and extensive (policy outside existing build regions) urban development scenarios with and without implementation of Best Management practices (BMPs). Water quantity and quality changes are simulated to assess effectiveness of five urban development scenarios. It is observed that optimal combination of intensive and extensive strategies can be used to sustain urban ecosystems. BMPs are found critical to reduce storm water and water quality impacts on urban development. Conservation zoning and incentives for voluntary adoption of BMPs can be used in sustaining urbanizing watersheds.

An Extension of the Partial Credit Model with an Application to the Measurement of Change.

ERIC Educational Resources Information Center

Fischer, Gerhard H.; Ponocny, Ivo

1994-01-01

An extension to the partial credit model, the linear partial credit model, is considered under the assumption of a certain linear decomposition of the item x category parameters into basic parameters. A conditional maximum likelihood algorithm for estimating basic parameters is presented and illustrated with simulation and an empirical study. (SLD)

Code Validation Studies of High-Enthalpy Flows

DTIC Science & Technology

2006-12-01

stage of future hypersonic vehicles. The development and design of such vehicles is aided by the use of experimentation and numerical simulation... numerical predictions and experimental measurements. 3. Summary of Previous Work We have studied extensively hypersonic double-cone flows with and in...the experimental measurements and the numerical predictions. When we accounted for that effect in numerical simulations, and also augmented the

Studying Variance in the Galactic Ultra-compact Binary Population

NASA Astrophysics Data System (ADS)

Larson, Shane L.; Breivik, Katelyn

2017-01-01

In the years preceding LISA, Milky Way compact binary population simulations can be used to inform the science capabilities of the mission. Galactic population simulation efforts generally focus on high fidelity models that require extensive computational power to produce a single simulated population for each model. Each simulated population represents an incomplete sample of the functions governing compact binary evolution, thus introducing variance from one simulation to another. We present a rapid Monte Carlo population simulation technique that can simulate thousands of populations on week-long timescales, thus allowing a full exploration of the variance associated with a binary stellar evolution model.

Drape simulation and subjective assessment of virtual drape

NASA Astrophysics Data System (ADS)

Buyukaslan, E.; Kalaoglu, F.; Jevsnik, S.

2017-10-01

In this study, a commercial 3D virtual garment simulation software (Optitex) is used to simulate drape behaviours of five different fabrics. Mechanical properties of selected fabrics are measured by Fabric Assurance by Simple Testing (FAST) method. Measured bending, shear and extension properties of fabrics are inserted to the simulation software to achieve more realistic simulations. Simulation images of fabrics are shown to 27 people and they are asked to match real drape images of fabrics with simulated drape images. Fabric simulations of two fabrics were correctly matched by the majority of the test group. However, the other three fabrics’ simulations were mismatched by most of the people.

Feasibility study for a numerical aerodynamic simulation facility. Volume 3: FMP language specification/user manual

NASA Technical Reports Server (NTRS)

Kenner, B. G.; Lincoln, N. R.

1979-01-01

The manual is intended to show the revisions and additions to the current STAR FORTRAN. The changes are made to incorporate an FMP (Flow Model Processor) for use in the Numerical Aerodynamic Simulation Facility (NASF) for the purpose of simulating fluid flow over three-dimensional bodies in wind tunnel environments and in free space. The FORTRAN programming language for the STAR-100 computer contains both CDC and unique STAR extensions to the standard FORTRAN. Several of the STAR FORTRAN extensions to standard FOR-TRAN allow the FORTRAN user to exploit the vector processing capabilities of the STAR computer. In STAR FORTRAN, vectors can be expressed with an explicit notation, functions are provided that return vector results, and special call statements enable access to any machine instruction.

Appendices to the model description document for a computer program for the emulation/simulation of a space station environmental control and life support system

NASA Technical Reports Server (NTRS)

Yanosy, James L.

1988-01-01

A Model Description Document for the Emulation Simulation Computer Model was already published. The model consisted of a detailed model (emulation) of a SAWD CO2 removal subsystem which operated with much less detailed (simulation) models of a cabin, crew, and condensing and sensible heat exchangers. The purpose was to explore the utility of such an emulation simulation combination in the design, development, and test of a piece of ARS hardware, SAWD. Extensions to this original effort are presented. The first extension is an update of the model to reflect changes in the SAWD control logic which resulted from test. Also, slight changes were also made to the SAWD model to permit restarting and to improve the iteration technique. The second extension is the development of simulation models for more pieces of air and water processing equipment. Models are presented for: EDC, Molecular Sieve, Bosch, Sabatier, a new condensing heat exchanger, SPE, SFWES, Catalytic Oxidizer, and multifiltration. The third extension is to create two system simulations using these models. The first system presented consists of one air and one water processing system. The second consists of a potential air revitalization system.

Appendices to the user's manual for a computer program for the emulation/simulation of a space station environmental control and life support system

NASA Technical Reports Server (NTRS)

Yanosy, James L.

1988-01-01

A user's Manual for the Emulation Simulation Computer Model was published previously. The model consisted of a detailed model (emulation) of a SAWD CO2 removal subsystem which operated with much less detailed (simulation) models of a cabin, crew, and condensing and sensible heat exchangers. The purpose was to explore the utility of such an emulation/simulation combination in the design, development, and test of a piece of ARS hardware - SAWD. Extensions to this original effort are presented. The first extension is an update of the model to reflect changes in the SAWD control logic which resulted from the test. In addition, slight changes were also made to the SAWD model to permit restarting and to improve the iteration technique. The second extension is the development of simulation models for more pieces of air and water processing equipment. Models are presented for: EDC, Molecular Sieve, Bosch, Sabatier, a new condensing heat exchanger, SPE, SFWES, Catalytic Oxidizer, and multifiltration. The third extension is to create two system simulations using these models. The first system presented consists of one air and one water processing system, the second a potential Space Station air revitalization system.

Middleware Trade Study for NASA Domain

NASA Technical Reports Server (NTRS)

Bowman, Dan

2007-01-01

This presentation presents preliminary results of a trade study designed to assess three distributed simulation middleware technologies for support of the NASA Constellation Distributed Space Exploration Simulation (DSES) project and Test and Verification Distributed System Integration Laboratory (DSIL). The technologies are: the High Level Architecture (HLA), the Test and Training Enabling Architecture (TENA), and an XML-based variant of Distributed Interactive Simulation (DIS-XML) coupled with the Extensible Messaging and Presence Protocol (XMPP). According to the criteria and weights determined in this study, HLA scores better than the other two for DSES as well as the DSIL

The Roland Maze Project school-based extensive air shower network

NASA Astrophysics Data System (ADS)

Feder, J.; Jȩdrzejczak, K.; Karczmarczyk, J.; Lewandowski, R.; Swarzyński, J.; Szabelska, B.; Szabelski, J.; Wibig, T.

2006-01-01

We plan to construct the large area network of extensive air shower detectors placed on the roofs of high school buildings in the city of Łódź. Detection points will be connected by INTERNET to the central server and their work will be synchronized by GPS. The main scientific goal of the project are studies of ultra high energy cosmic rays. Using existing town infrastructure (INTERNET, power supply, etc.) will significantly reduce the cost of the experiment. Engaging high school students in the research program should significantly increase their knowledge of science and modern technologies, and can be a very efficient way of science popularisation. We performed simulations of the projected network capabilities of registering Extensive Air Showers and reconstructing energies of primary particles. Results of the simulations and the current status of project realisation will be presented.

Faculty Perspectives on Effective Integration of Simulation into a Baccalaureate Nursing Curriculum

ERIC Educational Resources Information Center

Howell, Linda Jane

2017-01-01

Research shows that use of high fidelity simulation (HFS) as a teaching strategy requires extensive amounts of faculty time and financial resources for faculty development and equipment. This project study addressed the challenges encountered in the integration of HFS into a Midwestern metropolitan baccalaureate nursing program. The purpose of…

Evaluation of the effect of different stretching patterns on force decay and tensile properties of elastomeric ligatures

PubMed Central

Aminian, Amin; Nakhaei, Samaneh; Agahi, Raha Habib; Rezaeizade, Masoud; Aliabadi, Hamed Mirzazadeh; Heidarpour, Majid

2015-01-01

Background: There have been numerous researches on elastomeric ligatures, but clinical conditions in different stages of treatment are not exactly similar to laboratory conditions. The aim of this in vitro study was to simulate clinical conditions and evaluate the effect of three stretching patterns on the amount of force, tensile strength (TS) and extension to TS of the elastomers during 8 weeks. Materials and Methods: Forces, TS and extension to TS of two different brands of elastomers were measured at initial, 24 h and 2, 4, and 8-week intervals using a testing machine. During the study period, the elastomers were stored in three different types of jig (uniform stretching, 1 and 3 mm point stretching) designed by the computer-aided design and computer-aided manufacturing technique in order to simulate the different stages of orthodontic treatment. Results: The elastomeric ligatures under study exhibited a similar force decay pattern. The maximum force decay occurred during the first 24 h (49.9% ± 15%) and the amount of force decay was 75.7% ± 8% after 8 weeks. In general, the TS decreased during the study period, and the amount of extension to TS increased. Conclusion: Although the elastic behavior of all ligatures under study was similar, the amount of residual force, TS and extension to TS increased in elastomers under point stretching pattern. PMID:26759597

Evaluation of the effect of different stretching patterns on force decay and tensile properties of elastomeric ligatures.

PubMed

Aminian, Amin; Nakhaei, Samaneh; Agahi, Raha Habib; Rezaeizade, Masoud; Aliabadi, Hamed Mirzazadeh; Heidarpour, Majid

2015-01-01

There have been numerous researches on elastomeric ligatures, but clinical conditions in different stages of treatment are not exactly similar to laboratory conditions. The aim of this in vitro study was to simulate clinical conditions and evaluate the effect of three stretching patterns on the amount of force, tensile strength (TS) and extension to TS of the elastomers during 8 weeks. Forces, TS and extension to TS of two different brands of elastomers were measured at initial, 24 h and 2, 4, and 8-week intervals using a testing machine. During the study period, the elastomers were stored in three different types of jig (uniform stretching, 1 and 3 mm point stretching) designed by the computer-aided design and computer-aided manufacturing technique in order to simulate the different stages of orthodontic treatment. The elastomeric ligatures under study exhibited a similar force decay pattern. The maximum force decay occurred during the first 24 h (49.9% ± 15%) and the amount of force decay was 75.7% ± 8% after 8 weeks. In general, the TS decreased during the study period, and the amount of extension to TS increased. Although the elastic behavior of all ligatures under study was similar, the amount of residual force, TS and extension to TS increased in elastomers under point stretching pattern.

[Review on HSPF model for simulation of hydrology and water quality processes].

PubMed

Li, Zhao-fu; Liu, Hong-Yu; Li, Yan

2012-07-01

Hydrological Simulation Program-FORTRAN (HSPF), written in FORTRAN, is one ol the best semi-distributed hydrology and water quality models, which was first developed based on the Stanford Watershed Model. Many studies on HSPF model application were conducted. It can represent the contributions of sediment, nutrients, pesticides, conservatives and fecal coliforms from agricultural areas, continuously simulate water quantity and quality processes, as well as the effects of climate change and land use change on water quantity and quality. HSPF consists of three basic application components: PERLND (Pervious Land Segment) IMPLND (Impervious Land Segment), and RCHRES (free-flowing reach or mixed reservoirs). In general, HSPF has extensive application in the modeling of hydrology or water quality processes and the analysis of climate change and land use change. However, it has limited use in China. The main problems with HSPF include: (1) some algorithms and procedures still need to revise, (2) due to the high standard for input data, the accuracy of the model is limited by spatial and attribute data, (3) the model is only applicable for the simulation of well-mixed rivers, reservoirs and one-dimensional water bodies, it must be integrated with other models to solve more complex problems. At present, studies on HSPF model development are still undergoing, such as revision of model platform, extension of model function, method development for model calibration, and analysis of parameter sensitivity. With the accumulation of basic data and imorovement of data sharing, the HSPF model will be applied more extensively in China.

An actuator extension transformation for a motion simulator and an inverse transformation applying Newton-Raphson's method

NASA Technical Reports Server (NTRS)

Dieudonne, J. E.

1972-01-01

A set of equations which transform position and angular orientation of the centroid of the payload platform of a six-degree-of-freedom motion simulator into extensions of the simulator's actuators has been derived and is based on a geometrical representation of the system. An iterative scheme, Newton-Raphson's method, has been successfully used in a real time environment in the calculation of the position and angular orientation of the centroid of the payload platform when the magnitude of the actuator extensions is known. Sufficient accuracy is obtained by using only one Newton-Raphson iteration per integration step of the real time environment.

Boat, wake, and wave real-time simulation

NASA Astrophysics Data System (ADS)

Świerkowski, Leszek; Gouthas, Efthimios; Christie, Chad L.; Williams, Owen M.

2009-05-01

We describe the extension of our real-time scene generation software VIRSuite to include the dynamic simulation of small boats and their wakes within an ocean environment. Extensive use has been made of the programmabilty available in the current generation of GPUs. We have demonstrated that real-time simulation is feasible, even including such complexities as dynamical calculation of the boat motion, wake generation and calculation of an FFTgenerated sea state.

Simulated Radioscapholunate Fusion Alters Carpal Kinematics While Preserving Dart-Thrower's Motion

PubMed Central

Calfee, Ryan P.; Leventhal, Evan L.; Wilkerson, Jim; Moore, Douglas C.; Akelman, Edward; Crisco, Joseph J.

2014-01-01

Purpose Midcarpal degeneration is well documented after radioscapholunate fusion. This study tested the hypothesis that radioscapholunate fusion alters the kinematic behavior of the remaining lunotriquetral and midcarpal joints, with specific focus on the dart-thrower's motion. Methods Simulated radioscapholunate fusions were performed on 6 cadaveric wrists in an anatomically neutral posture. Two 0.060-in. carbon fiber pins were placed from proximal to distal across the radiolunate and radioscaphoid joints, respectively. The wrists were passively positioned in a custom jig toward a full range of motion along the orthogonal axes as well as oblique motions, with additional intermediate positions along the dart-thrower's path. Using a computed tomography– based markerless bone registration technique, each carpal bone's three-dimensional rotation was defined as a function of wrist flexion/extension from the pinned neutral position. Kinematic data was analyzed against data collected on the same wrist prior to fixation using hierarchical linear regression analysis and paired Student's t-tests. Results After simulated fusion, wrist motion was restricted to an average flexion-extension arc of 48°, reduced from 77°, and radial-ulnar deviation arc of 19°, reduced from 33°. The remaining motion was maximally preserved along the dart-thrower's path from radial-extension toward ulnar-flexion. The simulated fusion significantly increased rotation through the scaphotrapezial joint, scaphocapitate joint, triquetrohamate joint, and lunotriquetral joint. For example, in the pinned wrist, the rotation of the hamate relative to the triquetrum increased 85%. Therefore, during every 10° of total wrist motion, the hamate rotated an average of nearly 8° relative to the triquetrum after pinning versus 4° in the normal state. Conclusions Simulated radioscapholunate fusion altered midcarpal and lunotriquetral kinematics. The increased rotations across these remaining joints provide one potential explanation for midcarpal degeneration after radioscapholunate fusion. Additionally, this fusion model confirms the dart-thrower's hypothesis, as wrist motion after simulated radioscapholunate fusion was primarily preserved from radial-extension toward ulnar-flexion. PMID:18406953

Grandmothering and cognitive resources are required for the emergence of menopause and extensive post-reproductive lifespan.

PubMed

Aimé, Carla; André, Jean-Baptiste; Raymond, Michel

2017-07-01

Menopause, the permanent cessation of ovulation, occurs in humans well before the end of the expected lifespan, leading to an extensive post-reproductive period which remains a puzzle for evolutionary biologists. All human populations display this particularity; thus, it is difficult to empirically evaluate the conditions for its emergence. In this study, we used artificial neural networks to model the emergence and evolution of allocation decisions related to reproduction in simulated populations. When allocation decisions were allowed to freely evolve, both menopause and extensive post-reproductive life-span emerged under some ecological conditions. This result allowed us to test various hypotheses about the required conditions for the emergence of menopause and extensive post-reproductive life-span. Our findings did not support the Maternal Hypothesis (menopause has evolved to avoid the risk of dying in childbirth, which is higher in older women). In contrast, results supported a shared prediction from the Grandmother Hypothesis and the Embodied Capital Model. Indeed, we found that extensive post-reproductive lifespan allows resource reallocation to increase fertility of the children and survival of the grandchildren. Furthermore, neural capital development and the skill intensiveness of the foraging niche, rather than strength, played a major role in shaping the age profile of somatic and cognitive senescence in our simulated populations. This result supports the Embodied Capital Model rather than the Grand-Mother Hypothesis. Finally, in simulated populations where menopause had already evolved, we found that reduced post-reproductive lifespan lead to reduced children's fertility and grandchildren's survival. The results are discussed in the context of the evolutionary emergence of menopause and extensive post-reproductive life-span.

Preliminary study for a numerical aerodynamic simulation facility. Phase 1: Extension

NASA Technical Reports Server (NTRS)

Lincoln, N. R.

1978-01-01

Functional requirements and preliminary design data were identified for use in the design of all system components and in the construction of a facility to perform aerodynamic simulation for airframe design. A skeleton structure of specifications for the flow model processor and monitor, the operating system, and the language and its compiler is presented.

The Local Minima Problem in Hierarchical Classes Analysis: An Evaluation of a Simulated Annealing Algorithm and Various Multistart Procedures

ERIC Educational Resources Information Center

Ceulemans, Eva; Van Mechelen, Iven; Leenen, Iwin

2007-01-01

Hierarchical classes models are quasi-order retaining Boolean decomposition models for N-way N-mode binary data. To fit these models to data, rationally started alternating least squares (or, equivalently, alternating least absolute deviations) algorithms have been proposed. Extensive simulation studies showed that these algorithms succeed quite…

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.

Dry Volume Fracturing Simulation of Shale Gas Reservoir

NASA Astrophysics Data System (ADS)

Xu, Guixi; Wang, Shuzhong; Luo, Xiangrong; Jing, Zefeng

2017-11-01

Application of CO2 dry fracturing technology to shale gas reservoir development in China has advantages of no water consumption, little reservoir damage and promoting CH4 desorption. This paper uses Meyer simulation to study complex fracture network extension and the distribution characteristics of shale gas reservoirs in the CO2 dry volume fracturing process. The simulation results prove the validity of the modified CO2 dry fracturing fluid used in shale volume fracturing and provides a theoretical basis for the following study on interval optimization of the shale reservoir dry volume fracturing.

Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations.

PubMed

Einert, T R; Sing, C E; Alexander-Katz, A; Netz, R R

2011-12-01

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N (G) is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε < ε(s) with fast internal dynamics and a solid-like regime (for ε > ε(s) with slow internal dynamics. The cohesion strength ε(s) of this freezing transition depends on N (G) . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N (G) . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.

Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

NASA Astrophysics Data System (ADS)

Junghans, Christoph; Mniszewski, Susan; Voter, Arthur; Perez, Danny; Eidenbenz, Stephan

2014-03-01

We present an example of a new class of tools that we call application simulators, parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation (PDES). We demonstrate our approach with a TADSim application simulator that models the Temperature Accelerated Dynamics (TAD) method, which is an algorithmically complex member of the Accelerated Molecular Dynamics (AMD) family. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We further extend TADSim to model algorithm extensions to standard TAD, such as speculative spawning of the compute-bound stages of the algorithm, and predict performance improvements without having to implement such a method. Focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights into the TAD algorithm behavior and suggested extensions to the TAD method.

Primitive chain network simulations for entangled DNA solutions

NASA Astrophysics Data System (ADS)

Masubuchi, Yuichi; Furuichi, Kenji; Horio, Kazushi; Uneyama, Takashi; Watanabe, Hiroshi; Ianniruberto, Giovanni; Greco, Francesco; Marrucci, Giuseppe

2009-09-01

Molecular theories for polymer rheology are based on conformational dynamics of the polymeric chain. Hence, measurements directly related to molecular conformations appear more appealing than indirect ones obtained from rheology. In this study, primitive chain network simulations are compared to experimental data of entangled DNA solutions [Teixeira et al., Macromolecules 40, 2461 (2007)]. In addition to rheological comparisons of both linear and nonlinear viscoelasticities, a molecular extension measure obtained by Teixeira et al. through fluorescent microscopy is compared to simulations, in terms of both averages and distributions. The influence of flow on conformational distributions has never been simulated for the case of entangled polymers, and how DNA molecular individualism extends to the entangled regime is not known. The linear viscoelastic response and the viscosity growth curve in the nonlinear regime are found in good agreement with data for various DNA concentrations. Conversely, the molecular extension measure shows significant departures, even under equilibrium conditions. The reason for such discrepancies remains unknown.

Computers for real time flight simulation: A market survey

NASA Technical Reports Server (NTRS)

Bekey, G. A.; Karplus, W. J.

1977-01-01

An extensive computer market survey was made to determine those available systems suitable for current and future flight simulation studies at Ames Research Center. The primary requirement is for the computation of relatively high frequency content (5 Hz) math models representing powered lift flight vehicles. The Rotor Systems Research Aircraft (RSRA) was used as a benchmark vehicle for computation comparison studies. The general nature of helicopter simulations and a description of the benchmark model are presented, and some of the sources of simulation difficulties are examined. A description of various applicable computer architectures is presented, along with detailed discussions of leading candidate systems and comparisons between them.

Physics based modeling of a series parallel battery pack for asymmetry analysis, predictive control and life extension

NASA Astrophysics Data System (ADS)

Ganesan, Nandhini; Basu, Suman; Hariharan, Krishnan S.; Kolake, Subramanya Mayya; Song, Taewon; Yeo, Taejung; Sohn, Dong Kee; Doo, Seokgwang

2016-08-01

Lithium-Ion batteries used for electric vehicle applications are subject to large currents and various operation conditions, making battery pack design and life extension a challenging problem. With increase in complexity, modeling and simulation can lead to insights that ensure optimal performance and life extension. In this manuscript, an electrochemical-thermal (ECT) coupled model for a 6 series × 5 parallel pack is developed for Li ion cells with NCA/C electrodes and validated against experimental data. Contribution of the cathode to overall degradation at various operating conditions is assessed. Pack asymmetry is analyzed from a design and an operational perspective. Design based asymmetry leads to a new approach of obtaining the individual cell responses of the pack from an average ECT output. Operational asymmetry is demonstrated in terms of effects of thermal gradients on cycle life, and an efficient model predictive control technique is developed. Concept of reconfigurable battery pack is studied using detailed simulations that can be used for effective monitoring and extension of battery pack life.

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

Single polymer dynamics under large amplitude oscillatory extension

NASA Astrophysics Data System (ADS)

Zhou, Yuecheng; Schroeder, Charles M.

2016-09-01

Understanding the conformational dynamics of polymers in time-dependent flows is of key importance for controlling materials properties during processing. Despite this importance, however, it has been challenging to study polymer dynamics in controlled time-dependent or oscillatory extensional flows. In this work, we study the dynamics of single polymers in large-amplitude oscillatory extension (LAOE) using a combination of experiments and Brownian dynamics (BD) simulations. Two-dimensional LAOE flow is generated using a feedback-controlled stagnation point device known as the Stokes trap, thereby generating an oscillatory planar extensional flow with alternating principal axes of extension and compression. Our results show that polymers experience periodic cycles of compression, reorientation, and extension in LAOE, and dynamics are generally governed by a dimensionless flow strength (Weissenberg number Wi) and dimensionless frequency (Deborah number De). Single molecule experiments are compared to BD simulations with and without intramolecular hydrodynamic interactions (HI) and excluded volume (EV) interactions, and good agreement is obtained across a range of parameters. Moreover, transient bulk stress in LAOE is determined from simulations using the Kramers relation, which reveals interesting and unique rheological signatures for this time-dependent flow. We further construct a series of single polymer stretch-flow rate curves (defined as single molecule Lissajous curves) as a function of Wi and De, and we observe qualitatively different dynamic signatures (butterfly, bow tie, arch, and line shapes) across the two-dimensional Pipkin space defined by Wi and De. Finally, polymer dynamics spanning from the linear to nonlinear response regimes are interpreted in the context of accumulated fluid strain in LAOE.

A multi-species exchange model for fully fluctuating polymer field theory simulations.

PubMed

Düchs, Dominik; Delaney, Kris T; Fredrickson, Glenn H

2014-11-07

Field-theoretic models have been used extensively to study the phase behavior of inhomogeneous polymer melts and solutions, both in self-consistent mean-field calculations and in numerical simulations of the full theory capturing composition fluctuations. The models commonly used can be grouped into two categories, namely, species models and exchange models. Species models involve integrations of functionals that explicitly depend on fields originating both from species density operators and their conjugate chemical potential fields. In contrast, exchange models retain only linear combinations of the chemical potential fields. In the two-component case, development of exchange models has been instrumental in enabling stable complex Langevin (CL) simulations of the full complex-valued theory. No comparable stable CL approach has yet been established for field theories of the species type. Here, we introduce an extension of the exchange model to an arbitrary number of components, namely, the multi-species exchange (MSE) model, which greatly expands the classes of soft material systems that can be accessed by the complex Langevin simulation technique. We demonstrate the stability and accuracy of the MSE-CL sampling approach using numerical simulations of triblock and tetrablock terpolymer melts, and tetrablock quaterpolymer melts. This method should enable studies of a wide range of fluctuation phenomena in multiblock/multi-species polymer blends and composites.

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

PubMed

Dalby, Andrew; Shamsir, Mohd Shahir

2015-01-01

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

PubMed Central

Dalby, Andrew; Shamsir, Mohd Shahir

2015-01-01

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation. PMID:26539292

Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

DTIC Science & Technology

2009-01-01

implicit solvents on peptide structure and dynamics , we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two...end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those...to maintain the temperature of the systems. Introduction Molecular dynamics (MD) simulation techniques are widely used to study structure and

Lightweight computational steering of very large scale molecular dynamics simulations

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

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

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

Photomechanical Deformation of Azobenzene-Functionalized Polyimides Synthesized with Bulky Substituents (Postprint)

DTIC Science & Technology

2017-12-06

mechanical response of the azobenzene- functionalized polyimide is correlated to the rotational freedom of the polyimide chains (resulting in extensive... correlated to the rotational freedom of the polyimide chains (resulting in extensive segmental mobility) and fractional free volume (FFV > 0.1...response has been described,34 and a recent simulation study on the stress relaxation dynamics of azo-polyimides has provided insights into the correlation

Simulations of stretching a flexible polyelectrolyte with varying charge separation

DOE PAGES

Stevens, Mark J.; Saleh, Omar A.

2016-07-22

We calculated the force-extension curves for a flexible polyelectrolyte chain with varying charge separations by performing Monte Carlo simulations of a 5000 bead chain using a screened Coulomb interaction. At all charge separations, the force-extension curves exhibit a Pincus-like scaling regime at intermediate forces and a logarithmic regime at large forces. As the charge separation increases, the Pincus regime shifts to a larger range of forces and the logarithmic regime starts are larger forces. We also found that force-extension curve for the corresponding neutral chain has a logarithmic regime. Decreasing the diameter of bead in the neutral chain simulations removedmore » the logarithmic regime, and the force-extension curve tends to the freely jointed chain limit. In conclusion, this result shows that only excluded volume is required for the high force logarithmic regime to occur.« less

Neighbour-die effect on the measurement of wafer-level flip-chip LED dies in production lines

NASA Astrophysics Data System (ADS)

Chen, Tengfei; Wan, Zirui; Li, Bin

2017-11-01

The light from the side surfaces of the test flip-chip light-emitting diode (FCLED) dies is reflected, refracted or absorbed by neighbour dies during the measurement of wafer-level FCLED dies in production lines. A notable measurement deviation is caused by the neighbour-die effect, which is not considered in current industry practice. In this paper, Monte Carlo ray-tracing simulations are used to study the measurement deviations caused by the neighbour-die effect and extension ratios of the film. The simulation results show that the maximal deviation of radiant flux impinging the photodiode can reach 5.5%, if the die is tested without any neighbour dies, or is surrounded by a set of neighbour dies at an extension ratio of 1.1. Moreover, the dependence between the measurement results and neighbour cases for different extension ratios is also investigated. Then, a modified calibration method is proposed and studied. The proposed technique can be used to improve the calibration and measurement accuracy of the test equipment used for measurement of wafer-level FCLED dies in production lines.

A glacier runoff extension to the Precipitation Runoff Modeling System

USGS Publications Warehouse

Van Beusekom, Ashley E.; Viger, Roland

2016-01-01

A module to simulate glacier runoff, PRMSglacier, was added to PRMS (Precipitation Runoff Modeling System), a distributed-parameter, physical-process hydrological simulation code. The extension does not require extensive on-glacier measurements or computational expense but still relies on physical principles over empirical relations as much as is feasible while maintaining model usability. PRMSglacier is validated on two basins in Alaska, Wolverine, and Gulkana Glacier basin, which have been studied since 1966 and have a substantial amount of data with which to test model performance over a long period of time covering a wide range of climatic and hydrologic conditions. When error in field measurements is considered, the Nash-Sutcliffe efficiencies of streamflow are 0.87 and 0.86, the absolute bias fractions of the winter mass balance simulations are 0.10 and 0.08, and the absolute bias fractions of the summer mass balances are 0.01 and 0.03, all computed over 42 years for the Wolverine and Gulkana Glacier basins, respectively. Without taking into account measurement error, the values are still within the range achieved by the more computationally expensive codes tested over shorter time periods.

Simulation of Constrained Musculoskeletal Systems in Task Space.

PubMed

Stanev, Dimitar; Moustakas, Konstantinos

2018-02-01

This paper proposes an operational task space formalization of constrained musculoskeletal systems, motivated by its promising results in the field of robotics. The change of representation requires different algorithms for solving the inverse and forward dynamics simulation in the task space domain. We propose an extension to the direct marker control and an adaptation of the computed muscle control algorithms for solving the inverse kinematics and muscle redundancy problems, respectively. Experimental evaluation demonstrates that this framework is not only successful in dealing with the inverse dynamics problem, but also provides an intuitive way of studying and designing simulations, facilitating assessment prior to any experimental data collection. The incorporation of constraints in the derivation unveils an important extension of this framework toward addressing systems that use absolute coordinates and topologies that contain closed kinematic chains. Task space projection reveals a more intuitive encoding of the motion planning problem, allows for better correspondence between observed and estimated variables, provides the means to effectively study the role of kinematic redundancy, and most importantly, offers an abstract point of view and control, which can be advantageous toward further integration with high level models of the precommand level. Task-based approaches could be adopted in the design of simulation related to the study of constrained musculoskeletal systems.

Dissipative particle dynamics simulations of polymer chains: scaling laws and shearing response compared to DNA experiments.

PubMed

Symeonidis, Vasileios; Em Karniadakis, George; Caswell, Bruce

2005-08-12

Dissipative particle dynamics simulations of several bead-spring representations of polymer chains in dilute solution are used to demonstrate the correct static scaling laws for the radius of gyration. Shear flow results for the wormlike chain simulating single DNA molecules compare well with average extensions from experiments, irrespective of the number of beads. However, coarse graining with more than a few beads degrades the agreement of the autocorrelation of the extension.

The role of elasticity in simulating long-term tectonic extension

NASA Astrophysics Data System (ADS)

Olive, Jean-Arthur; Behn, Mark D.; Mittelstaedt, Eric; Ito, Garrett; Klein, Benjamin Z.

2016-05-01

While elasticity is a defining characteristic of the Earth's lithosphere, it is often ignored in numerical models of long-term tectonic processes in favour of a simpler viscoplastic description. Here we assess the consequences of this assumption on a well-studied geodynamic problem: the growth of normal faults at an extensional plate boundary. We conduct 2-D numerical simulations of extension in elastoplastic and viscoplastic layers using a finite difference, particle-in-cell numerical approach. Our models simulate a range of faulted layer thicknesses and extension rates, allowing us to quantify the role of elasticity on three key observables: fault-induced topography, fault rotation, and fault life span. In agreement with earlier studies, simulations carried out in elastoplastic layers produce rate-independent lithospheric flexure accompanied by rapid fault rotation and an inverse relationship between fault life span and faulted layer thickness. By contrast, models carried out with a viscoplastic lithosphere produce results that may qualitatively resemble the elastoplastic case, but depend strongly on the product of extension rate and layer viscosity U × ηL. When this product is high, fault growth initially generates little deformation of the footwall and hanging wall blocks, resulting in unrealistic, rigid block-offset in topography across the fault. This configuration progressively transitions into a regime where topographic decay associated with flexure is fully accommodated within the numerical domain. In addition, high U × ηL favours the sequential growth of multiple short-offset faults as opposed to a large-offset detachment. We interpret these results by comparing them to an analytical model for the fault-induced flexure of a thin viscous plate. The key to understanding the viscoplastic model results lies in the rate-dependence of the flexural wavelength of a viscous plate, and the strain rate dependence of the force increase associated with footwall and hanging wall bending. This behaviour produces unrealistic deformation patterns that can hinder the geological relevance of long-term rifting models that assume a viscoplastic rheology.

3D numerical simulations of multiphase continental rifting

NASA Astrophysics Data System (ADS)

Naliboff, J.; Glerum, A.; Brune, S.

2017-12-01

Observations of rifted margin architecture suggest continental breakup occurs through multiple phases of extension with distinct styles of deformation. The initial rifting stages are often characterized by slow extension rates and distributed normal faulting in the upper crust decoupled from deformation in the lower crust and mantle lithosphere. Further rifting marks a transition to higher extension rates and coupling between the crust and mantle lithosphere, with deformation typically focused along large-scale detachment faults. Significantly, recent detailed reconstructions and high-resolution 2D numerical simulations suggest that rather than remaining focused on a single long-lived detachment fault, deformation in this phase may progress toward lithospheric breakup through a complex process of fault interaction and development. The numerical simulations also suggest that an initial phase of distributed normal faulting can play a key role in the development of these complex fault networks and the resulting finite deformation patterns. Motivated by these findings, we will present 3D numerical simulations of continental rifting that examine the role of temporal increases in extension velocity on rifted margin structure. The numerical simulations are developed with the massively parallel finite-element code ASPECT. While originally designed to model mantle convection using advanced solvers and adaptive mesh refinement techniques, ASPECT has been extended to model visco-plastic deformation that combines a Drucker Prager yield criterion with non-linear dislocation and diffusion creep. To promote deformation localization, the internal friction angle and cohesion weaken as a function of accumulated plastic strain. Rather than prescribing a single zone of weakness to initiate deformation, an initial random perturbation of the plastic strain field combined with rapid strain weakening produces distributed normal faulting at relatively slow rates of extension in both 2D and 3D simulations. Our presentation will focus on both the numerical assumptions required to produce these results and variations in 3D rifted margin architecture arising from a transition from slow to rapid rates of extension.

A novel approach to study effects of asymmetric stiffness on parametric instabilities of multi-rotor-system

NASA Astrophysics Data System (ADS)

Jain, Anuj Kumar; Rastogi, Vikas; Agrawal, Atul Kumar

2018-01-01

The main focus of this paper is to study effects of asymmetric stiffness on parametric instabilities of multi-rotor-system through extended Lagrangian formalism, where symmetries are broken in terms of the rotor stiffness. The complete insight of dynamic behaviour of multi-rotor-system with asymmetries is evaluated through extension of Lagrangian equation with a case study. In this work, a dynamic mathematical model of a multi-rotor-system through a novel approach of extension of Lagrangian mechanics is developed, where the system is having asymmetries due to varying stiffness. The amplitude and the natural frequency of the rotor are obtained analytically through the proposed methodology. The bond graph modeling technique is used for modeling the asymmetric rotor. Symbol-shakti® software is used for the simulation of the model. The effects of the stiffness of multi-rotor-system on amplitude and frequencies are studied using numerical simulation. Simulation results show a considerable agreement with the theoretical results obtained through extended Lagrangian formalism. It is further shown that amplitude of the rotor increases inversely the stiffness of the rotor up to a certain limit, which is also affirmed theoretically.

SiMon: Simulation Monitor for Computational Astrophysics

NASA Astrophysics Data System (ADS)

Xuran Qian, Penny; Cai, Maxwell Xu; Portegies Zwart, Simon; Zhu, Ming

2017-09-01

Scientific discovery via numerical simulations is important in modern astrophysics. This relatively new branch of astrophysics has become possible due to the development of reliable numerical algorithms and the high performance of modern computing technologies. These enable the analysis of large collections of observational data and the acquisition of new data via simulations at unprecedented accuracy and resolution. Ideally, simulations run until they reach some pre-determined termination condition, but often other factors cause extensive numerical approaches to break down at an earlier stage. In those cases, processes tend to be interrupted due to unexpected events in the software or the hardware. In those cases, the scientist handles the interrupt manually, which is time-consuming and prone to errors. We present the Simulation Monitor (SiMon) to automatize the farming of large and extensive simulation processes. Our method is light-weight, it fully automates the entire workflow management, operates concurrently across multiple platforms and can be installed in user space. Inspired by the process of crop farming, we perceive each simulation as a crop in the field and running simulation becomes analogous to growing crops. With the development of SiMon we relax the technical aspects of simulation management. The initial package was developed for extensive parameter searchers in numerical simulations, but it turns out to work equally well for automating the computational processing and reduction of observational data reduction.

Simulating dynamic and mixed-severity fire regimes: a process-based fire extension for LANDIS-II

Treesearch

Brian R. Sturtevant; Robert M. Scheller; Brian R. Miranda; Douglas Shinneman; Alexandra Syphard

2009-01-01

Fire regimes result from reciprocal interactions between vegetation and fire that may be further affected by other disturbances, including climate, landform, and terrain. In this paper, we describe fire and fuel extensions for the forest landscape simulation model, LANDIS-II, that allow dynamic interactions among fire, vegetation, climate, and landscape structure, and...

Quantum chemical calculations of interatomic potentials for computer simulation of solids

NASA Technical Reports Server (NTRS)

1977-01-01

A comprehensive mathematical model by which the collective behavior of a very large number of atoms within a metal or alloy can accurately be simulated was developed. Work was done in order to predict and modify the strength of materials to suit our technological needs. The method developed is useful in studying atomic interactions related to dislocation motion and crack extension.

NASA/ESA CV-990 airborne simulation of Spacelab

NASA Technical Reports Server (NTRS)

Mulholland, D.; Neel, C.; De Waard, J.; Lovelett, R.; Weaver, L.; Parker, R.

1975-01-01

The paper describes the joint NASA/ESA extensive Spacelab simulation using the NASA CV-990 airborne laboratory. The scientific payload was selected to conduct studies in upper atmospheric physics and infrared astronomy. Two experiment operators from Europe and two from the U.S. were selected to live aboard the aircraft along with a mission manager for a six-day period and operate the experiments in behalf of the principal scientists. The mission was successful and provided extensive data relevant to Spacelab objectives on overall management of a complex international payload; experiment preparation, testing, and integration; training for proxy operation in space; data handling; multiexperimenter use of common experimenter facilities (telescopes); and schedule requirements to prepare for such a Spacelab mission.

NEVESIM: event-driven neural simulation framework with a Python interface.

PubMed

Pecevski, Dejan; Kappel, David; Jonke, Zeno

2014-01-01

NEVESIM is a software package for event-driven simulation of networks of spiking neurons with a fast simulation core in C++, and a scripting user interface in the Python programming language. It supports simulation of heterogeneous networks with different types of neurons and synapses, and can be easily extended by the user with new neuron and synapse types. To enable heterogeneous networks and extensibility, NEVESIM is designed to decouple the simulation logic of communicating events (spikes) between the neurons at a network level from the implementation of the internal dynamics of individual neurons. In this paper we will present the simulation framework of NEVESIM, its concepts and features, as well as some aspects of the object-oriented design approaches and simulation strategies that were utilized to efficiently implement the concepts and functionalities of the framework. We will also give an overview of the Python user interface, its basic commands and constructs, and also discuss the benefits of integrating NEVESIM with Python. One of the valuable capabilities of the simulator is to simulate exactly and efficiently networks of stochastic spiking neurons from the recently developed theoretical framework of neural sampling. This functionality was implemented as an extension on top of the basic NEVESIM framework. Altogether, the intended purpose of the NEVESIM framework is to provide a basis for further extensions that support simulation of various neural network models incorporating different neuron and synapse types that can potentially also use different simulation strategies.

NEVESIM: event-driven neural simulation framework with a Python interface

PubMed Central

Pecevski, Dejan; Kappel, David; Jonke, Zeno

2014-01-01

NEVESIM is a software package for event-driven simulation of networks of spiking neurons with a fast simulation core in C++, and a scripting user interface in the Python programming language. It supports simulation of heterogeneous networks with different types of neurons and synapses, and can be easily extended by the user with new neuron and synapse types. To enable heterogeneous networks and extensibility, NEVESIM is designed to decouple the simulation logic of communicating events (spikes) between the neurons at a network level from the implementation of the internal dynamics of individual neurons. In this paper we will present the simulation framework of NEVESIM, its concepts and features, as well as some aspects of the object-oriented design approaches and simulation strategies that were utilized to efficiently implement the concepts and functionalities of the framework. We will also give an overview of the Python user interface, its basic commands and constructs, and also discuss the benefits of integrating NEVESIM with Python. One of the valuable capabilities of the simulator is to simulate exactly and efficiently networks of stochastic spiking neurons from the recently developed theoretical framework of neural sampling. This functionality was implemented as an extension on top of the basic NEVESIM framework. Altogether, the intended purpose of the NEVESIM framework is to provide a basis for further extensions that support simulation of various neural network models incorporating different neuron and synapse types that can potentially also use different simulation strategies. PMID:25177291

Cislan-2 extension final document by University of Twente (Netherlands)

NASA Astrophysics Data System (ADS)

Niemegeers, Ignas; Baumann, Frank; Beuwer, Wim; Jordense, Marcel; Pras, Aiko; Schutte, Leon; Tracey, Ian

1992-01-01

Results of worked performed under the so called Cislan extension contract are presented. The adaptation of the Cislan 2 prototype design to an environment of interconnected Local Area Networks (LAN's) instead of a single 802.5 token ring LAN is considered. In order to extend the network architecture, the Interconnection Function (IF) protocol layer was subdivided into two protocol layers: a new IF layer, and below the Medium Enhancement (ME) protocol layer. Some small enhancements to the distributed bandwidth allocation protocol were developed, which in fact are also applicable to the 'normal' Cislan 2 system. The new services and protocols are described together with some scenarios and requirements for the new internetting Cislan 2 system. How to overcome the degradation of the quality of speech due to packet loss on the LAN subsystem was studied. Experiments were planned in order to measure this speech quality degradation. Simulations were performed of two Cislan subsystems, the bandwidth allocation protocol and the clock synchronization mechanism. Results on both simulations, performed on SUN workstations using QNAP as a simulation tool, are given. Results of the simulations of the clock synchronization mechanism, and results of the simulation of the distributed bandwidth allocation protocol are given.

A federated design for a neurobiological simulation engine: the CBI federated software architecture.

PubMed

Cornelis, Hugo; Coop, Allan D; Bower, James M

2012-01-01

Simulator interoperability and extensibility has become a growing requirement in computational biology. To address this, we have developed a federated software architecture. It is federated by its union of independent disparate systems under a single cohesive view, provides interoperability through its capability to communicate, execute programs, or transfer data among different independent applications, and supports extensibility by enabling simulator expansion or enhancement without the need for major changes to system infrastructure. Historically, simulator interoperability has relied on development of declarative markup languages such as the neuron modeling language NeuroML, while simulator extension typically occurred through modification of existing functionality. The software architecture we describe here allows for both these approaches. However, it is designed to support alternative paradigms of interoperability and extensibility through the provision of logical relationships and defined application programming interfaces. They allow any appropriately configured component or software application to be incorporated into a simulator. The architecture defines independent functional modules that run stand-alone. They are arranged in logical layers that naturally correspond to the occurrence of high-level data (biological concepts) versus low-level data (numerical values) and distinguish data from control functions. The modular nature of the architecture and its independence from a given technology facilitates communication about similar concepts and functions for both users and developers. It provides several advantages for multiple independent contributions to software development. Importantly, these include: (1) Reduction in complexity of individual simulator components when compared to the complexity of a complete simulator, (2) Documentation of individual components in terms of their inputs and outputs, (3) Easy removal or replacement of unnecessary or obsoleted components, (4) Stand-alone testing of components, and (5) Clear delineation of the development scope of new components.

A Federated Design for a Neurobiological Simulation Engine: The CBI Federated Software Architecture

PubMed Central

Cornelis, Hugo; Coop, Allan D.; Bower, James M.

2012-01-01

Simulator interoperability and extensibility has become a growing requirement in computational biology. To address this, we have developed a federated software architecture. It is federated by its union of independent disparate systems under a single cohesive view, provides interoperability through its capability to communicate, execute programs, or transfer data among different independent applications, and supports extensibility by enabling simulator expansion or enhancement without the need for major changes to system infrastructure. Historically, simulator interoperability has relied on development of declarative markup languages such as the neuron modeling language NeuroML, while simulator extension typically occurred through modification of existing functionality. The software architecture we describe here allows for both these approaches. However, it is designed to support alternative paradigms of interoperability and extensibility through the provision of logical relationships and defined application programming interfaces. They allow any appropriately configured component or software application to be incorporated into a simulator. The architecture defines independent functional modules that run stand-alone. They are arranged in logical layers that naturally correspond to the occurrence of high-level data (biological concepts) versus low-level data (numerical values) and distinguish data from control functions. The modular nature of the architecture and its independence from a given technology facilitates communication about similar concepts and functions for both users and developers. It provides several advantages for multiple independent contributions to software development. Importantly, these include: (1) Reduction in complexity of individual simulator components when compared to the complexity of a complete simulator, (2) Documentation of individual components in terms of their inputs and outputs, (3) Easy removal or replacement of unnecessary or obsoleted components, (4) Stand-alone testing of components, and (5) Clear delineation of the development scope of new components. PMID:22242154

Sialyldisaccharide conformations: a molecular dynamics perspective

NASA Astrophysics Data System (ADS)

Selvin, Jeyasigamani F. A.; Priyadarzini, Thanu R. K.; Veluraja, Kasinadar

2012-04-01

Sialyldisaccharides are significant terminal components of glycoconjugates and their negative charge and conformation are extensively utilized in molecular recognition processes. The conformation and flexibility of four biologically important sialyldisaccharides [Neu5Acα(2-3)Gal, Neu5Acα(2-6)Gal, Neu5Acα(2-8)Neu5Ac and Neu5Acα(2-9)Neu5Ac] are studied using Molecular Dynamics simulations of 20 ns duration to deduce the conformational preferences of the sialyldisaccharides and the interactions which stabilize the conformations. This study clearly describes the possible conformational models of sialyldisaccharides deduced from 20 ns Molecular Dynamics simulations and our results confirm the role of water in the structural stabilization of sialyldisaccharides. An extensive analysis on the sialyldisaccharide structures available in PDB also confirms the conformational regions found by experiments are detected in MD simulations of 20 ns duration. The three dimensional structural coordinates for all the MD derived sialyldisaccharide conformations are deposited in the 3DSDSCAR database and these conformational models will be useful for glycobiologists and biotechnologists to understand the biological functions of sialic acid containing glycoconjugates.

Evolution of Flow channels and Dipolarization Using THEMIS Observations and Global MHD Simulations

NASA Astrophysics Data System (ADS)

El-Alaoui, M.; McPherron, R. L.; Nishimura, Y.

2017-12-01

We have extensively analyzed a substorm on March 14, 2008 for which we have observations from THEMIS spacecraft located beyond 9 RE near 2100 local time. The available data include an extensive network of all sky cameras and ground magnetometers that establish the times of various auroral and magnetic events. This arrangement provided an excellent data set with which to investigate meso-scale structures in the plasma sheet. We have used a global magnetohydrodynamic simulation to investigate the structure and dynamics of the magnetotail current sheet during this substorm. Both earthward and tailward flows were found in the observations as well as the simulations. The simulation shows that the flow channels follow tortuous paths that are often reflected or deflected before arriving at the inner magnetosphere. The simulation shows a sequence of fast flows and dipolarization events similar to what is seen in the data, though not at precisely the same times or locations. We will use our simulation results combined with the observations to investigate the global convection systems and current sheet structure during this event, showing how meso-scale structures fit into the context of the overall tail dynamics during this event. Our study includes determining the location, timing and strength of several current wedges and expansion onsets during an 8-hour interval.

Quadriceps force during knee extension in different replacement scenarios with a modular partial prosthesis.

PubMed

Calliess, Tilman; Schado, Ssuheib; Richter, Berna I; Becher, Christoph; Ezechieli, Marco; Ostermeier, Sven

2014-02-01

Previous biomechanical studies have shown that bi-cruciate retaining knee replacement does not significantly alter normal knee kinematics, however, there are no data on the influence of a combined medial and patellofemoral bi-compartimental arthroplasty. The purpose of this in vitro study was to evaluate the effect of different replacement scenarios with a modular partial knee replacement system on the amount of quadriceps force required to extend the knee during an isokinetic extension cycle. Ten human knee specimens were tested in a kinematic knee simulator under (1) physiologic condition and after subsequent implantation of (2) a medial unicondylar and (3) a trochlear replacement. An isokinetic extension cycle of the knee with a constant extension moment of 31 Nm was simulated. The resulting quadriceps extension force was measured from 120° to full knee extension. The quadriceps force curve described a typically sinusoidal characteristic before and after each replacement scenario. The isolated medial replacement resulted in a slightly, but significantly higher maximum quadriceps force (1510 N vs. 1585 N, P = 0.006) as well as the subsequent trochlear replacement showed an additional increase (1801 N, P = 0.008). However, for both replacements no significant difference to the untreated condition could be detected in mid-flexion (10-50°). When considering a bi-compartimental replacement an increase of required maximum quadriceps force needed to extend the knee has to keep in mind. However, the close to physiological movement in mid-flexion suggests that patients with a bi-crutiate retaining arthroplasty might have an advantage in knee stability compared to total knee arthroplasty. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nanosecond Enhancements of the Atmospheric Electron Density by Extensive Air Showers

NASA Astrophysics Data System (ADS)

Rutjes, C.; Camporeale, E.; Ebert, U.; Buitink, S.; Scholten, O.; Trinh, G. T. N.; Witteveen, J.

2015-12-01

As is well known a sufficient density of free electrons and strong electric fields are the basic requirements to start any electrical discharge. In the context of thunderstorm discharges it has become clear that in addition droplets and or ice particles are required to enhance the electric field to values above breakdown. In our recent study [1] we have shown that these three ingredients have to interplay to allow for lightning inception, triggered by an extensive air shower event. The extensive air showers are a very stochastic natural phenomenon, creating highly coherent sub-nanosecond enhancements of the atmospheric electron density. Predicting these electron density enhancements accurately one has to take the uncertainty of the input variables into account. For this study we use the initial energy, inclination and altitude of first interaction, which will influence the evolution of the shower significantly. To this end, we use the stochastic collocation method, [2] to post-process our detailed Monte Carlo extensive air shower simulations, done with the CORSIKA [3] software package, which provides an efficient and elegant way to determine the distribution of the atmospheric electron density enhancements. [1] Dubinova, A., Rutjes, C., Ebert, E., Buitink, S., Scholten, O., and Trinh, G. T. N. "Prediction of Lightning Inception by Large Ice Particles and Extensive Air Showers." PRL 115 015002 (2015)[2] G.J.A. Loeven, J.A.S. Witteveen, H. Bijl, Probabilistic collocation: an efficient nonintrusive approach for arbitrarily distributed parametric uncertainties, 45th AIAA Aerospace Sciences Meeting, Reno, Nevada, 2007, AIAA-2007-317[3] Heck, Dieter, et al. CORSIKA: A Monte Carlo code to simulate extensive air showers. No. FZKA-6019. 1998.

Using Predictability for Lexical Segmentation

ERIC Educational Resources Information Center

Çöltekin, Çagri

2017-01-01

This study investigates a strategy based on predictability of consecutive sub-lexical units in learning to segment a continuous speech stream into lexical units using computational modeling and simulations. Lexical segmentation is one of the early challenges during language acquisition, and it has been studied extensively through psycholinguistic…

Matching the reaction-diffusion simulation to dynamic [18F]FMISO PET measurements in tumors: extension to a flow-limited oxygen-dependent model.

PubMed

Shi, Kuangyu; Bayer, Christine; Gaertner, Florian C; Astner, Sabrina T; Wilkens, Jan J; Nüsslin, Fridtjof; Vaupel, Peter; Ziegler, Sibylle I

2017-02-01

Positron-emission tomography (PET) with hypoxia specific tracers provides a noninvasive method to assess the tumor oxygenation status. Reaction-diffusion models have advantages in revealing the quantitative relation between in vivo imaging and the tumor microenvironment. However, there is no quantitative comparison of the simulation results with the real PET measurements yet. The lack of experimental support hampers further applications of computational simulation models. This study aims to compare the simulation results with a preclinical [ 18 F]FMISO PET study and to optimize the reaction-diffusion model accordingly. Nude mice with xenografted human squamous cell carcinomas (CAL33) were investigated with a 2 h dynamic [ 18 F]FMISO PET followed by immunofluorescence staining using the hypoxia marker pimonidazole and the endothelium marker CD 31. A large data pool of tumor time-activity curves (TAC) was simulated for each mouse by feeding the arterial input function (AIF) extracted from experiments into the model with different configurations of the tumor microenvironment. A measured TAC was considered to match a simulated TAC when the difference metric was below a certain, noise-dependent threshold. As an extension to the well-established Kelly model, a flow-limited oxygen-dependent (FLOD) model was developed to improve the matching between measurements and simulations. The matching rate between the simulated TACs of the Kelly model and the mouse PET data ranged from 0 to 28.1% (on average 9.8%). By modifying the Kelly model to an FLOD model, the matching rate between the simulation and the PET measurements could be improved to 41.2-84.8% (on average 64.4%). Using a simulation data pool and a matching strategy, we were able to compare the simulated temporal course of dynamic PET with in vivo measurements. By modifying the Kelly model to a FLOD model, the computational simulation was able to approach the dynamic [ 18 F]FMISO measurements in the investigated tumors.

Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit.

PubMed

Bernal, M A; Bordage, M C; Brown, J M C; Davídková, M; Delage, E; El Bitar, Z; Enger, S A; Francis, Z; Guatelli, S; Ivanchenko, V N; Karamitros, M; Kyriakou, I; Maigne, L; Meylan, S; Murakami, K; Okada, S; Payno, H; Perrot, Y; Petrovic, I; Pham, Q T; Ristic-Fira, A; Sasaki, T; Štěpán, V; Tran, H N; Villagrasa, C; Incerti, S

2015-12-01

Understanding the fundamental mechanisms involved in the induction of biological damage by ionizing radiation remains a major challenge of today's radiobiology research. The Monte Carlo simulation of physical, physicochemical and chemical processes involved may provide a powerful tool for the simulation of early damage induction. The Geant4-DNA extension of the general purpose Monte Carlo Geant4 simulation toolkit aims to provide the scientific community with an open source access platform for the mechanistic simulation of such early damage. This paper presents the most recent review of the Geant4-DNA extension, as available to Geant4 users since June 2015 (release 10.2 Beta). In particular, the review includes the description of new physical models for the description of electron elastic and inelastic interactions in liquid water, as well as new examples dedicated to the simulation of physicochemical and chemical stages of water radiolysis. Several implementations of geometrical models of biological targets are presented as well, and the list of Geant4-DNA examples is described. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Payload crew training complex simulation engineer's handbook

NASA Technical Reports Server (NTRS)

Shipman, D. L.

1984-01-01

The Simulation Engineer's Handbook is a guide for new engineers assigned to Experiment Simulation and a reference for engineers previously assigned. The experiment simulation process, development of experiment simulator requirements, development of experiment simulator hardware and software, and the verification of experiment simulators are discussed. The training required for experiment simulation is extensive and is only referenced in the handbook.

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

PubMed

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

2010-01-01

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

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

PubMed Central

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

2010-01-01

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

Time domain simulations of preliminary breakdown pulses in natural lightning.

PubMed

Carlson, B E; Liang, C; Bitzer, P; Christian, H

2015-06-16

Lightning discharge is a complicated process with relevant physical scales spanning many orders of magnitude. In an effort to understand the electrodynamics of lightning and connect physical properties of the channel to observed behavior, we construct a simulation of charge and current flow on a narrow conducting channel embedded in three-dimensional space with the time domain electric field integral equation, the method of moments, and the thin-wire approximation. The method includes approximate treatment of resistance evolution due to lightning channel heating and the corona sheath of charge surrounding the lightning channel. Focusing our attention on preliminary breakdown in natural lightning by simulating stepwise channel extension with a simplified geometry, our simulation reproduces the broad features observed in data collected with the Huntsville Alabama Marx Meter Array. Some deviations in pulse shape details are evident, suggesting future work focusing on the detailed properties of the stepping mechanism. Preliminary breakdown pulses can be reproduced by simulated channel extension Channel heating and corona sheath formation are crucial to proper pulse shape Extension processes and channel orientation significantly affect observations.

Time domain simulations of preliminary breakdown pulses in natural lightning

PubMed Central

Carlson, B E; Liang, C; Bitzer, P; Christian, H

2015-01-01

Lightning discharge is a complicated process with relevant physical scales spanning many orders of magnitude. In an effort to understand the electrodynamics of lightning and connect physical properties of the channel to observed behavior, we construct a simulation of charge and current flow on a narrow conducting channel embedded in three-dimensional space with the time domain electric field integral equation, the method of moments, and the thin-wire approximation. The method includes approximate treatment of resistance evolution due to lightning channel heating and the corona sheath of charge surrounding the lightning channel. Focusing our attention on preliminary breakdown in natural lightning by simulating stepwise channel extension with a simplified geometry, our simulation reproduces the broad features observed in data collected with the Huntsville Alabama Marx Meter Array. Some deviations in pulse shape details are evident, suggesting future work focusing on the detailed properties of the stepping mechanism. Key Points Preliminary breakdown pulses can be reproduced by simulated channel extension Channel heating and corona sheath formation are crucial to proper pulse shape Extension processes and channel orientation significantly affect observations PMID:26664815

Validation of the k- ω turbulence model for the thermal boundary layer profile of effusive cooled walls

NASA Astrophysics Data System (ADS)

Hink, R.

2015-09-01

The choice of materials for rocket chamber walls is limited by its thermal resistance. The thermal loads can be reduced substantially by the blowing out of gases through a porous surface. The k- ω-based turbulence models for computational fluid dynamic simulations are designed for smooth, non-permeable walls and have to be adjusted to account for the influence of injected fluids. Wilcox proposed therefore an extension for the k- ω turbulence model for the correct prediction of turbulent boundary layer velocity profiles. In this study, this extension is validated against experimental thermal boundary layer data from the Thermosciences Division of the Department of Mechanical Engineering from the Stanford University. All simulations are performed with a finite volume-based in-house code of the German Aerospace Center. Several simulations with different blowing settings were conducted and discussed in comparison to the results of the original model and in comparison to an additional roughness implementation. This study has permitted to understand that velocity profile corrections are necessary in contrast to additional roughness corrections to predict the correct thermal boundary layer profile of effusive cooled walls. Finally, this approach is applied to a two-dimensional simulation of an effusive cooled rocket chamber wall.

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

Düchs, Dominik; Delaney, Kris T., E-mail: kdelaney@mrl.ucsb.edu; Fredrickson, Glenn H., E-mail: ghf@mrl.ucsb.edu

Field-theoretic models have been used extensively to study the phase behavior of inhomogeneous polymer melts and solutions, both in self-consistent mean-field calculations and in numerical simulations of the full theory capturing composition fluctuations. The models commonly used can be grouped into two categories, namely, species models and exchange models. Species models involve integrations of functionals that explicitly depend on fields originating both from species density operators and their conjugate chemical potential fields. In contrast, exchange models retain only linear combinations of the chemical potential fields. In the two-component case, development of exchange models has been instrumental in enabling stable complexmore » Langevin (CL) simulations of the full complex-valued theory. No comparable stable CL approach has yet been established for field theories of the species type. Here, we introduce an extension of the exchange model to an arbitrary number of components, namely, the multi-species exchange (MSE) model, which greatly expands the classes of soft material systems that can be accessed by the complex Langevin simulation technique. We demonstrate the stability and accuracy of the MSE-CL sampling approach using numerical simulations of triblock and tetrablock terpolymer melts, and tetrablock quaterpolymer melts. This method should enable studies of a wide range of fluctuation phenomena in multiblock/multi-species polymer blends and composites.« less

An object oriented Python interface for atomistic simulations

NASA Astrophysics Data System (ADS)

Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

2016-01-01

Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins.

PubMed

Cossio-Pérez, Rodrigo; Palma, Juliana; Pierdominici-Sottile, Gustavo

2017-04-24

Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.

Scattering effects on the performance of carbon nanotube field effect transistor in a compact model

NASA Astrophysics Data System (ADS)

Hamieh, S. D.; Desgreys, P.; Naviner, J. F.

2010-01-01

Carbon nanotube field-effect transistors (CNTFET) are being extensively studied as possible successors to CMOS. Device simulators have been developed to estimate their performance in sub-10-nm and device structures have been fabricated. In this work, a new compact model of single-walled semiconducting CNTFET is proposed implementing the calculation of energy conduction sub-band minima and the treatment of scattering effects through energy shift in CNTFET. The developed model has been used to simulate I-V characteristics using VHDL-AMS simulator.

The statistical significance of error probability as determined from decoding simulations for long codes

NASA Technical Reports Server (NTRS)

Massey, J. L.

1976-01-01

The very low error probability obtained with long error-correcting codes results in a very small number of observed errors in simulation studies of practical size and renders the usual confidence interval techniques inapplicable to the observed error probability. A natural extension of the notion of a 'confidence interval' is made and applied to such determinations of error probability by simulation. An example is included to show the surprisingly great significance of as few as two decoding errors in a very large number of decoding trials.

Suppressing correlations in massively parallel simulations of lattice models

NASA Astrophysics Data System (ADS)

Kelling, Jeffrey; Ódor, Géza; Gemming, Sibylle

2017-11-01

For lattice Monte Carlo simulations parallelization is crucial to make studies of large systems and long simulation time feasible, while sequential simulations remain the gold-standard for correlation-free dynamics. Here, various domain decomposition schemes are compared, concluding with one which delivers virtually correlation-free simulations on GPUs. Extensive simulations of the octahedron model for 2 + 1 dimensional Kardar-Parisi-Zhang surface growth, which is very sensitive to correlation in the site-selection dynamics, were performed to show self-consistency of the parallel runs and agreement with the sequential algorithm. We present a GPU implementation providing a speedup of about 30 × over a parallel CPU implementation on a single socket and at least 180 × with respect to the sequential reference.

Evaluation of unsaturated-zone solute-transport models for studies of agricultural chemicals

USGS Publications Warehouse

Nolan, Bernard T.; Bayless, E. Randall; Green, Christopher T.; Garg, Sheena; Voss, Frank D.; Lampe, David C.; Barbash, Jack E.; Capel, Paul D.; Bekins, Barbara A.

2005-01-01

Of the models tested, RZWQM, HYDRUS2D, VS2DT, GLEAMS and PRZM had graphical user interfaces. Extensive documentation was available for RZWQM, HYDRUS2D, and VS2DT. RZWQM can explicitly simulate water and solute flux in macropores, and both HYDRUS2D and VS2DT can simulate water and solute flux in two dimensions. The version of RZWQM tested had a maximum simulation depth of 3 meters. The complex models simulate the formation, transport, and fate of degradates of up to three to five compounds including the parent, with the exception of VS2DT, which simulates the transport and fate of a single compound.

A New Numerical Simulation technology of Multistage Fracturing in Horizontal Well

NASA Astrophysics Data System (ADS)

Cheng, Ning; Kang, Kaifeng; Li, Jianming; Liu, Tao; Ding, Kun

2017-11-01

Horizontal multi-stage fracturing is recognized the effective development technology of unconventional oil resources. Geological mechanics in the numerical simulation of hydraulic fracturing technology occupies very important position, compared with the conventional numerical simulation technology, because of considering the influence of geological mechanics. New numerical simulation of hydraulic fracturing can more effectively optimize the design of fracturing and evaluate the production after fracturing. This paper studies is based on the three-dimensional stress and rock physics parameters model, using the latest fluid-solid coupling numerical simulation technology to engrave the extension process of fracture and describes the change of stress field in fracturing process, finally predict the production situation.

Guidance law simulation studies for complex approaches using the Microwave Landing System (MLS)

NASA Technical Reports Server (NTRS)

Feather, J. B.

1986-01-01

This report documents results for MLS guidance algorithm development conducted by DAC for NASA under the Advance Transport Operating Systems (ATOPS) Technology Studies program (NAS1-18028). The study consisted of evaluating guidance laws for vertical and lateral path control, as well as speed control, by simulating an MLS approach for the Washington National Airport. This work is an extension and generalization of a previous ATOPS contract (NAS1-16202) completed by DAC in 1985. The Washington river approach was simulated by six waypoints and one glideslope change and consisted of an eleven nautical mile approach path. Tracking performance was generated for 10 cases representing several different conditions, which included MLS noise, steady wind, turbulence, and windshear. Results of this simulation phase are suitable for use in future fixed-base simulator evaluations employing actual hardware (autopilot and a performance management system), as well as crew procedures and information requirements for MLS.

Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics.

PubMed

Panshenskov, Mikhail; Solov'yov, Ilia A; Solov'yov, Andrey V

2014-06-30

Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system. Copyright © 2014 Wiley Periodicals, Inc.

Numerical simulation of geomorphic, climatic and anthropogenic drivers of soil distribution on semi-arid hillslopes

NASA Astrophysics Data System (ADS)

Willgoose, G. R.; Cohen, S.; Svoray, T.; Sela, S.; Hancock, G. R.

2010-12-01

Numerical models are an important tool for studying landscape processes as they allow us to isolate specific processes and drivers and test various physics and spatio-temporal scenarios. Here we use a distributed physically-based soil evolution model (mARM4D) to describe the drivers and processes controlling soil-landscape evolution on a field-site at the fringe between the Mediterranean and desert regions of Israel. This study is an initial effort in a larger project aimed at improving our understanding of the mechanisms and drivers that led to the extensive removal of soils from the loess covered hillslopes of this region. This specific region is interesting as it is located between the Mediterranean climate region in which widespread erosion from hillslopes was attributed to human activity during the Holocene and the arid region in which extensive removal of loess from hillslopes was shown to have been driven by climatic changes during the late-Pleistocene. First we study the sediment transport mechanism of the soil-landscape evolution processes in our study-site. We simulate soil-landscape evolution with only one sediment transport process (fluvial or diffusive) at a time. We find that diffusive sediment transport is likely the dominant process in this site as it resulted in soil distributions that better corresponds to current observations. We then simulate several realistic climatic/anthropogenic scenarios (based on the literature) in order to quantify the sensitivity of the soil-landscape evolution process to temporal fluctuations. We find that this site is relatively insensitive to short term (several thousands of years) sharp, changes. This suggests that climate, rather then human activity, was the main driver for the extensive removal of loess from the hillslopes.

Comparative study of different stochastic weather generators for long-term climate data simulation

USDA-ARS?s Scientific Manuscript database

Climate is one of the single most important factors affecting watershed ecosystems and water resources. The effect of climate variability and change has been studied extensively in some places; in many places, however, assessments are hampered by limited availability of long term continuous climate ...

Relationship between movement time and hip moment impulse in the sagittal plane during sit-to-stand movement: a combined experimental and computer simulation study.

PubMed

Inai, Takuma; Takabayashi, Tomoya; Edama, Mutsuaki; Kubo, Masayoshi

2018-04-27

The association between repetitive hip moment impulse and the progression of hip osteoarthritis is a recently recognized area of study. A sit-to-stand movement is essential for daily life and requires hip extension moment. Although a change in the sit-to-stand movement time may influence the hip moment impulse in the sagittal plane, this effect has not been examined. The purpose of this study was to clarify the relationship between sit-to-stand movement time and hip moment impulse in the sagittal plane. Twenty subjects performed the sit-to-stand movement at a self-selected natural speed. The hip, knee, and ankle joint angles obtained from experimental trials were used to perform two computer simulations. In the first simulation, the actual sit-to-stand movement time obtained from the experiment was entered. In the second simulation, sit-to-stand movement times ranging from 0.5 to 4.0 s at intervals of 0.25 s were entered. Hip joint moments and hip moment impulses in the sagittal plane during sit-to-stand movements were calculated for both computer simulations. The reliability of the simulation model was confirmed, as indicated by the similarities in the hip joint moment waveforms (r = 0.99) and the hip moment impulses in the sagittal plane between the first computer simulation and the experiment. In the second computer simulation, the hip moment impulse in the sagittal plane decreased with a decrease in the sit-to-stand movement time, although the peak hip extension moment increased with a decrease in the movement time. These findings clarify the association between the sit-to-stand movement time and hip moment impulse in the sagittal plane and may contribute to the prevention of the progression of hip osteoarthritis.

Ground-based facilities for simulation of microgravity: organism-specific recommendations for their use, and recommended terminology.

PubMed

Herranz, Raul; Anken, Ralf; Boonstra, Johannes; Braun, Markus; Christianen, Peter C M; de Geest, Maarten; Hauslage, Jens; Hilbig, Reinhard; Hill, Richard J A; Lebert, Michael; Medina, F Javier; Vagt, Nicole; Ullrich, Oliver; van Loon, Jack J W A; Hemmersbach, Ruth

2013-01-01

Research in microgravity is indispensable to disclose the impact of gravity on biological processes and organisms. However, research in the near-Earth orbit is severely constrained by the limited number of flight opportunities. Ground-based simulators of microgravity are valuable tools for preparing spaceflight experiments, but they also facilitate stand-alone studies and thus provide additional and cost-efficient platforms for gravitational research. The various microgravity simulators that are frequently used by gravitational biologists are based on different physical principles. This comparative study gives an overview of the most frequently used microgravity simulators and demonstrates their individual capacities and limitations. The range of applicability of the various ground-based microgravity simulators for biological specimens was carefully evaluated by using organisms that have been studied extensively under the conditions of real microgravity in space. In addition, current heterogeneous terminology is discussed critically, and recommendations are given for appropriate selection of adequate simulators and consistent use of nomenclature.

Live tree carbon stock equivalence of fire and fuels extension to the Forest Vegetation Simulator and Forest Inventory and Analysis approaches

Treesearch

James E. Smith; Coeli M. Hoover

2017-01-01

The carbon reports in the Fire and Fuels Extension (FFE) to the Forest Vegetation Simulator (FVS) provide two alternate approaches to carbon estimates for live trees (Rebain 2010). These are (1) the FFE biomass algorithms, which are volumebased biomass equations, and (2) the Jenkins allometric equations (Jenkins and others 2003), which are diameter based. Here, we...

Modelling phosphorus (P), sulfur (S) and iron (Fe) interactions for dynamic simulations of anaerobic digestion processes.

PubMed

Flores-Alsina, Xavier; Solon, Kimberly; Kazadi Mbamba, Christian; Tait, Stephan; Gernaey, Krist V; Jeppsson, Ulf; Batstone, Damien J

2016-05-15

This paper proposes a series of extensions to functionally upgrade the IWA Anaerobic Digestion Model No. 1 (ADM1) to allow for plant-wide phosphorus (P) simulation. The close interplay between the P, sulfur (S) and iron (Fe) cycles requires a substantial (and unavoidable) increase in model complexity due to the involved three-phase physico-chemical and biological transformations. The ADM1 version, implemented in the plant-wide context provided by the Benchmark Simulation Model No. 2 (BSM2), is used as the basic platform (A0). Three different model extensions (A1, A2, A3) are implemented, simulated and evaluated. The first extension (A1) considers P transformations by accounting for the kinetic decay of polyphosphates (XPP) and potential uptake of volatile fatty acids (VFA) to produce polyhydroxyalkanoates (XPHA) by phosphorus accumulating organisms (XPAO). Two variant extensions (A2,1/A2,2) describe biological production of sulfides (SIS) by means of sulfate reducing bacteria (XSRB) utilising hydrogen only (autolithotrophically) or hydrogen plus organic acids (heterorganotrophically) as electron sources, respectively. These two approaches also consider a potential hydrogen sulfide ( [Formula: see text] inhibition effect and stripping to the gas phase ( [Formula: see text] ). The third extension (A3) accounts for chemical iron (III) ( [Formula: see text] ) reduction to iron (II) ( [Formula: see text] ) using hydrogen ( [Formula: see text] ) and sulfides (SIS) as electron donors. A set of pre/post interfaces between the Activated Sludge Model No. 2d (ASM2d) and ADM1 are furthermore proposed in order to allow for plant-wide (model-based) analysis and study of the interactions between the water and sludge lines. Simulation (A1 - A3) results show that the ratio between soluble/particulate P compounds strongly depends on the pH and cationic load, which determines the capacity to form (or not) precipitation products. Implementations A1 and A2,1/A2,2 lead to a reduction in the predicted methane/biogas production (and potential energy recovery) compared to reference ADM1 predictions (A0). This reduction is attributed to two factors: (1) loss of electron equivalents due to sulfate [Formula: see text] reduction by XSRB and storage of XPHA by XPAO; and, (2) decrease of acetoclastic and hydrogenotrophic methanogenesis due to [Formula: see text] inhibition. Model A3 shows the potential for iron to remove free SIS (and consequently inhibition) and instead promote iron sulfide (XFeS) precipitation. It also reduces the quantities of struvite ( [Formula: see text] ) and calcium phosphate ( [Formula: see text] ) that are formed due to its higher affinity for phosphate anions. This study provides a detailed analysis of the different model assumptions, the effect that operational/design conditions have on the model predictions and the practical implications of the proposed model extensions in view of plant-wide modelling/development of resource recovery strategies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Full Monte-Carlo description of the Moscow State University Extensive Air Shower experiment

NASA Astrophysics Data System (ADS)

Fomin, Yu. A.; Kalmykov, N. N.; Karpikov, I. S.; Kulikov, G. V.; Kuznetsov, M. Yu.; Rubtsov, G. I.; Sulakov, V. P.; Troitsky, S. V.

2016-08-01

The Moscow State University Extensive Air Shower (EAS-MSU) array studied high-energy cosmic rays with primary energies ~ (1-500) PeV in the Northern hemisphere. The EAS-MSU data are being revisited following recently found indications to an excess of muonless showers, which may be interpreted as the first observation of cosmic gamma rays at ~ 100 PeV. In this paper, we present a complete Monte-Carlo model of the surface detector which results in a good agreement between data and simulations. The model allows us to study the performance of the detector and will be used to obtain physical results in further studies.

Simulation of automatic precision departures and missed approaches using the microwave landing system

NASA Technical Reports Server (NTRS)

Feather, J. B.

1987-01-01

Results of simulated precision departures and missed approaches using MLS guidance concepts are presented. The study was conducted under the Terminal Configured Vehicle (TCV) Program, and is an extension of previous work by DAC under the Advanced Transport Operating System (ATOPS) Technology Studies Program. The study model included simulation of an MD-80 aircraft, an autopilot, and a MLS guidance computer that provided lateral and vertical steering commands. Precision departures were evaluated using a noise abatement procedure. Several curved path departures were simulated with MLS noise and under various environmental conditions. Missed approaches were considered for the same runway, where lateral MLS guidance maintained the aircraft along the extended runway centerline. In both the departures and the missed approach cases, pitch autopilot takeoff and go-around modes of operation were used in conjunction with MLS lateral guidance.

The Resource Usage Aware Backfilling

NASA Astrophysics Data System (ADS)

Guim, Francesc; Rodero, Ivan; Corbalan, Julita

Job scheduling policies for HPC centers have been extensively studied in the last few years, especially backfilling based policies. Almost all of these studies have been done using simulation tools. All the existent simulators use the runtime (either estimated or real) provided in the workload as a basis of their simulations. In our previous work we analyzed the impact on system performance of considering the resource sharing (memory bandwidth) of running jobs including a new resource model in the Alvio simulator. Based on this studies we proposed the LessConsume and LessConsume Threshold resource selection policies. Both are oriented to reduce the saturation of the shared resources thus increasing the performance of the system. The results showed how both resource allocation policies shown how the performance of the system can be improved by considering where the jobs are finally allocated.

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

Stevens, Mark J.; Saleh, Omar A.

We calculated the force-extension curves for a flexible polyelectrolyte chain with varying charge separations by performing Monte Carlo simulations of a 5000 bead chain using a screened Coulomb interaction. At all charge separations, the force-extension curves exhibit a Pincus-like scaling regime at intermediate forces and a logarithmic regime at large forces. As the charge separation increases, the Pincus regime shifts to a larger range of forces and the logarithmic regime starts are larger forces. We also found that force-extension curve for the corresponding neutral chain has a logarithmic regime. Decreasing the diameter of bead in the neutral chain simulations removedmore » the logarithmic regime, and the force-extension curve tends to the freely jointed chain limit. In conclusion, this result shows that only excluded volume is required for the high force logarithmic regime to occur.« less

An Investigation of the Impact of Aerodynamic Model Fidelity on Close-In Combat Effectiveness Prediction in Piloted Simulation

NASA Technical Reports Server (NTRS)

Persing, T. Ray; Bellish, Christine A.; Brandon, Jay; Kenney, P. Sean; Carzoo, Susan; Buttrill, Catherine; Guenther, Arlene

2005-01-01

Several aircraft airframe modeling approaches are currently being used in the DoD community for acquisition, threat evaluation, training, and other purposes. To date there has been no clear empirical study of the impact of airframe simulation fidelity on piloted real-time aircraft simulation study results, or when use of a particular level of fidelity is indicated. This paper documents a series of piloted simulation studies using three different levels of airframe model fidelity. This study was conducted using the NASA Langley Differential Maneuvering Simulator. Evaluations were conducted with three pilots for scenarios requiring extensive maneuvering of the airplanes during air combat. In many cases, a low-fidelity modified point-mass model may be sufficient to evaluate the combat effectiveness of the aircraft. However, in cases where high angle-of-attack flying qualities and aerodynamic performance are a factor or when precision tracking ability of the aircraft must be represented, use of high-fidelity models is indicated.

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations

PubMed Central

Skjaerven, Lars; Grant, Barry; Muga, Arturo; Teigen, Knut; McCammon, J. Andrew; Reuter, Nathalie; Martinez, Aurora

2011-01-01

GroEL is an ATP dependent molecular chaperone that promotes the folding of a large number of substrate proteins in E. coli. Large-scale conformational transitions occurring during the reaction cycle have been characterized from extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in the allosteric response to ATP and the nucleotide-driven reaction cycle are not completely established. Here we describe extensive (in total long) unbiased molecular dynamics (MD) simulations that probe the response of GroEL subunits to ATP binding. We observe nucleotide dependent conformational transitions, and show with multiple 100 ns long simulations that the ligand-induced shift in the conformational populations are intrinsically coded in the structure-dynamics relationship of the protein subunit. Thus, these simulations reveal a stabilization of the equatorial domain upon nucleotide binding and a concomitant “opening” of the subunit, which reaches a conformation close to that observed in the crystal structure of the subunits within the ADP-bound oligomer. Moreover, we identify changes in a set of unique intrasubunit interactions potentially important for the conformational transition. PMID:21423709

Leveraging simulation to evaluate system performance in presence of fixed pattern noise

NASA Astrophysics Data System (ADS)

Teaney, Brian P.

2017-05-01

The development of image simulation techniques which map the effects of a notional, modeled sensor system onto an existing image can be used to evaluate the image quality of camera systems prior to the development of prototype systems. In addition, image simulation or `virtual prototyping' can be utilized to reduce the time and expense associated with conducting extensive field trials. In this paper we examine the development of a perception study designed to assess the performance of the NVESD imager performance metrics as a function of fixed pattern noise. This paper discusses the development of the model theory and the implementation and execution of the perception study. In addition, other applications of the image simulation component including the evaluation of limiting resolution and other test targets is provided.

Modular space station, phase B extension. Information management advanced development. Volume 4: Data processing assembly

NASA Technical Reports Server (NTRS)

Gerber, C. R.

1972-01-01

The computation and logical functions which are performed by the data processing assembly of the modular space station are defined. The subjects discussed are: (1) requirements analysis, (2) baseline data processing assembly configuration, (3) information flow study, (4) throughput simulation, (5) redundancy study, (6) memory studies, and (7) design requirements specification.

Simulating direct shear tests with the Bullet physics library: A validation study.

PubMed

Izadi, Ehsan; Bezuijen, Adam

2018-01-01

This study focuses on the possible uses of physics engines, and more specifically the Bullet physics library, to simulate granular systems. Physics engines are employed extensively in the video gaming, animation and movie industries to create physically plausible scenes. They are designed to deliver a fast, stable, and optimal simulation of certain systems such as rigid bodies, soft bodies and fluids. This study focuses exclusively on simulating granular media in the context of rigid body dynamics with the Bullet physics library. The first step was to validate the results of the simulations of direct shear testing on uniform-sized metal beads on the basis of laboratory experiments. The difference in the average angle of mobilized frictions was found to be only 1.0°. In addition, a very close match was found between dilatancy in the laboratory samples and in the simulations. A comprehensive study was then conducted to determine the failure and post-failure mechanism. We conclude with the presentation of a simulation of a direct shear test on real soil which demonstrated that Bullet has all the capabilities needed to be used as software for simulating granular systems.

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Koh, Chuan Hock; Miyano, Satoru

2011-05-01

Mathematical modeling and simulation studies are playing an increasingly important role in helping researchers elucidate how living organisms function in cells. In systems biology, researchers typically tune many parameters manually to achieve simulation results that are consistent with biological knowledge. This severely limits the size and complexity of simulation models built. In order to break this limitation, we propose a computational framework to automatically estimate kinetic parameters for a given network structure. We utilized an online (on-the-fly) model checking technique (which saves resources compared to the offline approach), with a quantitative modeling and simulation architecture named hybrid functional Petri net with extension (HFPNe). We demonstrate the applicability of this framework by the analysis of the underlying model for the neuronal cell fate decision model (ASE fate model) in Caenorhabditis elegans. First, we built a quantitative ASE fate model containing 3327 components emulating nine genetic conditions. Then, using our developed efficient online model checker, MIRACH 1.0, together with parameter estimation, we ran 20-million simulation runs, and were able to locate 57 parameter sets for 23 parameters in the model that are consistent with 45 biological rules extracted from published biological articles without much manual intervention. To evaluate the robustness of these 57 parameter sets, we run another 20 million simulation runs using different magnitudes of noise. Our simulation results concluded that among these models, one model is the most reasonable and robust simulation model owing to the high stability against these stochastic noises. Our simulation results provide interesting biological findings which could be used for future wet-lab experiments.

A Taxonomy of Latent Structure Assumptions for Probability Matrix Decomposition Models.

ERIC Educational Resources Information Center

Meulders, Michel; De Boeck, Paul; Van Mechelen, Iven

2003-01-01

Proposed a taxonomy of latent structure assumptions for probability matrix decomposition (PMD) that includes the original PMD model and a three-way extension of the multiple classification latent class model. Simulation study results show the usefulness of the taxonomy. (SLD)

Behavior of stem cells under outer-space microgravity and ground-based microgravity simulation.

PubMed

Zhang, Cui; Li, Liang; Chen, Jianling; Wang, Jinfu

2015-06-01

With rapid development of space engineering, research on life sciences in space is being conducted extensively, especially cellular and molecular studies on space medicine. Stem cells, undifferentiated cells that can differentiate into specialized cells, are considered a key resource for regenerative medicine. Research on stem cells under conditions of microgravity during a space flight or a ground-based simulation has generated several excellent findings. To help readers understand the effects of outer space and ground-based simulation conditions on stem cells, we reviewed recent studies on the effects of microgravity (as an obvious environmental factor in space) on morphology, proliferation, migration, and differentiation of stem cells. © 2015 International Federation for Cell Biology.

Simulation studies for the PANDA experiment

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

Kopf, B.

2005-10-26

One main component of the planned Facility for Antiproton and Ion Research (FAIR) is the High Energy Storage Ring (HESR) at GSI, Darmstadt, which will provide cooled antiprotons with momenta between 1.5 and 15 GeV/c. The PANDA experiment will investigate p-barannihilations with internal hydrogen and nuclear targets. Due to the planned extensive physics program a multipurpose detector with nearly complete solid angle coverage, proper particle identification over a large momentum range, and high resolution calorimetry for neutral particles is required. For the optimization of the detector design simulation studies of several benchmark channels are in progress which are covering themore » most relevant physics topics. Some important simulation results are discussed here.« less

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

PubMed Central

Martinez, Michael; Romanowska, Julia; Kokh, Daria B.; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan

2015-01-01

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26123630

Extensible Adaptable Simulation Systems: Supporting Multiple Fidelity Simulations in a Common Environment

NASA Technical Reports Server (NTRS)

McLaughlin, Brian J.; Barrett, Larry K.

2012-01-01

Common practice in the development of simulation systems is meeting all user requirements within a single instantiation. The Joint Polar Satellite System (JPSS) presents a unique challenge to establish a simulation environment that meets the needs of a diverse user community while also spanning a multi-mission environment over decades of operation. In response, the JPSS Flight Vehicle Test Suite (FVTS) is architected with an extensible infrastructure that supports the operation of multiple observatory simulations for a single mission and multiple mission within a common system perimeter. For the JPSS-1 satellite, multiple fidelity flight observatory simulations are necessary to support the distinct user communities consisting of the Common Ground System development team, the Common Ground System Integration & Test team, and the Mission Rehearsal Team/Mission Operations Team. These key requirements present several challenges to FVTS development. First, the FVTS must ensure all critical user requirements are satisfied by at least one fidelity instance of the observatory simulation. Second, the FVTS must allow for tailoring of the system instances to function in diverse operational environments from the High-security operations environment at NOAA Satellite Operations Facility (NSOF) to the ground system factory floor. Finally, the FVTS must provide the ability to execute sustaining engineering activities on a subset of the system without impacting system availability to parallel users. The FVTS approach of allowing for multiple fidelity copies of observatory simulations represents a unique concept in simulator capability development and corresponds to the JPSS Ground System goals of establishing a capability that is flexible, extensible, and adaptable.

Towards a cosmic-ray mass-composition study at Tunka Radio Extension

NASA Astrophysics Data System (ADS)

Kostunin, D.; Bezyazeekov, P. A.; Budnev, N. M.; Fedorov, O.; Gress, O. A.; Haungs, A.; Hiller, R.; Huege, T.; Kazarina, Y.; Kleifges, M.; Korosteleva, E. E.; Krömer, O.; Kungel, V.; Kuzmichev, L. A.; Lubsandorzhiev, N.; Mirgazov, R. R.; Monkhoev, R.; Osipova, E. A.; Pakhorukov, A.; Pankov, L.; Prosin, V. V.; Rubtsov, G. I.; Schröder, F. G.; Wischnewski, R.; Zagorodnikov, A.

2017-03-01

The Tunka Radio Extension (Tunka-Rex) is a radio detector at the TAIGA facility located in Siberia nearby the southern tip of Lake Baikal. Tunka-Rex measures air-showers induced by high-energy cosmic rays, in particular, the lateral distribution of the radio pulses. The depth of the air-shower maximum, statistically depends on the mass of the primary particle, is determined from the slope of the lateral distribution function (LDF). Using a model-independent approach, we have studied possible features of the one-dimensional slope method and tried to find improvements for the reconstruction of primary mass. To study the systematic uncertainties given by different primary particles, we have performed simulations using the CONEX and CoREAS software packages of the recently released CORSIKA v7.5 including the modern high-energy hadronic models QGSJet-II.04 and EPOS-LHC. The simulations have shown that the largest systematic uncertainty in the energy deposit is due to the unknown primary particle. Finally, we studied the relation between the polarization and the asymmetry of the LDF.

Ground-Based Facilities for Simulation of Microgravity: Organism-Specific Recommendations for Their Use, and Recommended Terminology

PubMed Central

Anken, Ralf; Boonstra, Johannes; Braun, Markus; Christianen, Peter C.M.; de Geest, Maarten; Hauslage, Jens; Hilbig, Reinhard; Hill, Richard J.A.; Lebert, Michael; Medina, F. Javier; Vagt, Nicole; Ullrich, Oliver

2013-01-01

Abstract Research in microgravity is indispensable to disclose the impact of gravity on biological processes and organisms. However, research in the near-Earth orbit is severely constrained by the limited number of flight opportunities. Ground-based simulators of microgravity are valuable tools for preparing spaceflight experiments, but they also facilitate stand-alone studies and thus provide additional and cost-efficient platforms for gravitational research. The various microgravity simulators that are frequently used by gravitational biologists are based on different physical principles. This comparative study gives an overview of the most frequently used microgravity simulators and demonstrates their individual capacities and limitations. The range of applicability of the various ground-based microgravity simulators for biological specimens was carefully evaluated by using organisms that have been studied extensively under the conditions of real microgravity in space. In addition, current heterogeneous terminology is discussed critically, and recommendations are given for appropriate selection of adequate simulators and consistent use of nomenclature. Key Words: 2-D clinostat—3-D clinostat—Gravity—Magnetic levitation—Random positioning machine—Simulated microgravity—Space biology. Astrobiology 13, 1–17. PMID:23252378

A framework for visualization of battlefield network behavior

NASA Astrophysics Data System (ADS)

Perzov, Yury; Yurcik, William

2006-05-01

An extensible network simulation application was developed to study wireless battlefield communications. The application monitors node mobility and depicts broadcast and unicast traffic as expanding rings and directed links. The network simulation was specially designed to support fault injection to show the impact of air strikes on disabling nodes. The application takes standard ns-2 trace files as an input and provides for performance data output in different graphical forms (histograms and x/y plots). Network visualization via animation of simulation output can be saved in AVI format that may serve as a basis for a real-time battlefield awareness system.

Muscle contributions to knee extension in the early stance phase in patients with knee osteoarthritis.

PubMed

Ogaya, Shinya; Kubota, Ryo; Chujo, Yuta; Hirooka, Eiko; Kwang-Ho, Kim; Hase, Kimitaka

2017-10-01

The aim of this study was to analyze individual muscle contributions to knee angular acceleration using a musculoskeletal simulation analysis and evaluate knee extension mechanics in the early stance phase in patients with knee osteoarthritis (OA). The subjects comprised 15 patients with medial knee OA and 14 healthy elderly individuals. All participants underwent gait performance test using 8 infrared cameras and two force plates to measure the kinetic and kinematic data. The simulation was driven by 92 Hill-type muscle-tendon units of the lower extremities and a trunk with 23° of freedom. We analyzed each muscle contribution to knee angular acceleration in the 5%-15% and 15%-25% periods of the stance phase (% SP) using an induced acceleration analysis. We compared accelerations by individual muscles between the two groups using an analysis of covariance for controlling gait speed. Patients with knee OA had a significantly lesser knee extension acceleration by the vasti muscles and higher knee acceleration by hip adductors than those in controls in 5-15% SP. In addition, knee OA resulted in significantly lesser knee extension acceleration by the vasti muscles in 15-25% SP. These results indicate that patients with knee OA have decreased dependency on the vasti muscles to control knee movements during early stance phase. Hip adductor muscles, which mainly control mediolateral motion, partly compensate for the weak knee extension by the vasti muscles in patients with knee OA. Copyright © 2017 Elsevier B.V. All rights reserved.

ASSESSING POPULATION EXPOSURES TO MULTIPLE AIR POLLUTANTS USING A MECHANISTIC SOURCE-TO-DOSE MODELING FRAMEWORK

EPA Science Inventory

The Modeling Environment for Total Risks studies (MENTOR) system, combined with an extension of the SHEDS (Stochastic Human Exposure and Dose Simulation) methodology, provide a mechanistically consistent framework for conducting source-to-dose exposure assessments of multiple pol...

Sensitivity studies of pediatric material properties on juvenile lumbar spine responses using finite element analysis.

PubMed

Jebaseelan, D Davidson; Jebaraj, C; Yoganandan, Narayan; Rajasekaran, S; Kanna, Rishi M

2012-05-01

The objective of the study was to determine the sensitivity of material properties of the juvenile spine to its external and internal responses using a finite element model under compression, and flexion-extension bending moments. The methodology included exercising the 8-year-old juvenile lumbar spine using parametric procedures. The model included the vertebral centrum, growth plates, laminae, pedicles, transverse processes and spinous processes; disc annulus and nucleus; and various ligaments. The sensitivity analysis was conducted by varying the modulus of elasticity for various components. The first simulation was done using mean material properties. Additional simulations were done for each component corresponding to low and high material property variations. External displacement/rotation and internal stress-strain responses were determined under compression and flexion-extension bending. Results indicated that, under compression, disc properties were more sensitive than bone properties, implying an elevated role of the disc under this mode. Under flexion-extension moments, ligament properties were more dominant than the other components, suggesting that various ligaments of the juvenile spine play a key role in modulating bending behaviors. Changes in the growth plate stress associated with ligament properties explained the importance of the growth plate in the pediatric spine with potential implications in progressive deformities.

North Pacific Mesoscale Coupled Air-Ocean Simulations Compared with Observations

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

Koracin, Darko; Cerovecki, Ivana; Vellore, Ramesh

2013-04-11

Executive summary The main objective of the study was to investigate atmospheric and ocean interaction processes in the western Pacific and, in particular, effects of significant ocean heat loss in the Kuroshio and Kuroshio Extension regions on the lower and upper atmosphere. It is yet to be determined how significant are these processes are on climate scales. The understanding of these processes led us also to development of the methodology of coupling the Weather and Research Forecasting model with the Parallel Ocean Program model for western Pacific regional weather and climate simulations. We tested NCAR-developed research software Coupler 7 formore » coupling of the WRF and POP models and assessed its usability for regional-scale applications. We completed test simulations using the Coupler 7 framework, but implemented a standard WRF model code with options for both one- and two-way mode coupling. This type of coupling will allow us to seamlessly incorporate new WRF updates and versions in the future. We also performed a long-term WRF simulation (15 years) covering the entire North Pacific as well as high-resolution simulations of a case study which included extreme ocean heat losses in the Kuroshio and Kuroshio Extension regions. Since the extreme ocean heat loss occurs during winter cold air outbreaks (CAO), we simulated and analyzed a case study of a severe CAO event in January 2000 in detail. We found that the ocean heat loss induced by CAOs is amplified by additional advection from mesocyclones forming on the southern part of the Japan Sea. Large scale synoptic patterns with anomalously strong anticyclone over Siberia and Mongolia, deep Aleutian Low, and the Pacific subtropical ridge are a crucial setup for the CAO. It was found that the onset of the CAO is related to the breaking of atmospheric Rossby waves and vertical transport of vorticity that facilitates meridional advection. The study also indicates that intrinsic parameterization of the surface fluxes within the WRF model needs more evaluation and analysis.« less

Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins

NASA Astrophysics Data System (ADS)

Dahlke, K.; Sing, C. E.

2018-02-01

Interactions between nucleoid associated proteins (NAPs) and DNA affect DNA polymer conformation, leading to phenomena such as concentration dependent force-extension behavior. These effects, in turn, also impact the local binding behavior of the protein, such as high forces causing proteins to unbind, or proteins binding favorably to locally bent DNA. We develop a coarse-grained NAP-DNA simulation model that incorporates both force- and concentration-dependent behaviors, in order to study the interplay between NAP binding and DNA conformation. This model system includes multi-state protein binding and unbinding, motivated by prior work, but is now dependent on the local structure of the DNA, which is related to external forces acting on the DNA strand. We observe the expected qualitative binding behavior, where more proteins are bound at lower forces than at higher forces. Our model also includes NAP-induced DNA bending, which affects DNA elasticity. We see semi-quantitative matching of our simulated force-extension behavior to the reported experimental data. By using a coarse-grained simulation, we are also able to look at non-equilibrium behaviors, such as dynamic extension of a DNA strand. We stretch a DNA strand at different rates and at different NAP concentrations to observe how the time scales of the system (such as pulling time and unbinding time) work in concert. When these time scales are similar, we observe measurable rate-dependent changes in the system, which include the number of proteins bound and the force required to extend the DNA molecule. This suggests that the relative time scales of different dynamic processes play an important role in the behavior of NAP-DNA systems.

From conscious thought to automatic action: A simulation account of action planning.

PubMed

Martiny-Huenger, Torsten; Martiny, Sarah E; Parks-Stamm, Elizabeth J; Pfeiffer, Elisa; Gollwitzer, Peter M

2017-10-01

We provide a theoretical framework and empirical evidence for how verbally planning an action creates direct perception-action links and behavioral automaticity. We argue that planning actions in an if (situation)-then (action) format induces sensorimotor simulations (i.e., activity patterns reenacting the event in the sensory and motor brain areas) of the anticipated situation and the intended action. Due to their temporal overlap, these activity patterns become linked. Whenever the previously simulated situation is encountered, the previously simulated action is partially reactivated through spreading activation and thus more likely to be executed. In 4 experiments (N = 363), we investigated the relation between specific if-then action plans worded to activate simulations of elbow flexion versus extension movements and actual elbow flexion versus extension movements in a subsequent, ostensibly unrelated categorization task. As expected, linking a critical stimulus to intended actions that implied elbow flexion movements (e.g., grabbing it for consumption) subsequently facilitated elbow flexion movements upon encountering the critical stimulus. However, linking a critical stimulus to actions that implied elbow extension movements (e.g., pointing at it) subsequently facilitated elbow extension movements upon encountering the critical stimulus. Thus, minor differences (i.e., exchanging the words "point at" with "grab") in verbally formulated action plans (i.e., conscious thought) had systematic consequences on subsequent actions. The question of how conscious thought can induce stimulus-triggered action is illuminated by the provided theoretical framework and the respective empirical evidence, facilitating the understanding of behavioral automaticity and human agency. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A Comparative Study on Multifactor Dimensionality Reduction Methods for Detecting Gene-Gene Interactions with the Survival Phenotype

PubMed Central

Lee, Seungyeoun; Kim, Yongkang; Kwon, Min-Seok; Park, Taesung

2015-01-01

Genome-wide association studies (GWAS) have extensively analyzed single SNP effects on a wide variety of common and complex diseases and found many genetic variants associated with diseases. However, there is still a large portion of the genetic variants left unexplained. This missing heritability problem might be due to the analytical strategy that limits analyses to only single SNPs. One of possible approaches to the missing heritability problem is to consider identifying multi-SNP effects or gene-gene interactions. The multifactor dimensionality reduction method has been widely used to detect gene-gene interactions based on the constructive induction by classifying high-dimensional genotype combinations into one-dimensional variable with two attributes of high risk and low risk for the case-control study. Many modifications of MDR have been proposed and also extended to the survival phenotype. In this study, we propose several extensions of MDR for the survival phenotype and compare the proposed extensions with earlier MDR through comprehensive simulation studies. PMID:26339630

Electrolytes in a nanometer slab-confinement: Ion-specific structure and solvation forces

NASA Astrophysics Data System (ADS)

Kalcher, Immanuel; Schulz, Julius C. F.; Dzubiella, Joachim

2010-10-01

We study the liquid structure and solvation forces of dense monovalent electrolytes (LiCl, NaCl, CsCl, and NaI) in a nanometer slab-confinement by explicit-water molecular dynamics (MD) simulations, implicit-water Monte Carlo (MC) simulations, and modified Poisson-Boltzmann (PB) theories. In order to consistently coarse-grain and to account for specific hydration effects in the implicit methods, realistic ion-ion and ion-surface pair potentials have been derived from infinite-dilution MD simulations. The electrolyte structure calculated from MC simulations is in good agreement with the corresponding MD simulations, thereby validating the coarse-graining approach. The agreement improves if a realistic, MD-derived dielectric constant is employed, which partially corrects for (water-mediated) many-body effects. Further analysis of the ionic structure and solvation pressure demonstrates that nonlocal extensions to PB (NPB) perform well for a wide parameter range when compared to MC simulations, whereas all local extensions mostly fail. A Barker-Henderson mapping of the ions onto a charged, asymmetric, and nonadditive binary hard-sphere mixture shows that the strength of structural correlations is strongly related to the magnitude and sign of the salt-specific nonadditivity. Furthermore, a grand canonical NPB analysis shows that the Donnan effect is dominated by steric correlations, whereas solvation forces and overcharging effects are mainly governed by ion-surface interactions. However, steric corrections to solvation forces are strongly repulsive for high concentrations and low surface charges, while overcharging can also be triggered by steric interactions in strongly correlated systems. Generally, we find that ion-surface and ion-ion correlations are strongly coupled and that coarse-grained methods should include both, the latter nonlocally and nonadditive (as given by our specific ionic diameters), when studying electrolytes in highly inhomogeneous situations.

Decrypting the structural, dynamic, and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation.

PubMed

Chakraborty, Srirupa; Zheng, Wenjun

2015-01-27

We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO, and ATP state) of a human kinesin-1 monomer in complex with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin-tubulin complex by the Knossow lab, we have used flexible fitting of cryo-electron-microscopy maps to construct new structural models of the kinesin-tubulin complex in APO and ATP state, and then conducted extensive MD simulations (total 400 ns for each state), followed by flexibility analysis, principal component analysis, hydrogen bond analysis, and binding free energy analysis. Our modeling and simulation have revealed key nucleotide-dependent changes in the structure and flexibility of the nucleotide-binding pocket (featuring a highly flexible and open switch I in APO state) and the tubulin-binding site, and allosterically coupled motions driving the APO to ATP transition. In addition, our binding free energy analysis has identified a set of key residues involved in kinesin-tubulin binding. On the basis of our simulation, we have attempted to address several outstanding issues in kinesin study, including the possible roles of β-sheet twist and neck linker docking in regulating nucleotide release and binding, the structural mechanism of ADP release, and possible extension and shortening of α4 helix during the ATPase cycle. This study has provided a comprehensive structural and dynamic picture of kinesin's major ATPase states, and offered promising targets for future mutational and functional studies to investigate the molecular mechanism of kinesin motors.

An operational GLS model for hydrologic regression

USGS Publications Warehouse

Tasker, Gary D.; Stedinger, J.R.

1989-01-01

Recent Monte Carlo studies have documented the value of generalized least squares (GLS) procedures to estimate empirical relationships between streamflow statistics and physiographic basin characteristics. This paper presents a number of extensions of the GLS method that deal with realities and complexities of regional hydrologic data sets that were not addressed in the simulation studies. These extensions include: (1) a more realistic model of the underlying model errors; (2) smoothed estimates of cross correlation of flows; (3) procedures for including historical flow data; (4) diagnostic statistics describing leverage and influence for GLS regression; and (5) the formulation of a mathematical program for evaluating future gaging activities. ?? 1989.

Extreme events in a vortex gas simulation of a turbulent half-jet

NASA Astrophysics Data System (ADS)

Suryanarayanan, Saikishan; Pathikonda, Gokul; Narasimha, Roddam

2012-11-01

Extensive simulations [arXiv:1008.2876v1 [physics.flu-dyn], BAPS.2010.DFD.LE.4] have shown that the temporally evolving vortex gas mixing layer has 3 regimes, including one which has a universal spreading rate. The present study explores the development of spatially evolving mixing layers, using a vortex gas model based on Basu et al. (1995 Appl. Math. Modelling). The effects of the velocity ratio (r) are analyzed via the most extensive simulations of this kind till date, involving up to 10000 vortices and averaging over up to 1000 convective times. While the temporal limit is approached as r approaches unity, striking features such as extreme events involving coherent structures, bending, deviation of the convection velocity from mean velocity, spatial feedback and greater sensitivity to downstream and free stream boundary conditions are observed in the half-jet (r = 0) limit. A detailed statistical analysis reveals possible causes for the large scatter across experiments, as opposed to the commonly adopted explanation of asymptotic dependence on initial conditions. Supported in part by contract no. Intel/RN/4288.

Swarm Counter-Asymmetric-Threat (CAT) 6-DOF Dynamics Simulation

DTIC Science & Technology

2005-07-01

NAWCWD TP 8593 Swarm Counter-Asymmetric-Threat ( CAT ) 6-DOF Dynamics Simulation by James Bobinchak Weapons and Energetics...mathematical models used in the swarm counter- asymmetric-threat ( CAT ) simulation and the results of extensive Monte Carlo simulations. The swarm CAT ...Asymmetric-Threat ( CAT ) 6-DOF Dynamics Simulation (U) 6. AUTHOR(S) James Bobinchak and Gary Hewer 7. PERFORMING ORGANIZATION NAME(S) AND

A Modular and Extensible Architecture Integrating Sensors, Dynamic Displays of Anatomy and Physiology, and Automated Instruction for Innovations in Clinical Education

ERIC Educational Resources Information Center

Nelson, Douglas Allen, Jr.

2017-01-01

Adoption of simulation in healthcare education has increased tremendously over the past two decades. However, the resources necessary to perform simulation are immense. Simulators are large capital investments and require specialized training for both instructors and simulation support staff to develop curriculum using the simulator and to use the…

The virtual morphology and the main movements of the human neck simulations used for car crash studies

NASA Astrophysics Data System (ADS)

Ciunel, St.; Tica, B.

2016-08-01

The paper presents the studies made on a similar biomechanical system composed by neck, head and thorax bones. The models were defined in a CAD environment which includes Adams algorithm for dynamic simulations. The virtual models and the entire morphology were obtained starting with CT images made on a living human subject. The main movements analyzed were: axial rotation (left-right), lateral bending (left-right) and flexion- extension movement. After simulation was obtained the entire biomechanical behavior based on data tables or diagrams. That virtual model composed by neck and head can be included in complex system (as a car system) and supposed to several impact simulations (virtual crash tests). Also, our research team built main components of a testing device for dummy car crash neck-head system using anatomical data.

Structure and dynamics of solvated polyethylenimine chains

NASA Astrophysics Data System (ADS)

Beu, Titus A.; Farcaş, Alexandra

2017-12-01

Polimeric gene-delivery carriers have attracted great interest in recent years, owing to their applicability in gene therapy. In particular, cationic polymers represent the most promising delivery vectors for nucleic acids into the cells. This study presents extensive atomistic molecular dynamics simulations of linear polyethylenimine chains. The simulations show that the variation of the chain size and protonation fraction causes a substantial change of the diffusion coefficient. Examination of the solvated chains suggests the possibility of controlling the polymer diffusion mobility in solution.

NETL - Chemical Looping Reactor

ScienceCinema

None

2018-02-14

NETL's Chemical Looping Reactor unit is a high-temperature integrated CLC process with extensive instrumentation to improve computational simulations. A non-reacting test unit is also used to study solids flow at ambient temperature. The CLR unit circulates approximately 1,000 pounds per hour at temperatures around 1,800 degrees Fahrenheit.

Macroscopic Relationships Among Latent Heating, Precipitation, Organized Convection, and the Environment

NASA Technical Reports Server (NTRS)

Moncrieff, Mitchell

2003-01-01

The two studies summarized below represent the results of a one-year extension to the original award grant. These studies involve cloud-resolving simulation, theory and parameterization of multi-scale convective systems in the Tropics. It is a contribution to the basic scientific objectives of TRMM and the prospective NASA Global Precipitation Mission.

An Extension of Least Squares Estimation of IRT Linking Coefficients for the Graded Response Model

ERIC Educational Resources Information Center

Kim, Seonghoon

2010-01-01

The three types (generalized, unweighted, and weighted) of least squares methods, proposed by Ogasawara, for estimating item response theory (IRT) linking coefficients under dichotomous models are extended to the graded response model. A simulation study was conducted to confirm the accuracy of the extended formulas, and a real data study was…

Meta-Analysis of Correlations Revisited: Attempted Replication and Extension of Field's (2001) Simulation Studies

ERIC Educational Resources Information Center

Hafdahl, Adam R.; Williams, Michelle A.

2009-01-01

In 2 Monte Carlo studies of fixed- and random-effects meta-analysis for correlations, A. P. Field (2001) ostensibly evaluated Hedges-Olkin-Vevea Fisher-[zeta] and Schmidt-Hunter Pearson-r estimators and tests in 120 conditions. Some authors have cited those results as evidence not to meta-analyze Fisher-[zeta] correlations, especially with…

In Vivo Investigation of the Effectiveness of a Hyper-viscoelastic Model in Simulating Brain Retraction

NASA Astrophysics Data System (ADS)

Li, Ping; Wang, Weiwei; Zhang, Chenxi; An, Yong; Song, Zhijian

2016-07-01

Intraoperative brain retraction leads to a misalignment between the intraoperative positions of the brain structures and their previous positions, as determined from preoperative images. In vitro swine brain sample uniaxial tests showed that the mechanical response of brain tissue to compression and extension could be described by the hyper-viscoelasticity theory. The brain retraction caused by the mechanical process is a combination of brain tissue compression and extension. In this paper, we first constructed a hyper-viscoelastic framework based on the extended finite element method (XFEM) to simulate intraoperative brain retraction. To explore its effectiveness, we then applied this framework to an in vivo brain retraction simulation. The simulation strictly followed the clinical scenario, in which seven swine were subjected to brain retraction. Our experimental results showed that the hyper-viscoelastic XFEM framework is capable of simulating intraoperative brain retraction and improving the navigation accuracy of an image-guided neurosurgery system (IGNS).

Tests of local Lorentz invariance violation of gravity in the standard model extension with pulsars.

PubMed

Shao, Lijing

2014-03-21

The standard model extension is an effective field theory introducing all possible Lorentz-violating (LV) operators to the standard model and general relativity (GR). In the pure-gravity sector of minimal standard model extension, nine coefficients describe dominant observable deviations from GR. We systematically implemented 27 tests from 13 pulsar systems to tightly constrain eight linear combinations of these coefficients with extensive Monte Carlo simulations. It constitutes the first detailed and systematic test of the pure-gravity sector of minimal standard model extension with the state-of-the-art pulsar observations. No deviation from GR was detected. The limits of LV coefficients are expressed in the canonical Sun-centered celestial-equatorial frame for the convenience of further studies. They are all improved by significant factors of tens to hundreds with existing ones. As a consequence, Einstein's equivalence principle is verified substantially further by pulsar experiments in terms of local Lorentz invariance in gravity.

TOWARDS ICE FORMATION CLOSURE IN MIXED-PHASE BOUNDARY LAYER CLOUDS DURING ISDAC

NASA Astrophysics Data System (ADS)

Avramov, A.; Ackerman, A. S.; Fridlind, A. M.; van Diedenhoven, B.; Korolev, A. V.

2009-12-01

Mixed-phase stratus clouds are ubiquitous in the Arctic during the winter and transition seasons. Despite their important role in various climate feedback mechanisms they are not well understood and are difficult to represent faithfully in cloud models. In particular, models of all types experience difficulties reproducing observed ice concentrations and liquid/ice water partitioning in these clouds. Previous studies have demonstrated that simulated ice concentrations and ice water content are critically dependent on ice nucleation modes and ice crystal habit assumed in simulations. In this study we use large-eddy simulations with size-resolved microphysics to determine whether uncertainties in ice nucleus concentrations, ice nucleation mechanisms, ice crystal habits and large-scale forcing are sufficient to account for the difference between simulated and observed quantities. We present results of simulations of two case studies based on observations taken during the recent Indirect and Semi-Direct Aerosol Campaign (ISDAC) on April 8 and 26, 2008. The model simulations are evaluated through extensive comparison with in-situ observations and ground-based remote sensing measurements.

A comparison of stress in cracked fibrous tissue specimens with varied crack location, loading, and orientation using finite element analysis.

PubMed

Peloquin, John M; Elliott, Dawn M

2016-04-01

Cracks in fibrous soft tissue, such as intervertebral disc annulus fibrosus and knee meniscus, cause pain and compromise joint mechanics. A crack concentrates stress at its tip, making further failure and crack extension (fracture) more likely. Ex vivo mechanical testing is an important tool for studying the loading conditions required for crack extension, but prior work has shown that it is difficult to reproduce crack extension. Most prior work used edge crack specimens in uniaxial tension, with the crack 90° to the edge of the specimen. This configuration does not necessarily represent the loading conditions that cause in vivo crack extension. To find a potentially better choice for experiments aiming to reproduce crack extension, we used finite element analysis to compare, in factorial combination, (1) center crack vs. edge crack location, (2) biaxial vs. uniaxial loading, and (3) crack-fiber angles ranging from 0° to 90°. The simulated material was annulus fibrosus fibrocartilage with a single fiber family. We hypothesized that one of the simulated test cases would produce a stronger stress concentration than the commonly used uniaxially loaded 90° crack-fiber angle edge crack case. Stress concentrations were compared between cases in terms of fiber-parallel stress (representing risk of fiber rupture), fiber-perpendicular stress (representing risk of matrix rupture), and fiber shear stress (representing risk of fiber sliding). Fiber-perpendicular stress and fiber shear stress concentrations were greatest in edge crack specimens (of any crack-fiber angle) and center crack specimens with a 90° crack-fiber angle. However, unless the crack is parallel to the fiber direction, these stress components alone are insufficient to cause crack opening and extension. Fiber-parallel stress concentrations were greatest in center crack specimens with a 45° crack-fiber angle, either biaxially or uniaxially loaded. We therefore recommend that the 45° center crack case be tried in future experiments intended to study crack extension by fiber rupture. Copyright © 2015 Elsevier Ltd. All rights reserved.

A simple polymeric model describes cell nuclear mechanical response

NASA Astrophysics Data System (ADS)

Banigan, Edward; Stephens, Andrew; Marko, John

The cell nucleus must continually resist inter- and intracellular mechanical forces, and proper mechanical response is essential to basic cell biological functions as diverse as migration, differentiation, and gene regulation. Experiments probing nuclear mechanics reveal that the nucleus stiffens under strain, leading to two characteristic regimes of force response. This behavior depends sensitively on the intermediate filament protein lamin A, which comprises the outer layer of the nucleus, and the properties of the chromatin interior. To understand these mechanics, we study a simulation model of a polymeric shell encapsulating a semiflexible polymer. This minimalistic model qualitatively captures the typical experimental nuclear force-extension relation and observed nuclear morphologies. Using a Flory-like theory, we explain the simulation results and mathematically estimate the force-extension relation. The model and experiments suggest that chromatin organization is a dominant contributor to nuclear mechanics, while the lamina protects cell nuclei from large deformations.

NASA/ESA CV-990 spacelab simulation

NASA Technical Reports Server (NTRS)

1975-01-01

Due to interest in the application of simplified techniques used to conduct airborne science missions at NASA's Ames Research Center, a joint NASA/ESA endeavor was established to conduct an extensive Spacelab simulation using the NASA CV-990 airborne laboratory. The scientific payload was selected to perform studies in upper atmospheric physics and infrared astronomy with principal investigators from France, the Netherlands, England, and several groups from the United States. Communication links between the 'Spacelab' and a ground based mission operations center were limited consistent with Spacelab plans. The mission was successful and provided extensive data relevant to Spacelab objectives on overall management of a complex international payload; experiment preparation, testing, and integration; training for proxy operation in space; data handling; multiexperimenter use of common experimenter facilities (telescopes); multiexperiment operation by experiment operators; selection criteria for Spacelab experiment operators; and schedule requirements to prepare for such a Spacelab mission.

Estimating canopy bulk density and canopy base height for conifer stands in the interior Western United States using the Forest Vegetation Simulator Fire and Fuels Extension.

Treesearch

Seth Ex; Frederick Smith; Tara Keyser; Stephanie Rebain

2017-01-01

The Forest Vegetation Simulator Fire and Fuels Extension (FFE-FVS) is often used to estimate canopy bulk density (CBD) and canopy base height (CBH), which are key indicators of crown fire hazard for conifer stands in the Western United States. Estimated CBD from FFE-FVS is calculated as the maximum 4 m running mean bulk density of predefined 0.3 m thick canopy layers (...

Closed Environment Module - Modularization and extension of the Virtual Habitat

NASA Astrophysics Data System (ADS)

Plötner, Peter; Czupalla, Markus; Zhukov, Anton

2013-12-01

The Virtual Habitat (V-HAB), is a Life Support System (LSS) simulation, created to perform dynamic simulation of LSS's for future human spaceflight missions. It allows the testing of LSS robustness by means of computer simulations, e.g. of worst case scenarios.

A Component-Based Extension Framework for Large-Scale Parallel Simulations in NEURON

PubMed Central

King, James G.; Hines, Michael; Hill, Sean; Goodman, Philip H.; Markram, Henry; Schürmann, Felix

2008-01-01

As neuronal simulations approach larger scales with increasing levels of detail, the neurosimulator software represents only a part of a chain of tools ranging from setup, simulation, interaction with virtual environments to analysis and visualizations. Previously published approaches to abstracting simulator engines have not received wide-spread acceptance, which in part may be to the fact that they tried to address the challenge of solving the model specification problem. Here, we present an approach that uses a neurosimulator, in this case NEURON, to describe and instantiate the network model in the simulator's native model language but then replaces the main integration loop with its own. Existing parallel network models are easily adopted to run in the presented framework. The presented approach is thus an extension to NEURON but uses a component-based architecture to allow for replaceable spike exchange components and pluggable components for monitoring, analysis, or control that can run in this framework alongside with the simulation. PMID:19430597

Resonant scattering experiments with radioactive nuclear beams - Recent results and future plans

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

Teranishi, T.; Sakaguchi, S.; Uesaka, T.

2013-04-19

Resonant scattering with low-energy radioactive nuclear beams of E < 5 MeV/u have been studied at CRIB of CNS and at RIPS of RIKEN. As an extension to the present experimental technique, we will install an advanced polarized proton target for resonant scattering experiments. A Monte-Carlo simulation was performed to study the feasibility of future experiments with the polarized target. In the Monte-Carlo simulation, excitation functions and analyzing powers were calculated using a newly developed R-matrix calculation code. A project of a small-scale radioactive beam facility at Kyushu University is also briefly described.

Automating the solution of PDEs on the sphere and other manifolds in FEniCS 1.2

NASA Astrophysics Data System (ADS)

Rognes, M. E.; Ham, D. A.; Cotter, C. J.; McRae, A. T. T.

2013-12-01

Differential equations posed over immersed manifolds are of particular importance in studying geophysical flows; for instance, ocean and atmosphere simulations crucially rely on the capability to solve equations over the sphere. This paper presents the extension of the FEniCS software components to the automated solution of finite element formulations of differential equations defined over general, immersed manifolds. We describe the implementation and, in particular detail, how the required extensions essentially reduce to the extension of the FEniCS form compiler to cover this case. The resulting implementation has all the properties of the FEniCS pipeline and we demonstrate its flexibility by an extensive range of numerical examples covering a number of geophysical benchmark examples and test cases. The results are all in agreement with the expected values. The description here relates to DOLFIN/FEniCS 1.2.

Automating the solution of PDEs on the sphere and other manifolds in FEniCS 1.2

NASA Astrophysics Data System (ADS)

Rognes, M. E.; Ham, D. A.; Cotter, C. J.; McRae, A. T. T.

2013-07-01

Differential equations posed over immersed manifolds are of particular importance in studying geophysical flows; for instance, ocean and atmosphere simulations crucially rely on the capability to solve equations over the sphere. This paper presents the extension of the FEniCS software components to the automated solution of finite element formulations of differential equations defined over general, immersed manifolds. We describe the implementation and in particular detail how the required extensions essentially reduce to the extension of the FEniCS form compiler to cover this case. The resulting implementation has all the properties of the FEniCS pipeline and we demonstrate its flexibility by an extensive range of numerical examples covering a number of geophysical benchmark examples and test cases. The results are all in agreement with the expected values. The description here relates to DOLFIN/FEniCS 1.2.

Status of the EDDA experiment at COSY

NASA Astrophysics Data System (ADS)

Scobel, W.; EDDA Collaboration; Bisplinghoff, J.; Bollmann, R.; Cloth, P.; Dohrmann, F.; Dorner, G.; Drüke, V.; Ernst, J.; Eversheim, P. D.; Filges, D.; Gasthuber, M.; Gebel, R.; Groß, A.; Groß-Hardt, R.; Hinterberger, F.; Jahn, R.; Lahr, U.; Langkau, R.; Lippert, G.; Mayer-Kuckuk, T.; Maschuw, R.; Mertler, G.; Metsch, B.; Mosel, F.; Paetz gen Schieck, H.; Petry, H. R.; Prasuhn, D.; von Przewoski, B.; Rohdjeß, H.; Rosendaal, D.; von Rossen, P.; Scheid, H.; Schirm, N.; Schwandt, F.; Stein, H.; Theis, D.; Weber, J.; Wiedmann, W.; Woller, K.; Ziegler, R.

1993-07-01

The EDDA experiment is designed to study p + p excitation functions with high energy resolution and narrow step size in the kinetic energy range from 250 MeV to 2500 MeV at the Cooler Synchrotron COSY. Measurements during the accelertion phase in conjunction with internal targets will allow to achieve a fast and precise energy variation. Prototypes of the detector elements and the fiber target have been extensively tested with proton and electron beams; the detector performance and trigger efficiency have been studied in Monte Carlo simulations. In this contribution, results concerning detector design, prototype studies, Monte Carlo simulations and the anticipated detector resolutions will be reported.

ReaxFF Study of the Oxidation of Softwood Lignin in View of Carbon Fiber Production

DOE PAGES

Beste, Ariana

2014-10-06

We investigate the oxidative, thermal conversion of softwood lignin by performing molecular dynamics simulations based on a reactive force field (ReaxFF). The lignin samples are constructed from coniferyl alcohol units, which are connected through linkages that are randomly selected from a natural distribution of linkages in softwood. The goal of this work is to simulate the oxidative stabilization step during carbon fiber production from lignin precursor. We find that at simulation conditions where stabilization reactions occur, the lignin fragments have already undergone extensive degradation. The 5-5 linkage shows the highest reactivity towards cyclization and dehydrogenation.

Low Gravity Freefall Facilities

NASA Technical Reports Server (NTRS)

1981-01-01

Composite of Marshall Space Flight Center's Low-Gravity Free Fall Facilities.These facilities include a 100-meter drop tower and a 100-meter drop tube. The drop tower simulates in-flight microgravity conditions for up to 4.2 seconds for containerless processing experiments, immiscible fluids and materials research, pre-flight hardware design test and flight experiment simulation. The drop tube simulates in-flight microgravity conditions for up to 4.6 seconds and is used extensively for ground-based microgravity convection research in which extremely small samples are studied. The facility can provide deep undercooling for containerless processing experiments that require materials to remain in a liquid phase when cooled below the normal solidification temperature.

Microgravity

NASA Image and Video Library

1981-03-30

Composite of Marshall Space Flight Center's Low-Gravity Free Fall Facilities.These facilities include a 100-meter drop tower and a 100-meter drop tube. The drop tower simulates in-flight microgravity conditions for up to 4.2 seconds for containerless processing experiments, immiscible fluids and materials research, pre-flight hardware design test and flight experiment simulation. The drop tube simulates in-flight microgravity conditions for up to 4.6 seconds and is used extensively for ground-based microgravity convection research in which extremely small samples are studied. The facility can provide deep undercooling for containerless processing experiments that require materials to remain in a liquid phase when cooled below the normal solidification temperature.

Dynamical evolution of globular-cluster systems in clusters of galaxies

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

Muzzio, J.C.

1987-04-01

The dynamical processes that affect globular-cluster systems in clusters of galaxies are analyzed. Two-body and impulsive approximations are utilized to study dynamical friction, drag force, tidal stripping, tidal radii, globular-cluster swapping, tidal accretion, and galactic cannibalism. The evolution of galaxies and the collision of galaxies are simulated numerically; the steps involved in the simulation are described. The simulated data are compared with observations. Consideration is given to the number of galaxies, halo extension, location of the galaxies, distribution of the missing mass, nonequilibrium initial conditions, mass dependence, massive central galaxies, globular-cluster distribution, and lost globular clusters. 116 references.

ARC-1969-AC-42137

NASA Image and Video Library

1969-02-05

Height-Control Test Apparatus (HICONTA) Simulator mounted to the exterior of the 40x80ft W.T. Building N-221B and provided extensive vertical motion simulating airplanes, helicopter and V/STOL aircraft

Empirical Evaluation of Directional-Dependence Tests

ERIC Educational Resources Information Center

Thoemmes, Felix

2015-01-01

Testing of directional dependence is a method to infer causal direction that recently has attracted some attention. Previous examples by e.g. von Eye and DeShon (2012a) and extensive simulation studies by Pornprasertmanit and Little (2012) have demonstrated that under specific assumptions, directional-dependence tests can recover the true causal…

Documentation of the GLAS fourth order general circulation model. Volume 1: Model documentation

NASA Technical Reports Server (NTRS)

Kalnay, E.; Balgovind, R.; Chao, W.; Edelmann, J.; Pfaendtner, J.; Takacs, L.; Takano, K.

1983-01-01

The volume 1, of a 3 volume technical memoranda which contains a documentation of the GLAS Fourth Order General Circulation Model is presented. Volume 1 contains the documentation, description of the stratospheric/tropospheric extension, user's guide, climatological boundary data, and some climate simulation studies.

Sequential Dependencies in Driving

ERIC Educational Resources Information Center

Doshi, Anup; Tran, Cuong; Wilder, Matthew H.; Mozer, Michael C.; Trivedi, Mohan M.

2012-01-01

The effect of recent experience on current behavior has been studied extensively in simple laboratory tasks. We explore the nature of sequential effects in the more naturalistic setting of automobile driving. Driving is a safety-critical task in which delayed response times may have severe consequences. Using a realistic driving simulator, we find…

Constructing the Exact Significance Level for a Person-Fit Statistic.

ERIC Educational Resources Information Center

Liou, Michelle; Chang, Chih-Hsin

1992-01-01

An extension is proposed for the network algorithm introduced by C.R. Mehta and N.R. Patel to construct exact tail probabilities for testing the general hypothesis that item responses are distributed according to the Rasch model. A simulation study indicates the efficiency of the algorithm. (SLD)

Simulation of orientational coherent effects via Geant4

NASA Astrophysics Data System (ADS)

Bagli, E.; Asai, M.; Brandt, D.; Dotti, A.; Guidi, V.; Verderi, M.; Wright, D.

2017-10-01

Simulation of orientational coherent effects via Geant4 beam manipulation of high-and very-high-energy particle beams is a hot topic in accelerator physics. Coherent effects of ultra-relativistic particles in bent crystals allow the steering of particle trajectories thanks to the strong electrical field generated between atomic planes. Recently, a collimation experiment with bent crystals was carried out at the CERN-LHC, paving the way to the usage of such technology in current and future accelerators. Geant4 is a widely used object-oriented tool-kit for the Monte Carlo simulation of the interaction of particles with matter in high-energy physics. Moreover, its areas of application include also nuclear and accelerator physics, as well as studies in medical and space science. We present the first Geant4 extension for the simulation of orientational effects in straight and bent crystals for high energy charged particles. The model allows the manipulation of particle trajectories by means of straight and bent crystals and the scaling of the cross sections of hadronic and electromagnetic processes for channeled particles. Based on such a model, an extension of the Geant4 toolkit has been developed. The code and the model have been validated by comparison with published experimental data regarding the deflection efficiency via channeling and the variation of the rate of inelastic nuclear interactions.

Signal treatments to reduce heavy vehicle crash-risk at metropolitan highway intersections.

PubMed

Archer, Jeffery; Young, William

2009-05-01

Heavy vehicle red-light running at intersections is a common safety problem that has severe consequences. This paper investigates alternative signal treatments that address this issue. A micro-simulation analysis approach was adopted as a precursor to a field trial. The simulation model emulated traffic conditions at a known problem intersection and provided a baseline measure to compare the effects of: an extension of amber time; an extension of green for heavy vehicles detected in the dilemma zone at the onset of amber; an extension of the all-red safety-clearance time based on the detection of vehicles considered likely to run the red light at two detector locations during amber; an extension of the all-red safety-clearance time based on the detection of potential red-light runners during amber or red; and a combination of the second and fourth alternatives. Results suggested safety improvements for all treatments. An extension of amber provided the best safety effect but is known to be prone to behavioural adaptation effects and wastes traffic movement time unnecessarily. A green extension for heavy vehicles detected in the dilemma zone and an all-red extension for potential red-light runners were deemed to provide a sustainable safety improvement and operational efficiency.

Alborz-I array: A simulation on performance and properties of the array around the knee of the cosmic ray spectrum

NASA Astrophysics Data System (ADS)

Abdollahi, Soheila; Bahmanabadi, Mahmud; Pezeshkian, Yousef; Mortazavi Moghaddam, Saba

2016-03-01

The first phase of the Alborz Observatory Array (Alborz-I) consists of 20 plastic scintillation detectors each one with surface area of 0.25 m2spread over an area of 40 × 40 m2 realized to the study of Extensive Air Showers around the knee at the Sharif University of Technology campus. The first stage of the project including construction and operation of a prototype system has now been completed and the electronics that will be used in the array instrument has been tested under field conditions. In order to achieve a realistic estimate of the array performance, a large number of simulated CORSIKA showers have been used. In the present work, theoretical results obtained in the study of different array layouts and trigger conditions are described. Using Monte Carlo simulations of showers the rate of detected events per day and the trigger probability functions, i.e., the probability for an extensive air shower to trigger a ground based array as a function of the shower core distance to the center of array are presented for energies above 1 TeV and zenith angles up to 60°. Moreover, the angular resolution of the Alborz-I array is obtained.

Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments.

PubMed

Wiechert, W; de Graaf, A A

1997-07-05

The extension of metabolite balancing with carbon labeling experiments, as described by Marx et al. (Biotechnol. Bioeng. 49: 11-29), results in a much more detailed stationary metabolic flux analysis. As opposed to basic metabolite flux balancing alone, this method enables both flux directions of bidirectional reaction steps to be quantitated. However, the mathematical treatment of carbon labeling systems is much more complicated, because it requires the solution of numerous balance equations that are bilinear with respect to fluxes and fractional labeling. In this study, a universal modeling framework is presented for describing the metabolite and carbon atom flux in a metabolic network. Bidirectional reaction steps are extensively treated and their impact on the system's labeling state is investigated. Various kinds of modeling assumptions, as usually made for metabolic fluxes, are expressed by linear constraint equations. A numerical algorithm for the solution of the resulting linear constrained set of nonlinear equations is developed. The numerical stability problems caused by large bidirectional fluxes are solved by a specially developed transformation method. Finally, the simulation of carbon labeling experiments is facilitated by a flexible software tool for network synthesis. An illustrative simulation study on flux identifiability from available flux and labeling measurements in the cyclic pentose phosphate pathway of a recombinant strain of Zymomonas mobilis concludes this contribution.

The role of potassium, magnesium and calcium in the Enhanced Biological Phosphorus Removal treatment plants.

PubMed

Barat, R; Montoya, T; Seco, A; Ferrer, J

2005-09-01

Cations as potassium and magnesium play an important role in maintaining the stability of Enhanced Biological Phosphorus Removal (EBPR) process. In this paper potassium, magnesium and calcium behaviour in EBPR treatment plants has been studied. An ASM2d model extension which takes into account the role of potassium and magnesium in the EBPR process has been developed. Finally, a simulation of the effect on P removal of a shortage of K and Mg was studied. The experimental results showed that K and Mg play an important role in the EBPR process being cotransported with P into and out of bacterial cells. It has been observed that calcium is not involved in P release and uptake. The values of the molar ratios K/P (0.28 mol K mol P(-1)) and Mg/P (0.36 mol Mg mol P(-1)) were obtained accomplishing the charge balance, with different K/Mg mass ratios and without phosphorus precipitation. Model predictions accurately reproduced experimental data. The simulations carried out showed the important effect of the K and Mg influent concentration for P removal efficiency. The results illustrate that the proposed ASM2d model extension must be considered in order to accurately simulate the phosphorus removal process.

Assessing uncertainties in crop and pasture ensemble model simulations of productivity and N2O emissions

USDA-ARS?s Scientific Manuscript database

Simulation models are extensively used to predict agricultural productivity and greenhouse gas (GHG) emissions. However, the uncertainties of (reduced) model ensemble simulations have not been assessed systematically for variables affecting food security and climate change mitigation, within multisp...

Dual Interlocked Logic for Single-Event Transient Mitigation

DTIC Science & Technology

2017-03-01

SPICE simulation and fault-injection analysis. Exemplar SPICE simulations have been performed in a 32nm partially- depleted silicon-on-insulator...in this work. The model has been validated at the 32nm SOI technology node with extensive heavy-ion data [7]. For the SPICE simulations, three

Extending MAM5 Meta-Model and JaCalIV E Framework to Integrate Smart Devices from Real Environments.

PubMed

Rincon, J A; Poza-Lujan, Jose-Luis; Julian, V; Posadas-Yagüe, Juan-Luis; Carrascosa, C

2016-01-01

This paper presents the extension of a meta-model (MAM5) and a framework based on the model (JaCalIVE) for developing intelligent virtual environments. The goal of this extension is to develop augmented mirror worlds that represent a real and virtual world coupled, so that the virtual world not only reflects the real one, but also complements it. A new component called a smart resource artifact, that enables modelling and developing devices to access the real physical world, and a human in the loop agent to place a human in the system have been included in the meta-model and framework. The proposed extension of MAM5 has been tested by simulating a light control system where agents can access both virtual and real sensor/actuators through the smart resources developed. The results show that the use of real environment interactive elements (smart resource artifacts) in agent-based simulations allows to minimize the error between simulated and real system.

Extending MAM5 Meta-Model and JaCalIV E Framework to Integrate Smart Devices from Real Environments

PubMed Central

2016-01-01

This paper presents the extension of a meta-model (MAM5) and a framework based on the model (JaCalIVE) for developing intelligent virtual environments. The goal of this extension is to develop augmented mirror worlds that represent a real and virtual world coupled, so that the virtual world not only reflects the real one, but also complements it. A new component called a smart resource artifact, that enables modelling and developing devices to access the real physical world, and a human in the loop agent to place a human in the system have been included in the meta-model and framework. The proposed extension of MAM5 has been tested by simulating a light control system where agents can access both virtual and real sensor/actuators through the smart resources developed. The results show that the use of real environment interactive elements (smart resource artifacts) in agent-based simulations allows to minimize the error between simulated and real system. PMID:26926691

LOOS: an extensible platform for the structural analysis of simulations.

PubMed

Romo, Tod D; Grossfield, Alan

2009-01-01

We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.

Stress in Lumbar Intervertebral Discs during Distraction

PubMed Central

Gay, Ralph E.; Ilharreborde, Brice; Zhao, Kristin D.; Berglund, Lawrence J.; Bronfort, Gert; An, Kai-Nan

2008-01-01

BACKGROUND CONTEXT The intervertebral disc is a common source of low back pain. Prospective studies suggest that treatments that intermittently distract the disc might be beneficial for chronic low back pain. Although the potential exists for distraction therapies to affect the disc biomechanically their effect on intradiscal stress is debated. PURPOSE To determine if distraction alone, distraction combined with flexion or distraction combined with extension can reduce nucleus pulposus pressure and posterior anulus compressive stress in cadaveric lumbar discs compared to simulated standing or lying. STUDY DESIGN Laboratory study using single cadaveric motion segments. OUTCOME MEASURES Strain gauge measures of nucleus pulposus pressure and compressive stress in the anterior and posterior annulus fibrosus METHODS Intradiscal stress profilometry was performed on 15 motion segments during 5 simulated conditions: standing, lying, and 3 distracted conditions. Disc degeneration was graded by inspection from 1 (normal) to 4 (severe degeneration). RESULTS All distraction conditions markedly reduced nucleus pressure compared to either simulated standing or lying. There was no difference between distraction with flexion and distraction with extension in regard to posterior annulus compressive stress. Discs with little or no degeneration appeared to distributed compressive stress differently than those with moderate or severe degeneration. CONCLUSIONS Distraction appears to predictably reduce nucleus pulposus pressure. The effect of distraction therapy on the distribution of compressive stress may be dependent in part on the health of the disc. PMID:17981092

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

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

Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul

2015-01-21

The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, whichmore » is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.« less

Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.

PubMed

Havrila, Marek; Zgarbová, Marie; Jurečka, Petr; Banáš, Pavel; Krepl, Miroslav; Otyepka, Michal; Šponer, Jiří

2015-12-10

We report an extensive set of explicit solvent molecular dynamics (MD) simulations (∼25 μs of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson-Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Waals interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions.

Addition of lateral bending range of motion measurement to standard sagittal measurement to improve diagnosis sensitivity of ligamentous injury in the human lower cervical spine.

PubMed

Leahy, P Devin; Puttlitz, Christian M

2016-01-01

This study examined the cervical spine range of motion (ROM) resulting from whiplash-type hyperextension and hyperflexion type ligamentous injuries, and sought to improve the accuracy of specific diagnosis of these injuries. The study was accomplished by measurement of ROM throughout axial rotation, lateral bending, and flexion and extension, using a validated finite element model of the cervical spine that was modified to simulate hyperextension and/or hyperflexion injuries. It was found that the kinematic difference between hyperextension and hyperflexion injuries was minimal throughout the combined flexion and extension ROM measurement that is commonly used for clinical diagnosis of cervical ligamentous injury. However, the two injuries demonstrated substantially different ROM under axial rotation and lateral bending. It is recommended that other bending axes beyond flexion and extension are incorporated into clinical diagnosis of cervical ligamentous injury.

Surgical stent planning: simulation parameter study for models based on DICOM standards.

PubMed

Scherer, S; Treichel, T; Ritter, N; Triebel, G; Drossel, W G; Burgert, O

2011-05-01

Endovascular Aneurysm Repair (EVAR) can be facilitated by a realistic simulation model of stent-vessel-interaction. Therefore, numerical feasibility and integrability in the clinical environment was evaluated. The finite element method was used to determine necessary simulation parameters for stent-vessel-interaction in EVAR. Input variables and result data of the simulation model were examined for their standardization using DICOM supplements. The study identified four essential parameters for the stent-vessel simulation: blood pressure, intima constitution, plaque occurrence and the material properties of vessel and plaque. Output quantities such as radial force of the stent and contact pressure between stent/vessel can help the surgeon to evaluate implant fixation and sealing. The model geometry can be saved with DICOM "Surface Segmentation" objects and the upcoming "Implant Templates" supplement. Simulation results can be stored using the "Structured Report". A standards-based general simulation model for optimizing stent-graft selection may be feasible. At present, there are limitations due to specification of individual vessel material parameters and for simulating the proximal fixation of stent-grafts with hooks. Simulation data with clinical relevance for documentation and presentation can be stored using existing or new DICOM extensions.

Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase.

PubMed

Isaksen, Geir Villy; Hopmann, Kathrin Helen; Åqvist, Johan; Brandsdal, Bjørn Olav

2016-04-12

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides and 2'-deoxyribonucleosides, yielding the purine base and (2'-deoxy)ribose 1-phosphate as products. While this enzyme has been extensively studied, several questions with respect to the catalytic mechanism have remained largely unanswered. The role of the phosphate and key amino acid residues in the catalytic reaction as well as the purine ring protonation state is elucidated using density functional theory calculations and extensive empirical valence bond (EVB) simulations. Free energy surfaces for adenosine, inosine, and guanosine are fitted to ab initio data and yield quantitative agreement with experimental data when the surfaces are used to model the corresponding enzymatic reactions. The cognate substrates 6-aminopurines (inosine and guanosine) interact with PNP through extensive hydrogen bonding, but the substrate specificity is found to be a direct result of the electrostatic preorganization energy along the reaction coordinate. Asn243 has previously been identified as a key residue providing substrate specificity. Mutation of Asn243 to Asp has dramatic effects on the substrate specificity, making 6-amino- and 6-oxopurines equally good as substrates. The principal effect of this particular mutation is the change in the electrostatic preorganization energy between the native enzyme and the Asn243Asp mutant, clearly favoring adenosine over inosine and guanosine. Thus, the EVB simulations show that this particular mutation affects the electrostatic preorganization of the active site, which in turn can explain the substrate specificity.

Extension of a Kinetic Approach to Chemical Reactions to Electronic Energy Levels and Reactions Involving Charged Species with Application to DSMC Simulations

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2014-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties are extended in the current work to include electronic energy level transitions and reactions involving charged particles. These extensions are shown to agree favorably with reported transition and reaction rates from the literature for near-equilibrium conditions. Also, the extensions are applied to the second flight of the Project FIRE flight experiment at 1634 seconds with a Knudsen number of 0.001 at an altitude of 76.4 km. In order to accomplish this, NASA's direct simulation Monte Carlo code DAC was rewritten to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced chemistry model, and to include the extensions presented in this work. The 1634 second data point was chosen for comparisons to be made in order to include a CFD solution. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid because, although near-transitional, the flow is still considered to be continuum. It is shown that the inclusion of electronic energy levels in the DSMC simulation is necessary for flows of this nature and is required for comparison to the CFD solution. The flow field solutions are also post-processed by the nonequilibrium radiation code HARA to compute the radiative portion.

Evaluation of DNA Force Fields in Implicit Solvation

PubMed Central

Gaillard, Thomas; Case, David A.

2011-01-01

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

Primary damage formation in bcc iron

NASA Astrophysics Data System (ADS)

Stoller, R. E.; Odette, G. R.; Wirth, B. D.

1997-11-01

Primary defect formation in bee iron has been extensively investigated using the methods of molecular dynamics (MD) and Monte Carlo (MC) simulation. This research has employed a modified version of the Finnis-Sinclair interatomic potential. MD was used in the simulation of displacement cascades with energies up to 40 keV and to examine the migration of the interstitial clusters that were observed to form in the cascade simulations. Interstitial cluster binding energies and the stable cluster configurations were determined by structural relaxation and energy minimization using a MC method with simulated annealing. Clusters containing up to 19 interstitials were examined. Taken together with the previous work, these new simulations provide a reasonably complete description of primary defect formation in iron. The results of the displacement cascade simulations have been used to characterize the energy and temperature dependence of primary defect formation in terms of two parameters: (1) the number of surviving point defects and (2) the fraction of the surviving defects that are contained in clusters. The number of surviving point defects is expressed as a fraction of the atomic displacements calculated using the secondary displacement model of Norgett-Robinson-Torrens (NRT). Although the results of the high energy simulations are generally consistent with those obtained at lower energies, two notable exceptions were observed. The first is that extensive subcascade formation at 40 keV leads to a higher defect survival fraction than would be predicted from extrapolation of the results obtained for energies up to 20 keV. The stable defect fraction obtained from the MD simulations is a smoothly decreasing function up to 20 keV. Subcascade formation leads to a slight increase in this ratio at 40 keV, where the value is about the same as at 10 keV. Secondly, the potential for a significant level of in-cascade vacancy clustering was observed. Previous cascade studies employing this potential have reported extensive interstitial clustering, but little evidence of vacancy clustering. Interstitial clusters were found to be strongly bound, with binding energies in excess of 1 eV. The larger clusters exhibited a complex, 3D structure and were composed of <111> crowdions. These clusters were observed to migrate by collective <111> translations with an activation energy on the order of 0.1 eV.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

PubMed

Eastman, Peter; Friedrichs, Mark S; Chodera, John D; Radmer, Randall J; Bruns, Christopher M; Ku, Joy P; Beauchamp, Kyle A; Lane, Thomas J; Wang, Lee-Ping; Shukla, Diwakar; Tye, Tony; Houston, Mike; Stich, Timo; Klein, Christoph; Shirts, Michael R; Pande, Vijay S

2013-01-08

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

PubMed Central

Eastman, Peter; Friedrichs, Mark S.; Chodera, John D.; Radmer, Randall J.; Bruns, Christopher M.; Ku, Joy P.; Beauchamp, Kyle A.; Lane, Thomas J.; Wang, Lee-Ping; Shukla, Diwakar; Tye, Tony; Houston, Mike; Stich, Timo; Klein, Christoph; Shirts, Michael R.; Pande, Vijay S.

2012-01-01

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added. PMID:23316124

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

PubMed

Decherchi, Sergio; Berteotti, Anna; Bottegoni, Giovanni; Rocchia, Walter; Cavalli, Andrea

2015-01-27

The study of biomolecular interactions between a drug and its biological target is of paramount importance for the design of novel bioactive compounds. In this paper, we report on the use of molecular dynamics (MD) simulations and machine learning to study the binding mechanism of a transition state analogue (DADMe-immucillin-H) to the purine nucleoside phosphorylase (PNP) enzyme. Microsecond-long MD simulations allow us to observe several binding events, following different dynamical routes and reaching diverse binding configurations. These simulations are used to estimate kinetic and thermodynamic quantities, such as kon and binding free energy, obtaining a good agreement with available experimental data. In addition, we advance a hypothesis for the slow-onset inhibition mechanism of DADMe-immucillin-H against PNP. Combining extensive MD simulations with machine learning algorithms could therefore be a fruitful approach for capturing key aspects of drug-target recognition and binding.

Evaluation of urban surface parameterizations in the WRF model using measurements during the Texas Air Quality Study 2006 field campaign

NASA Astrophysics Data System (ADS)

Lee, S.-H.; Kim, S.-W.; Angevine, W. M.; Bianco, L.; McKeen, S. A.; Senff, C. J.; Trainer, M.; Tucker, S. C.; Zamora, R. J.

2011-03-01

The performance of different urban surface parameterizations in the WRF (Weather Research and Forecasting) in simulating urban boundary layer (UBL) was investigated using extensive measurements during the Texas Air Quality Study 2006 field campaign. The extensive field measurements collected on surface (meteorological, wind profiler, energy balance flux) sites, a research aircraft, and a research vessel characterized 3-dimensional atmospheric boundary layer structures over the Houston-Galveston Bay area, providing a unique opportunity for the evaluation of the physical parameterizations. The model simulations were performed over the Houston metropolitan area for a summertime period (12-17 August) using a bulk urban parameterization in the Noah land surface model (original LSM), a modified LSM, and a single-layer urban canopy model (UCM). The UCM simulation compared quite well with the observations over the Houston urban areas, reducing the systematic model biases in the original LSM simulation by 1-2 °C in near-surface air temperature and by 200-400 m in UBL height, on average. A more realistic turbulent (sensible and latent heat) energy partitioning contributed to the improvements in the UCM simulation. The original LSM significantly overestimated the sensible heat flux (~200 W m-2) over the urban areas, resulting in warmer and higher UBL. The modified LSM slightly reduced warm and high biases in near-surface air temperature (0.5-1 °C) and UBL height (~100 m) as a result of the effects of urban vegetation. The relatively strong thermal contrast between the Houston area and the water bodies (Galveston Bay and the Gulf of Mexico) in the LSM simulations enhanced the sea/bay breezes, but the model performance in predicting local wind fields was similar among the simulations in terms of statistical evaluations. These results suggest that a proper surface representation (e.g. urban vegetation, surface morphology) and explicit parameterizations of urban physical processes are required for accurate urban atmospheric numerical modeling.

Molecular Optical Simulation Environment (MOSE): A Platform for the Simulation of Light Propagation in Turbid Media

PubMed Central

Ren, Shenghan; Chen, Xueli; Wang, Hailong; Qu, Xiaochao; Wang, Ge; Liang, Jimin; Tian, Jie

2013-01-01

The study of light propagation in turbid media has attracted extensive attention in the field of biomedical optical molecular imaging. In this paper, we present a software platform for the simulation of light propagation in turbid media named the “Molecular Optical Simulation Environment (MOSE)”. Based on the gold standard of the Monte Carlo method, MOSE simulates light propagation both in tissues with complicated structures and through free-space. In particular, MOSE synthesizes realistic data for bioluminescence tomography (BLT), fluorescence molecular tomography (FMT), and diffuse optical tomography (DOT). The user-friendly interface and powerful visualization tools facilitate data analysis and system evaluation. As a major measure for resource sharing and reproducible research, MOSE aims to provide freeware for research and educational institutions, which can be downloaded at http://www.mosetm.net. PMID:23577215

Use of high performance networks and supercomputers for real-time flight simulation

NASA Technical Reports Server (NTRS)

Cleveland, Jeff I., II

1993-01-01

In order to meet the stringent time-critical requirements for real-time man-in-the-loop flight simulation, computer processing operations must be consistent in processing time and be completed in as short a time as possible. These operations include simulation mathematical model computation and data input/output to the simulators. In 1986, in response to increased demands for flight simulation performance, NASA's Langley Research Center (LaRC), working with the contractor, developed extensions to the Computer Automated Measurement and Control (CAMAC) technology which resulted in a factor of ten increase in the effective bandwidth and reduced latency of modules necessary for simulator communication. This technology extension is being used by more than 80 leading technological developers in the United States, Canada, and Europe. Included among the commercial applications are nuclear process control, power grid analysis, process monitoring, real-time simulation, and radar data acquisition. Personnel at LaRC are completing the development of the use of supercomputers for mathematical model computation to support real-time flight simulation. This includes the development of a real-time operating system and development of specialized software and hardware for the simulator network. This paper describes the data acquisition technology and the development of supercomputing for flight simulation.

A non-iterative extension of the multivariate random effects meta-analysis.

PubMed

Makambi, Kepher H; Seung, Hyunuk

2015-01-01

Multivariate methods in meta-analysis are becoming popular and more accepted in biomedical research despite computational issues in some of the techniques. A number of approaches, both iterative and non-iterative, have been proposed including the multivariate DerSimonian and Laird method by Jackson et al. (2010), which is non-iterative. In this study, we propose an extension of the method by Hartung and Makambi (2002) and Makambi (2001) to multivariate situations. A comparison of the bias and mean square error from a simulation study indicates that, in some circumstances, the proposed approach perform better than the multivariate DerSimonian-Laird approach. An example is presented to demonstrate the application of the proposed approach.

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

Majzoobi, A.; Joshi, R. P., E-mail: ravi.joshi@ttu.edu; Neuber, A. A.

Particle-in-cell simulations are performed to analyze the efficiency, output power and leakage currents in a 12-Cavity, 12-Cathode rising-sun magnetron with diffraction output (MDO). The central goal is to conduct a parameter study of a rising-sun magnetron that comprehensively incorporates performance enhancing features such as transparent cathodes, axial extraction, the use of endcaps, and cathode extensions. Our optimum results demonstrate peak output power of about 2.1 GW, with efficiencies of ∼70% and low leakage currents at a magnetic field of 0.45 Tesla, a 400 kV bias with a single endcap, for a range of cathode extensions between 3 and 6 centimeters.

Optimizing the network topology of block copolymer liquid crystal elastomers for enhanced extensibility and toughness

NASA Astrophysics Data System (ADS)

Nowak, Christian; Escobedo, Fernando A.

2017-08-01

Molecular simulations are used to study the effect of synthesis conditions on the tensile response of liquid-crystalline elastomers formed by block copolymer chains. Remarkably, it is found that despite the significant presence of trapped entanglements, these networks can exhibit the sawtooth tensile response previously predicted for ideal unentangled networks. It is also found that the monomer concentration during crosslinking can be tuned to limit the extent of entanglements and inhomogeneities while also maximizing network extensibility. It is predicted that networks synthesized at a "critical" concentration will have the greatest toughness.

Influence of hip joint simulator design and mechanics on the wear and creep of metal-on-polyethylene bearings

PubMed Central

Ali, Murat; Al-Hajjar, Mazen; Partridge, Susan; Williams, Sophie; Fisher, John; Jennings, Louise M

2016-01-01

Hip joint simulators are used extensively for preclinical testing of hip replacements. The variation in simulator design and test conditions used worldwide can affect the tribological performance of polyethylene. The aim of this study was to assess the effects of simulator mechanics and design on the wear and creep of ultra-high-molecular-weight polyethylene. In the first part of this study, an electromechanical simulator and pneumatic simulator were used to compare the wear and creep of metal-on-polyethylene components under the same standard gait conditions. In the second part of the study, the same electromechanical hip joint simulator was used to investigate the influence of kinematics on wear. Higher wear rates and penetration depths were observed from the electromechanical simulator compared with the pneumatic simulator. When adduction/abduction was introduced to the gait cycle, there was no significant difference in wear with that obtained under the gait cycle condition without adduction/abduction. This study confirmed the influence of hip simulator design and loading conditions on the wear of polyethylene, and therefore direct comparisons of absolute wear rates between different hip joint simulators should be avoided. This study also confirmed that the resulting wear path was the governing factor in obtaining clinically relevant wear rates, and this can be achieved with either two axes or three axes of rotations. However, three axes of rotation (with the inclusion of adduction/abduction) more closely replicate clinical conditions and should therefore be the design approach for newly developed hip joint simulators used for preclinical testing. PMID:27160559

Influence of hip joint simulator design and mechanics on the wear and creep of metal-on-polyethylene bearings.

PubMed

Ali, Murat; Al-Hajjar, Mazen; Partridge, Susan; Williams, Sophie; Fisher, John; Jennings, Louise M

2016-05-01

Hip joint simulators are used extensively for preclinical testing of hip replacements. The variation in simulator design and test conditions used worldwide can affect the tribological performance of polyethylene. The aim of this study was to assess the effects of simulator mechanics and design on the wear and creep of ultra-high-molecular-weight polyethylene. In the first part of this study, an electromechanical simulator and pneumatic simulator were used to compare the wear and creep of metal-on-polyethylene components under the same standard gait conditions. In the second part of the study, the same electromechanical hip joint simulator was used to investigate the influence of kinematics on wear. Higher wear rates and penetration depths were observed from the electromechanical simulator compared with the pneumatic simulator. When adduction/abduction was introduced to the gait cycle, there was no significant difference in wear with that obtained under the gait cycle condition without adduction/abduction. This study confirmed the influence of hip simulator design and loading conditions on the wear of polyethylene, and therefore direct comparisons of absolute wear rates between different hip joint simulators should be avoided. This study also confirmed that the resulting wear path was the governing factor in obtaining clinically relevant wear rates, and this can be achieved with either two axes or three axes of rotations. However, three axes of rotation (with the inclusion of adduction/abduction) more closely replicate clinical conditions and should therefore be the design approach for newly developed hip joint simulators used for preclinical testing. © IMechE 2016.

Dissolution curve comparisons through the F(2) parameter, a Bayesian extension of the f(2) statistic.

PubMed

Novick, Steven; Shen, Yan; Yang, Harry; Peterson, John; LeBlond, Dave; Altan, Stan

2015-01-01

Dissolution (or in vitro release) studies constitute an important aspect of pharmaceutical drug development. One important use of such studies is for justifying a biowaiver for post-approval changes which requires establishing equivalence between the new and old product. We propose a statistically rigorous modeling approach for this purpose based on the estimation of what we refer to as the F2 parameter, an extension of the commonly used f2 statistic. A Bayesian test procedure is proposed in relation to a set of composite hypotheses that capture the similarity requirement on the absolute mean differences between test and reference dissolution profiles. Several examples are provided to illustrate the application. Results of our simulation study comparing the performance of f2 and the proposed method show that our Bayesian approach is comparable to or in many cases superior to the f2 statistic as a decision rule. Further useful extensions of the method, such as the use of continuous-time dissolution modeling, are considered.

Viscous relaxation as a prerequisite for tectonic resurfacing on Ganymede: Insights from numerical models of lithospheric extension

USGS Publications Warehouse

Bland, Michael T.; McKinnon, William B.

2018-01-01

Ganymede’s bright terrain formed during a near-global resurfacing event (or events) that produced both heavily tectonized and relatively smooth terrains. The mechanism(s) by which resurfacing occurred on Ganymede (e.g., cryovolcanic or tectonic), and the relationship between the older, dark and the younger, bright terrain are fundamental to understanding the geological evolution of the satellite. Using a two-dimensional numerical model of lithospheric extension that has previously been used to successfully simulate surface deformation consistent with grooved terrain morphologies, we investigate whether large-amplitude preexisting topography can be resurfaced (erased) by extension (i.e., tectonic resurfacing). Using synthetically produced initial topography, we show that when the total relief of the initial topography is larger than 25–50 m, periodic groove-like structures fail to form. Instead, extension is localized in a few individual, isolated troughs. These results pose a challenge to the tectonic resurfacing hypothesis. We further investigate the effects of preexisting topography by performing suites of simulations initialized with topography derived from digital terrain models of Ganymede’s surface. These include dark terrain, fresh (relatively deep) impact craters, smooth bright terrain, and a viscously relaxed impact crater. The simulations using dark terrain and fresh impact craters are consistent with our simulations using synthetic topography: periodic groove-like deformation fails to form. In contrast, when simulations were initialized with bright smooth terrain topography, groove-like deformation results from a wide variety of heat flow and surface temperature conditions. Similarly, when a viscously relaxed impact crater was used, groove-like structures were able to form during extension. These results suggest that tectonic resurfacing may require that the amplitude of the initial topography be reduced before extension begins. We emphasize that viscous relaxation may be the key to enabling tectonic resurfacing, as the heat fluxes associated with groove terrain formation are also capable of reducing crater topography through viscous relaxation. For long-wavelength topography (large craters) viscous relaxation is unavoidable. We propose that the resurfacing of Ganymede occurred through a combination of viscous relaxation, tectonic resurfacing, cryovolcanism and, at least in a few cases, band formation. Variations in heat flow and strain magnitudes across Ganymede likely produced the complex variety of terrain types currently observed.

Viscous relaxation as a prerequisite for tectonic resurfacing on Ganymede: Insights from numerical models of lithospheric extension

NASA Astrophysics Data System (ADS)

Bland, Michael T.; McKinnon, William B.

2018-05-01

Ganymede's bright terrain formed during a near-global resurfacing event (or events) that produced both heavily tectonized and relatively smooth terrains. The mechanism(s) by which resurfacing occurred on Ganymede (e.g., cryovolcanic or tectonic), and the relationship between the older, dark and the younger, bright terrain are fundamental to understanding the geological evolution of the satellite. Using a two-dimensional numerical model of lithospheric extension that has previously been used to successfully simulate surface deformation consistent with grooved terrain morphologies, we investigate whether large-amplitude preexisting topography can be resurfaced (erased) by extension (i.e., tectonic resurfacing). Using synthetically produced initial topography, we show that when the total relief of the initial topography is larger than 25-50 m, periodic groove-like structures fail to form. Instead, extension is localized in a few individual, isolated troughs. These results pose a challenge to the tectonic resurfacing hypothesis. We further investigate the effects of preexisting topography by performing suites of simulations initialized with topography derived from digital terrain models of Ganymede's surface. These include dark terrain, fresh (relatively deep) impact craters, smooth bright terrain, and a viscously relaxed impact crater. The simulations using dark terrain and fresh impact craters are consistent with our simulations using synthetic topography: periodic groove-like deformation fails to form. In contrast, when simulations were initialized with bright smooth terrain topography, groove-like deformation results from a wide variety of heat flow and surface temperature conditions. Similarly, when a viscously relaxed impact crater was used, groove-like structures were able to form during extension. These results suggest that tectonic resurfacing may require that the amplitude of the initial topography be reduced before extension begins. We emphasize that viscous relaxation may be the key to enabling tectonic resurfacing, as the heat fluxes associated with groove terrain formation are also capable of reducing crater topography through viscous relaxation. For long-wavelength topography (large craters) viscous relaxation is unavoidable. We propose that the resurfacing of Ganymede occurred through a combination of viscous relaxation, tectonic resurfacing, cryovolcanism and, at least in a few cases, band formation. Variations in heat flow and strain magnitudes across Ganymede likely produced the complex variety of terrain types currently observed.

Reinventing atomic magnetic simulations with spin-orbit coupling

DOE PAGES

Perera, Meewanage Dilina N.; Eisenbach, Markus; Nicholson, Don M.; ...

2016-02-10

We propose a powerful extension to the combined molecular and spin dynamics method that fully captures the coupling between the atomic and spin subsystems via spin-orbit interactions. Moreover, the foundation of this method lies in the inclusion of the local magnetic anisotropies that arise as a consequence of the lattice symmetry breaking due to phonons or crystallographic defects. By using canonical simulations of bcc iron with the system coupled to a phonon heat bath, we show that our extension enables the previously unachievable angular momentum exchange between the atomic and spin degrees of freedom.

Surgical simulation: a urological perspective.

PubMed

Wignall, Geoffrey R; Denstedt, John D; Preminger, Glenn M; Cadeddu, Jeffrey A; Pearle, Margaret S; Sweet, Robert M; McDougall, Elspeth M

2008-05-01

Surgical education is changing rapidly as several factors including budget constraints and medicolegal concerns limit opportunities for urological trainees. New methods of skills training such as low fidelity bench trainers and virtual reality simulators offer new avenues for surgical education. In addition, surgical simulation has the potential to allow practicing surgeons to develop new skills and maintain those they already possess. We provide a review of the background, current status and future directions of surgical simulators as they pertain to urology. We performed a literature review and an overview of surgical simulation in urology. Surgical simulators are in various stages of development and validation. Several simulators have undergone extensive validation studies and are in use in surgical curricula. While virtual reality simulators offer the potential to more closely mimic reality and present entire operations, low fidelity simulators remain useful in skills training, particularly for novices and junior trainees. Surgical simulation remains in its infancy. However, the potential to shorten learning curves for difficult techniques and practice surgery without risk to patients continues to drive the development of increasingly more advanced and realistic models. Surgical simulation is an exciting area of surgical education. The future is bright as advancements in computing and graphical capabilities offer new innovations in simulator technology. Simulators must continue to undergo rigorous validation studies to ensure that time spent by trainees on bench trainers and virtual reality simulators will translate into improved surgical skills in the operating room.

Performance of the S - [chi][squared] Statistic for Full-Information Bifactor Models

ERIC Educational Resources Information Center

Li, Ying; Rupp, Andre A.

2011-01-01

This study investigated the Type I error rate and power of the multivariate extension of the S - [chi][squared] statistic using unidimensional and multidimensional item response theory (UIRT and MIRT, respectively) models as well as full-information bifactor (FI-bifactor) models through simulation. Manipulated factors included test length, sample…

EXTENSION OF SELF-MODELING CURVE RESOLUTION TO MIXTURES OF MORE THAN THREE COMPONENTS. PART 3. ATMOSPHERIC AEROSOL DATA SIMULATION STUDIES. (R826238)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Heart Rate Variability during Simulated Hemorrhage with Lower Body Negative Pressure in High and Low Tolerant Subjects

DTIC Science & Technology

2011-11-01

Army Institute of Surgical Research, Fort Sam Houston, TX, USA 2 Department of Health and Kinesiology , University of Texas at San Antonio, San Antonio...reduced HRV (Thayer and Sternberg, 2006).HRVhas been extensively studied in hospital settings such as intensive care units to assess cardiovascular

Electroencephalographic Correlates of Pilot Performance: Simulation and In-Flight Studies

DTIC Science & Technology

1988-02-01

a11Hzinlet n 1ig-r Hz acomparaesthve inmlsiio of sgnitradnitat 4-7rc andfectsH in ef and rle rigt nral oreetent durin thre pioteoflht condi...mu rhythm concept bears further consideration. It will be recalled from our initial coments that an extensive animal literature has shown that

A Driving Simulator Evaluation of Red Arrows and Flashing Yellow Arrows in Right-Turn Applications : Establishing the Foundation for Future Research

DOT National Transportation Integrated Search

2017-11-01

Driver understanding of flashing yellow arrow (FYA) indications for left turns has been studied extensively; however, the use of FYA for right-turn applications is an area that needs to be better understood through evaluations focused on actual drive...

Simulation of solar array slewing of Indian remote sensing satellite

NASA Astrophysics Data System (ADS)

Maharana, P. K.; Goel, P. S.

The effect of flexible arrays on sun tracking for the IRS satellite is studied. Equations of motion of satellites carrying a rotating flexible appendage are developed following the Newton-Euler approach and utilizing the constrained modes of the appendage. The drive torque, detent torque and friction torque in the SADA are included in the model. Extensive simulations of the slewing motion are carried out. The phenomena of back-stepping, step-missing, step-slipping and the influences of array flexibility in the acquisition mode are observed for certain combinations of parameters.

Eccentric and concentric muscle performance following 7 days of simulated weightlessness

NASA Technical Reports Server (NTRS)

Hayes, Judith C.; Roper, Mary L.; Mazzocca, Augustus D.; Mcbrine, John J.; Barrows, Linda H.; Harris, Bernard A.; Siconolfi, Steven F.

1992-01-01

Changes in skeletal muscle strength occur in response to chronic disuse or insufficient functional loading. The purpose of this study was to examine changes in muscle performance of the lower extremity and torso prior to and immediately after 7 days of simulated weightlessness (horizontal bed rest). A Biodex was used to determine concentric and eccentric peak torque and angle at peak torque for the back, abdomen, quadriceps, hamstring, soleus, and tibialis anterior. A reference angle of 0 degrees was set at full extension. Data were analyzed by ANOVA.

Advances in the computation of transonic separated flows over finite wings

NASA Technical Reports Server (NTRS)

Kaynak, Unver; Flores, Jolen

1989-01-01

Problems encountered in numerical simulations of transonic wind-tunnel experiments with low-aspect-ratio wings are surveyed and illustrated. The focus is on the zonal Euler/Navier-Stokes program developed by Holst et al. (1985) and its application to shock-induced separation. The physical basis and numerical implementation of the method are reviewed, and results are presented from studies of the effects of artificial dissipation, boundary conditions, grid refinement, the turbulence model, and geometry representation on the simulation accuracy. Extensive graphs and diagrams and typical flow visualizations are provided.

Freak waves in random oceanic sea states.

PubMed

Onorato, M; Osborne, A R; Serio, M; Bertone, S

2001-06-18

Freak waves are very large, rare events in a random ocean wave train. Here we study their generation in a random sea state characterized by the Joint North Sea Wave Project spectrum. We assume, to cubic order in nonlinearity, that the wave dynamics are governed by the nonlinear Schrödinger (NLS) equation. We show from extensive numerical simulations of the NLS equation how freak waves in a random sea state are more likely to occur for large values of the Phillips parameter alpha and the enhancement coefficient gamma. Comparison with linear simulations is also reported.

Gyrokinetic continuum simulations of turbulence in the Texas Helimak

NASA Astrophysics Data System (ADS)

Bernard, T. N.; Shi, E. L.; Hammett, G. W.; Hakim, A.; Taylor, E. I.

2017-10-01

We have used the Gkeyll code to perform 3x-2v full-f gyrokinetic continuum simulations of electrostatic plasma turbulence in the Texas Helimak. The Helimak is an open field-line experiment with magnetic curvature and shear. It is useful for validating numerical codes due to its extensive diagnostics and simple, helical geometry, which is similar to the scrape-off layer region of tokamaks. Interchange and drift-wave modes are the main turbulence mechanisms in the device, and potential biasing is applied to study the effect of velocity shear on turbulence reduction. With Gkeyll, we varied field-line pitch angle and simulated biased and unbiased cases to study different turbulent regimes and turbulence reduction. These are the first kinetic simulations of the Helimak and resulting plasma profiles agree fairly well with experimental data. This research demonstrates Gkeyll's progress towards 5D simulations of the SOL region of fusion devices. Supported by the U.S. DOE SCGSR program under contract DE-SC0014664, the Max-Planck/Princeton Center for Plasma Physics, the SciDAC Center for the Study of Plasma Microturbulence, and DOE contract DE-AC02-09CH11466.

Mass production of extensive air showers for the Pierre Auger Collaboration using Grid Technology

NASA Astrophysics Data System (ADS)

Lozano Bahilo, Julio; Pierre Auger Collaboration

2012-06-01

When ultra-high energy cosmic rays enter the atmosphere they interact producing extensive air showers (EAS) which are the objects studied by the Pierre Auger Observatory. The number of particles involved in an EAS at these energies is of the order of billions and the generation of a single simulated EAS requires many hours of computing time with current processors. In addition, the storage space consumed by the output of one simulated EAS is very high. Therefore we have to make use of Grid resources to be able to generate sufficient quantities of showers for our physics studies in reasonable time periods. We have developed a set of highly automated scripts written in common software scripting languages in order to deal with the high number of jobs which we have to submit regularly to the Grid. In spite of the low number of sites supporting our Virtual Organization (VO) we have reached the top spot on CPU consumption among non LHC (Large Hadron Collider) VOs within EGI (European Grid Infrastructure).

Modeling interactions of agriculture and groundwater nitrate contaminants: application of The STICS-Eau-Dyssée coupled models over the Seine River Basin

NASA Astrophysics Data System (ADS)

Tavakoly, A. A.; Habets, F.; Saleh, F.; Yang, Z. L.

2017-12-01

Human activities such as the cultivation of N-fixing crops, burning of fossil fuels, discharging of industrial and domestic effluents, and extensive usage of fertilizers have recently accelerated the nitrogen loading to watersheds worldwide. Increasing nitrate concentration in surface water and groundwater is a major concern in watersheds with extensive agricultural activities. Nutrient enrichment is one of the major environmental problems in the French coastal zone. To understand and predict interactions between agriculture, surface water and groundwater nitrate contaminants, this study presents a modeling framework that couples the agronomic STICS model with Eau-Dyssée, a distributed hydrologic modeling system to simulate groundwater-surface water interaction. The coupled system is implemented on the Seine River Basin with an area of 88,000 km2 to compute daily nitrate contaminants. Representing a sophisticated hydrosystem with several aquifers and including the megalopolis of Paris, the Seine River Basin is well-known as one of the most productive agricultural areas in France. The STICS-EauDyssée framework is evaluated for a long-term simulation covering 39 years (1971-2010). Model results show that the simulated nitrate highly depends on the inflow produced by surface and subsurface waters. Daily simulation shows that the model captures the seasonal variation of observations and that the overall long-term simulation of nitrate contaminant is satisfactory at the regional scale.

A multibody knee model with discrete cartilage prediction of tibio-femoral contact mechanics.

PubMed

Guess, Trent M; Liu, Hongzeng; Bhashyam, Sampath; Thiagarajan, Ganesh

2013-01-01

Combining musculoskeletal simulations with anatomical joint models capable of predicting cartilage contact mechanics would provide a valuable tool for studying the relationships between muscle force and cartilage loading. As a step towards producing multibody musculoskeletal models that include representation of cartilage tissue mechanics, this research developed a subject-specific multibody knee model that represented the tibia plateau cartilage as discrete rigid bodies that interacted with the femur through deformable contacts. Parameters for the compliant contact law were derived using three methods: (1) simplified Hertzian contact theory, (2) simplified elastic foundation contact theory and (3) parameter optimisation from a finite element (FE) solution. The contact parameters and contact friction were evaluated during a simulated walk in a virtual dynamic knee simulator, and the resulting kinematics were compared with measured in vitro kinematics. The effects on predicted contact pressures and cartilage-bone interface shear forces during the simulated walk were also evaluated. The compliant contact stiffness parameters had a statistically significant effect on predicted contact pressures as well as all tibio-femoral motions except flexion-extension. The contact friction was not statistically significant to contact pressures, but was statistically significant to medial-lateral translation and all rotations except flexion-extension. The magnitude of kinematic differences between model formulations was relatively small, but contact pressure predictions were sensitive to model formulation. The developed multibody knee model was computationally efficient and had a computation time 283 times faster than a FE simulation using the same geometries and boundary conditions.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

In Vivo Investigation of the Effectiveness of a Hyper-viscoelastic Model in Simulating Brain Retraction

PubMed Central

Li, Ping; Wang, Weiwei; Zhang, Chenxi; An, Yong; Song, Zhijian

2016-01-01

Intraoperative brain retraction leads to a misalignment between the intraoperative positions of the brain structures and their previous positions, as determined from preoperative images. In vitro swine brain sample uniaxial tests showed that the mechanical response of brain tissue to compression and extension could be described by the hyper-viscoelasticity theory. The brain retraction caused by the mechanical process is a combination of brain tissue compression and extension. In this paper, we first constructed a hyper-viscoelastic framework based on the extended finite element method (XFEM) to simulate intraoperative brain retraction. To explore its effectiveness, we then applied this framework to an in vivo brain retraction simulation. The simulation strictly followed the clinical scenario, in which seven swine were subjected to brain retraction. Our experimental results showed that the hyper-viscoelastic XFEM framework is capable of simulating intraoperative brain retraction and improving the navigation accuracy of an image-guided neurosurgery system (IGNS). PMID:27387301

Simulation of Radiation Damage to Neural Cells with the Geant4-DNA Toolkit

NASA Astrophysics Data System (ADS)

Bayarchimeg, Lkhagvaa; Batmunkh, Munkhbaatar; Belov, Oleg; Lkhagva, Oidov

2018-02-01

To help in understanding the physical and biological mechanisms underlying effects of cosmic and therapeutic types of radiation on the central nervous system (CNS), we have developed an original neuron application based on the Geant4 Monte Carlo simulation toolkit, in particular on its biophysical extension Geant4-DNA. The applied simulation technique provides a tool for the simulation of physical, physico-chemical and chemical processes (e.g. production of water radiolysis species in the vicinity of neurons) in realistic geometrical model of neural cells exposed to ionizing radiation. The present study evaluates the microscopic energy depositions and water radiolysis species yields within a detailed structure of a selected neuron taking into account its soma, dendrites, axon and spines following irradiation with carbon and iron ions.

Normal Brain-Skull Development with Hybrid Deformable VR Models Simulation.

PubMed

Jin, Jing; De Ribaupierre, Sandrine; Eagleson, Roy

2016-01-01

This paper describes a simulation framework for a clinical application involving skull-brain co-development in infants, leading to a platform for craniosynostosis modeling. Craniosynostosis occurs when one or more sutures are fused early in life, resulting in an abnormal skull shape. Surgery is required to reopen the suture and reduce intracranial pressure, but is difficult without any predictive model to assist surgical planning. We aim to study normal brain-skull growth by computer simulation, which requires a head model and appropriate mathematical methods for brain and skull growth respectively. On the basis of our previous model, we further specified suture model into fibrous and cartilaginous sutures and develop algorithm for skull extension. We evaluate the resulting simulation by comparison with datasets of cases and normal growth.

Direct Numerical Simulations of Aerofoils with Serrated Trailing-Edge Extensions

NASA Astrophysics Data System (ADS)

Shahab, Muhammad Farrukh; Omidyeganeh, Mohammad; Pinelli, Alfredo

2017-11-01

Owl-feather-inspired technology motivates engineers to develop quieter wings. Direct numerical simulations of NACA-4412 aerofoil with retrofitted flat plate, serrated sawtooth shaped and porous (serrations with filaments) extensions have been performed to study the effects of these modifications on the hydrodynamic characteristics of the turbulent wake and their upstream influence on the interacting boundary layer. A chord based Reynolds number of 100,000 and an angle of attack of 5° has been chosen for all simulations, moreover the surface boundary layers are tripped using a a volume forcing method. This contribution will present a detailed statistical analysis of the mean and fluctuating behaviour of the flow and the key differences in the flow topologies will be highlighted. The preliminary analysis of results identifies a system of counter rotating streamwise vortices for the case of saw-tooth shaped serrations. The presence of the latter is generally considered responsible for an increased parasitic higher frequency noise for serrated aerofoils. To palliate the effect of aforementioned system of streamwise vortices, a filamentous layer occupying the voids of the serrations has been added which is expected to improve the aeroacoustic performance of the system.

Fixed gain and adaptive techniques for rotorcraft vibration control

NASA Technical Reports Server (NTRS)

Roy, R. H.; Saberi, H. A.; Walker, R. A.

1985-01-01

The results of an analysis effort performed to demonstrate the feasibility of employing approximate dynamical models and frequency shaped cost functional control law desgin techniques for helicopter vibration suppression are presented. Both fixed gain and adaptive control designs based on linear second order dynamical models were implemented in a detailed Rotor Systems Research Aircraft (RSRA) simulation to validate these active vibration suppression control laws. Approximate models of fuselage flexibility were included in the RSRA simulation in order to more accurately characterize the structural dynamics. The results for both the fixed gain and adaptive approaches are promising and provide a foundation for pursuing further validation in more extensive simulation studies and in wind tunnel and/or flight tests.

Use of Flowtran Simulation in Education

ERIC Educational Resources Information Center

Clark, J. Peter; Sommerfeld, Jude T.

1976-01-01

Describes the use in chemical engineering education of FLOWTRAN, a large steady-state simulator of chemical processes with extensive facilities for physical and thermodynamic data-handling and a large library of equipment modules, including cost estimation capability. (MLH)

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems.

PubMed

Pan, Albert C; Weinreich, Thomas M; Piana, Stefano; Shaw, David E

2016-03-08

Molecular dynamics (MD) simulations can describe protein motions in atomic detail, but transitions between protein conformational states sometimes take place on time scales that are infeasible or very expensive to reach by direct simulation. Enhanced sampling methods, the aim of which is to increase the sampling efficiency of MD simulations, have thus been extensively employed. The effectiveness of such methods when applied to complex biological systems like proteins, however, has been difficult to establish because even enhanced sampling simulations of such systems do not typically reach time scales at which convergence is extensive enough to reliably quantify sampling efficiency. Here, we obtain sufficiently converged simulations of three proteins to evaluate the performance of simulated tempering, a member of a widely used class of enhanced sampling methods that use elevated temperature to accelerate sampling. Simulated tempering simulations with individual lengths of up to 100 μs were compared to (previously published) conventional MD simulations with individual lengths of up to 1 ms. With two proteins, BPTI and ubiquitin, we evaluated the efficiency of sampling of conformational states near the native state, and for the third, the villin headpiece, we examined the rate of folding and unfolding. Our comparisons demonstrate that simulated tempering can consistently achieve a substantial sampling speedup of an order of magnitude or more relative to conventional MD.

Evaluation of a computational model to predict elbow range of motion

PubMed Central

Nishiwaki, Masao; Johnson, James A.; King, Graham J. W.; Athwal, George S.

2014-01-01

Computer models capable of predicting elbow flexion and extension range of motion (ROM) limits would be useful for assisting surgeons in improving the outcomes of surgical treatment of patients with elbow contractures. A simple and robust computer-based model was developed that predicts elbow joint ROM using bone geometries calculated from computed tomography image data. The model assumes a hinge-like flexion-extension axis, and that elbow passive ROM limits can be based on terminal bony impingement. The model was validated against experimental results with a cadaveric specimen, and was able to predict the flexion and extension limits of the intact joint to 0° and 3°, respectively. The model was also able to predict the flexion and extension limits to 1° and 2°, respectively, when simulated osteophytes were inserted into the joint. Future studies based on this approach will be used for the prediction of elbow flexion-extension ROM in patients with primary osteoarthritis to help identify motion-limiting hypertrophic osteophytes, and will eventually permit real-time computer-assisted navigated excisions. PMID:24841799

Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation

NASA Astrophysics Data System (ADS)

Lee, Joonseong; Kim, Seonghoon; Chang, Rakwoo; Jayanthi, Lakshmi; Gebremichael, Yeshitila

2013-01-01

The present study examines the effects of the model dependence, ionic strength, divalent ions, and hydrophobic interaction on the structural organization of the human neurofilament (NF) brush, using canonical ensemble Monte Carlo (MC) simulations of a coarse-grained model with the amino-acid resolution. The model simplifies the interactions between the NF core and the sidearm or between the sidearms by the sum of excluded volume, electrostatic, and hydrophobic interactions, where both monovalent salt ions and solvents are implicitly incorporated into the electrostatic interaction potential. Several important observations are made from the MC simulations of the coarse-grained model NF systems. First, the mean-field type description of monovalent salt ions works reasonably well in the NF system. Second, the manner by which the NF sidearms are arranged on the surface of the NF backbone core has little influence on the lateral extension of NF sidearms. Third, the lateral extension of the NF sidearms is highly affected by the ionic strength of the system: at low ionic strength, NF-M is most extended but at high ionic strength, NF-H is more stretched out because of the effective screening of the electrostatic interaction. Fourth, the presence of Ca2 + ions induces the attraction between negatively charged residues, which leads to the contraction of the overall NF extension. Finally, the introduction of hydrophobic interaction does not change the general structural organization of the NF sidearms except that the overall extension is contracted.

A biomechanical study of artificial cervical discs using computer simulation.

PubMed

Ahn, Hyung Soo; DiAngelo, Denis J

2008-04-15

A virtual simulation model of the subaxial cervical spine was used to study the biomechanical effects of various disc prosthesis designs. To study the biomechanics of different design features of cervical disc arthroplasty devices. Disc arthroplasty is an alternative approach to cervical fusion surgery for restoring and maintaining motion at a diseased spinal segment. Different types of cervical disc arthroplasty devices exist and vary based on their placement and degrees of motion offered. A virtual dynamic model of the subaxial cervical spine was used to study 3 different prosthetic disc designs (PDD): (1) PDD-I: The center of rotation of a spherical joint located at the mid C5-C6 disc, (2) PDD-II: The center of rotation of a spherical joint located 6.5 mm below the mid C5-C6 disc, and (3) PDD-III: The center of rotation of a spherical joint in a plane located at the C5-C6 disc level. A constrained spherical joint placed at the disc level (PDD-I) significantly increased facet loads during extension. Lowering the rotational axis of the spherical joint towards the subjacent body (PDD-II) caused a marginal increase in facet loading during flexion, extension, and lateral bending. Lastly, unconstraining the spherical joint to move freely in a plane (PDD-III) minimized facet load build up during all loading modes. The simulation model showed the impact simple design changes may have on cervical disc dynamics. The predicted facet loads calculated from computer model have to be validated in the experimental study.

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

PubMed

Curuksu, Jeremy; Zacharias, Martin

2009-03-14

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

Computational simulation of concurrent engineering for aerospace propulsion systems

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Singhal, S. N.

1992-01-01

Results are summarized of an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulations methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties - fundamental in developing such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering for propulsion systems and systems in general. Benefits and facets needing early attention in the development are outlined.

Computational simulation for concurrent engineering of aerospace propulsion systems

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Singhal, S. N.

1993-01-01

Results are summarized for an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulation methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties--fundamental to develop such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering of propulsion systems and systems in general. Benefits and issues needing early attention in the development are outlined.

Computational simulation for concurrent engineering of aerospace propulsion systems

NASA Astrophysics Data System (ADS)

Chamis, C. C.; Singhal, S. N.

1993-02-01

Results are summarized for an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulation methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties--fundamental to develop such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering of propulsion systems and systems in general. Benefits and issues needing early attention in the development are outlined.

In-flight simulation studies at the NASA Dryden Flight Research Facility

NASA Technical Reports Server (NTRS)

Shafer, Mary F.

1992-01-01

Since the late 1950's, the National Aeronautics and Space Administration's Dryden Flight Research Facility has found in-flight simulation to be an invaluable tool. In-flight simulation has been used to address a wide variety of flying qualities questions, including low-lift-to-drag ratio approach characteristics for vehicles like the X-15, the lifting bodies, and the Space Shuttle; the effects of time delays on controllability of aircraft with digital flight-control systems, the causes and cures of pilot-induced oscillation in a variety of aircraft, and flight-control systems for such diverse aircraft as the X-15 and the X-29. In-flight simulation has also been used to anticipate problems and to avoid them and to solve problems once they appear. Presented here is an account of the in-flight simulation at the Dryden Flight Research Facility and some discussion. An extensive bibliography is included.

Building Airport Surface HITL Simulation Capability

NASA Technical Reports Server (NTRS)

Chinn, Fay Cherie

2016-01-01

FutureFlight Central is a high fidelity, real-time simulator designed to study surface operations and automation. As an air traffic control tower simulator, FFC allows stakeholders such as the FAA, controllers, pilots, airports, and airlines to develop and test advanced surface and terminal area concepts and automation including NextGen and beyond automation concepts and tools. These technologies will improve the safety, capacity and environmental issues facing the National Airspace system. FFC also has extensive video streaming capabilities, which combined with the 3-D database capability makes the facility ideal for any research needing an immersive virtual and or video environment. FutureFlight Central allows human in the loop testing which accommodates human interactions and errors giving a more complete picture than fast time simulations. This presentation describes FFCs capabilities and the components necessary to build an airport surface human in the loop simulation capability.

In-flight simulation studies at the NASA Dryden Flight Research Facility

NASA Technical Reports Server (NTRS)

Shafer, Mary F.

1994-01-01

Since the late 1950's the National Aeronautics and Space Administration's Dryden Flight Research Facility has found in-flight simulation to be an invaluable tool. In-flight simulation has been used to address a wide variety of flying qualities questions, including low lift-to-drag ratio approach characteristics for vehicles like the X-15, the lifting bodies, and the space shuttle; the effects of time delays on controllability of aircraft with digital flight control systems; the causes and cures of pilot-induced oscillation in a variety of aircraft; and flight control systems for such diverse aircraft as the X-15 and the X-29. In-flight simulation has also been used to anticipate problems, avoid them, and solve problems once they appear. This paper presents an account of the in-flight simulation at the Dryden Flight Research Facility and some discussion. An extensive bibliography is included.

5D Tempest simulations of kinetic edge turbulence

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Xiong, Z.; Cohen, B. I.; Cohen, R. H.; Dorr, M. R.; Hittinger, J. A.; Kerbel, G. D.; Nevins, W. M.; Rognlien, T. D.; Umansky, M. V.; Qin, H.

2006-10-01

Results are presented from the development and application of TEMPEST, a nonlinear five dimensional (3d2v) gyrokinetic continuum code. The simulation results and theoretical analysis include studies of H-mode edge plasma neoclassical transport and turbulence in real divertor geometry and its relationship to plasma flow generation with zero external momentum input, including the important orbit-squeezing effect due to the large electric field flow-shear in the edge. In order to extend the code to 5D, we have formulated a set of fully nonlinear electrostatic gyrokinetic equations and a fully nonlinear gyrokinetic Poisson's equation which is valid for both neoclassical and turbulence simulations. Our 5D gyrokinetic code is built on 4D version of Tempest neoclassical code with extension to a fifth dimension in binormal direction. The code is able to simulate either a full torus or a toroidal segment. Progress on performing 5D turbulence simulations will be reported.

Extending quantum mechanics entails extending special relativity

NASA Astrophysics Data System (ADS)

Aravinda, S.; Srikanth, R.

2016-05-01

The complementarity between signaling and randomness in any communicated resource that can simulate singlet statistics is generalized by relaxing the assumption of free will in the choice of measurement settings. We show how to construct an ontological extension for quantum mechanics (QMs) through the oblivious embedding of a sound simulation protocol in a Newtonian spacetime. Minkowski or other intermediate spacetimes are ruled out as the locus of the embedding by virtue of hidden influence inequalities. The complementarity transferred from a simulation to the extension unifies a number of results about quantum non-locality, and implies that special relativity has a different significance for the ontological model and for the operational theory it reproduces. Only the latter, being experimentally accessible, is required to be Lorentz covariant. There may be certain Lorentz non-covariant elements at the ontological level, but they will be inaccessible at the operational level in a valid extension. Certain arguments against the extendability of QM, due to Conway and Kochen (2009) and Colbeck and Renner (2012), are attributed to their assumption that the spacetime at the ontological level has Minkowski causal structure.

A dynamic motion simulator for future European docking systems

NASA Technical Reports Server (NTRS)

Brondino, G.; Marchal, PH.; Grimbert, D.; Noirault, P.

1990-01-01

Europe's first confrontation with docking in space will require extensive testing to verify design and performance and to qualify hardware. For this purpose, a Docking Dynamics Test Facility (DDTF) was developed. It allows reproduction on the ground of the same impact loads and relative motion dynamics which would occur in space during docking. It uses a 9 degree of freedom, servo-motion system, controlled by a real time computer, which simulates the docking spacecraft in a zero-g environment. The test technique involves and active loop based on six axis force and torque detection, a mathematical simulation of individual spacecraft dynamics, and a 9 degree of freedom servomotion of which 3 DOFs allow extension of the kinematic range to 5 m. The configuration was checked out by closed loop tests involving spacecraft control models and real sensor hardware. The test facility at present has an extensive configuration that allows evaluation of both proximity control and docking systems. It provides a versatile tool to verify system design, hardware items and performance capabilities in the ongoing HERMES and COLUMBUS programs. The test system is described and its capabilities are summarized.

Computational aeroacoustics and numerical simulation of supersonic jets

NASA Technical Reports Server (NTRS)

Morris, Philip J.; Long, Lyle N.

1996-01-01

The research project has been a computational study of computational aeroacoustics algorithms and numerical simulations of the flow and noise of supersonic jets. During this study a new method for the implementation of solid wall boundary conditions for complex geometries in three dimensions has been developed. In addition, a detailed study of the simulation of the flow in and noise from supersonic circular and rectangular jets has been conducted. Extensive comparisons have been made with experimental measurements. A summary of the results of the research program are attached as the main body of this report in the form of two publications. Also, the report lists the names of the students who were supported by this grant, their degrees, and the titles of their dissertations. In addition, a list of presentations and publications made by the Principal Investigators and the research students is also included.

The Bern Simple Climate Model (BernSCM) v1.0: an extensible and fully documented open-source re-implementation of the Bern reduced-form model for global carbon cycle-climate simulations

NASA Astrophysics Data System (ADS)

Strassmann, Kuno M.; Joos, Fortunat

2018-05-01

The Bern Simple Climate Model (BernSCM) is a free open-source re-implementation of a reduced-form carbon cycle-climate model which has been used widely in previous scientific work and IPCC assessments. BernSCM represents the carbon cycle and climate system with a small set of equations for the heat and carbon budget, the parametrization of major nonlinearities, and the substitution of complex component systems with impulse response functions (IRFs). The IRF approach allows cost-efficient yet accurate substitution of detailed parent models of climate system components with near-linear behavior. Illustrative simulations of scenarios from previous multimodel studies show that BernSCM is broadly representative of the range of the climate-carbon cycle response simulated by more complex and detailed models. Model code (in Fortran) was written from scratch with transparency and extensibility in mind, and is provided open source. BernSCM makes scientifically sound carbon cycle-climate modeling available for many applications. Supporting up to decadal time steps with high accuracy, it is suitable for studies with high computational load and for coupling with integrated assessment models (IAMs), for example. Further applications include climate risk assessment in a business, public, or educational context and the estimation of CO2 and climate benefits of emission mitigation options.

A Phenomenological Model and Validation of Shortening Induced Force Depression during Muscle Contractions

PubMed Central

McGowan, C.P.; Neptune, R.R.; Herzog, W.

2009-01-01

History dependent effects on muscle force development following active changes in length have been measured in a number of experimental studies. However, few muscle models have included these properties or examined their impact on force and power output in dynamic cyclic movements. The goal of this study was to develop and validate a modified Hill-type muscle model that includes shortening induced force depression and assess its influence on locomotor performance. The magnitude of force depression was defined by empirical relationships based on muscle mechanical work. To validate the model, simulations incorporating force depression were developed to emulate single muscle in situ and whole muscle group leg extension experiments. There was excellent agreement between simulation and experimental values, with in situ force patterns closely matching the experimental data (average RMS error < 1.5 N) and force depression in the simulated leg extension exercise being similar in magnitude to experimental values (6.0% vs 6.5%, respectively). To examine the influence of force depression on locomotor performance, simulations of maximum power pedaling with and without force depression were generated. Force depression decreased maximum crank power by 20% – 40%, depending on the relationship between force depression and muscle work used. These results indicate that force depression has the potential to substantially influence muscle power output in dynamic cyclic movements. However, to fully understand the impact of this phenomenon on human movement, more research is needed to characterize the relationship between force depression and mechanical work in large muscles with different morphologies. PMID:19879585

Evaluation of total knee mechanics using a crouching simulator with a synthetic knee substitute.

PubMed

Lowry, Michael; Rosenbaum, Heather; Walker, Peter S

2016-05-01

Mechanical evaluation of total knees is frequently required for aspects such as wear, strength, kinematics, contact areas, and force transmission. In order to carry out such tests, we developed a crouching simulator, based on the Oxford-type machine, with novel features including a synthetic knee including ligaments. The instrumentation and data processing methods enabled the determination of contact area locations and interface forces and moments, for a full flexion-extension cycle. To demonstrate the use of the simulator, we carried out a comparison of two different total knee designs, cruciate retaining and substituting. The first part of the study describes the simulator design and the methodology for testing the knees without requiring cadaveric knee specimens. The degrees of freedom of the anatomic hip and ankle joints were reproduced. Flexion-extension was obtained by changing quadriceps length, while variable hamstring forces were applied using springs. The knee joint was represented by three-dimensional printed blocks on to which the total knee components were fixed. Pretensioned elastomeric bands of realistic stiffnesses passed through holes in the block at anatomical locations to represent ligaments. Motion capture of the knees during flexion, together with laser scanning and computer modeling, was used to reconstruct contact areas on the bearing surfaces. A method was also developed for measuring tibial component interface forces and moments as a comparative assessment of fixation. The method involved interposing Tekscan pads at locations on the interface. Overall, the crouching machine and the methodology could be used for many different mechanical measurements of total knee designs, adapted especially for comparative or parametric studies. © IMechE 2016.

Comparative study on gene set and pathway topology-based enrichment methods.

PubMed

Bayerlová, Michaela; Jung, Klaus; Kramer, Frank; Klemm, Florian; Bleckmann, Annalen; Beißbarth, Tim

2015-10-22

Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions. In contrast, the new group of so called pathway topology-based methods integrates the topological structure of a pathway into the analysis. We comparatively investigated gene set and pathway topology-based enrichment approaches, considering three gene set and four topological methods. These methods were compared in two extensive simulation studies and on a benchmark of 36 real datasets, providing the same pathway input data for all methods. In the benchmark data analysis both types of methods showed a comparable ability to detect enriched pathways. The first simulation study was conducted with KEGG pathways, which showed considerable gene overlaps between each other. In this study with original KEGG pathways, none of the topology-based methods outperformed the gene set approach. Therefore, a second simulation study was performed on non-overlapping pathways created by unique gene IDs. Here, methods accounting for pathway topology reached higher accuracy than the gene set methods, however their sensitivity was lower. We conducted one of the first comprehensive comparative works on evaluating gene set against pathway topology-based enrichment methods. The topological methods showed better performance in the simulation scenarios with non-overlapping pathways, however, they were not conclusively better in the other scenarios. This suggests that simple gene set approach might be sufficient to detect an enriched pathway under realistic circumstances. Nevertheless, more extensive studies and further benchmark data are needed to systematically evaluate these methods and to assess what gain and cost pathway topology information introduces into enrichment analysis. Both types of methods for enrichment analysis require further improvements in order to deal with the problem of pathway overlaps.

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

Chremos, Alexandros, E-mail: achremos@imperial.ac.uk; Nikoubashman, Arash, E-mail: arashn@princeton.edu; Panagiotopoulos, Athanassios Z.

In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is importantmore » from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.« less

ATTDES: An Expert System for Satellite Attitude Determination and Control. 2

NASA Technical Reports Server (NTRS)

Mackison, Donald L.; Gifford, Kevin

1996-01-01

The design, analysis, and flight operations of satellite attitude determintion and attitude control systems require extensive mathematical formulations, optimization studies, and computer simulation. This is best done by an analyst with extensive education and experience. The development of programs such as ATTDES permit the use of advanced techniques by those with less experience. Typical tasks include the mission analysis to select stabilization and damping schemes, attitude determination sensors and algorithms, and control system designs to meet program requirements. ATTDES is a system that includes all of these activities, including high fidelity orbit environment models that can be used for preliminary analysis, parameter selection, stabilization schemes, the development of estimators covariance analyses, and optimization, and can support ongoing orbit activities. The modification of existing simulations to model new configurations for these purposes can be an expensive, time consuming activity that becomes a pacing item in the development and operation of such new systems. The use of an integrated tool such as ATTDES significantly reduces the effort and time required for these tasks.

A simulation study on few parameters of Cherenkov photons in extensive air showers of different primaries incident at various zenith angles over a high altitude observation level

NASA Astrophysics Data System (ADS)

Das, G. S.; Hazarika, P.; Goswami, U. D.

2018-07-01

We have studied the distribution patterns of lateral density, arrival time and angular position of Cherenkov photons generated in Extensive Air Showers (EASs) initiated by γ-ray, proton and iron primaries incident with various energies and at various zenith angles. This study is the extension of our earlier work [1] to cover a wide energy range of ground based γ-ray astronomy with a wide range of zenith angles (≤40°) of primary particles, as well as the extension to study the angular distribution patterns of Cherenkov photons in EASs. This type of study is important for distinguishing the γ-ray initiated showers from the hadronic showers in the ground based γ-ray astronomy, where Atmospheric Cherenkov Technique (ACT) is being used. Importantly, such study gives an insight on the nature of γ-ray and hadronic showers in general. In this work, the CORSIKA 6.990 simulation code is used for generation of EASs. Similarly to the case of Ref. [1], this study also revealed that, the lateral density and arrival time distributions of Cherenkov photons vary almost in accordance with the functions: ρch(r) =ρ0e-βr and tch(r) =t0eΓ/rλ respectively by taking different values of the parameters of functions for the type, energy and zenith angle of the primary particle. The distribution of Cherenkov photon's angular positions with respect to shower axis shows distinctive features depending on the primary type, its energy and the zenith angle. As a whole this distribution pattern for the iron primary is noticeably different from those for γ-ray and proton primaries. The value of the angular position at which the maximum number of Cherenkov photons are concentrated, increases with increase in energy of vertically incident primary, but for inclined primary it lies within a small value (≤1°) for almost all energies and primary types. No significant difference in the results obtained by using the high energy hadronic interaction models, viz., QGSJETII and EPOS has been observed.

Monte Carlo Simulation Using HyperCard and Lotus 1-2-3.

ERIC Educational Resources Information Center

Oulman, Charles S.; Lee, Motoko Y.

Monte Carlo simulation is a computer modeling procedure for mimicking observations on a random variable. A random number generator is used in generating the outcome for the events that are being modeled. The simulation can be used to obtain results that otherwise require extensive testing or complicated computations. This paper describes how Monte…

Ionization in MHD-Gas interactions

NASA Astrophysics Data System (ADS)

Wilson, A.; Diver, D. A.

2013-09-01

The study of partially ionized plasmas is important in a number of astrophysical situations and is vital for the study of laboratory plasmas. The interactions between a neutral gas and a plasma define a hybrid medium that has aspects of each, but does not only sustain the pure modes of the individual species. Previously we have shown that momentum coupling between the gas and the magnetized plasma alters the behaviour of both; as an extension of that simulation, we present results for the extension to the coupling in which the relative motion between the species provides enough kinetic energy in the flow to allow a measure of species exchange Alfvén ionization (AI) (also known as critical velocity ionization), allowing the ionization fraction to evolve as the dynamics evolve.

System crash as dynamics of complex networks.

PubMed

Yu, Yi; Xiao, Gaoxi; Zhou, Jie; Wang, Yubo; Wang, Zhen; Kurths, Jürgen; Schellnhuber, Hans Joachim

2016-10-18

Complex systems, from animal herds to human nations, sometimes crash drastically. Although the growth and evolution of systems have been extensively studied, our understanding of how systems crash is still limited. It remains rather puzzling why some systems, appearing to be doomed to fail, manage to survive for a long time whereas some other systems, which seem to be too big or too strong to fail, crash rapidly. In this contribution, we propose a network-based system dynamics model, where individual actions based on the local information accessible in their respective system structures may lead to the "peculiar" dynamics of system crash mentioned above. Extensive simulations are carried out on synthetic and real-life networks, which further reveal the interesting system evolution leading to the final crash. Applications and possible extensions of the proposed model are discussed.

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.

Development and Simulation Testing of a Computerized Adaptive Version of the Philadelphia Naming Test

ERIC Educational Resources Information Center

Hula, William D.; Kellough, Stacey; Fergadiotis, Gerasimos

2015-01-01

Purpose: The purpose of this study was to develop a computerized adaptive test (CAT) version of the Philadelphia Naming Test (PNT; Roach, Schwartz, Martin, Grewal, & Brecher, 1996), to reduce test length while maximizing measurement precision. This article is a direct extension of a companion article (Fergadiotis, Kellough, & Hula, 2015),…

Estimating Causal Effects of Education Interventions Using a Two-Rating Regression Discontinuity Design: Lessons from a Simulation Study

ERIC Educational Resources Information Center

Porter, Kristin E.; Reardon, Sean F.; Unlu, Fatih; Bloom, Howard S.; Robinson-Cimpian, Joseph P.

2014-01-01

A valuable extension of the single-rating regression discontinuity design (RDD) is a multiple-rating RDD (MRRDD). To date, four main methods have been used to estimate average treatment effects at the multiple treatment frontiers of an MRRDD: the "surface" method, the "frontier" method, the "binding-score" method, and…

A synoptic climatology for forest fires in the NE US and future implications for GCM simulations

Treesearch

Yan Qing; Ronald Sabo; Yiqiang Wu; J.Y. Zhu

1994-01-01

We studied surface-pressure patterns corresponding to reduced precipitation, high evaporation potential, and enhanced forest-fire danger for West Virginia, which experienced extensive forest-fire damage in November 1987. From five years of daily weather maps we identified eight weather patterns that describe distinctive flow situations throughout the year. Map patterns...

Near-term hybrid vehicle program, phase 1. Appendix B: Design trade-off studies report. Volume 3: Computer program listings

NASA Technical Reports Server (NTRS)

1979-01-01

A description and listing is presented of two computer programs: Hybrid Vehicle Design Program (HYVELD) and Hybrid Vehicle Simulation Program (HYVEC). Both of the programs are modifications and extensions of similar programs developed as part of the Electric and Hybrid Vehicle System Research and Development Project.

Using Monte-Carlo Simulations to Study the Disk Structure in Cygnus X-1

NASA Technical Reports Server (NTRS)

Yao, Y.; Zhang, S. N.; Zhang, X. L.; Feng, Y. X.

2002-01-01

As the first dynamically determined black hole X-ray binary system, Cygnus X-1 has been studied extensively. However, its broad-band spectra in hard state with BeppoSAX is still not well understood. Besides the soft excess described by the multi-color disk model (MCD), the power- law component and a broad excess feature above 10 keV (disk reflection component), there is also an additional soft component around 1 keV, whose origin is not known currently.We propose that the additional soft component is due to the thermal Comptonization process between the s oft disk photon and the warm plasma cloud just above the disk.i.e., a warm layer. We use Monte-Carlo technique t o simulate this Compton scattering process and build several table models based on our simulation results.

A Three-Dimensional Eulerian Code for Simulation of High-Speed Multimaterial Interactions

DTIC Science & Technology

2011-08-01

PDE -based extension. The extension process is done on only the host cells on a particular processor. After extension the parallel communication is...condensation shocks, explosive debris transport, detonation in heterogeneous media and so on. In these flows complex interactions occur between the...A.22] and ijΩ is the spin tensor. The Jaumann derivative is used to ensure objectivity of the stress tensor with respect to rotation

Community Level Impact Assessment--Extension Applications.

ERIC Educational Resources Information Center

Woods, Mike D.; Doeksen, Gerald A.

Using the Oklahoma State University (OSU) computerized community simulation model, extension professionals can provide local decision makers with information derived from an impact model that is dynamic, community specific, and easy to adapt to different communities. The four main sections of the OSU model are an economic account, a capital…

Extensive Air Showers in the Classroom

ERIC Educational Resources Information Center

Badala, A.; Blanco, F.; La Rocca, P.; Pappalardo, G. S.; Pulvirenti, A.; Riggi, F.

2007-01-01

The basic properties of extensive air showers of particles produced in the interaction of a high-energy primary cosmic ray in the Earth's atmosphere are discussed in the context of educational cosmic ray projects involving undergraduate students and high-school teams. Simulation results produced by an air shower development code were made…

Active and hibernating turbulence in drag-reducing plane Couette flows

NASA Astrophysics Data System (ADS)

Pereira, Anselmo S.; Mompean, Gilmar; Thais, Laurent; Soares, Edson J.; Thompson, Roney L.

2017-08-01

In this paper we analyze the active and hibernating turbulence in drag-reducing plane Couette flows using direct numerical simulations of the viscoelastic finitely extensible nonlinear elastic model with the Peterlin approximation fluids. The polymer-turbulence interactions are studied from an energetic standpoint for a range of Weissenberg numbers (from 2 up to 30), fixing the Reynolds number based on the plate velocities at 4000, the viscosity ratio at 0.9, and the maximum polymer molecule extensibility at 100. The qualitative picture that emerges from this investigation is a cyclic mechanism of energy exchange between the polymers and turbulence that drives the flow through an oscillatory behavior.

A study comparing precision of the maximum multipoint heterogeneity LOD statistic to three model-free multipoint linkage methods.

PubMed

Finch, S J; Chen, C H; Gordon, D; Mendell, N R

2001-12-01

This study compared the performance of the maximum lod (MLOD), maximum heterogeneity lod (MHLOD), maximum non-parametric linkage score (MNPL), maximum Kong and Cox linear extension (MKC(lin)) of NPL, and maximum Kong and Cox exponential extension (MKC(exp)) of NPL as calculated in Genehunter 1.2 and Genehunter-Plus. Our performance measure was the distance between the marker with maximum value for each linkage statistic and the trait locus. We performed a simulation study considering: 1) four modes of transmission, 2) 100 replicates for each model, 3) 58 pedigrees (with 592 subjects) per replicate, 4) three linked marker loci each having three equally frequent alleles, and 5) either 0% unlinked families (linkage homogeneity) or 50% unlinked families (linkage heterogeneity). For each replicate, we obtained the Haldane map position of the location at which each of the five statistics is maximized. The MLOD and MHLOD were obtained by maximizing over penetrances, phenocopy rate, and risk-allele frequencies. For the models simulated, MHLOD appeared to be the best statistic both in terms of identifying a marker locus having the smallest mean distance from the trait locus and in terms of the strongest negative correlation between maximum linkage statistic and distance of the identified position and the trait locus. The marker loci with maximum value of the Kong and Cox extensions of the NPL statistic also were closer to the trait locus than the marker locus with maximum value of the NPL statistic. Copyright 2001 Wiley-Liss, Inc.

Validation of a Wave Data Assimilation System Based on SWAN

NASA Astrophysics Data System (ADS)

Flampourisi, Stylianos; Veeramony, Jayaram; Orzech, Mark D.; Ngodock, Hans E.

2013-04-01

SWAN is one of the most broadly used models for wave predictions in the nearshore, with known and extensively studied limitations due to the physics and/or to the numerical implementation. In order to improve the performance of the model, a 4DVAR data assimilation system based on a tangent linear code and the corresponding adjoint from the numerical SWAN model has been developed at NRL(Orzech et. al., 2013), by implementing the methodology of Bennett 2002. The assimilation system takes into account the nonlinear triad and quadruplet interactions, depth-limited breaking, wind forcing, bottom friction and white-capping. Using conjugate gradient method, the assimilation system minimizes a quadratic penalty functional (which represents the overall error of the simulation) and generates the correction of the forward simulation in spatial, temporal and spectral domain. The weights are given to the output of the adjoint by calculating the covariance to an ensemble of forward simulations according to Evensen 2009. This presentation will focus on the extension of the system to a weak-constrainted data assimilation system and on the extensive validation of the system by using wave spectra for forcing, assimilation and validation, from FRF Duck, North Carolina, during August 2011. During this period, at the 17 m waverider buoy location, the wind speed was up to 35 m/s (due to Hurricane Irene) and the significant wave height varied from 0.5 m to 6 m and the peak period between 5 s and 18 s. In general, this study shows significant improvement of the integrated spectral properties, but the main benefit of assimilating the wave spectra (and not only their integrated properties) is that the accurate simulation of separated, in frequency and in direction, wave systems is possible even nearshore, where non-linear phenomena are dominant. The system is ready to be used for more precise reanalysis of the wave climate and climate variability, and determination of coastal hazards in regional or local scales, in case of available wave data. References: Orzech, M.D., J. Veeramony, and H.E. Ngodock, 2013: A variational assimilation system for nearshore wave modeling. J. Atm. & Oc. Tech., in press.

Flexible polyelectrolyte chain in a strong electrolyte solution: Insight into equilibrium properties and force-extension behavior from mesoscale simulation

NASA Astrophysics Data System (ADS)

Malekzadeh Moghani, Mahdy; Khomami, Bamin

2016-01-01

Macromolecules with ionizable groups are ubiquitous in biological and synthetic systems. Due to the complex interaction between chain and electrostatic decorrelation lengths, both equilibrium properties and micro-mechanical response of dilute solutions of polyelectrolytes (PEs) are more complex than their neutral counterparts. In this work, the bead-rod micromechanical description of a chain is used to perform hi-fidelity Brownian dynamics simulation of dilute PE solutions to ascertain the self-similar equilibrium behavior of PE chains with various linear charge densities, scaling of the Kuhn step length (lE) with salt concentration cs and the force-extension behavior of the PE chain. In accord with earlier theoretical predictions, our results indicate that for a chain with n Kuhn segments, lE ˜ cs-0.5 as linear charge density approaches 1/n. Moreover, the constant force ensemble simulation results accurately predict the initial non-linear force-extension region of PE chain recently measured via single chain experiments. Finally, inspired by Cohen's extraction of Warner's force law from the inverse Langevin force law, a novel numerical scheme is developed to extract a new elastic force law for real chains from our discrete set of force-extension data similar to Padè expansion, which accurately depicts the initial non-linear region where the total Kuhn length is less than the thermal screening length.

Flexible polyelectrolyte chain in a strong electrolyte solution: Insight into equilibrium properties and force-extension behavior from mesoscale simulation.

PubMed

Malekzadeh Moghani, Mahdy; Khomami, Bamin

2016-01-14

Macromolecules with ionizable groups are ubiquitous in biological and synthetic systems. Due to the complex interaction between chain and electrostatic decorrelation lengths, both equilibrium properties and micro-mechanical response of dilute solutions of polyelectrolytes (PEs) are more complex than their neutral counterparts. In this work, the bead-rod micromechanical description of a chain is used to perform hi-fidelity Brownian dynamics simulation of dilute PE solutions to ascertain the self-similar equilibrium behavior of PE chains with various linear charge densities, scaling of the Kuhn step length (lE) with salt concentration cs and the force-extension behavior of the PE chain. In accord with earlier theoretical predictions, our results indicate that for a chain with n Kuhn segments, lE ∼ cs (-0.5) as linear charge density approaches 1/n. Moreover, the constant force ensemble simulation results accurately predict the initial non-linear force-extension region of PE chain recently measured via single chain experiments. Finally, inspired by Cohen's extraction of Warner's force law from the inverse Langevin force law, a novel numerical scheme is developed to extract a new elastic force law for real chains from our discrete set of force-extension data similar to Padè expansion, which accurately depicts the initial non-linear region where the total Kuhn length is less than the thermal screening length.

The Behavior of TCP and Its Extensions in Space

NASA Technical Reports Server (NTRS)

Wang, Ruhai; Horan, Stephen

2001-01-01

The performance of Transmission Control Protocol (TCP) in space has been examined from the observations of simulation and experimental tests for several years at National Aeronautics and Space Administration (NASA), Department of Defense (DoD) and universities. At New Mexico State University (NMSU), we have been concentrating on studying the performance of two protocol suites: the file transfer protocol (ftp) running over Transmission Control Protocol/Internet Protocol (TCP/IP) stack and the file protocol (fp) running over the Space Communications Protocol Standards (SCPS)-Transport Protocol (TP) developed under the Consultative Committee for Space Data Systems (CCSDS) standards process. SCPS-TP is considered to be TCP's extensions for space communications. This dissertation experimentally studies the behavior of TCP and SCPS-TP by running the protocol suites over both the Space-to-Ground Link Simulator (SGLS) test-bed and realistic satellite link. The study concentrates on comparing protocol behavior by plotting the averaged file transfer times for different experimental configurations and analyzing them using Statistical Analysis System (SAS) based procedures. The effects of different link delays and various Bit-Error-Rates (BERS) on each protocol performance are also studied and linear regression models are built for experiments over SGLS test-bed to reflect the relationships between the file transfer time and various transmission conditions.

Lunar Regolith Simulant Materials: Recommendations for Standardization, Production, and Usage

NASA Technical Reports Server (NTRS)

Sibille, L.; Carpenter, P.; Schlagheck, R.; French, R. A.

2006-01-01

Experience gained during the Apollo program demonstrated the need for extensive testing of surface systems in relevant environments, including regolith materials similar to those encountered on the lunar surface. As NASA embarks on a return to the Moon, it is clear that the current lunar sample inventory is not only insufficient to support lunar surface technology and system development, but its scientific value is too great to be consumed by destructive studies. Every effort must be made to utilize standard simulant materials, which will allow developers to reduce the cost, development, and operational risks to surface systems. The Lunar Regolith Simulant Materials Workshop held in Huntsville, AL, on January 24 26, 2005, identified the need for widely accepted standard reference lunar simulant materials to perform research and development of technologies required for lunar operations. The workshop also established a need for a common, traceable, and repeatable process regarding the standardization, characterization, and distribution of lunar simulants. This document presents recommendations for the standardization, production and usage of lunar regolith simulant materials.

Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph.

PubMed

Mörschel, Konstantin; Breit, Markus; Queisser, Gillian

2017-07-01

Generating realistic and complex computational domains for numerical simulations is often a challenging task. In neuroscientific research, more and more one-dimensional morphology data is becoming publicly available through databases. This data, however, only contains point and diameter information not suitable for detailed three-dimensional simulations. In this paper, we present a novel framework, AnaMorph, that automatically generates water-tight surface meshes from one-dimensional point-diameter files. These surface triangulations can be used to simulate the electrical and biochemical behavior of the underlying cell. In addition to morphology generation, AnaMorph also performs quality control of the semi-automatically reconstructed cells coming from anatomical reconstructions. This toolset allows an extension from the classical dimension-reduced modeling and simulation of cellular processes to a full three-dimensional and morphology-including method, leading to novel structure-function interplay studies in the medical field. The developed numerical methods can further be employed in other areas where complex geometries are an essential component of numerical simulations.

Spatial awareness comparisons between large-screen, integrated pictorial displays and conventional EFIS displays during simulated landing approaches

NASA Technical Reports Server (NTRS)

Parrish, Russell V.; Busquets, Anthony M.; Williams, Steven P.; Nold, Dean E.

1994-01-01

An extensive simulation study was performed to determine and compare the spatial awareness of commercial airline pilots on simulated landing approaches using conventional flight displays with their awareness using advanced pictorial 'pathway in the sky' displays. Sixteen commercial airline pilots repeatedly made simulated complex microwave landing system approaches to closely spaced parallel runways with an extremely short final segment. Scenarios involving conflicting traffic situation assessments and recoveries from flight path offset conditions were used to assess spatial awareness (own ship position relative the the desired flight route, the runway, and other traffic) with the various display formats. The situation assessment tools are presented, as well as the experimental designs and the results. The results demonstrate that the integrated pictorial displays substantially increase spatial awareness over conventional electronic flight information systems display formats.

Extension of a Kinetic Approach to Chemical Reactions to Electronic Energy Levels and Reactions Involving Charged Species With Application to DSMC Simulations

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2013-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties are extended in the current work to include electronic energy level transitions and reactions involving charged particles. These extensions are shown to agree favorably with reported transition and reaction rates from the literature for nearequilibrium conditions. Also, the extensions are applied to the second flight of the Project FIRE flight experiment at 1634 seconds with a Knudsen number of 0.001 at an altitude of 76.4 km. In order to accomplish this, NASA's direct simulation Monte Carlo code DAC was rewritten to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced chemistry model, and to include the extensions presented in this work. The 1634 second data point was chosen for comparisons to be made in order to include a CFD solution. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid because, although near-transitional, the flow is still considered to be continuum. It is shown that the inclusion of electronic energy levels in the DSMC simulation is necessary for flows of this nature and is required for comparison to the CFD solution. The flow field solutions are also post-processed by the nonequilibrium radiation code HARA to compute the radiative portion of the heating and is then compared to the total heating measured in flight.

Multispectral Resource Sampler (MRS): Proof of concept. Study on bidirectional reflectance. A simulation analysis of bidirectional reflectance properties and their effects on scene radiance. Implications for the MRS

NASA Technical Reports Server (NTRS)

Smith, J. A.

1980-01-01

A study was performed to evaluate the geometrical implication of a Multispectral Resource Sampler; a pointable sensor. Several vegetative targets representative of natural and agricultural canopies were considered in two wavelength bands. All combinations of Sun and view angles between 5 and 85 degrees zenith for a range of azimuths were simulated to examine geometrical dependance arising from seasonal as well as latitudinal variation. The effects of three different atmospheres corresponding to clear, medium and heavy haze conditions are included. An extensive model data base was generated to provide investigators with means for possible further study of atmospheric correction procedures and sensor design questions.

Optimization of MLS receivers for multipath environments

NASA Technical Reports Server (NTRS)

Mcalpine, G. A.; Irwin, S. H.; NELSON; Roleyni, G.

1977-01-01

Optimal design studies of MLS angle-receivers and a theoretical design-study of MLS DME-receivers are reported. The angle-receiver results include an integration of the scan data processor and tracking filter components of the optimal receiver into a unified structure. An extensive simulation study comparing the performance of the optimal and threshold receivers in a wide variety of representative dynamical interference environments was made. The optimal receiver was generally superior. A simulation of the performance of the threshold and delay-and-compare receivers in various signal environments was performed. An analysis of combined errors due to lateral reflections from vertical structures with small differential path delays, specular ground reflections with neglible differential path delays, and thermal noise in the receivers is provided.

The discovery of the causes of leprosy: A computational analysis

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

Corruble, V.; Ganascia, J.G.

1996-12-31

The role played by the inductive inference has been studied extensively in the field of Scientific Discovery. The work presented here tackles the problem of induction in medical research. The discovery of the causes of leprosy is analyzed and simulated using computational means. An inductive algorithm is proposed, which is successful in simulating some essential steps in the progress of the understanding of the disease. It also allows us to simulate the false reasoning of previous centuries through the introduction of some medical a priori inherited form archaic medicine. Corroborating previous research, this problem illustrates the importance of the socialmore » and cultural environment on the way the inductive inference is performed in medicine.« less

Multi-Fluid Simulations of Field Reversed Configuration Formation

NASA Astrophysics Data System (ADS)

Sousa, Eder; Martin, Robert

2017-10-01

The use of field reversed configuration (FRC) have been studied extensively for fusion application but here we investigate them for propulsion purposes. FRCs have the potential to produce highly variable thrust and specific impulse using different gases as propellant. Aspects of the FRC formation physics, using a rotating magnetic field (RMF) at low power, are simulated using a multi-fluid plasma model. Results are compared with experimental observations with emphasis in the development of instabilities and robustness of the field reversal. The use of collisional radiative models are used to help compare experiment versus simulation results. Distribution A: Approved for public release; distribution unlimited; Clearance No. 17445. This work is supported by the Air Force Office of Scientific Research Grant Number 17RQCOR465.

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

PubMed

Kuriata, Aleksander; Gierut, Aleksandra Maria; Oleniecki, Tymoteusz; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

2018-05-14

Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

Qualitative modeling of normal blood coagulation and its pathological states using stochastic activity networks.

PubMed

Mounts, W M; Liebman, M N

1997-07-01

We have developed a method for representing biological pathways and simulating their behavior based on the use of stochastic activity networks (SANs). SANs, an extension of the original Petri net, have been used traditionally to model flow systems including data-communications networks and manufacturing processes. We apply the methodology to the blood coagulation cascade, a biological flow system, and present the representation method as well as results of simulation studies based on published experimental data. In addition to describing the dynamic model, we also present the results of its utilization to perform simulations of clinical states including hemophilia's A and B as well as sensitivity analysis of individual factors and their impact on thrombin production.

Study of the Time Response of a Simulated Hydroelectric System

NASA Astrophysics Data System (ADS)

Simani, S.; Alvisi, S.; Venturini, M.

2014-12-01

This paper addresses the design of an advanced control strategy for a typical hydroelectric dynamic process, performed in the Matlab and Simulink environments. The hydraulic system consists of a high water head and a long penstock with upstream and downstream surge tanks, and is equipped with a Francis turbine. The nonlinear characteristics of hydraulic turbine and the inelastic water hammer effects were considered to calculate and simulate the hydraulic transients. With reference to the control solution, the proposed methodology relies on an adaptive control designed by means of the on-line identification of the system model under monitoring. Extensive simulations and comparison with respect to a classic hydraulic turbine speed PID regulator show the effectiveness of the proposed modelling and control tools.

Emissions from Open Burning of Simulated Military Waste from Forward Operating Bases

EPA Science Inventory

Emissions from open burning of simulated military waste from forward operating bases (FOBs) were extensively characterized as an initial step in assessing potential inhalation exposure of FOB personnel and future disposal alternatives. Emissions from two different burning scenar...

Campus Energy Model for Control and Performance Validation

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

2014-09-19

The core of the modeling platform is an extensible block library for the MATLAB/Simulink software suite. The platform enables true co-simulation (interaction at each simulation time step) with NREL's state-of-the-art modeling tools and other energy modeling software.

Simulating Multivariate Nonnormal Data Using an Iterative Algorithm

ERIC Educational Resources Information Center

Ruscio, John; Kaczetow, Walter

2008-01-01

Simulating multivariate nonnormal data with specified correlation matrices is difficult. One especially popular method is Vale and Maurelli's (1983) extension of Fleishman's (1978) polynomial transformation technique to multivariate applications. This requires the specification of distributional moments and the calculation of an intermediate…

Learning about Fossil Formation by Classroom Simulation.

ERIC Educational Resources Information Center

Schlenker, Richard M.; Yoshida, Sarah J.

1991-01-01

Activities in which students build their own simulations of fossils, using seashells, chicken bones, toy dinosaurs, or leaves as models and plaster of paris, sand, mud, clay, or a mixture of gravel and clay as a matrix are presented. Curriculum extensions are included. (KR)

Measuring Human Performance in Simulated Nuclear Power Plant Control Rooms Using Eye Tracking

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

Kovesdi, Casey Robert; Rice, Brandon Charles; Bower, Gordon Ross

Control room modernization will be an important part of life extension for the existing light water reactor fleet. As part of modernization efforts, personnel will need to gain a full understanding of how control room technologies affect performance of human operators. Recent advances in technology enables the use of eye tracking technology to continuously measure an operator’s eye movement, which correlates with a variety of human performance constructs such as situation awareness and workload. This report describes eye tracking metrics in the context of how they will be used in nuclear power plant control room simulator studies.

Tutoring electronic troubleshooting in a simulated maintenance work environment

NASA Technical Reports Server (NTRS)

Gott, Sherrie P.

1987-01-01

A series of intelligent tutoring systems, or intelligent maintenance simulators, is being developed based on expert and novice problem solving data. A graded series of authentic troubleshooting problems provides the curriculum, and adaptive instructional treatments foster active learning in trainees who engage in extensive fault isolation practice and thus in conditionalizing what they know. A proof of concept training study involving human tutoring was conducted as a precursor to the computer tutors to assess this integrated, problem based approach to task analysis and instruction. Statistically significant improvements in apprentice technicians' troubleshooting efficiency were achieved after approximately six hours of training.

Guidelines for Computing Longitudinal Dynamic Stability Characteristics of a Subsonic Transport

NASA Technical Reports Server (NTRS)

Thompson, Joseph R.; Frank, Neal T.; Murphy, Patrick C.

2010-01-01

A systematic study is presented to guide the selection of a numerical solution strategy for URANS computation of a subsonic transport configuration undergoing simulated forced oscillation about its pitch axis. Forced oscillation is central to the prevalent wind tunnel methodology for quantifying aircraft dynamic stability derivatives from force and moment coefficients, which is the ultimate goal for the computational simulations. Extensive computations are performed that lead in key insights of the critical numerical parameters affecting solution convergence. A preliminary linear harmonic analysis is included to demonstrate the potential of extracting dynamic stability derivatives from computational solutions.

Flame-Generated Vorticity Production in Premixed Flame-Vortex Interactions

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

2003-01-01

In this study, we use detailed time-dependent, multi-dimensional numerical simulations to investigate the relative importance of the processes leading to FGV in flame-vortex interactions in normal gravity and microgravity and to determine if the production of vorticity in flames in gravity is the same as that in zero gravity except for the contribution of the gravity term. The numerical simulations will be performed using the computational model developed at NRL, FLAME3D. FLAME3D is a parallel, multi-dimensional (either two- or three-dimensional) flame model based on FLIC2D, which has been used extensively to study the structure and stability of premixed hydrogen and methane flames.

Spacecraft applications of advanced global positioning system technology

NASA Technical Reports Server (NTRS)

1988-01-01

This is the final report on the Texas Instruments Incorporated (TI) simulations study of Spacecraft Application of Advanced Global Positioning System (GPS) Technology. This work was conducted for the NASA Johnson Space Center (JSC) under contract NAS9-17781. GPS, in addition to its baselined capability as a highly accurate spacecraft navigation system, can provide traffic control, attitude control, structural control, and uniform time base. In Phase 1 of this program, another contractor investigated the potential of GPS in these four areas and compared GPS to other techniques. This contract was for the Phase 2 effort, to study the performance of GPS for these spacecraft applications through computer simulations. TI had previously developed simulation programs for GPS differential navigation and attitude measurement. These programs were adapted for these specific spacecraft applications. In addition, TI has extensive expertise in the design and production of advanced GPS receivers, including space-qualified GPS receivers. We have drawn on this background to augment the simulation results in the system level overview, which is Section 2 of this report.

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

Sotomayor, Marcos

Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictionsmore » must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.« less

Simulation studies on the standing and traveling wave thermoacoustic prime movers

NASA Astrophysics Data System (ADS)

Skaria, Mathew; Rasheed, K. K. Abdul; Shafi, K. A.; Kasthurirengan, S.; Behera, Upendra

2014-01-01

Thermoacoustic systems have been a focus of recent research due to its structural simplicity, high reliability due to absence of moving parts, and can be driven by low grade energy such as fuel, gas, solar energy, waste heat etc. There has been extensive research on both standing wave and traveling wave systems. Towards the development of such systems, simulations can be carried out by several methods such as (a) solving the energy equation, (b) enthalpy flow model, (c) DeltaEC, a free software available from LANL, USA (d) Computational Fluid Dynamics (CFD) etc. We present here the simulation studies of standing wave and traveling wave thermoacoustic prime movers using CFD and DeltaEC. The CFD analysis is carried out using Fluent 6.3.26, incorporating the necessary boundary conditions with different working fluids at different operating pressures. The results obtained by CFD are compared with those obtained using DeltaEC. Also, the CFD simulation of the thermoacoustically driven refrigerator is presented.

Simulation studies on the standing and traveling wave thermoacoustic prime movers

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

Skaria, Mathew; Rasheed, K. K. Abdul; Shafi, K. A.

Thermoacoustic systems have been a focus of recent research due to its structural simplicity, high reliability due to absence of moving parts, and can be driven by low grade energy such as fuel, gas, solar energy, waste heat etc. There has been extensive research on both standing wave and traveling wave systems. Towards the development of such systems, simulations can be carried out by several methods such as (a) solving the energy equation, (b) enthalpy flow model, (c) DeltaEC, a free software available from LANL, USA (d) Computational Fluid Dynamics (CFD) etc. We present here the simulation studies of standingmore » wave and traveling wave thermoacoustic prime movers using CFD and DeltaEC. The CFD analysis is carried out using Fluent 6.3.26, incorporating the necessary boundary conditions with different working fluids at different operating pressures. The results obtained by CFD are compared with those obtained using DeltaEC. Also, the CFD simulation of the thermoacoustically driven refrigerator is presented.« less

MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery

PubMed Central

Li, Rongzhong; Macnamara, Lindsay M.; Leuchter, Jessica D.; Alexander, Rebecca W.; Cho, Samuel S.

2015-01-01

While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes. PMID:26184179

Experimental and Computational Study of Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Fletcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock-shear-layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Higher representations on the lattice: Numerical simulations, SU(2) with adjoint fermions

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

Del Debbio, Luigi; Patella, Agostino; Pica, Claudio

2010-05-01

We discuss the lattice formulation of gauge theories with fermions in arbitrary representations of the color group and present in detail the implementation of the hybrid Monte Carlo (HMC)/rational HMC algorithm for simulating dynamical fermions. We discuss the validation of the implementation through an extensive set of tests and the stability of simulations by monitoring the distribution of the lowest eigenvalue of the Wilson-Dirac operator. Working with two flavors of Wilson fermions in the adjoint representation, benchmark results for realistic lattice simulations are presented. Runs are performed on different lattice sizes ranging from 4{sup 3}x8 to 24{sup 3}x64 sites. Formore » the two smallest lattices we also report the measured values of benchmark mesonic observables. These results can be used as a baseline for rapid cross-checks of simulations in higher representations. The results presented here are the first steps toward more extensive investigations with controlled systematic errors, aiming at a detailed understanding of the phase structure of these theories, and of their viability as candidates for strong dynamics beyond the standard model.« less

Systematic Validation of Protein Force Fields against Experimental Data

PubMed Central

Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

2012-01-01

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field—the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins—one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins. PMID:22384157

Simulating fuel treatment effects in dry forests of the western United States: testing the principles of a fire-safe forest

Treesearch

Morris C. Johnson; Maureen C Kennedy; David L. Peterson

2011-01-01

We used the Fire and Fuels Extension to the Forest Vegetation Simulator (FFE-FVS) to simulate fuel treatment effects on stands in low- to midelevation dry forests (e.g., ponderosa pine (Pinus ponderosa Dougl. ex. P. & C. Laws.) and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) of the western United States. We...

Mathematical modeling of high-pH chemical flooding

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

Bhuyan, D.; Lake, L.W.; Pope, G.A.

1990-05-01

This paper describes a generalized compositional reservoir simulator for high-pH chemical flooding processes. This simulator combines the reaction chemistry associated with these processes with the extensive physical- and flow-property modeling schemes of an existing micellar/polymer flood simulator, UTCHEM. Application of the model is illustrated for cases from a simple alkaline preflush to surfactant-enhanced alkaline-polymer flooding.

Radiographic diagnosis of sagittal plane rotational displacement in pelvic fractures: a cadaveric model and clinical case study.

PubMed

Shui, Xiaolong; Ying, Xiaozhou; Kong, Jianzhong; Feng, Yongzeng; Hu, Wei; Guo, Xiaoshan; Wang, Gang

2015-08-01

Our objective was to measure the sagittal plane rotational (flexion and extension) displacement of hemipelvis radiologically and analyze the ratio of flexion and extension displacement of unstable pelvic fractures. We used 8 cadaveric models to study the radiographic evidence of pelvic fractures in the sagittal plane. We performed pelvic osteotomy on 8 cadavers to simulate anterior and posterior pelvic ring injury. Radiological data were measured in the flexion and extension group under different angles (5°, 10°, 15°, 20°, and 25°). We retrospectively reviewed 164 patients who were diagnosed with a unilateral fracture of the pelvis. Pelvic ring displacement was identified and recorded radiographically in cadaveric models. The flexion and extension displacement of pelvic fractures was measured in terms of the vertical distance of fracture from the top of iliac crest to the pubic tubercle (CD) or from the top of iliac crest to the lowest point of ischial tuberosity (AB). Fifty-seven pelves showed flexion displacement and 15 showed extension displacement. Closed reduction including internal fixation and external fixation was successfully used in 141 cases (86.0 %). The success rates of closed reduction in flexion and extension displacement groups were 77 and 73 %, respectively, which were lower than in unstable pelvic ring fractures. The sagittal plane rotation (flexion and extension) displacement of pelvic fractures could be measured by special points and lines on the radiographs. Minimally invasive reduction should be based on clearly identified differences between the sagittal plane rotation and the vertical displacement of pelvic fractures.

Transient Side Load Analysis of Out-of-Round Film-Cooled Nozzle Extensions

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Lin, Jeff; Ruf, Joe; Guidos, Mike

2012-01-01

There was interest in understanding the impact of out-of-round nozzle extension on the nozzle side load during transient startup operations. The out-of-round nozzle extension could be the result of asymmetric internal stresses, deformation induced by previous tests, and asymmetric loads induced by hardware attached to the nozzle. The objective of this study was therefore to computationally investigate the effect of out-of-round nozzle extension on the nozzle side loads during an engine startup transient. The rocket engine studied encompasses a regeneratively cooled chamber and nozzle, along with a film cooled nozzle extension. The computational methodology is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, and transient inlet boundary flow properties derived from an engine system simulation. Six three-dimensional cases were performed with the out-of-roundness achieved by three different degrees of ovalization, elongated on lateral y and z axes: one slightly out-of-round, one more out-of-round, and one significantly out-of-round. The results show that the separation line jump was the primary source of the peak side loads. Comparing to the peak side load of the perfectly round nozzle, the peak side loads increased for the slightly and more ovalized nozzle extensions, and either increased or decreased for the two significantly ovalized nozzle extensions. A theory based on the counteraction of the flow destabilizing effect of an exacerbated asymmetrical flow caused by a lower degree of ovalization, and the flow stabilizing effect of a more symmetrical flow, created also by ovalization, is presented to explain the observations obtained in this effort.

Variance in binary stellar population synthesis

NASA Astrophysics Data System (ADS)

Breivik, Katelyn; Larson, Shane L.

2016-03-01

In the years preceding LISA, Milky Way compact binary population simulations can be used to inform the science capabilities of the mission. Galactic population simulation efforts generally focus on high fidelity models that require extensive computational power to produce a single simulated population for each model. Each simulated population represents an incomplete sample of the functions governing compact binary evolution, thus introducing variance from one simulation to another. We present a rapid Monte Carlo population simulation technique that can simulate thousands of populations in less than a week, thus allowing a full exploration of the variance associated with a binary stellar evolution model.

Research in the Aloha system

NASA Technical Reports Server (NTRS)

Abramson, N.

1974-01-01

The Aloha system was studied and developed and extended to advanced forms of computer communications networks. Theoretical and simulation studies of Aloha type radio channels for use in packet switched communications networks were performed. Improved versions of the Aloha communications techniques and their extensions were tested experimentally. A packet radio repeater suitable for use with the Aloha system operational network was developed. General studies of the organization of multiprocessor systems centered on the development of the BCC 500 computer were concluded.

Multislice spiral CT simulator for dynamic cardiopulmonary studies

NASA Astrophysics Data System (ADS)

De Francesco, Silvia; Ferreira da Silva, Augusto M.

2002-04-01

We've developed a Multi-slice Spiral CT Simulator modeling the acquisition process of a real tomograph over a 4-dimensional phantom (4D MCAT) of the human thorax. The simulator allows us to visually characterize artifacts due to insufficient temporal sampling and a priori evaluate the quality of the images obtained in cardio-pulmonary studies (both with single-/multi-slice and ECG gated acquisition processes). The simulating environment allows both for conventional and spiral scanning modes and includes a model of noise in the acquisition process. In case of spiral scanning, reconstruction facilities include longitudinal interpolation methods (360LI and 180LI both for single and multi-slice). Then, the reconstruction of the section is performed through FBP. The reconstructed images/volumes are affected by distortion due to insufficient temporal sampling of the moving object. The developed simulating environment allows us to investigate the nature of the distortion characterizing it qualitatively and quantitatively (using, for example, Herman's measures). Much of our work is focused on the determination of adequate temporal sampling and sinogram regularization techniques. At the moment, the simulator model is limited to the case of multi-slice tomograph, being planned as a next step of development the extension to cone beam or area detectors.

skelesim: an extensible, general framework for population genetic simulation in R.

PubMed

Parobek, Christian M; Archer, Frederick I; DePrenger-Levin, Michelle E; Hoban, Sean M; Liggins, Libby; Strand, Allan E

2017-01-01

Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier and a steep conceptual learning curve. skelesim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics and organizing data output, in a reproducible pipeline within the R environment. skelesim is designed to be an extensible framework that can 'wrap' around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skelesim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skelesim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skelesim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny). © 2016 John Wiley & Sons Ltd.

skeleSim: an extensible, general framework for population genetic simulation in R

PubMed Central

Parobek, Christian M.; Archer, Frederick I.; DePrenger-Levin, Michelle E.; Hoban, Sean M.; Liggins, Libby; Strand, Allan E.

2016-01-01

Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares’ complex capabilities, composing code and input files, a daunting bioinformatics barrier, and a steep conceptual learning curve. skeleSim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics, and organizing data output, in a reproducible pipeline within the R environment. skeleSim is designed to be an extensible framework that can ‘wrap’ around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skeleSim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skeleSim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skeleSim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny). PMID:27736016

Railroads and the Environment : Estimation of Fuel Consumption in Rail Transportation : Volume 3. Comparison of Computer Simulations with Field Measurements

DOT National Transportation Integrated Search

1978-09-01

This report documents comparisons between extensive rail freight service measurements (previously presented in Volume II) and simulations of the same operations using a sophisticated train performance calculator computer program. The comparisons cove...

The muon component in extensive air showers and new p+C data in fixed target experiments

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

Meurer, C.; Bluemer, J.; Engel, R.

2007-03-19

One of the most promising approaches to determine the energy spectrum and composition of the cosmic rays with energies above 1015 eV is the measurement of the number of electrons and muons produced in extensive air showers (EAS). Therefore simulation of air showers using electromagnetic and hadronic interaction models are necessary. These simulations show uncertainties which come mainly from hadronic interaction models. One aim of this work is to specify the low energy hadronic interactions which are important for the muon production in EAS. Therefore we simulate extensive air showers with a modified version of the simulation package CORSIKA. Inmore » particular we investigate in detail the energy and the phase space regions of secondary particle production, which are most important for muon production. This phase space region is covered by fixed target experiments at CERN. In the second part of this work we present preliminary momentum spectra of secondary {pi}+ and {pi}- in p+C collisions at 12 GeV/c measured with the HARP spectrometer at the PS accelerator at CERN. In addition we use the new p+C NA49 data at 158 GeV/c to check the reliability of hadronic interaction models for muon production in EAS. Finally, possibilities to measure relevant quantities of hadron production in existing and planned accelerator experiments are discussed.« less

High performance real-time flight simulation at NASA Langley

NASA Technical Reports Server (NTRS)

Cleveland, Jeff I., II

1994-01-01

In order to meet the stringent time-critical requirements for real-time man-in-the-loop flight simulation, computer processing operations must be deterministic and be completed in as short a time as possible. This includes simulation mathematical model computational and data input/output to the simulators. In 1986, in response to increased demands for flight simulation performance, personnel at NASA's Langley Research Center (LaRC), working with the contractor, developed extensions to a standard input/output system to provide for high bandwidth, low latency data acquisition and distribution. The Computer Automated Measurement and Control technology (IEEE standard 595) was extended to meet the performance requirements for real-time simulation. This technology extension increased the effective bandwidth by a factor of ten and increased the performance of modules necessary for simulator communications. This technology is being used by more than 80 leading technological developers in the United States, Canada, and Europe. Included among the commercial applications of this technology are nuclear process control, power grid analysis, process monitoring, real-time simulation, and radar data acquisition. Personnel at LaRC have completed the development of the use of supercomputers for simulation mathematical model computational to support real-time flight simulation. This includes the development of a real-time operating system and the development of specialized software and hardware for the CAMAC simulator network. This work, coupled with the use of an open systems software architecture, has advanced the state of the art in real time flight simulation. The data acquisition technology innovation and experience with recent developments in this technology are described.

Estimating Causal Effects of Education Interventions Using a Two-Rating Regression Discontinuity Design: Lessons from a Simulation Study and an Application

ERIC Educational Resources Information Center

Porter, Kristin E.; Reardon, Sean F.; Unlu, Fatih; Bloom, Howard S.; Cimpian, Joseph R.

2017-01-01

A valuable extension of the single-rating regression discontinuity design (RDD) is a multiple-rating RDD (MRRDD). To date, four main methods have been used to estimate average treatment effects at the multiple treatment frontiers of an MRRDD: the "surface" method, the "frontier" method, the "binding-score" method, and…

Teaching an Old Game New Tricks: Long-Term Feedback on a Re-Designed Online Role Play

ERIC Educational Resources Information Center

Hardy, Mat; Totman, Sally

2017-01-01

Despite an extensive history of use in teaching Political Science subjects, long-term scholarly studies of online role plays are uncommon. This paper redresses that balance by presenting five years of data on the Middle East Politics Simulation. This online role play has been run since the 1990s and underwent significant technical upgrade in…

Response of black ash wetland gaseous soil carbon fluxes to a simulated emerald ash borer infestation

Treesearch

Matthew Van Grinsven; Joseph Shannon; Nicholas Bolton; Joshua Davis; Nam Noh; Joseph Wagenbrenner; Randall Kolka; Thomas Pypker

2018-01-01

The rapid and extensive expansion of emerald ash borer (EAB) in North America since 2002 may eliminate most existing ash stands, likely affecting critical ecosystem services associated with water and carbon cycling. To our knowledge, no studies have evaluated the coupled response of black ash (Fraxinus nigra Marsh.) wetland water tables, soil...

Discrete Optimization of Electronic Hyperpolarizabilities in a Chemical Subspace

DTIC Science & Technology

2009-05-01

molecular design. Methods for optimization in discrete spaces have been studied extensively and recently reviewed ( 5). Optimization methods include...integer programming, as in branch-and-bound techniques (including dead-end elimination [ 6]), simulated annealing ( 7), and genetic algorithms ( 8...These algorithms have found renewed interest and application in molecular and materials design (9- 12) . Recently, new approaches have been

Early MIMD experience on the CRAY X-MP

NASA Astrophysics Data System (ADS)

Rhoades, Clifford E.; Stevens, K. G.

1985-07-01

This paper describes some early experience with converting four physics simulation programs to the CRAY X-MP, a current Multiple Instruction, Multiple Data (MIMD) computer consisting of two processors each with an architecture similar to that of the CRAY-1. As a multi-processor, the CRAY X-MP together with the high speed Solid-state Storage Device (SSD) in an ideal machine upon which to study MIMD algorithms for solving the equations of mathematical physics because it is fast enough to run real problems. The computer programs used in this study are all FORTRAN versions of original production codes. They range in sophistication from a one-dimensional numerical simulation of collisionless plasma to a two-dimensional hydrodynamics code with heat flow to a couple of three-dimensional fluid dynamics codes with varying degrees of viscous modeling. Early research with a dual processor configuration has shown speed-ups ranging from 1.55 to 1.98. It has been observed that a few simple extensions to FORTRAN allow a typical programmer to achieve a remarkable level of efficiency. These extensions involve the concept of memory local to a concurrent subprogram and memory common to all concurrent subprograms.

Link Connectivity and Coverage of Underwater Cognitive Acoustic Networks under Spectrum Constraint

PubMed Central

Wang, Qiu; Cheang, Chak Fong

2017-01-01

Extensive attention has been given to the use of cognitive radio technology in underwater acoustic networks since the acoustic spectrum became scarce due to the proliferation of human aquatic activities. Most of the recent studies on underwater cognitive acoustic networks (UCANs) mainly focus on spectrum management or protocol design. Few efforts have addressed the quality-of-service (QoS) of UCANs. In UCANs, secondary users (SUs) have lower priority to use acoustic spectrum than primary users (PUs) with higher priority to access spectrum. As a result, the QoS of SUs is difficult to ensure in UCANs. This paper proposes an analytical model to investigate the link connectivity and the probability of coverage of SUs in UCANs. In particular, this model takes both topological connectivity and spectrum availability into account, though spectrum availability has been ignored in most recent studies. We conduct extensive simulations to evaluate the effectiveness and the accuracy of our proposed model. Simulation results show that our proposed model is quite accurate. Besides, our results also imply that the link connectivity and the probability of coverage of SUs heavily depend on both the underwater acoustic channel conditions and the activities of PUs. PMID:29215561

Simulation of Wind Profile Perturbations for Launch Vehicle Design

NASA Technical Reports Server (NTRS)

Adelfang, S. I.

2004-01-01

Ideally, a statistically representative sample of measured high-resolution wind profiles with wavelengths as small as tens of meters is required in design studies to establish aerodynamic load indicator dispersions and vehicle control system capability. At most potential launch sites, high- resolution wind profiles may not exist. Representative samples of Rawinsonde wind profiles to altitudes of 30 km are more likely to be available from the extensive network of measurement sites established for routine sampling in support of weather observing and forecasting activity. Such a sample, large enough to be statistically representative of relatively large wavelength perturbations, would be inadequate for launch vehicle design assessments because the Rawinsonde system accurately measures wind perturbations with wavelengths no smaller than 2000 m (1000 m altitude increment). The Kennedy Space Center (KSC) Jimsphere wind profiles (150/month and seasonal 2 and 3.5-hr pairs) are the only adequate samples of high resolution profiles approx. 150 to 300 m effective resolution, but over-sampled at 25 m intervals) that have been used extensively for launch vehicle design assessments. Therefore, a simulation process has been developed for enhancement of measured low-resolution Rawinsonde profiles that would be applicable in preliminary launch vehicle design studies at launch sites other than KSC.

Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases.

PubMed

Moffett, Alexander S; Bender, Kyle W; Huber, Steven C; Shukla, Diwakar

2017-07-28

The structural motifs responsible for activation and regulation of eukaryotic protein kinases in animals have been studied extensively in recent years, and a coherent picture of their activation mechanisms has begun to emerge. In contrast, non-animal eukaryotic protein kinases are not as well understood from a structural perspective, representing a large knowledge gap. To this end, we investigated the conformational dynamics of two key Arabidopsis thaliana receptor-like kinases, brassinosteroid-insensitive 1 (BRI1) and BRI1-associated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphorylated kinase domains. Molecular dynamics simulations calculate the motion of each atom in a protein based on classical approximations of interatomic forces, giving researchers insight into protein function at unparalleled spatial and temporal resolutions. We found that in an otherwise "active" BAK1 the αC helix is highly disordered, a hallmark of deactivation, whereas the BRI1 αC helix is moderately disordered and displays swinging behavior similar to numerous animal kinases. An analysis of all known sequences in the A. thaliana kinome found that αC helix disorder may be a common feature of plant kinases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

How do energetic ions damage metallic surfaces?

DOE PAGES

Osetskiy, Yury N.; Calder, Andrew F.; Stoller, Roger E.

2015-02-20

Surface modification under bombardment by energetic ions observed under different conditions in structural and functional materials and can be either unavoidable effect of the conditions or targeted modification to enhance materials properties. Understanding basic mechanisms is necessary for predicting properties changes. The mechanisms activated during ion irradiation are of atomic scale and atomic scale modeling is the most suitable tool to study these processes. In this paper we present results of an extensive simulation program aimed at developing an understanding of primary surface damage in iron by energetic particles. We simulated 25 keV self-ion bombardment of Fe thin films withmore » (100) and (110) surfaces at room temperature. A large number of simulations, ~400, were carried out allow a statistically significant treatment of the results. The particular mechanism of surface damage depends on how the destructive supersonic shock wave generated by the displacement cascade interacts with the free surface. Three basic scenarios were observed, with the limiting cases being damage created far below the surface with little or no impact on the surface itself, and extensive direct surface damage on the timescale of a few picoseconds. In some instances, formation of large <100> vacancy loops beneath the free surface was observed, which may explain some earlier experimental observations.« less

Can physical joint simulators be used to anticipate clinical wear problems of new joint replacement implants prior to market release?

PubMed

Medley, John B

2016-05-01

One of the most important mandates of physical joint simulators is to provide test results that allow the implant manufacturer to anticipate and perhaps avoid clinical wear problems with their new products. This is best done before market release. This study gives four steps to follow in conducting such wear simulator testing. Two major examples involving hip wear simulators are discussed in which attempts had been made to predict clinical wear performance prior to market release. The second one, involving the DePuy ASR implant systems, is chosen for more extensive treatment by making it an illustrative example to explore whether wear simulator testing can anticipate clinical wear problems. It is concluded that hip wear simulator testing did provide data in the academic literature that indicated some risk of clinical wear problems prior to market release of the ASR implant systems. This supports the idea that physical joint simulators have an important role in the pre-market testing of new joint replacement implants. © IMechE 2016.

Direct simulations of chemically reacting turbulent mixing layers, part 2

NASA Technical Reports Server (NTRS)

Metcalfe, Ralph W.; Mcmurtry, Patrick A.; Jou, Wen-Huei; Riley, James J.; Givi, Peyman

1988-01-01

The results of direct numerical simulations of chemically reacting turbulent mixing layers are presented. This is an extension of earlier work to a more detailed study of previous three dimensional simulations of cold reacting flows plus the development, validation, and use of codes to simulate chemically reacting shear layers with heat release. Additional analysis of earlier simulations showed good agreement with self similarity theory and laboratory data. Simulations with a two dimensional code including the effects of heat release showed that the rate of chemical product formation, the thickness of the mixing layer, and the amount of mass entrained into the layer all decrease with increasing rates of heat release. Subsequent three dimensional simulations showed similar behavior, in agreement with laboratory observations. Baroclinic torques and thermal expansion in the mixing layer were found to produce changes in the flame vortex structure that act to diffuse the pairing vortices, resulting in a net reduction in vorticity. Previously unexplained anomalies observed in the mean velocity profiles of reacting jets and mixing layers were shown to result from vorticity generation by baroclinic torques.

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

Alexeev, A. V.; Maltseva, D. V.; Ivanov, V. A., E-mail: ivanov@polly.phys.msu.ru

We study force-extension curves of a single semiflexible chain consisting of several rigid rods connected by flexible spacers. The atomic force microscopy and laser optical or magnetic tweezers apparatus stretching these rod-coil macromolecules are discussed. In addition, the stretching by external isotropic force is analyzed. The main attention is focused on computer simulation and analytical results. We demonstrate that the force-extension curves for rod-coil chains composed of two or three rods of equal length differ not only quantitatively but also qualitatively in different probe methods. These curves have an anomalous shape for a chain of two rods. End-to-end distributions ofmore » rod-coil chains are calculated by Monte Carlo method and compared with analytical equations. The influence of the spacer’s length on the force-extension curves in different probe methods is analyzed. The results can be useful for interpreting experiments on the stretching of rod-coil block-copolymers.« less

Observation and Modeling of the Generation Mechanism of Ion Upflow during Sudden Commencement

NASA Astrophysics Data System (ADS)

Zou, S.; Ozturk, D. S.; Li, C.; Varney, R. H.; Reimer, A.

2017-12-01

Sudden commencement (SC) induced by solar wind pressure enhancement can produce significant global impact on the coupled magnetosphere-ionosphere (MI) system, and its effects have been studied extensively using ground magnetometers and coherent scatter radars. However, very limited observations have been reported about the effects of SC on the ionospheric plasma. We study the ionosphere response to the SC using the Poker Flat incoherent scatter radar (PFISR) and numerical simulations. A detailed case study of SC during the 17 March 2015 storm was conducted. PFISR observed lifting of the F region ionosphere, transient field-aligned ion upflow, prompt but short-lived ion temperature increase, subsequent F region density decrease, and persistent electron temperature increase. A global magnetohydrodynamic (MHD) simulation has been carried out to characterize the SC-induced current, convection, and magnetic perturbations. Simulated magnetic perturbations at Poker Flat show a satisfactory agreement with observations. The simulation provides a global context for linking localized PFISR observations to large-scale dynamic processes in the MI system. Following the case study, we also perform a statistical study of the effects of SC on the ionosphere focusing on the magnetic local time and latitudinal asymmetries using PFISR and GPS TEC.

Activity coefficients from molecular simulations using the OPAS method

NASA Astrophysics Data System (ADS)

Kohns, Maximilian; Horsch, Martin; Hasse, Hans

2017-10-01

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

Finite element simulation of adaptive aerospace structures with SMA actuators

NASA Astrophysics Data System (ADS)

Frautschi, Jason; Seelecke, Stefan

2003-07-01

The particular demands of aerospace engineering have spawned many of the developments in the field of adaptive structures. Shape memory alloys are particularly attractive as actuators in these types of structures due to their large strains, high specific work output and potential for structural integration. However, the requisite extensive physical testing has slowed development of potential applications and highlighted the need for a simulation tool for feasibility studies. In this paper we present an implementation of an extended version of the M'ller-Achenbach SMA model into a commercial finite element code suitable for such studies. Interaction between the SMA model and the solution algorithm for the global FE equations is thoroughly investigated with respect to the effect of tolerances and time step size on convergence, computational cost and accuracy. Finally, a simulation of a SMA-actuated flexible trailing edge of an aircraft wing modeled with beam elements is presented.

Extension and Validation of a Hybrid Particle-Finite Element Method for Hypervelocity Impact Simulation. Chapter 2

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.; Shivarama, Ravishankar

2004-01-01

The hybrid particle-finite element method of Fahrenthold and Horban, developed for the simulation of hypervelocity impact problems, has been extended to include new formulations of the particle-element kinematics, additional constitutive models, and an improved numerical implementation. The extended formulation has been validated in three dimensional simulations of published impact experiments. The test cases demonstrate good agreement with experiment, good parallel speedup, and numerical convergence of the simulation results.

Evaluation of Upland Disposal of Oakland Harbor, California, Sediment; Volume I: Turning Basin Sediments

DTIC Science & Technology

1992-10-01

infiltration studies ( Westerdahl and Skogerboe 1982). Extensive field 53 verification studies have been conducted with the WES Rainfall Simulator...Lysimeter System on a wide range of Corps project sites ( Westerdahl and Skogerboe 1982, Lee and Skogerboe 1984, Skogerboe et al. 1987). The WES Rain- fall...Vicksburg, MS. Winer, B. J. 1971. Statistical Principles in Experimental Design, McGraw- Hill Book Company, New York. Westerdahl , H. E., and Skogerboe, J

Energy simulation and optimization for a small commercial building through Modelica

NASA Astrophysics Data System (ADS)

Rivas, Bryan

Small commercial buildings make up the majority of buildings in the United States. Energy consumed by these buildings is expected to drastically increase in the next few decades, with a large percentage of the energy consumed attributed to cooling systems. This work presents the simulation and optimization of a thermostat schedule to minimize energy consumption in a small commercial building test bed during the cooling season. The simulation occurs through the use of the multi-engineering domain Dymola environment based on the Modelica open source programming language and is optimized with the Java based optimization program GenOpt. The simulation uses both physically based modeling utilizing heat transfer principles for the building and regression analysis for energy consumption. GenOpt is dynamically coupled to Dymola through various interface files. There are very few studies that have coupled GenOpt to a building simulation program and even fewer studies have used Dymola for building simulation as extensively as the work presented here. The work presented proves Dymola as a viable alternative to other building simulation programs such as EnergyPlus and MatLab. The model developed is used to simulate the energy consumption of a test bed, a commissioned real world small commercial building, while maintaining indoor thermal comfort. Potential applications include smart or intelligent building systems, predictive simulation of small commercial buildings, and building diagnostics.

The effect of lunate position on range of motion after a four-corner arthrodesis: a biomechanical simulation study.

PubMed

Dvinskikh, N A; Blankevoort, L; Strackee, S D; Grimbergen, C A; Streekstra, G J

2011-04-29

A four-corner arthrodesis of the wrist is a salvage procedure for the treatment of specific wrist disorders, to achieve a movable, stable and pain free joint. However, a partial arthrodesis limits the postoperative range of motion (ROM). The goal of this study is to understand the mechanism of the reduction of the ROM and to evaluate the effect of the orientation of the lunate in the four-corner arthrodesis on the range of motion by using a biomechanical model, containing articular contacts and ligaments. Multi-body models of a normal wrist and a four-corner arthrodesis wrist with different orientation of the lunate were used for simulations of flexion-extension motion (FEM) and radial-ulnar deviation motion (RUD). The ROM of the postoperative wrist was reduced from 145° to 82° of the total arc of FEM and from 73° to 41.5° of the total arc of RUD. The model simulations show that the range of motion reduction is caused by overtension of the extrinsic wrist ligaments. Different positioning of the lunate changes the balance between the contact forces and ligament forces in the wrist. This explains the effect on the postoperative range of motion. The 20° flexed lunate did not give any gain in the extension motion of the wrist, caused joint luxation in flexion and limitation in RUD. The 30° extended lunate caused overtension of the extrinsic ligaments attached to the lunate. The ROM in this case is dramatically reduced. The model simulations suggest that the neutral position of the lunate seems to be most favorable for mobility of the wrist after a four-corner arthrodesis procedure. Copyright © 2011 Elsevier Ltd. All rights reserved.

On-Chip Transport of Biological Fluids in MEMS Devices

DTIC Science & Technology

1999-02-01

this model has been extended for multi-dimensional geometries to simulate electroosmotic flow in microdevices. Electrophoresis model in CFD- ACE + will...integrated with CFD- ACE +. 7.0 REFERENCES 1. N. A. Patankar and H. H. Hu, "Numerical Simulation of Electroosmotic Flow," Analytical Chemistry, 70...Electroosmosis has been developed and successfully integrated with CFD- ACE + code. (ii) Extension of the above-mentioned model to simulate

Local-Area-Network Simulator

NASA Technical Reports Server (NTRS)

Gibson, Jim; Jordan, Joe; Grant, Terry

1990-01-01

Local Area Network Extensible Simulator (LANES) computer program provides method for simulating performance of high-speed local-area-network (LAN) technology. Developed as design and analysis software tool for networking computers on board proposed Space Station. Load, network, link, and physical layers of layered network architecture all modeled. Mathematically models according to different lower-layer protocols: Fiber Distributed Data Interface (FDDI) and Star*Bus. Written in FORTRAN 77.

Impact of model development, calibration and validation decisions on hydrological simulations in West Lake Erie Basin

USDA-ARS?s Scientific Manuscript database

Watershed simulation models are used extensively to investigate hydrologic processes, landuse and climate change impacts, pollutant load assessments and best management practices (BMPs). Developing, calibrating and validating these models require a number of critical decisions that will influence t...

AN ENVIRONMENTAL SIMULATION MODEL FOR TRANSPORT AND FATE OF MERCURY IN SMALL RURAL CATCHMENTS

EPA Science Inventory

The development of an extensively modified version of the environmental model GLEAMS to simulate fate and transport of mercury in small catchments is presented. Methods for parameter estimation are proposed and in some cases simple relationships for mercury processes are derived....

User's guide [Chapter 3

Treesearch

Nicholas L. Crookston; Donald C. E. Robinson; Sarah J. Beukema

2003-01-01

The Fire and Fuels Extension (FFE) to the Forest Vegetation Simulator (FVS) simulates fuel dynamics and potential fire behavior over time, in the context of stand development and management. This chapter presents the model's options, provides annotated examples, describes the outputs, and describes how to use and apply the model.

Purpose and applications [Chapter 1

Treesearch

Nicholas L. Crookston

2003-01-01

The Fire and Fuels Extension (FFE) to the Forest Vegetation Simulator (FVS) simulates fuel dynamics and potential fire behavior over time, in the context of stand development and management. This chapter provides an introduction to the model by illustrating its purpose and chronicling some of the applications it has supported.

An evaluation of edge effects in nutritional accessibility and availability measures: a simulation study

PubMed Central

2010-01-01

Background This paper addresses the statistical use of accessibility and availability indices and the effect of study boundaries on these measures. The measures are evaluated via an extensive simulation based on cluster models for local outlet density. We define outlet to mean either food retail store (convenience store, supermarket, gas station) or restaurant (limited service or full service restaurants). We designed a simulation whereby a cluster outlet model is assumed in a large study window and an internal subset of that window is constructed. We performed simulations on various criteria including one scenario representing an urban area with 2000 outlets as well as a non-urban area simulated with only 300 outlets. A comparison is made between estimates obtained with the full study area and estimates using only the subset area. This allows the study of the effect of edge censoring on accessibility measures. Results The results suggest that considerable bias is found at the edges of study regions in particular for accessibility measures. Edge effects are smaller for availability measures (when not smoothed) and also for short range accessibility Conclusions It is recommended that any study utilizing these measures should correct for edge effects. The use of edge correction via guard areas is recommended and the avoidance of large range distance-based accessibility measures is also proposed. PMID:20663199

Challenges in reducing the computational time of QSTS simulations for distribution system analysis.

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

Deboever, Jeremiah; Zhang, Xiaochen; Reno, Matthew J.

The rapid increase in penetration of distributed energy resources on the electric power distribution system has created a need for more comprehensive interconnection modelling and impact analysis. Unlike conventional scenario - based studies , quasi - static time - series (QSTS) simulation s can realistically model time - dependent voltage controllers and the diversity of potential impacts that can occur at different times of year . However, to accurately model a distribution system with all its controllable devices, a yearlong simulation at 1 - second resolution is often required , which could take conventional computers a computational time of 10more » to 120 hours when an actual unbalanced distribution feeder is modeled . This computational burden is a clear l imitation to the adoption of QSTS simulation s in interconnection studies and for determining optimal control solutions for utility operations . Our ongoing research to improve the speed of QSTS simulation has revealed many unique aspects of distribution system modelling and sequential power flow analysis that make fast QSTS a very difficult problem to solve. In this report , the most relevant challenges in reducing the computational time of QSTS simulations are presented: number of power flows to solve, circuit complexity, time dependence between time steps, multiple valid power flow solutions, controllable element interactions, and extensive accurate simulation analysis.« less

A virtual source model for Monte Carlo simulation of helical tomotherapy.

PubMed

Yuan, Jiankui; Rong, Yi; Chen, Quan

2015-01-08

The purpose of this study was to present a Monte Carlo (MC) simulation method based on a virtual source, jaw, and MLC model to calculate dose in patient for helical tomotherapy without the need of calculating phase-space files (PSFs). Current studies on the tomotherapy MC simulation adopt a full MC model, which includes extensive modeling of radiation source, primary and secondary jaws, and multileaf collimator (MLC). In the full MC model, PSFs need to be created at different scoring planes to facilitate the patient dose calculations. In the present work, the virtual source model (VSM) we established was based on the gold standard beam data of a tomotherapy unit, which can be exported from the treatment planning station (TPS). The TPS-generated sinograms were extracted from the archived patient XML (eXtensible Markup Language) files. The fluence map for the MC sampling was created by incorporating the percentage leaf open time (LOT) with leaf filter, jaw penumbra, and leaf latency contained from sinogram files. The VSM was validated for various geometry setups and clinical situations involving heterogeneous media and delivery quality assurance (DQA) cases. An agreement of < 1% was obtained between the measured and simulated results for percent depth doses (PDDs) and open beam profiles for all three jaw settings in the VSM commissioning. The accuracy of the VSM leaf filter model was verified in comparing the measured and simulated results for a Picket Fence pattern. An agreement of < 2% was achieved between the presented VSM and a published full MC model for heterogeneous phantoms. For complex clinical head and neck (HN) cases, the VSM-based MC simulation of DQA plans agreed with the film measurement with 98% of planar dose pixels passing on the 2%/2 mm gamma criteria. For patient treatment plans, results showed comparable dose-volume histograms (DVHs) for planning target volumes (PTVs) and organs at risk (OARs). Deviations observed in this study were consistent with literature. The VSM-based MC simulation approach can be feasibly built from the gold standard beam model of a tomotherapy unit. The accuracy of the VSM was validated against measurements in homogeneous media, as well as published full MC model in heterogeneous media.

A virtual source model for Monte Carlo simulation of helical tomotherapy

PubMed Central

Yuan, Jiankui; Rong, Yi

2015-01-01

The purpose of this study was to present a Monte Carlo (MC) simulation method based on a virtual source, jaw, and MLC model to calculate dose in patient for helical tomotherapy without the need of calculating phase‐space files (PSFs). Current studies on the tomotherapy MC simulation adopt a full MC model, which includes extensive modeling of radiation source, primary and secondary jaws, and multileaf collimator (MLC). In the full MC model, PSFs need to be created at different scoring planes to facilitate the patient dose calculations. In the present work, the virtual source model (VSM) we established was based on the gold standard beam data of a tomotherapy unit, which can be exported from the treatment planning station (TPS). The TPS‐generated sinograms were extracted from the archived patient XML (eXtensible Markup Language) files. The fluence map for the MC sampling was created by incorporating the percentage leaf open time (LOT) with leaf filter, jaw penumbra, and leaf latency contained from sinogram files. The VSM was validated for various geometry setups and clinical situations involving heterogeneous media and delivery quality assurance (DQA) cases. An agreement of <1% was obtained between the measured and simulated results for percent depth doses (PDDs) and open beam profiles for all three jaw settings in the VSM commissioning. The accuracy of the VSM leaf filter model was verified in comparing the measured and simulated results for a Picket Fence pattern. An agreement of <2% was achieved between the presented VSM and a published full MC model for heterogeneous phantoms. For complex clinical head and neck (HN) cases, the VSM‐based MC simulation of DQA plans agreed with the film measurement with 98% of planar dose pixels passing on the 2%/2 mm gamma criteria. For patient treatment plans, results showed comparable dose‐volume histograms (DVHs) for planning target volumes (PTVs) and organs at risk (OARs). Deviations observed in this study were consistent with literature. The VSM‐based MC simulation approach can be feasibly built from the gold standard beam model of a tomotherapy unit. The accuracy of the VSM was validated against measurements in homogeneous media, as well as published full MC model in heterogeneous media. PACS numbers: 87.53.‐j, 87.55.K‐ PMID:25679157

Simulating pre-galactic metal enrichment for JWST deep-field observations

NASA Astrophysics Data System (ADS)

Jaacks, Jason

2017-08-01

We propose to create a new suite of mesoscale cosmological volume simulations with custom built sub-grid physics in which we independently track the contribution from Population III and Population II star formation to the total metals in the interstellar medium (ISM) of the first galaxies, and in the diffuse IGM at an epoch prior to reionization. These simulations will fill a gap in our simulation knowledge about chemical enrichment in the pre-reionization universe, which is a crucial need given the impending observational push into this epoch with near-future ground and space-based telescopes. This project is the natural extension of our successful Cycle 24 theory proposal (HST-AR-14569.001-A; PI Jaacks) in which we developed a new Pop III star formation sub-grid model which is currently being utilized to study the baseline metal enrichment of pre-reionization systems.

Diffusion-coupled cohesive interface simulations of stress corrosion intergranular cracking in polycrystalline materials

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

Pu, Chao; Gao, Yanfei; Wang, Yanli

To study the stress corrosion intergranular cracking mechanism, a diffusion-coupled cohesive zone model (CZM) is proposed for the simulation of the stress-assisted diffusional process along grain boundaries and the mechanical response of grain boundary sliding and separation. This simulation methodology considers the synergistic effects of impurity diffusion driven by pressure gradient and degradation of grain boundary strength by impurity concentration. The diffusion-coupled CZM is combined with crystal plasticity finite element model (CPFEM) to simulate intergranular fracture of polycrystalline material under corrosive environment. Significant heterogeneity of the stress field and extensive impurity accumulation is observed at grain boundaries and junction points.more » Deformation mechanism maps are constructed with respect to the grain boundary degradation factor and applied strain rate, which dictate the transition from internal to near-surface intergranular fracture modes under various strain amplitudes and grain sizes.« less

Numerical simulation of turbulent jet noise, part 2

NASA Technical Reports Server (NTRS)

Metcalfe, R. W.; Orszag, S. A.

1976-01-01

Results on the numerical simulation of jet flow fields were used to study the radiated sound field, and in addition, to extend and test the capabilities of the turbulent jet simulation codes. The principal result of the investigation was the computation of the radiated sound field from a turbulent jet. In addition, the computer codes were extended to account for the effects of compressibility and eddy viscosity, and the treatment of the nonlinear terms of the Navier-Stokes equations was modified so that they can be computed in a semi-implicit way. A summary of the flow model and a description of the numerical methods used for its solution are presented. Calculations of the radiated sound field are reported. In addition, the extensions that were made to the fundamental dynamical codes are described. Finally, the current state-of-the-art for computer simulation of turbulent jet noise is summarized.

Detailed Comparison of DNS to PSE for Oblique Breakdown at Mach 3

NASA Technical Reports Server (NTRS)

Mayer, Christian S. J.; Fasel, Hermann F.; Choudhari, Meelan; Chang, Chau-Lyan

2010-01-01

A pair of oblique waves at low amplitudes is introduced in a supersonic flat-plate boundary layer. Their downstream development and the concomitant process of laminar to turbulent transition is then investigated numerically using Direct Numerical Simulations (DNS) and Parabolized Stability Equations (PSE). This abstract is the last part of an extensive study of the complete transition process initiated by oblique breakdown at Mach 3. In contrast to the previous simulations, the symmetry condition in the spanwise direction is removed for the simulation presented in this abstract. By removing the symmetry condition, we are able to confirm that the flow is indeed symmetric over the entire computational domain. Asymmetric modes grow in the streamwise direction but reach only small amplitude values at the outflow. Furthermore, this abstract discusses new time-averaged data from our previous simulation CASE 3 and compares PSE data obtained from NASA's LASTRAC code to DNS results.

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.

PubMed

Luginbühl, P; Güntert, P; Billeter, M; Wüthrich, K

1996-09-01

A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.

Sampling Simulations for Assessing the Accuracy of U.S. Agricultural Crop Mapping from Remotely Sensed Imagery

NASA Astrophysics Data System (ADS)

Dwyer, Linnea; Yadav, Kamini; Congalton, Russell G.

2017-04-01

Providing adequate food and water for a growing, global population continues to be a major challenge. Mapping and monitoring crops are useful tools for estimating the extent of crop productivity. GFSAD30 (Global Food Security Analysis Data at 30m) is a program, funded by NASA, that is producing global cropland maps by using field measurements and remote sensing images. This program studies 8 major crop types, and includes information on cropland area/extent, if crops are irrigated or rainfed, and the cropping intensities. Using results from the US and the extensive reference data available, CDL (USDA Crop Data Layer), we will experiment with various sampling simulations to determine optimal sampling for thematic map accuracy assessment. These simulations will include varying the sampling unit, the sampling strategy, and the sample number. Results of these simulations will allow us to recommend assessment approaches to handle different cropping scenarios.

Morphology, surface temperatures, and northern limits of columnar cacti in the Sonoran Desert

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

Nobel, P.S.

1980-02-01

Interspecific morphological differences and intraspecific morphological changes with latitude were evaluated to help examine the distributional ranges of Carnegiea gigantea, Lemaireocereus thurberi, Lophocereus schottii, Pachycereus pecten-aboriginum, and P. pringlei in the Sonoran Desert (US and Mexico). A computer model, which predicted the average surface temperature of the stem within 1/sup 0/C of that measured hourly throughout a 24-h period, was particularly useful in studying the thermal relations of the stem apex, where the lowest surface temperature occurred. Simulated increases in stem diameter raised the minimum apical temperature for C. gigantea and may help account for the extension of its rangemore » to higher latitudes than the other species studied. However, diameter increases led to a slight decrease in minimum apical temperatures for Lophocereus schottii. The immature stems of L. schottii are morphologically distinct from the mature stems, which caused minimum apical temperatures to be 1.6/sup 0/C lower for the immature stems under given environmental conditions; thus, freezing damage to the immature stems could limit the northward extension of the range of this species. As the apical pubescence in the simulations was increased up to the normal amount (10 mm), the minimum apical temperature for the stem of C. gigantea increased 2.4/sup 0/C. Simulated increases in spine shading of the apexalso raised the minimum apical temperatures, again indicating the influence of morphological features on the temperature of the meristematic region.« less

Fatigue reassessment for lifetime extension of offshore wind monopile substructures

NASA Astrophysics Data System (ADS)

Ziegler, Lisa; Muskulus, Michael

2016-09-01

Fatigue reassessment is required to decide about lifetime extension of aging offshore wind farms. This paper presents a methodology to identify important parameters to monitor during the operational phase of offshore wind turbines. An elementary effects method is applied to analyze the global sensitivity of residual fatigue lifetimes to environmental, structural and operational parameters. Therefore, renewed lifetime simulations are performed for a case study which consists of a 5 MW turbine with monopile substructure in 20 m water depth. Results show that corrosion, turbine availability, and turbulence intensity are the most influential parameters. This can vary strongly for other settings (water depth, turbine size, etc.) making case-specific assessments necessary.

Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation

NASA Technical Reports Server (NTRS)

Afjeh, Abdollah A.; Reed, John A.

2003-01-01

The following reports are presented on this project:A first year progress report on: Development of a Dynamically Configurable,Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; A second year progress report on: Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; An Extensible, Interchangeable and Sharable Database Model for Improving Multidisciplinary Aircraft Design; Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration; and Improving the Aircraft Design Process Using Web-based Modeling and Simulation.

Oceanic dispersion of Fukushima-derived Cs-137 in the coastal, offshore, and open oceans simulated by multiple oceanic general circulation models

NASA Astrophysics Data System (ADS)

Kawamura, H.; Furuno, A.; Kobayashi, T.; In, T.; Nakayama, T.; Ishikawa, Y.; Miyazawa, Y.; Usui, N.

2017-12-01

To understand the concentration and amount of Fukushima-derived Cs-137 in the ocean, this study simulates the oceanic dispersion of Cs-137 by an oceanic dispersion model SEA-GEARN-FDM developed at Japan Atomic Energy Agency (JAEA) and multiple oceanic general circulation models. The Cs-137 deposition amounts at the sea surface were used as the source term in oceanic dispersion simulations, which were estimated by atmospheric dispersion simulations with a Worldwide version of System for Prediction of Environmental Emergency Dose Information version II (WSPEEDI-II) developed at JAEA. The direct release from the Fukushima Daiichi Nuclear Power Plant into the ocean based on in situ Cs-137 measurements was used as the other source term in oceanic dispersion simulations. The simulated air Cs-137 concentrations qualitatively replicated those measured around the North Pacific. The accumulated Cs-137 ground deposition amount in the eastern Japanese Islands was consistent with that estimated by aircraft measurements. The oceanic dispersion simulations relatively well reproduced the measured Cs-137 concentrations in the coastal and offshore oceans during the first few months after the Fukushima disaster, and in the open ocean during the first year post-disaster. It was suggested that Cs-137 dispersed along the coast in the north-south direction during the first few months post-disaster, and were subsequently dispersed offshore by the Kuroshio Current and Kuroshio Extension. Mesoscale eddies accompanied by the Kuroshio Current and Kuroshio Extension played an important role in dilution of Cs-137. The Cs-137 amounts were quantified in the coastal, offshore, and open oceans during the first year post-disaster. It was demonstrated that Cs-137 actively dispersed from the coastal and offshore oceans to the open ocean, and from the surface layer to the deeper layer in the North Pacific.

Simulator certification methods and the vertical motion simulator

NASA Technical Reports Server (NTRS)

Showalter, T. W.

1981-01-01

The vertical motion simulator (VMS) is designed to simulate a variety of experimental helicopter and STOL/VTOL aircraft as well as other kinds of aircraft with special pitch and Z axis characteristics. The VMS includes a large motion base with extensive vertical and lateral travel capabilities, a computer generated image visual system, and a high speed CDC 7600 computer system, which performs aero model calculations. Guidelines on how to measure and evaluate VMS performance were developed. A survey of simulation users was conducted to ascertain they evaluated and certified simulators for use. The results are presented.

Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

NASA Astrophysics Data System (ADS)

Degrève, Léo; Fuzo, Carlos A.; Caliri, Antonio

2012-12-01

The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in the unprotonated form, the protein structure is very stable for ionic strengths ranging from 0 to 225 mM. Therefore, our findings support the hypothesis that the histidines constitute the hot points that induce configurational changes of E protein in acid pH, and give extra motivation to the development of new ideas for antivirus compound design.

Anticipation of the landing shock phenomenon in flight simulation

NASA Technical Reports Server (NTRS)

Mcfarland, Richard E.

1987-01-01

An aircraft landing may be described as a controlled crash because a runway surface is intercepted. In a simulation model the transition from aerodynamic flight to weight on wheels involves a single computational cycle during which stiff differential equations are activated; with a significant probability these initial conditions are unrealistic. This occurs because of the finite cycle time, during which large restorative forces will accompany unrealistic initial oleo compressions. This problem was recognized a few years ago at Ames Research Center during simulation studies of a supersonic transport. The mathematical model of this vehicle severely taxed computational resources, and required a large cycle time. The ground strike problem was solved by a described technique called anticipation equations. This extensively used technique has not been previously reported. The technique of anticipating a significant event is a useful tool in the general field of discrete flight simulation. For the differential equations representing a landing gear model stiffness, rate of interception and cycle time may combine to produce an unrealistic simulation of the continuum.

Development of the simulation system {open_quotes}IMPACT{close_quotes} for analysis of nuclear power plant severe accidents

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

Naitoh, Masanori; Ujita, Hiroshi; Nagumo, Hiroichi

1997-07-01

The Nuclear Power Engineering Corporation (NUPEC) has initiated a long-term program to develop the simulation system {open_quotes}IMPACT{close_quotes} for analysis of hypothetical severe accidents in nuclear power plants. IMPACT employs advanced methods of physical modeling and numerical computation, and can simulate a wide spectrum of senarios ranging from normal operation to hypothetical, beyond-design-basis-accident events. Designed as a large-scale system of interconnected, hierarchical modules, IMPACT`s distinguishing features include mechanistic models based on first principles and high speed simulation on parallel processing computers. The present plan is a ten-year program starting from 1993, consisting of the initial one-year of preparatory work followed bymore » three technical phases: Phase-1 for development of a prototype system; Phase-2 for completion of the simulation system, incorporating new achievements from basic studies; and Phase-3 for refinement through extensive verification and validation against test results and available real plant data.« less

Comparison of simulated and actual wind shear radar data products

NASA Technical Reports Server (NTRS)

Britt, Charles L.; Crittenden, Lucille H.

1992-01-01

Prior to the development of the NASA experimental wind shear radar system, extensive computer simulations were conducted to determine the performance of the radar in combined weather and ground clutter environments. The simulation of the radar used analytical microburst models to determine weather returns and synthetic aperture radar (SAR) maps to determine ground clutter returns. These simulations were used to guide the development of hazard detection algorithms and to predict their performance. The structure of the radar simulation is reviewed. Actual flight data results from the Orlando and Denver tests are compared with simulated results. Areas of agreement and disagreement of actual and simulated results are shown.

The effect of the remplissage procedure on shoulder range of motion: a cadaveric study.

PubMed

Omi, Rei; Hooke, Alexander W; Zhao, Kristin D; Matsuhashi, Tomoya; Goto, Akira; Yamamoto, Nobuyuki; Sperling, John W; Steinmann, Scott P; Itoi, Eiji; An, Kai-Nan

2014-02-01

The purpose of this in vitro biomechanical study was to assess the effects of the remplissage procedure for small- and large-sized Hill-Sachs lesions (HSLs) on shoulder range of motion (ROM) with a special interest in the apprehension position. HSLs of 50% and 100% of the glenoid width were simulated in 7 cadaveric shoulders as small and large lesions, respectively, and the postoperative condition was reproduced by placing suture anchors on the articular surface and tying down the infraspinatus at the medial edge of the would-be lesion site. ROMs were measured in abduction, internal rotation, and external rotation with the humerus in the adducted and abducted position. In addition, the ROM was measured in the anterior apprehension position, in which 2 torques of external rotation and extension were applied simultaneously, and external rotation and horizontal extension ROMs were measured with the humerus in different abduction angles (20°, 40°, and 60°). For standard ROMs, the procedure for the 50% HSL maintained complete ROMs, whereas the procedure for the 100% HSL significantly decreased external rotation ROM with the humerus in both the adducted and abducted positions, as well as abduction ROM. In the apprehension position, remplissage for the 50% HSL decreased extension ROM with the humerus abducted to 40° and 60°. Remplissage for the 100% HSL significantly decreased both external and extension ROMs regardless of the humeral abduction angle. In the cadaveric model with an intact humeral head and the simulated postoperative condition, the remplissage procedure for a large HSL caused significant restrictions in ROM of abduction in the scapular plane and external rotation with the humerus in both adduction and abduction. It also caused significant restrictions in both external rotation and extension ROMs in the apprehension position. The indication for the remplissage procedure for the larger HSL should be considered carefully, especially for the competitive throwing athlete who needs exceptional external rotation ROM for optimal overhead throwing performance. Copyright © 2014 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Deductibles in health insurance

NASA Astrophysics Data System (ADS)

Dimitriyadis, I.; Öney, Ü. N.

2009-11-01

This study is an extension to a simulation study that has been developed to determine ruin probabilities in health insurance. The study concentrates on inpatient and outpatient benefits for customers of varying age bands. Loss distributions are modelled through the Allianz tool pack for different classes of insureds. Premiums at different levels of deductibles are derived in the simulation and ruin probabilities are computed assuming a linear loading on the premium. The increase in the probability of ruin at high levels of the deductible clearly shows the insufficiency of proportional loading in deductible premiums. The PH-transform pricing rule developed by Wang is analyzed as an alternative pricing rule. A simple case, where an insured is assumed to be an exponential utility decision maker while the insurer's pricing rule is a PH-transform is also treated.

Improved simulation of river water and groundwater exchange in an alluvial plain using the SWAT model

USDA-ARS?s Scientific Manuscript database

Hydrological interaction between surface and subsurface water systems has a significant impact on water quality, ecosystems and biogeochemistry cycling of both systems. Distributed models have been developed to simulate this function, but they require detailed spatial inputs and extensive computati...

ESTIMATION OF INFILTRATION RATE IN THE VADOSE ZONE: COMPILATION OF SIMPLE MATHEMATICAL MODELS - VOLUME I

EPA Science Inventory

The unsaturated or vadose zone provides a complex system for the simulation of water movement and contaminant transport and fate. Numerous models are available for performing simulations related to the movement of water. There exists extensive documentation of these models. Ho...

Simulated and Virtual Science Laboratory Experiments: Improving Critical Thinking and Higher-Order Learning Skills

ERIC Educational Resources Information Center

Simon, Nicole A.

2013-01-01

Virtual laboratory experiments using interactive computer simulations are not being employed as viable alternatives to laboratory science curriculum at extensive enough rates within higher education. Rote traditional lab experiments are currently the norm and are not addressing inquiry, Critical Thinking, and cognition throughout the laboratory…

No Friends but the Mountains: A Simulation on Kurdistan.

ERIC Educational Resources Information Center

Major, Marc R.

1996-01-01

Presents a simulation that focuses on Kurdish nationalism and the struggle for autonomy and independence from the states that rule over Kurdish lands. Students assume the roles of either one of the countries directly involved or the governing body of the United Nations. Includes extensive background material. (MJP)

Chapter 4: Variant descriptions

Treesearch

Duncan C. Lutes; Donald C. E. Robinson

2003-01-01

The Fire and Fuels Extension (FFE) to the Forest Vegetation Simulator (FVS) simulates fuel dynamics and potential fire behavior over time, in the context of stand development and management. This report documents differences between geographic variants of the FFE. It is a companion document to the FFE "Model Description" and "User's Guide."...

Helicopter simulator qualification

NASA Technical Reports Server (NTRS)

Hampson, Brian

1992-01-01

CAE has extensive experience in building helicopter simulators and has participated in group working sessions for fixed-wing advisory circulars. Against this background, issues that should be addressed in establishing helicopter approval criteria were highlighted. Some of these issues are not immediately obvious and may, indeed, be more important than the criteria a themselves.

CCSI and the role of advanced computing in accelerating the commercial deployment of carbon capture systems

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

Miller, David; Agarwal, Deborah A.; Sun, Xin

2011-09-01

The Carbon Capture Simulation Initiative is developing state-of-the-art computational modeling and simulation tools to accelerate the commercialization of carbon capture technology. The CCSI Toolset consists of an integrated multi-scale modeling and simulation framework, which includes extensive use of reduced order models (ROMs) and a comprehensive uncertainty quantification (UQ) methodology. This paper focuses on the interrelation among high performance computing, detailed device simulations, ROMs for scale-bridging, UQ and the integration framework.

CCSI and the role of advanced computing in accelerating the commercial deployment of carbon capture systems

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

Miller, D.; Agarwal, D.; Sun, X.

2011-01-01

The Carbon Capture Simulation Initiative is developing state-of-the-art computational modeling and simulation tools to accelerate the commercialization of carbon capture technology. The CCSI Toolset consists of an integrated multi-scale modeling and simulation framework, which includes extensive use of reduced order models (ROMs) and a comprehensive uncertainty quantification (UQ) methodology. This paper focuses on the interrelation among high performance computing, detailed device simulations, ROMs for scale-bridging, UQ and the integration framework.

Experimental and numerical study of wastewater pollution in Yuhui channel, Jiashan city

NASA Astrophysics Data System (ADS)

Fu, Lei; Peng, Zhenhua; You, Aiju

2018-02-01

Due to the development of economics and society in China, the huge amount of wastewater becomes a serious problem in most of the Chinese cities. Therefore, the construction of wastewater treatment plant draws much more attentions than before. The discharge from the wastewater treatment plant is then considered as a point source in most of the important rivers and channels in China. In this study, a typical wastewater treatment plant extension project is introduced as a case study, a filed monitoring experiment is designed and executed to observe required data, then, a two-dimensional model is estabilished to simulate the water quality downsteam of the wastewater treatment plant, CODCr is considered as a typical pollutant during the simulation. The simulation results indicate that different discharge conditions will lead to different CODCr concentration downstream of the wastewater treatment plant, and an emergency plan should be prepared to minimize the risk of the pollution in the channel under unusual and accident conditions.

Derivation and Applicability of Asymptotic Results for Multiple Subtests Person-Fit Statistics

PubMed Central

Albers, Casper J.; Meijer, Rob R.; Tendeiro, Jorge N.

2016-01-01

In high-stakes testing, it is important to check the validity of individual test scores. Although a test may, in general, result in valid test scores for most test takers, for some test takers, test scores may not provide a good description of a test taker’s proficiency level. Person-fit statistics have been proposed to check the validity of individual test scores. In this study, the theoretical asymptotic sampling distribution of two person-fit statistics that can be used for tests that consist of multiple subtests is first discussed. Second, simulation study was conducted to investigate the applicability of this asymptotic theory for tests of finite length, in which the correlation between subtests and number of items in the subtests was varied. The authors showed that these distributions provide reasonable approximations, even for tests consisting of subtests of only 10 items each. These results have practical value because researchers do not have to rely on extensive simulation studies to simulate sampling distributions. PMID:29881053

A service life extension (SLEP) approach to operating aging aircraft beyond their original design lives

NASA Astrophysics Data System (ADS)

Pentz, Alan Carter

With today's uncertain funding climate (including sequestration and continuing budget resolutions), decision makers face severe budgetary challenges to maintain dominance through all aspects of the Department of Defense (DoD). To meet war-fighting capabilities, the DoD continues to extend aircraft programs beyond their design service lives by up to ten years, and occasionally much more. The budget requires a new approach to traditional extension strategies (i.e., reuse, reset, and reclamation) for structural hardware. While extending service life without careful controls can present a safety concern, future operations planning does not consider how much risk is present when operating within sound structural principles. Traditional structural hardware extension methods drive increased costs. Decision makers often overlook the inherent damage tolerance and fatigue capability of structural components and rely on simple time- and flight-based cycle accumulation when determining aircraft retirement lives. This study demonstrates that decision makers should consider risk in addition to the current extension strategies. Through an evaluation of eight military aircraft programs and the application and simulation of F-18 turbine engine usage data, this dissertation shows that insight into actual aircraft mission data, consideration of fatigue capability, and service extension length are key factors to consider. Aircraft structural components, as well as many critical safety components and system designs, have a predefined level of conservatism and inherent damage tolerance. The methods applied in this study would apply to extensions of other critical structures such as bridges. Understanding how much damage tolerance is built into the design compared to the original design usage requirements presents the opportunity to manage systems based on risk. The study presents the sensitivity of these factors and recommends avenues for further research.

Monte-Carlo simulations of a coarse-grained model for α-oligothiophenes

NASA Astrophysics Data System (ADS)

Almutairi, Amani; Luettmer-Strathmann, Jutta

The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. Oligothiophenes are small, π-conjugated molecules with applications in organic electronics that also serve as small-molecule models for polythiophenes. α-hexithiophene (6T) is a six-ring molecule, whose adsorption on noble metal surfaces has been studied extensively (see, e.g., Ref.). In this work, we develop a coarse-grained model for α-oligothiophenes. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. We perform Monte Carlo simulations to study the structure of isolated and adsorbed molecules

The hydrological behaviour of extensive and intensive green roofs in a dry climate.

PubMed

Razzaghmanesh, M; Beecham, S

2014-11-15

This paper presents the results of a hydrological investigation of four medium scale green roofs that were set up at the University of South Australia. In this study, the potential of green roofs as a source control device was investigated over a 2 year period using four medium size green roof beds comprised of two growth media types and two media depths. During the term of this study, 226 rainfall events were recorded and these were representative of the Adelaide climate. In general, there were no statistically significant differences between the rainfall and runoff parameters for the intensive and extensive beds except for peak attenuation and peak runoff delay, for which higher values were recorded in the intensive beds. Longer dry periods generally resulted in higher retention coefficients and higher retention was also recorded in warmer seasons. The average retention coefficient for intensive systems (89%) was higher than for extensive systems (74%). It was shown that rainfall depth, intensity, duration and also average dry weather period between events can change the retention performance and runoff volume of the green roofs. Comparison of green and simulated conventional roofs indicated that the former were able to mitigate the peak of runoff and could delay the start of runoff. These characteristics are important for most source control measures. The recorded rainfall and runoff data displayed a non-linear relationship. Also, the results indicated that continuous time series modelling would be a more appropriate technique than using peak rainfall intensity methods for green roof design and simulation. Copyright © 2014 Elsevier B.V. All rights reserved.

Prevention of distal extension cantilever fracture in mandibular overdentures.

PubMed

Quirynen, Thomas; Quirynen, Marc; Duyck, Joke

2015-09-01

Fractures of distal bar extensions, supporting a mandibular overdenture, do occur with significant functional and economic consequences for the patient. This study therefore aims to evaluate the effect of different bar cross-sectional shapes and surfaces, bar extension lengths and the placement of a support rib under the distal bar extension on fracture resistance. The 2nd moment area and static strength were calculated for 11 frequently used bar designs using finite element analysis (FEA). For two specific designs (Ackermann round Ø 1.8mm and Dolder-Y macro, the former with and without a support rib) additional physical static and fatigue strength tests were included. The FEA static strength data corresponded well to the 2nd moment area (a similar ranking when maximum allowed force was considered). The application of a rib support (Ackermann Ø 1.8mm) and limitations of the bar extension length (6mm for the Ackermann Ø 1.8mm, 8mm for the Dolder-Y macro) allowed the bars to exceed 5 × 10(6) cycles of 120 and 250N, respectively, before fracture. The region of highest stresses in FEA corresponded well with the locations of the fractures observed in static- and fatigue-testing. With some simple guidelines/modifications, the number of bar extension fractures can be reduced significantly. This study focusses on distal bar extensions which improve the positioning of an implant supported overdenture. By combining laboratory testing and finite element simulations we aim to: (1) explain why fractures occur (dependent on physical characteristics of the bar), and (2) give clinical guidelines on how to prevent such fractures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Studying Scientific Discovery by Computer Simulation.

DTIC Science & Technology

1983-03-30

Mendel’s laws of inheritance, the law of Gay- Lussac for gaseous reactions, tile law of Dulong and Petit, the derivation of atomic weights by Avogadro...neceseary mid identify by block number) scientific discovery -ittri sic properties physical laws extensive terms data-driven heuristics intensive...terms theory-driven heuristics conservation laws 20. ABSTRACT (Continue on revere. side It necessary and identify by block number) Scientific discovery

Versatile RED-based buffer management mechanism for the efficient support of internet traffic

NASA Astrophysics Data System (ADS)

Nelissen, Jordi; De Cnodder, Stefaan

1999-11-01

This paper presents an evaluation of various GFR (Guaranteed Frame Rate) implementation proposals. By means of extensive simulations performed in different network environments we compare two ATM Forum example implementations, namely the `simple FIFO-based GFR.2 implementation' and the `per-VC threshold and scheduling implementation'. The lessons learned from this study are as well applicable to non-ATM network technologies.

Southwestern Oregon's Biscuit Fire: An Analysis of Forest Resources, Fire Severity, and Fire Hazard

Treesearch

David L. Azuma; Glenn A. Christensen

2005-01-01

This study compares pre-fire field inventory data (collected from 1993 to 1997) in relation to post-fire mapped fire severity classes and the Fire and Fuels Extension of the Forest Vegetation Simulator growth and yield model measures of fire hazard for the portion of the Siskiyou National Forest in the 2002 Biscuit fire perimeter of southwestern Oregon. Post-fire...

A Numerical Study on Microwave Coagulation Therapy

DTIC Science & Technology

2013-01-01

hepatocellular carcinoma (small size liver tumor). Through extensive numerical simulations, we reveal the mathematical relationships between some critical parameters in the therapy, including input power, frequency, temperature, and regions of impact. It is shown that these relationships can be approximated using simple polynomial functions. Compared to solutions of partial differential equations, these functions are significantly easier to compute and simpler to analyze for engineering design and clinical

Determination of the thermodynamic correction factor of fluids confined in nano-metric slit pores from molecular simulation

NASA Astrophysics Data System (ADS)

Collell, Julien; Galliero, Guillaume

2014-05-01

The multi-component diffusive mass transport is generally quantified by means of the Maxwell-Stefan diffusion coefficients when using molecular simulations. These coefficients can be related to the Fick diffusion coefficients using the thermodynamic correction factor matrix, which requires to run several simulations to estimate all the elements of the matrix. In a recent work, Schnell et al. ["Thermodynamics of small systems embedded in a reservoir: A detailed analysis of finite size effects," Mol. Phys. 110, 1069-1079 (2012)] developed an approach to determine the full matrix of thermodynamic factors from a single simulation in bulk. This approach relies on finite size effects of small systems on the density fluctuations. We present here an extension of their work for inhomogeneous Lennard Jones fluids confined in slit pores. We first verified this extension by cross validating the results obtained from this approach with the results obtained from the simulated adsorption isotherms, which allows to determine the thermodynamic factor in porous medium. We then studied the effects of the pore width (from 1 to 15 molecular sizes), of the solid-fluid interaction potential (Lennard Jones 9-3, hard wall potential) and of the reduced fluid density (from 0.1 to 0.7 at a reduced temperature T* = 2) on the thermodynamic factor. The deviation of the thermodynamic factor compared to its equivalent bulk value decreases when increasing the pore width and becomes insignificant for reduced pore width above 15. We also found that the thermodynamic factor is sensitive to the magnitude of the fluid-fluid and solid-fluid interactions, which softens or exacerbates the density fluctuations.

Determination of the thermodynamic correction factor of fluids confined in nano-metric slit pores from molecular simulation

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

Collell, Julien; Galliero, Guillaume, E-mail: guillaume.galliero@univ-pau.fr

2014-05-21

The multi-component diffusive mass transport is generally quantified by means of the Maxwell-Stefan diffusion coefficients when using molecular simulations. These coefficients can be related to the Fick diffusion coefficients using the thermodynamic correction factor matrix, which requires to run several simulations to estimate all the elements of the matrix. In a recent work, Schnell et al. [“Thermodynamics of small systems embedded in a reservoir: A detailed analysis of finite size effects,” Mol. Phys. 110, 1069–1079 (2012)] developed an approach to determine the full matrix of thermodynamic factors from a single simulation in bulk. This approach relies on finite size effectsmore » of small systems on the density fluctuations. We present here an extension of their work for inhomogeneous Lennard Jones fluids confined in slit pores. We first verified this extension by cross validating the results obtained from this approach with the results obtained from the simulated adsorption isotherms, which allows to determine the thermodynamic factor in porous medium. We then studied the effects of the pore width (from 1 to 15 molecular sizes), of the solid-fluid interaction potential (Lennard Jones 9-3, hard wall potential) and of the reduced fluid density (from 0.1 to 0.7 at a reduced temperature T* = 2) on the thermodynamic factor. The deviation of the thermodynamic factor compared to its equivalent bulk value decreases when increasing the pore width and becomes insignificant for reduced pore width above 15. We also found that the thermodynamic factor is sensitive to the magnitude of the fluid-fluid and solid-fluid interactions, which softens or exacerbates the density fluctuations.« less

Extended computational kernels in a massively parallel implementation of the Trotter-Suzuki approximation

NASA Astrophysics Data System (ADS)

Wittek, Peter; Calderaro, Luca

2015-12-01

We extended a parallel and distributed implementation of the Trotter-Suzuki algorithm for simulating quantum systems to study a wider range of physical problems and to make the library easier to use. The new release allows periodic boundary conditions, many-body simulations of non-interacting particles, arbitrary stationary potential functions, and imaginary time evolution to approximate the ground state energy. The new release is more resilient to the computational environment: a wider range of compiler chains and more platforms are supported. To ease development, we provide a more extensive command-line interface, an application programming interface, and wrappers from high-level languages.

MCNP calculations for container inspection with tagged neutrons

NASA Astrophysics Data System (ADS)

Boghen, G.; Donzella, A.; Filippini, V.; Fontana, A.; Lunardon, M.; Moretto, S.; Pesente, S.; Zenoni, A.

2005-12-01

We are developing an innovative tagged neutrons inspection system (TNIS) for cargo containers: the system will allow us to assay the chemical composition of suspect objects, previously identified by a standard X-ray radiography. The operation of the system is extensively being simulated by using the MCNP Monte Carlo code to study different inspection geometries, cargo loads and hidden threat materials. Preliminary simulations evaluating the signal and the signal over background ratio expected as a function of the system parameters are presented. The results for a selection of cases are briefly discussed and demonstrate that the system can operate successfully in different filling conditions.

Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

NASA Astrophysics Data System (ADS)

Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha; Kalinkin, Alexander A.

2017-02-01

Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, which is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,'bottom-up' and 'top-down', are illustrated. Preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.

A Simulation Analysis of an Extension of One-Dimensional Speckle Correlation Method for Detection of General In-Plane Translation

PubMed Central

Hrabovský, Miroslav

2014-01-01

The purpose of the study is to show a proposal of an extension of a one-dimensional speckle correlation method, which is primarily intended for determination of one-dimensional object's translation, for detection of general in-plane object's translation. In that view, a numerical simulation of a displacement of the speckle field as a consequence of general in-plane object's translation is presented. The translation components a x and a y representing the projections of a vector a of the object's displacement onto both x- and y-axes in the object plane (x, y) are evaluated separately by means of the extended one-dimensional speckle correlation method. Moreover, one can perform a distinct optimization of the method by reduction of intensity values representing detected speckle patterns. The theoretical relations between the translation components a x and a y of the object and the displacement of the speckle pattern for selected geometrical arrangement are mentioned and used for the testifying of the proposed method's rightness. PMID:24592180

Multi-day activity scheduling reactions to planned activities and future events in a dynamic model of activity-travel behavior

NASA Astrophysics Data System (ADS)

Nijland, Linda; Arentze, Theo; Timmermans, Harry

2014-01-01

Modeling multi-day planning has received scarce attention in activity-based transport demand modeling so far. However, new dynamic activity-based approaches are being developed at the current moment. The frequency and inflexibility of planned activities and events in activity schedules of individuals indicate the importance of incorporating those pre-planned activities in the new generation of dynamic travel demand models. Elaborating and combining previous work on event-driven activity generation, the aim of this paper is to develop and illustrate an extension of a need-based model of activity generation that takes into account possible influences of pre-planned activities and events. This paper describes the theory and shows the results of simulations of the extension. The simulation was conducted for six different activities, and the parameter values used were consistent with an earlier estimation study. The results show that the model works well and that the influences of the parameters are consistent, logical, and have clear interpretations. These findings offer further evidence of face and construct validity to the suggested modeling approach.

Simulation of the time structure of Extensive Air Showers with CORSIKA initiated by various primary particles at Alborz-I observatory level

NASA Astrophysics Data System (ADS)

Bahmanabadi, Mahmud; Moghaddam, Saba Mortazavi

2018-05-01

A detailed simulation of showers with various zenith angles in atmosphere produced by different primary particles including gamma, proton, carbon, and iron at Alborz-I observatory level (35∘43‧N, 51∘20‧E, 1200 m a.s.l= 890 gcm-2), in the energy range 3 × 1013 eV-3 × 1015 eV, has been performed by means of the CORSIKA Monte Carlo code. The aim of this study is to examine the time structure of secondary particles in Extensive Air Showers (EAS) produced by the different primary particles. For each primary particle, the distribution of the mean values of the time delays of secondary particles relative to the first particle hitting the ground level in each EAS, <τi > = , and the distribution of their mean standard deviations, < σi > in terms of distance from the shower core are obtained. The mean thickness and profile of showers as a function of their energy, primary mass, and zenith angle is described.

DAKOTA Design Analysis Kit for Optimization and Terascale

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

Adams, Brian M.; Dalbey, Keith R.; Eldred, Michael S.

2010-02-24

The DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a flexible and extensible interface between simulation codes (computational models) and iterative analysis methods. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the DAKOTA toolkit provides a flexible and extensible problem-solving environment for design and analysis of computational models on high performance computers.A user provides a set of DAKOTA commands in an input file and launches DAKOTA. DAKOTA invokes instances of the computational models, collects their results, and performs systems analyses. DAKOTA contains algorithms for optimization with gradient and nongradient-basedmore » methods; uncertainty quantification with sampling, reliability, polynomial chaos, stochastic collocation, and epistemic methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Services for parallel computing, simulation interfacing, approximation modeling, fault tolerance, restart, and graphics are also included.« less

Sub-half-micron contact window design with 3D photolithography simulator

NASA Astrophysics Data System (ADS)

Brainerd, Steve K.; Bernard, Douglas A.; Rey, Juan C.; Li, Jiangwei; Granik, Yuri; Boksha, Victor V.

1997-07-01

In state of the art IC design and manufacturing certain lithography layers have unique requirements. Latitudes and tolerances that apply to contacts and polysilicon gates are tight for such critical layers. Industry experts are discussing the most cost effective ways to use feature- oriented equipment and materials already developed for these layers. Such requirements introduce new dimensions into the traditionally challenging task for the photolithography engineer when considering various combinations of multiple factors to optimize and control the process. In addition, he/she faces a rapidly increasing cost of experiments, limited time and scarce access to equipment to conduct them. All the reasons presented above support simulation as an ideal method to satisfy these demands. However lithography engineers may be easily dissatisfied with a simulation tool when discovering disagreement between the simulation and experimental data. The problem is that several parameters used in photolithography simulation are very process specific. Calibration, i.e. matching experimental and simulation data using a specific set of procedures allows one to effectively use the simulation tool. We present results of a simulation based approach to optimize photolithography processes for sub-0.5 micron contact windows. Our approach consists of: (1) 3D simulation to explore different lithographic options, (2) calibration to a range of process conditions with extensive use of specifically developed optimization techniques. The choice of a 3D simulator is essential because of 3D nature of the problem of contact window design. We use DEPICT 4.1. This program performs fast aerial image simulation as presented before. For 3D exposure the program uses an extension to three-dimensions of the high numerical aperture model combined with Fast Fourier Transforms for maximum performance and accuracy. We use Kim (U.C. Berkeley) model and the fast marching Level Set method respectively for the calculation of resist development rates and resist surface movement during development process. Calibration efforts were aimed at matching experimental results on contact windows obtained after exposure of a binary mask. Additionally, simulation was applied to conduct quantitative analysis of PSM design capabilities, optical proximity correction, and stepper parameter optimization. Extensive experiments covered exposure (ASML 5500/100D stepper), pre- and post-exposure bake and development (2.38% TMAH, puddle process) of JSR IX725D2G and TOK iP3500 photoresists films on 200 mm test wafers. `Aquatar' was used as top antireflective coating, SEM pictures of developed patterns were analyzed and compared with simulation results for different values of defocus, exposure energies, numerical aperture and partial coherence.

REVIEWS OF TOPICAL PROBLEMS: Population synthesis in astrophysics

NASA Astrophysics Data System (ADS)

Popov, S. B.; Prokhorov, M. E.

2007-11-01

Population synthesis is a method for numerical simulation of the population of objects with a complex evolution. This method is widely used in astrophysics. We consider its main applications to studying astronomical objects. Examples of modeling evolution are given for populations of close binaries and isolated neutron stars. The application of the method to studying active galactic nuclei and the integral spectral characteristics of galaxies is briefly discussed. An extensive bibliography on all the topics covered is provided.

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

PubMed Central

2015-01-01

As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level. In this paper, we introduce iBIOMES Lite, a lightweight tool for biomolecular simulation data indexing and summarization. The main goal of iBIOMES Lite is to provide a simple interface to summarize computational experiments in a setting where the user might have limited privileges and limited access to IT resources. A command-line interface allows the user to summarize, publish, and search local simulation data sets. Published data sets are accessible via static hypertext markup language (HTML) pages that summarize the simulation protocols and also display data analysis graphically. The publication process is customized via extensible markup language (XML) descriptors while the HTML summary template is customized through extensible stylesheet language (XSL). iBIOMES Lite was tested on different platforms and at several national computing centers using various data sets generated through classical and quantum molecular dynamics, quantum chemistry, and QM/MM. The associated parsers currently support AMBER, GROMACS, Gaussian, and NWChem data set publication. The code is available at https://github.com/jcvthibault/ibiomes. PMID:24830957

Stable White Coatings

NASA Technical Reports Server (NTRS)

Zerlaut, Gene A.; Gilligan, J. E.; Harada, Y.

1965-01-01

In a previous research program for the Jet Propulsion- Laboratory, extensive studies led to the development and specifications of three zinc oxide-pigmented thermal-control coatings. The principal objectives of this program are: improvement of the three paints (as engineering materials), determination of the validity of our accelerated space-simulation testing, and continuation of the zinc oxide photolysis studies begun in the preceding program. Specific tasks that are discussed include: improvement of potassium silicate coatings as engineering materials and elucidation of their storage and handling problems; improvement of methyl silicone coatings as engineering materials; studies of zinc oxide photolysis to establish reasons for the observed stability of zinc oxide; and determination of space-simulation parameters such as long-term stability (to 8000 ESH), effect of coating surface temperature on the rate of degradation, and validity of accelerated testing (by reciprocity and wavelength dependency studies).

Preliminary design of CERN Future Circular Collider tunnel: first evaluation of the radiation environment in critical areas for electronics

NASA Astrophysics Data System (ADS)

Infantino, Angelo; Alía, Rubén García; Besana, Maria Ilaria; Brugger, Markus; Cerutti, Francesco

2017-09-01

As part of its post-LHC high energy physics program, CERN is conducting a study for a new proton-proton collider, called Future Circular Collider (FCC-hh), running at center-of-mass energies of up to 100 TeV in a new 100 km tunnel. The study includes a 90-350 GeV lepton collider (FCC-ee) as well as a lepton-hadron option (FCC-he). In this work, FLUKA Monte Carlo simulation was extensively used to perform a first evaluation of the radiation environment in critical areas for electronics in the FCC-hh tunnel. The model of the tunnel was created based on the original civil engineering studies already performed and further integrated in the existing FLUKA models of the beam line. The radiation levels in critical areas, such as the racks for electronics and cables, power converters, service areas, local tunnel extensions was evaluated.

Psychometric testing on the NLN Student Satisfaction and Self-Confidence in Learning, Simulation Design Scale, and Educational Practices Questionnaire using a sample of pre-licensure novice nurses.

PubMed

Franklin, Ashley E; Burns, Paulette; Lee, Christopher S

2014-10-01

In 2006, the National League for Nursing published three measures related to novice nurses' beliefs about self-confidence, scenario design, and educational practices associated with simulation. Despite the extensive use of these measures, little is known about their reliability and validity. The psychometric properties of the Student Satisfaction and Self-Confidence in Learning Scale, Simulation Design Scale, and Educational Practices Questionnaire were studied among a sample of 2200 surveys completed by novice nurses from a liberal arts university in the southern United States. Psychometric tests included item analysis, confirmatory and exploratory factor analyses in randomly-split subsamples, concordant and discordant validity, and internal consistency. All three measures have sufficient reliability and validity to be used in education research. There is room for improvement in content validity with the Student Satisfaction and Self-Confidence in Learning and Simulation Design Scale. This work provides robust evidence to ensure that judgments made about self-confidence after simulation, simulation design and educational practices are valid and reliable. Copyright © 2014 Elsevier Ltd. All rights reserved.

Simulation methods to estimate design power: an overview for applied research.

PubMed

Arnold, Benjamin F; Hogan, Daniel R; Colford, John M; Hubbard, Alan E

2011-06-20

Estimating the required sample size and statistical power for a study is an integral part of study design. For standard designs, power equations provide an efficient solution to the problem, but they are unavailable for many complex study designs that arise in practice. For such complex study designs, computer simulation is a useful alternative for estimating study power. Although this approach is well known among statisticians, in our experience many epidemiologists and social scientists are unfamiliar with the technique. This article aims to address this knowledge gap. We review an approach to estimate study power for individual- or cluster-randomized designs using computer simulation. This flexible approach arises naturally from the model used to derive conventional power equations, but extends those methods to accommodate arbitrarily complex designs. The method is universally applicable to a broad range of designs and outcomes, and we present the material in a way that is approachable for quantitative, applied researchers. We illustrate the method using two examples (one simple, one complex) based on sanitation and nutritional interventions to improve child growth. We first show how simulation reproduces conventional power estimates for simple randomized designs over a broad range of sample scenarios to familiarize the reader with the approach. We then demonstrate how to extend the simulation approach to more complex designs. Finally, we discuss extensions to the examples in the article, and provide computer code to efficiently run the example simulations in both R and Stata. Simulation methods offer a flexible option to estimate statistical power for standard and non-traditional study designs and parameters of interest. The approach we have described is universally applicable for evaluating study designs used in epidemiologic and social science research.

Simulation methods to estimate design power: an overview for applied research

PubMed Central

2011-01-01

Background Estimating the required sample size and statistical power for a study is an integral part of study design. For standard designs, power equations provide an efficient solution to the problem, but they are unavailable for many complex study designs that arise in practice. For such complex study designs, computer simulation is a useful alternative for estimating study power. Although this approach is well known among statisticians, in our experience many epidemiologists and social scientists are unfamiliar with the technique. This article aims to address this knowledge gap. Methods We review an approach to estimate study power for individual- or cluster-randomized designs using computer simulation. This flexible approach arises naturally from the model used to derive conventional power equations, but extends those methods to accommodate arbitrarily complex designs. The method is universally applicable to a broad range of designs and outcomes, and we present the material in a way that is approachable for quantitative, applied researchers. We illustrate the method using two examples (one simple, one complex) based on sanitation and nutritional interventions to improve child growth. Results We first show how simulation reproduces conventional power estimates for simple randomized designs over a broad range of sample scenarios to familiarize the reader with the approach. We then demonstrate how to extend the simulation approach to more complex designs. Finally, we discuss extensions to the examples in the article, and provide computer code to efficiently run the example simulations in both R and Stata. Conclusions Simulation methods offer a flexible option to estimate statistical power for standard and non-traditional study designs and parameters of interest. The approach we have described is universally applicable for evaluating study designs used in epidemiologic and social science research. PMID:21689447

Benchmark Simulation Model No 2: finalisation of plant layout and default control strategy.

PubMed

Nopens, I; Benedetti, L; Jeppsson, U; Pons, M-N; Alex, J; Copp, J B; Gernaey, K V; Rosen, C; Steyer, J-P; Vanrolleghem, P A

2010-01-01

The COST/IWA Benchmark Simulation Model No 1 (BSM1) has been available for almost a decade. Its primary purpose has been to create a platform for control strategy benchmarking of activated sludge processes. The fact that the research work related to the benchmark simulation models has resulted in more than 300 publications worldwide demonstrates the interest in and need of such tools within the research community. Recent efforts within the IWA Task Group on "Benchmarking of control strategies for WWTPs" have focused on an extension of the benchmark simulation model. This extension aims at facilitating control strategy development and performance evaluation at a plant-wide level and, consequently, includes both pretreatment of wastewater as well as the processes describing sludge treatment. The motivation for the extension is the increasing interest and need to operate and control wastewater treatment systems not only at an individual process level but also on a plant-wide basis. To facilitate the changes, the evaluation period has been extended to one year. A prolonged evaluation period allows for long-term control strategies to be assessed and enables the use of control handles that cannot be evaluated in a realistic fashion in the one week BSM1 evaluation period. In this paper, the finalised plant layout is summarised and, as was done for BSM1, a default control strategy is proposed. A demonstration of how BSM2 can be used to evaluate control strategies is also given.

Blind ethics: Closing one's eyes polarizes moral judgments and discourages dishonest behavior.

PubMed

Caruso, Eugene M; Gino, Francesca

2011-02-01

Four experiments demonstrate that closing one's eyes affects ethical judgment and behavior because it induces people to mentally simulate events more extensively. People who considered situations with their eyes closed rather than open judged immoral behaviors as more unethical and moral behaviors as more ethical. In addition, considering potential decisions with closed eyes decreased stated intentions to behave ethically and actual self-interested behavior. This relationship was mediated by the more extensive mental simulation that occurred with eyes closed rather than open, which, in turn, intensified emotional reactions to the ethical situation. We discuss the implications of these findings for moral psychology and ethical decision making. Copyright © 2010 Elsevier B.V. All rights reserved.

Monte Carlo simulation of EAS generated by 10(14) - 10(16) eV protons

NASA Technical Reports Server (NTRS)

Fenyves, E. J.; Yunn, B. C.; Stanev, T.

1985-01-01

Detailed Monte Carlo simulations of extensive air showers to be detected by the Homestake Surface Underground Telescope and other similar detectors located at sea level and mountain altitudes have been performed for 10 to the 14th power to 10 to the 16th power eV primary energies. The results of these Monte Carlo calculations will provide an opportunity to compare the experimental data with different models for the composition and spectra of primaries and for the development of air showers. The results obtained for extensive air showers generated by 10 to the 14th power to 10 to the 16th power eV primary protons are reported.

Extending the impulse response in order to reduce errors due to impulse noise and signal fading

NASA Technical Reports Server (NTRS)

Webb, Joseph A.; Rolls, Andrew J.; Sirisena, H. R.

1988-01-01

A finite impulse response (FIR) digital smearing filter was designed to produce maximum intersymbol interference and maximum extension of the impulse response of the signal in a noiseless binary channel. A matched FIR desmearing filter at the receiver then reduced the intersymbol interference to zero. Signal fades were simulated by means of 100 percent signal blockage in the channel. Smearing and desmearing filters of length 256, 512, and 1024 were used for these simulations. Results indicate that impulse response extension by means of bit smearing appears to be a useful technique for correcting errors due to impulse noise or signal fading in a binary channel.

TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.

PubMed

Li, Min; Liu, Fengjiao; Zhang, John Z H

2016-12-13

Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.

The use of real-time, hardware-in-the-loop simulation in the design and development of the new Hughes HS601 spacecraft attitude control system

NASA Technical Reports Server (NTRS)

Slafer, Loren I.

1989-01-01

Realtime simulation and hardware-in-the-loop testing is being used extensively in all phases of the design, development, and testing of the attitude control system (ACS) for the new Hughes HS601 satellite bus. Realtime, hardware-in-the-loop simulation, integrated with traditional analysis and pure simulation activities is shown to provide a highly efficient and productive overall development program. Implementation of high fidelity simulations of the satellite dynamics and control system algorithms, capable of real-time execution (using applied Dynamics International's System 100), provides a tool which is capable of being integrated with the critical flight microprocessor to create a mixed simulation test (MST). The MST creates a highly accurate, detailed simulated on-orbit test environment, capable of open and closed loop ACS testing, in which the ACS design can be validated. The MST is shown to provide a valuable extension of traditional test methods. A description of the MST configuration is presented, including the spacecraft dynamics simulation model, sensor and actuator emulators, and the test support system. Overall system performance parameters are presented. MST applications are discussed; supporting ACS design, developing on-orbit system performance predictions, flight software development and qualification testing (augmenting the traditional software-based testing), mission planning, and a cost-effective subsystem-level acceptance test. The MST is shown to provide an ideal tool in which the ACS designer can fly the spacecraft on the ground.

Painful ophthalmoplegia secondary to a mucocele involving the sella turcica, superior orbital fissure, and sphenoid sinus.

PubMed

Clarke, H; Clarke, V; Gill, J; St John, A; Lashley, M

1992-03-01

A case of painful ophthalmoplegia associated with an extensive lesion involving the sella turcica, superior orbital fissure, and sphenoid sinus in a 57-year-old man is reported. Even though nasal and ocular symptoms and signs represent the usual features of sphenoidal mucoceles, extension to the intracranial cavity as seen in this lesion is rare. Surgical exploration via a sublabial, transseptal approach revealed a mucocele of the sphenoid sinus. This case exhibited extensive and aggressive behavior simulating a malignant neoplasm.

No rationale for 1 variable per 10 events criterion for binary logistic regression analysis.

PubMed

van Smeden, Maarten; de Groot, Joris A H; Moons, Karel G M; Collins, Gary S; Altman, Douglas G; Eijkemans, Marinus J C; Reitsma, Johannes B

2016-11-24

Ten events per variable (EPV) is a widely advocated minimal criterion for sample size considerations in logistic regression analysis. Of three previous simulation studies that examined this minimal EPV criterion only one supports the use of a minimum of 10 EPV. In this paper, we examine the reasons for substantial differences between these extensive simulation studies. The current study uses Monte Carlo simulations to evaluate small sample bias, coverage of confidence intervals and mean square error of logit coefficients. Logistic regression models fitted by maximum likelihood and a modified estimation procedure, known as Firth's correction, are compared. The results show that besides EPV, the problems associated with low EPV depend on other factors such as the total sample size. It is also demonstrated that simulation results can be dominated by even a few simulated data sets for which the prediction of the outcome by the covariates is perfect ('separation'). We reveal that different approaches for identifying and handling separation leads to substantially different simulation results. We further show that Firth's correction can be used to improve the accuracy of regression coefficients and alleviate the problems associated with separation. The current evidence supporting EPV rules for binary logistic regression is weak. Given our findings, there is an urgent need for new research to provide guidance for supporting sample size considerations for binary logistic regression analysis.

A Monte Carlo study of Weibull reliability analysis for space shuttle main engine components

NASA Technical Reports Server (NTRS)

Abernethy, K.

1986-01-01

The incorporation of a number of additional capabilities into an existing Weibull analysis computer program and the results of Monte Carlo computer simulation study to evaluate the usefulness of the Weibull methods using samples with a very small number of failures and extensive censoring are discussed. Since the censoring mechanism inherent in the Space Shuttle Main Engine (SSME) data is hard to analyze, it was decided to use a random censoring model, generating censoring times from a uniform probability distribution. Some of the statistical techniques and computer programs that are used in the SSME Weibull analysis are described. The methods documented in were supplemented by adding computer calculations of approximate (using iteractive methods) confidence intervals for several parameters of interest. These calculations are based on a likelihood ratio statistic which is asymptotically a chisquared statistic with one degree of freedom. The assumptions built into the computer simulations are described. The simulation program and the techniques used in it are described there also. Simulation results are tabulated for various combinations of Weibull shape parameters and the numbers of failures in the samples.

Three Dimensional Simulation of the Baneberry Nuclear Event

NASA Astrophysics Data System (ADS)

Lomov, Ilya N.; Antoun, Tarabay H.; Wagoner, Jeff; Rambo, John T.

2004-07-01

Baneberry, a 10-kiloton nuclear event, was detonated at a depth of 278 m at the Nevada Test Site on December 18, 1970. Shortly after detonation, radioactive gases emanating from the cavity were released into the atmosphere through a shock-induced fissure near surface ground zero. Extensive geophysical investigations, coupled with a series of 1D and 2D computational studies were used to reconstruct the sequence of events that led to the catastrophic failure. However, the geological profile of the Baneberry site is complex and inherently three-dimensional, which meant that some geological features had to be simplified or ignored in the 2D simulations. This left open the possibility that features unaccounted for in the 2D simulations could have had an important influence on the eventual containment failure of the Baneberry event. This paper presents results from a high-fidelity 3D Baneberry simulation based on the most accurate geologic and geophysical data available. The results are compared with available data, and contrasted against the results of the previous 2D computational studies.

Transport simulations of linear plasma generators with the B2.5-Eirene and EMC3-Eirene codes

DOE PAGES

Rapp, Juergen; Owen, Larry W.; Bonnin, X.; ...

2014-12-20

Linear plasma generators are cost effective facilities to simulate divertor plasma conditions of present and future fusion reactors. For this research, the codes B2.5-Eirene and EMC3-Eirene were extensively used for design studies of the planned Material Plasma Exposure eXperiment (MPEX). Effects on the target plasma of the gas fueling and pumping locations, heating power, device length, magnetic configuration and transport model were studied with B2.5-Eirene. Effects of tilted or vertical targets were calculated with EMC3-Eirene and showed that spreading the incident flux over a larger area leads to lower density, higher temperature and off-axis profile peaking in front of themore » target. In conclusion, the simulations indicate that with sufficient heating power MPEX can reach target plasma conditions that are similar to those expected in the ITER divertor. B2.5-Eirene simulations of the MAGPIE experiment have been carried out in order to establish an additional benchmark with experimental data from a linear device with helicon wave heating.« less

Patient-Specific Simulations of Reactivity in Models of the Pulmonary Vasculature: A 3-D Numerical Study with Fluid-Structure Interaction

NASA Astrophysics Data System (ADS)

Hunter, Kendall; Zhang, Yanhang; Lanning, Craig

2005-11-01

Insight into the progression of pulmonary hypertension may be obtained from thorough study of vascular flow during reactivity testing, an invasive diagnostic procedure which can dramatically alter vascular hemodynamics. Diagnostic imaging methods, however, are limited in their ability to provide extensive data. Here we present detailed flow and wall deformation results from simulations of pulmonary arteries undergoing this procedure. Patient-specific 3-D geometric reconstructions of the first four branches of the pulmonary vasculature were obtained clinically and meshed for use with computational software. Transient simulations in normal and reactive states were obtained from four such models were completed with patient-specific velocity inlet conditions and flow impedance exit conditions. A microstructurally based orthotropic hyperelastic model that simulates pulmonary artery mechanics under normotensive and hypoxic hypertensive conditions treated wall constitutive changes due to pressure reactivity and arterial remodeling. Pressure gradients, velocity fields, arterial deformation, and complete topography of shear stress were obtained. These models provide richer detail of hemodynamics than can be obtained from current imaging techniques, and should allow maximum characterization of vascular function in the clinical situation.

Time-temperature-stress capabilities of composite materials for advanced supersonic technology application

NASA Technical Reports Server (NTRS)

Kerr, James R.; Haskins, James F.

1987-01-01

Advanced composites will play a key role in the development of the technology for the design and fabrication of future supersonic vehicles. However, incorporating the material into vehicle usage is contingent on accelerating the demonstration of service capacity and design technology. Because of the added material complexity and lack of extensive data, laboratory replication of the flight service will provide the most rapid method to document the airworthiness of advanced composite systems. Consequently, a laboratory program was conducted to determine the time-temperature-stress capabilities of several high temperature composites. Tests included were thermal aging, environmental aging, fatigue, creep, fracture, tensile, and real-time flight simulation exposure. The program had two phases. The first included all the material property determinations and aging and simulation exposures up through 10,000 hours. The second continued these tests up to 50,000 cumulative hours. This report presents the results of the Phase 1 baseline and 10,000-hr aging and flight simulation studies, the Phase 2 50,000-hr aging studies, and the Phase 2 flight simulation tests, some of which extended to almost 40,000 hours.

Climate Change Impact on Air Quality in High Resolution Simulation for Central Europe

NASA Astrophysics Data System (ADS)

Halenka, T.; Huszar, P.; Belda, M.

2009-04-01

Recently the effects of climate change on air-quality and vice-versa are studied quite extensively. In fact, even at regional and local scale especially the impact of climate change on the atmospheric composition and photochemical smog formation conditions can be significant when expecting e.g. more frequent appearance of heat waves etc. For the purpose of qualifying and quantifying the magnitude of such effects and to study the potential of climate forcing due to atmospheric chemistry/aerosols on regional scale, chemistry-transport model was coupled to RegCM on the Department of Meteorology and Environmental Protection, Faculty of Mathematics and Physics, Charles University in Prague, for the simulations in framework of the EC FP6 Project CECILIA. Off-line one way coupling enables the simulation of distribution of pollutants over 1991-2001 in very high resolution of 10 km is compared to the EMEP observations for the area of Central Europe. Simulations driven by climate change boundary conditions for time slices 1991-2000, 2041-2050 and 2091-2100 are presented to show the effect of climate change on the air quality in the region.

A Computer Model for Teaching the Dynamic Behavior of AC Contactors

ERIC Educational Resources Information Center

Ruiz, J.-R. R.; Espinosa, A. G.; Romeral, L.

2010-01-01

Ac-powered contactors are extensively used in industry in applications such as automatic electrical devices, motor starters, and heaters. In this work, a practical session that allows students to model and simulate the dynamic behavior of ac-powered electromechanical contactors is presented. Simulation is carried out using a rigorous parametric…

Spatial application of WEPS for estimating wind erosion in the Pacific Northwest

USDA-ARS?s Scientific Manuscript database

The Wind Erosion Prediction System (WEPS) is used to simulate soil erosion on croplands and was originally designed to run field scale simulations. This research is an extension of the WEPS model to run on multiple fields (grids) covering a larger region. We modified the WEPS source code to allow it...

LANES 1 Users' Guide

NASA Technical Reports Server (NTRS)

Jordan, J.

1985-01-01

This document is intended for users of the Local Area Network Extensible Simulator, version I. This simulator models the performance of a Fiber Optic network under a variety of loading conditions and network characteristics. The options available to the user for defining the network conditions are described in this document. Computer hardware and software requirements are also defined.

Enhancing Pre-Service Special Educator Preparation through Combined Use of Virtual Simulation and Instructional Coaching

ERIC Educational Resources Information Center

Peterson-Ahmad, Maria

2018-01-01

To meet the ever-increasing teaching standards, pre-service special educators need extensive and advanced opportunities for pedagogical preparation prior to entering the classroom. Providing opportunities for pre-service special educators to practice such strategies within a virtual simulation environment offers teacher preparation programs a way…

REVEAL: An Extensible Reduced Order Model Builder for Simulation and Modeling

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

Agarwal, Khushbu; Sharma, Poorva; Ma, Jinliang

2013-04-30

Many science domains need to build computationally efficient and accurate representations of high fidelity, computationally expensive simulations. These computationally efficient versions are known as reduced-order models. This paper presents the design and implementation of a novel reduced-order model (ROM) builder, the REVEAL toolset. This toolset generates ROMs based on science- and engineering-domain specific simulations executed on high performance computing (HPC) platforms. The toolset encompasses a range of sampling and regression methods that can be used to generate a ROM, automatically quantifies the ROM accuracy, and provides support for an iterative approach to improve ROM accuracy. REVEAL is designed to bemore » extensible in order to utilize the core functionality with any simulator that has published input and output formats. It also defines programmatic interfaces to include new sampling and regression techniques so that users can ‘mix and match’ mathematical techniques to best suit the characteristics of their model. In this paper, we describe the architecture of REVEAL and demonstrate its usage with a computational fluid dynamics model used in carbon capture.« less

Promoting Simulation Globally: Networking with Nursing Colleagues Across Five Continents.

PubMed

Alfes, Celeste M; Madigan, Elizabeth A

Simulation education is gaining momentum internationally and may provide the opportunity to enhance clinical education while disseminating evidence-based practice standards for clinical simulation and learning. There is a need to develop a cohesive leadership group that fosters support, networking, and sharing of simulation resources globally. The Frances Payne Bolton School of Nursing at Case Western Reserve University has had the unique opportunity to establish academic exchange programs with schools of nursing across five continents. Although the joint and mutual simulation activities have been extensive, each international collaboration has also provided insight into the innovations developed by global partners.

Simulation of a synergistic six-post motion system on the flight simulator for advanced aircraft at NASA-Ames

NASA Technical Reports Server (NTRS)

Bose, S. C.; Parris, B. L.

1977-01-01

Motion system drive philosophy and corresponding real-time software have been developed for the purpose of simulating the characteristics of a typical synergistic Six-Post Motion System (SPMS) on the Flight Simulator for Advanced Aircraft (FSAA) at NASA-Ames which is a non-synergistic motion system. This paper gives a brief description of these two types of motion systems and the general methods of producing motion cues of the FSAA. An actuator extension transformation which allows the simulation of a typical SPMS by appropriate drive washout and variable position limiting is described.

The Kepler End-to-End Model: Creating High-Fidelity Simulations to Test Kepler Ground Processing

NASA Technical Reports Server (NTRS)

Bryson, Stephen T.; Jenkins, Jon M.; Peters, Dan J.; Tenenbaum, Peter P.; Klaus, Todd C.; Gunter, Jay P.; Cote, Miles T.; Caldwell, Douglas A.

2010-01-01

The Kepler mission is designed to detect the transit of Earth-like planets around Sun-like stars by observing 100,000 stellar targets. Developing and testing the Kepler ground-segment processing system, in particular the data analysis pipeline, requires high-fidelity simulated data. This simulated data is provided by the Kepler End-to-End Model (ETEM). ETEM simulates the astrophysics of planetary transits and other phenomena, properties of the Kepler spacecraft and the format of the downlinked data. Major challenges addressed by ETEM include the rapid production of large amounts of simulated data, extensibility and maintainability.

A fast recursive algorithm for molecular dynamics simulation

NASA Technical Reports Server (NTRS)

Jain, A.; Vaidehi, N.; Rodriguez, G.

1993-01-01

The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

Hydrological performance of an extensive green roof: a case study from the central Europe (Bustehrad, Czech Republic)

NASA Astrophysics Data System (ADS)

Tománková, Klára; Sněhota, Michal; Jelínková, Vladimíra

2016-04-01

Extensive green roofs with a thin growing medium require minimal maintenance, and in general no irrigation. The proper functioning of such systems rests with their structural constituents, especially with the substrate used for planting. An extensive green roof with poorly developed vegetation and with a soil layer of a maximum thickness of 5 cm mixed with local stripped topsoil with crushed bricks and green waste was studied with respect to the hydrological behavior. The substrate classified as loam comprises a significant proportion of very fine particles and thus it is prone to clogging up of soil pores and forming of fissures on the surface. The green roof studied is well equipped for measuring meteorological data including air temperature, wind speed and direction, net radiation, relative humidity, and rainfall intensity. The meteorological information on the site is completed by soil temperature measurement. The 12 m long transect is equipped with eight time domain reflectometry probes (TDR) to monitor soil water content. Soil physical properties (bulk density, porosity, grain size distribution) and soil hydraulic characteristics (soil water retention curve) were obtained. The numerical modeling of transient soil water movement in the green roof substrate was performed using a two-dimensional model based on the Richards' equation. Results were compared with the soil water content data acquired. Six alternative scenarios were formulated to discuss possible improvement of green roof functioning and four selected scenarios were simulated. The study helped us to improve our understanding of the flow processes through the green roof soil system under study. The alternative scenario simulations allowed hydrological assessment of roof construction amendments. The research was realized as a part of the University Centre for Energy Efficient Buildings supported by the EU and with financial support from the Czech Science Foundation under project number 14-10455P.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

PubMed

Bergmann, Frank T; Cooper, Jonathan; Le Novère, Nicolas; Nickerson, David; Waltemath, Dagmar

2015-09-04

The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines. This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

PubMed

Bergmann, Frank T; Cooper, Jonathan; Le Novère, Nicolas; Nickerson, David; Waltemath, Dagmar

2015-06-01

The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines. This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

DOE PAGES

Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.; ...

2015-04-16

Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family ofmore » molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.« less

Radiation Protection Methods for the Interventionalist’s Hands: Use of an Extension Tube

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

Dixon, Shaheen, E-mail: shaheen7noorani@gmail.com; Schick, Daniel, E-mail: Daniel.Schick@health.qld.gov.au; Harper, John, E-mail: John-Harper@health.qld.gov.au

2015-04-15

PurposeCumulative radiation exposure to the hands during certain interventional procedures may be high. It is important to decrease the amount of radiation to the operator due to the possibility of deterministic effects. We performed a pilot study to demonstrate a significant decrease in operator dose when using extension tubing (ET) in combination with shielding and collimation during a simulated percutaneous transhepatic cholangiogram (PTC) procedure.MethodsA whole body, anthropomorphic phantom was used to simulate the patient. A Unfors-Xi Survey detector (to measure scatter) supported by a retort stand and trolley was placed in various positions to simulate the position of hands andmore » eyes/thyroid of an interventionalist. Radiation dose was measured simulating left and right-sided PTC punctures with and without a lead shield, and with and without ET.ResultsRegarding the radiation dose to the hands; the use of an ET reduces dose by 54 % in right-sided PTC punctures without a shield and by 91 % if used in combination with a shield. For left-sided PTC punctures, ET reduces hand dose by 75 %. The use of collimation decreases hand dose by approximately 60 %. The use of shielding reduces dose to the eyes/thyroid by 98 %.ConclusionsThe dose to the hands can be significantly reduced with the appropriate use of a shield, ET, and tight collimation. The use of a shield is paramount to reduce dose to the eyes/thyroid. It is important for interventionalists to adhere to radiation protective practice considering the potential deterministic effects during a lifelong career.« less

Derivation of Cumulus Cloud Dimensions and Shape from the Airborne Measurements by the Research Scanning Polarimeter

NASA Technical Reports Server (NTRS)

Alexandrov, Mikhail D.; Cairns, Brian; Emde, Claudia; Ackerman, Andrew S.; Ottaviani, Matteo; Wasilewski, Andrzej P.

2016-01-01

The Research Scanning Polarimeter (RSP) is an airborne instrument, whose measurements have been extensively used for retrievals of microphysical properties of clouds. In this study we show that for cumulus clouds the information content of the RSP data can be extended by adding the macroscopic parameters of the cloud, such as its geometric shape, dimensions, and height above the ground. This extension is possible by virtue of the high angular resolution and high frequency of the RSP measurements, which allow for geometric constraint of the cloud's 2D cross section between a number of tangent lines of view. The retrieval method is tested on realistic 3D radiative transfer simulations and applied to actual RSP data.

Correlation of high energy muons with primary composition in extensive air shower

NASA Technical Reports Server (NTRS)

Chou, C.; Higashi, S.; Hiraoka, N.; Ozaki, S.; Sato, T.; Suwada, T.; Takahasi, T.; Umeda, H.

1985-01-01

An experimental investigation of high energy muons above 200 GeV in extensive air showers has been made for studying high energy interaction and primary composition of cosmic rays of energies in the range 10 to the 14th power approx. 10 to the 15th power eV. The muon energies are estimated from the burst sizes initiated by the muons in the rock, which are measured by four layers of proportional counters, each of area 5 x 2.6 sq m, placed at 30 m.w.e. deep, Funasaka tunnel vertically below the air shower array. These results are compared with Monte Carlo simulations based on the scaling model and the fireball model for two primary compositions, all proton and mixed.

An Extensible, Interchangeable and Sharable Database Model for Improving Multidisciplinary Aircraft Design

NASA Technical Reports Server (NTRS)

Lin, Risheng; Afjeh, Abdollah A.

2003-01-01

Crucial to an efficient aircraft simulation-based design is a robust data modeling methodology for both recording the information and providing data transfer readily and reliably. To meet this goal, data modeling issues involved in the aircraft multidisciplinary design are first analyzed in this study. Next, an XML-based. extensible data object model for multidisciplinary aircraft design is constructed and implemented. The implementation of the model through aircraft databinding allows the design applications to access and manipulate any disciplinary data with a lightweight and easy-to-use API. In addition, language independent representation of aircraft disciplinary data in the model fosters interoperability amongst heterogeneous systems thereby facilitating data sharing and exchange between various design tools and systems.

Impact of random discrete dopant in extension induced fluctuation in gate-source/drain underlap FinFET

NASA Astrophysics Data System (ADS)

Wang, Yijiao; Huang, Peng; Xin, Zheng; Zeng, Lang; Liu, Xiaoyan; Du, Gang; Kang, Jinfeng

2014-01-01

In this work, three dimensional technology computer-aided design (TCAD) simulations are performed to investigate the impact of random discrete dopant (RDD) including extension induced fluctuation in 14 nm silicon-on-insulator (SOI) gate-source/drain (G-S/D) underlap fin field effect transistor (FinFET). To fully understand the RDD impact in extension, RDD effect is evaluated in channel and extension separately and together. The statistical variability of FinFET performance parameters including threshold voltage (Vth), subthreshold slope (SS), drain induced barrier lowering (DIBL), drive current (Ion), and leakage current (Ioff) are analyzed. The results indicate that RDD in extension can lead to substantial variability, especially for SS, DIBL, and Ion and should be taken into account together with that in channel to get an accurate estimation on RDF. Meanwhile, higher doping concentration of extension region is suggested from the perspective of overall variability control.

Search for Spatially Extended Fermi-LAT Sources Using Two Years of Data

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

Lande, Joshua; Ackermann, Markus; Allafort, Alice

2012-07-13

Spatial extension is an important characteristic for correctly associating {gamma}-ray-emitting sources with their counterparts at other wavelengths and for obtaining an unbiased model of their spectra. We present a new method for quantifying the spatial extension of sources detected by the Large Area Telescope (LAT), the primary science instrument on the Fermi Gamma-ray Space Telescope (Fermi). We perform a series of Monte Carlo simulations to validate this tool and calculate the LAT threshold for detecting the spatial extension of sources. We then test all sources in the second Fermi -LAT catalog (2FGL) for extension. We report the detection of sevenmore » new spatially extended sources.« less

Feasibility of four-dimensional preoperative simulation for elbow debridement arthroplasty.

PubMed

Yamamoto, Michiro; Murakami, Yukimi; Iwatsuki, Katsuyuki; Kurimoto, Shigeru; Hirata, Hitoshi

2016-04-02

Recent advances in imaging modalities have enabled three-dimensional preoperative simulation. A four-dimensional preoperative simulation system would be useful for debridement arthroplasty of primary degenerative elbow osteoarthritis because it would be able to detect the impingement lesions. We developed a four-dimensional simulation system by adding the anatomical axis to the three-dimensional computed tomography scan data of the affected arm in one position. Eleven patients with primary degenerative elbow osteoarthritis were included. A "two rings" method was used to calculate the flexion-extension axis of the elbow by converting the surface of the trochlea and capitellum into two rings. A four-dimensional simulation movie was created and showed the optimal range of motion and the impingement area requiring excision. To evaluate the reliability of the flexion-extension axis, interobserver and intraobserver reliabilities regarding the assessment of bony overlap volumes were calculated twice for each patient by two authors. Patients were treated by open or arthroscopic debridement arthroplasties. Pre- and postoperative examinations included elbow range of motion measurement, and completion of the patient-rated questionnaire Hand20, Japanese Orthopaedic Association-Japan Elbow Society Elbow Function Score, and the Mayo Elbow Performance Score. Measurement of the bony overlap volume showed an intraobserver intraclass correlation coefficient of 0.93 and 0.90, and an interobserver intraclass correlation coefficient of 0.94. The mean elbow flexion-extension arc significantly improved from 101° to 125°. The mean Hand20 score significantly improved from 52 to 22. The mean Japanese Orthopaedic Association-Japan Elbow Society Elbow Function Score significantly improved from 67 to 88. The mean Mayo Elbow Performance Score significantly improved from 71 to 91 at the final follow-up evaluation. We showed that four-dimensional, preoperative simulation can be generated by adding the rotation axis to the one-position, three-dimensional computed tomography image of the affected arm. This method is feasible for elbow debridement arthroplasty.

Relative Contributions of the Midcarpal and Radiocarpal Joints to Dart-Thrower's Motion at the Wrist.

PubMed

Kane, Patrick M; Vopat, Bryan G; Mansuripur, P Kaveh; Gaspar, Michael P; Wolfe, Scott W; Crisco, Joseph J; Got, Christopher

2018-03-01

To identify the relative contributions of the radiocarpal (RC) and midcarpal (MC) joints to dart-thrower's motion (DTM) of the wrist. Six cadaveric upper extremities were fixed to a custom-designed loading jig allowing for pure moment-rotation analysis in 24 different directions of wrist motion. Each specimen was tested in 3 states: intact, simulated radiocarpal fusion (sRCF) and simulated pancarpal fusion (sPCF). Moments of ± 1.5 Nm were applied at each of 24 directions for each state and the resulting wrist rotation recorded. Data from each specimen were reduced to compute the range of motion (ROM) envelopes and the orientation of the ROM for the 3 different states. The ROM was significantly decreased in the sRCF and sPCF groups compared with the intact group in the directions of the pure extension, radial extension, ulnar flexion, and ulnar deviation. No significant difference in ROM was detected between the sRCF and sPCF groups in any direction. The ROM envelopes for the intact, sRCF, and sPCF groups were all oriented obliquely to the axis of pure wrist flexion-extension near a path of ulnar flexion-radial extension, consistent with prior reports on DTM. Although both simulated fusion types decreased ROM compared with the intact wrist, the principal direction of wrist motion along the path of DTM was not significantly altered by simulated RCF or PCF. These findings suggest that the RC and MC joints can each contribute to a similar mechanical axis of motion located along the path of DTM when the other joint has been eliminated via fusion. Surgical options such as partial wrist fusions may maintain the native wrist's mechanical axis if either the RC or the MC joint is preserved, despite significant reduction in overall ROM. Copyright © 2018 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

PubMed

Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe

2015-08-01

The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

State estimation of stochastic non-linear hybrid dynamic system using an interacting multiple model algorithm.

PubMed

Elenchezhiyan, M; Prakash, J

2015-09-01

In this work, state estimation schemes for non-linear hybrid dynamic systems subjected to stochastic state disturbances and random errors in measurements using interacting multiple-model (IMM) algorithms are formulated. In order to compute both discrete modes and continuous state estimates of a hybrid dynamic system either an IMM extended Kalman filter (IMM-EKF) or an IMM based derivative-free Kalman filters is proposed in this study. The efficacy of the proposed IMM based state estimation schemes is demonstrated by conducting Monte-Carlo simulation studies on the two-tank hybrid system and switched non-isothermal continuous stirred tank reactor system. Extensive simulation studies reveal that the proposed IMM based state estimation schemes are able to generate fairly accurate continuous state estimates and discrete modes. In the presence and absence of sensor bias, the simulation studies reveal that the proposed IMM unscented Kalman filter (IMM-UKF) based simultaneous state and parameter estimation scheme outperforms multiple-model UKF (MM-UKF) based simultaneous state and parameter estimation scheme. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

CFD Simulation On The Pressure Distribution For An Isolated Single-Story House With Extension: Grid Sensitivity Analysis

NASA Astrophysics Data System (ADS)

Yahya, W. N. W.; Zaini, S. S.; Ismail, M. A.; Majid, T. A.; Deraman, S. N. C.; Abdullah, J.

2018-04-01

Damage due to wind-related disasters is increasing due to global climate change. Many studies have been conducted to study the wind effect surrounding low-rise building using wind tunnel tests or numerical simulations. The use of numerical simulation is relatively cheap but requires very good command in handling the software, acquiring the correct input parameters and obtaining the optimum grid or mesh. However, before a study can be conducted, a grid sensitivity test must be conducted to get a suitable cell number for the final to ensure an accurate result with lesser computing time. This study demonstrates the numerical procedures for conducting a grid sensitivity analysis using five models with different grid schemes. The pressure coefficients (CP) were observed along the wall and roof profile and compared between the models. The results showed that medium grid scheme can be used and able to produce high accuracy results compared to finer grid scheme as the difference in terms of the CP values was found to be insignificant.

Quantitative risk management in gas injection project: a case study from Oman oil and gas industry

NASA Astrophysics Data System (ADS)

Khadem, Mohammad Miftaur Rahman Khan; Piya, Sujan; Shamsuzzoha, Ahm

2017-09-01

The purpose of this research was to study the recognition, application and quantification of the risks associated in managing projects. In this research, the management of risks in an oil and gas project is studied and implemented within a case company in Oman. In this study, at first, the qualitative data related to risks in the project were identified through field visits and extensive interviews. These data were then translated into numerical values based on the expert's opinion. Further, the numerical data were used as an input to Monte Carlo simulation. RiskyProject Professional™ software was used to simulate the system based on the identified risks. The simulation result predicted a delay of about 2 years as a worse case with no chance of meeting the project's on stream date. Also, it has predicted 8% chance of exceeding the total estimated budget. The result of numerical analysis from the proposed model is validated by comparing it with the result of qualitative analysis, which was obtained through discussion with various project managers of company.

Noise and Dissipation on Coadjoint Orbits

NASA Astrophysics Data System (ADS)

Arnaudon, Alexis; De Castro, Alex L.; Holm, Darryl D.

2018-02-01

We derive and study stochastic dissipative dynamics on coadjoint orbits by incorporating noise and dissipation into mechanical systems arising from the theory of reduction by symmetry, including a semidirect product extension. Random attractors are found for this general class of systems when the Lie algebra is semi-simple, provided the top Lyapunov exponent is positive. We study in details two canonical examples, the free rigid body and the heavy top, whose stochastic integrable reductions are found and numerical simulations of their random attractors are shown.

Study of Gaussian Doped Double Gate JunctionLess (GD-DG-JL) transistor including source drain depletion length: Model for sub-threshold behavior

NASA Astrophysics Data System (ADS)

Kumari, Vandana; Kumar, Ayush; Saxena, Manoj; Gupta, Mridula

2018-01-01

The sub-threshold model formulation of Gaussian Doped Double Gate JunctionLess (GD-DG-JL) FET including source/drain depletion length is reported in the present work under the assumption that the ungated regions are fully depleted. To provide deeper insight into the device performance, the impact of gaussian straggle, channel length, oxide and channel thickness and high-k gate dielectric has been studied using extensive TCAD device simulation.

Design and operational energy studies in a new high-rise office building. Volume 5. DOE-2: comparison with measured data

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

Not Available

1984-03-01

The purpose of the DOE-2 comparison study is to compare the energy consumption for the Park Plaza building predicted by the DOE-2.1 simulation with actual energy consumption measured by the data collection system at the building. The extensive and detailed output of the data collection system provides a basis for verifying the accuracy of DOE-2.1 at a component level over short intervals of time in each of the four seasons.

BOREAS Level-0 ER-2 Daedalus TMS Imagery Digital Counts in BIL Format

NASA Technical Reports Server (NTRS)

Newcomer, Jeffrey A.; Dominguez, Roseanne; Hall, Forrest G. (Editor)

2000-01-01

The level-0 Daedalus Thematic Mapper Simulator (TMS) imagery, along with the other remotely sensed images, was collected to provide spatially extensive information about radiant energy over the primary BOReal Ecosystem-Atmosphere Study (BOREAS) study areas. This information includes detailed land cover and biophysical parameter maps such as fraction of Photosynthetically Active Radiation (fPAR) and Leaf Area Index (LAI). Two flights of the Daedalus TMS instrument were made onboard the ER-2 aircraft on 16-Sep-1994 and 17-Sep-1994.

From scale-free to Erdos-Rényi networks.

PubMed

Gómez-Gardeñes, Jesús; Moreno, Yamir

2006-05-01

We analyze a model that interpolates between scale-free and Erdos-Rényi networks. The model introduced generates a one-parameter family of networks and allows one to analyze the role of structural heterogeneity. Analytical calculations are compared with extensive numerical simulations in order to describe the transition between these two important classes of networks. Finally, an application of the proposed model to the study of the percolation transition is presented.

Numerical Experiments Investigating the Source of Explosion S-Waves

DTIC Science & Technology

2007-09-01

simulations in this study are based on the well-recorded 1993 Nonproliferation experiment (NPE) ( chemical kiloton). A regional 3-dimensional model...1-kiloton chemical explosion at the NTS. NPE details and research reports can be found in Denny and Stull (1994). Figure 3 shows the extensive...T., D. Helmberger, and G. Engen (1985). Evidence for tectonic release from underground nuclear explosions in long period S waves, Bull. Seismol. Soc

Two-Dimensional Signal Processing and Storage and Theory and Applications of Electromagnetic Measurements.

DTIC Science & Technology

1983-06-01

system, provides a convenient, low- noise , fully parallel method of improving contrast and enhancing structural detail in an image prior to input to a...directed towards problems in deconvolution, reconstruction from projections, bandlimited extrapolation, and shift varying deblurring of images...deconvolution algorithm has been studied with promising 5 results [I] for simulated motion blurs. Future work will focus on noise effects and the extension

Urban water-quality modelling: implementing an extension to Multi-Hydro platform for real case studies

NASA Astrophysics Data System (ADS)

Hong, Yi; Giangola-Murzyn, Agathe; Bonhomme, Celine; Chebbo, Ghassan; Schertzer, Daniel

2015-04-01

During the last few years, the physically based and fully distributed numerical platform Multi-Hydro (MH) has been developed to simulate hydrological behaviours in urban/peri-urban areas (El-Tabach et al. , 2009 ; Gires et al., 2013 ; Giangola-Murzyn et al., 2014). This hydro-dynamical platform is open-access and has a modular structure, which is designed to be easily scalable and transportable, in order to simulate the dynamics and complex interactions of the water cycle processes in urban or peri-urban environment (surface hydrology, urban groundwater infrastructures and infiltration). Each hydrological module relies on existing and widely validated open source models, such as TREX model (Velleux, 2005) for the surface module, SWMM model (Rossman, 2010) for the drainage module and VS2DT model (Lappala et al., 1987) for the soil module. In our recent studies, an extension of MH has been set up by connecting the already available water-quality computational components among different modules, to introduce a pollutant transport modelling into the hydro-dynamical platform. As for the surface module in two-dimensions, the concentration of particles in flow is expressed by sediment advection equation, the settling of suspended particles is calculated with a simplified settling velocity formula, while the pollutant wash-off from a given land-use is represented as a mass rate of particle removal from the bottom boundary over time, based on transport capacity, which is computed by a modified form of Universal Soil Loss Equation (USLE). Considering that the USLE is originally conceived to predict soil losses caused by runoff in agriculture areas, several adaptations were needed to use it for urban areas, such as the alterations of USLE parameters according to different criterions, the definition of the appropriate initial dust thickness corresponding to various land-uses, etc. Concerning the drainage module, water quality routing within pipes assumes that the conduit behaves as a continuously stirred tank reactor. This extension of Multi-Hydro was tested on two peri-urban catchments located near Paris, the Villecresnes (France, 0.7 km²) and the Le Perreux-sur-Marne (France, 0.2 km²). As the Villecresnes had been analyzed within several European projects (FP7 SMARTeST, KIC-Climate BlueGreenDream, Interreg RainGain), the robustness of the new extension of MH was firstly tested on this basin by comparing the water quantity simulation outcomes with the results already obtained in previous works. Benefiting from the large datasets that are collected in the framework of the ANR (French National Agency for Research) Trafipollu project, the water quality modelling performance of the extension was then illustrated on the catchment of Le Perreux-sur-Marne.

LANDSAT-D investigations in snow hydrology

NASA Technical Reports Server (NTRS)

Dozier, J. (Principal Investigator)

1982-01-01

The sample LANDSAT-4 TM tape (7 bands) of NE Arkansas/Tennessee area was received and displayed. Snow reflectance in all 6 TM reflective bands, i.e. 1, 2, 3, 4, 5, and 7 was simulated, using Wiscombe and Warren's (1980) delta-Eddington model. Snow reflectance in bands 4, 5, and 7 appear sensitive to grain size. One of the objectives is to interpret surface optical grain size of snow, for spectral extension of albedo. While TM data of the study area are not received, simulation results are encouraging. It also appears that the TM filters resemble a "square-wave" closely enough to permit assuming a square-wave in calculations. Integrated band reflectance over the actual response functions was simulated, using sensor data supplied by Santa Barbara Research Center. Differences between integrating over the actual response functions and the equivalent square wave were negligible.

Membrane Fusion Involved in Neurotransmission: Glimpse from Electron Microscope and Molecular Simulation

PubMed Central

Yang, Zhiwei; Gou, Lu; Chen, Shuyu; Li, Na; Zhang, Shengli; Zhang, Lei

2017-01-01

Membrane fusion is one of the most fundamental physiological processes in eukaryotes for triggering the fusion of lipid and content, as well as the neurotransmission. However, the architecture features of neurotransmitter release machinery and interdependent mechanism of synaptic membrane fusion have not been extensively studied. This review article expounds the neuronal membrane fusion processes, discusses the fundamental steps in all fusion reactions (membrane aggregation, membrane association, lipid rearrangement and lipid and content mixing) and the probable mechanism coupling to the delivery of neurotransmitters. Subsequently, this work summarizes the research on the fusion process in synaptic transmission, using electron microscopy (EM) and molecular simulation approaches. Finally, we propose the future outlook for more exciting applications of membrane fusion involved in synaptic transmission, with the aid of stochastic optical reconstruction microscopy (STORM), cryo-EM (cryo-EM), and molecular simulations. PMID:28638320

Computer simulations of space-borne meteorological systems on the CYBER 205

NASA Technical Reports Server (NTRS)

Halem, M.

1984-01-01

Because of the extreme expense involved in developing and flight testing meteorological instruments, an extensive series of numerical modeling experiments to simulate the performance of meteorological observing systems were performed on CYBER 205. The studies compare the relative importance of different global measurements of individual and composite systems of the meteorological variables needed to determine the state of the atmosphere. The assessments are made in terms of the systems ability to improve 12 hour global forecasts. Each experiment involves the daily assimilation of simulated data that is obtained from a data set called nature. This data is obtained from two sources: first, a long two-month general circulation integration with the GLAS 4th Order Forecast Model and second, global analysis prepared by the National Meteorological Center, NOAA, from the current observing systems twice daily.

Measuring technical and mathematical investigation of multiple reignitions at the switching of a motor using vacuum circuit breakers

NASA Astrophysics Data System (ADS)

Luxa, Andreas

The necessary conditions in switching system and vacuum circuit breaker for the occurrence of multiple re-ignitions and accompanying effects were examined. The shape of the occurring voltages was determined in relationship to other types of overvoltage. A phenomenological model of the arc, based on an extension of the Mayr equation for arcs was used with the simulation program NETOMAC for the switching transients. Factors which affect the arc parameters were analyzed. The results were statistically verified by 3000 three-phase switching tests on 3 standard vacuum circuit breakers under realistic systems conditions; the occurring overvoltage level was measured. Dimensioning criteria for motor simulation circuits in power plants were formulated on the basis of a theoretical equivalence analysis and experimental studies. The simulation model allows a sufficiently correct estimation of all effects.

A large eddy lattice Boltzmann simulation of magnetohydrodynamic turbulence

NASA Astrophysics Data System (ADS)

Flint, Christopher; Vahala, George

2018-02-01

Large eddy simulations (LES) of a lattice Boltzmann magnetohydrodynamic (LB-MHD) model are performed for the unstable magnetized Kelvin-Helmholtz jet instability. This algorithm is an extension of Ansumali et al. [1] to MHD in which one performs first an expansion in the filter width on the kinetic equations followed by the usual low Knudsen number expansion. These two perturbation operations do not commute. Closure is achieved by invoking the physical constraint that subgrid effects occur at transport time scales. The simulations are in very good agreement with direct numerical simulations.

The ν process in the innermost supernova ejecta

NASA Astrophysics Data System (ADS)

Sieverding, Andre; Martínez Pinedo, Gabriel; Langanke, Karlheinz; Harris, J. Austin; Hix, W. Raphael

2018-01-01

The neutrino-induced nucleosynthesis (ν process) in supernova explosions of massive stars of solar metallicity with initial main sequence masses between 13 and 30 M⊙ has been studied with an analytic explosion model using a new extensive set of neutrino-nucleus cross-sections and spectral properties that agree with modern supernova simulations. The production factors for the nuclei 7Li, 11B, 19F, 138La and 180Ta, are still significantly enhanced but do not reproduce the full solar abundances. We study the possible contribution of the innermost supernova eject to the production of the light elements 7Li and 11B with tracer particles based on a 2D supernova simulation of a 12 M⊙ progenitor and conclude, that a contribution exists but is negligible for the total yield for this explosion model.

A novel computational method to simulate non-enzymatic self-replication. [Abstract only

NASA Technical Reports Server (NTRS)

Navarro-Gonzalez, Rafael; Reggia, James A.; Wu, Jayoung; Chou, Hui-Hsien

1994-01-01

Non-enzymatic, template-directed synthesis of oligonucleotides has been extensively studied in the laboratory as a model to understand the kind of chemical processes that might have contributed to the origin of life on Earth. Several oligonucleotides have been shown to catalyze the synthesis of their complements from activated mononucleotides; however, a restricted number of them have been found to self-replicate. Recently we developed an efficient modified cellular automata method that supports the study of self-replicating oligonucleotides. With this method the oligonucleotide molecules are represented as active cells imbedded in a two-dimensional array of inactive cells symbolizing the environment. Random movements and probability-governed chemical reactions occurring in a cellular space can effectively simulate the experimental behavior observed in self-directed replication of oligonucleotides.

Influence of circumferential notch and fatigue crack on the mechanical integrity of biodegradable magnesium-based alloy in simulated body fluid.

PubMed

Bobby Kannan, M; Singh Raman, R K; Witte, F; Blawert, C; Dietzel, W

2011-02-01

Applications of magnesium alloys as biodegradable orthopaedic implants are critically dependent on the mechanical integrity of the implant during service. In this study, the mechanical integrity of an AZ91 magnesium alloy was studied using a constant extension rate tensile (CERT) method. The samples in two different geometries that is, circumferentially notched (CN), and circumferentially notched and fatigue cracked (CNFC), were tested in air and in simulated body fluid (SBF). The test results show that the mechanical integrity of the AZ91 magnesium alloy decreased substantially (∼50%) in both the CN and CNFC samples exposed to SBF. Fracture surface analysis revealed secondary cracks suggesting stress corrosion cracking susceptibility of the alloy in SBF. Copyright © 2010 Wiley Periodicals, Inc.

CFD analysis of onshore oil pipelines in permafrost

NASA Astrophysics Data System (ADS)

Nardecchia, Fabio; Gugliermetti, Luca; Gugliermetti, Franco

2017-07-01

Underground pipelines are built all over the world and the knowledge of their thermal interaction with the soil is crucial for their design. This paper studies the "thermal influenced zone" produced by a buried pipeline and the parameters that can influence its extension by 2D-steady state CFD simulations with the aim to improve the design of new pipelines in permafrost. In order to represent a real case, the study is referred to the Eastern Siberia-Pacific Ocean Oil Pipeline at the three stations of Mo'he, Jiagedaqi and Qiqi'har. Different burial depth sand diameters of the pipe are analyzed; the simulation results show that the effect of the oil pipeline diameter on the thermal field increases with the increase of the distance from the starting station.

Effects of Network Characteristics on Reaching the Payoff-Dominant Equilibrium in Coordination Games: A Simulation study.

PubMed

Buskens, Vincent; Snijders, Chris

2016-01-01

We study how payoffs and network structure affect reaching the payoff-dominant equilibrium in a [Formula: see text] coordination game that actors play with their neighbors in a network. Using an extensive simulation analysis of over 100,000 networks with 2-25 actors, we show that the importance of network characteristics is restricted to a limited part of the payoff space. In this part, we conclude that the payoff-dominant equilibrium is chosen more often if network density is larger, the network is more centralized, and segmentation of the network is smaller. Moreover, it is more likely that heterogeneity in behavior persists if the network is more segmented and less centralized. Persistence of heterogeneous behavior is not related to network density.

An important role of the moisture supply from the Kuroshio Current/Kuroshio Extension in the rapid development of an explosive cyclone

NASA Astrophysics Data System (ADS)

Hirata, H.; Kawamura, R.; Kato, M.; Shinoda, T.

2014-12-01

We investigated how the moisture supply from the Kuroshio Current/Kuroshio Extension affects the rapid intensification of an explosive cyclone using a couple atmosphere-ocean non-hydrostatic model, CReSS-NHOES. The Cloud-Resolving Storm Simulator (CReSS) and the Non-Hydrostatic Ocean model for the Earth Simulator (NHOES) have been developed by the Hydrospheric Atmospheric Research Center of Nagoya University and the Japan Agency for Marine-Earth Science and Technology, respectively. We performed a numerical simulation of an extratropical cyclone migrating along the southern periphery of the Kuroshio Current on January 14, 2013, that developed most rapidly in recent years in the vicinity of Japan. The evolutions of surface fronts related to the cyclone simulated by the CReSS-NHOES closely resemble Shapiro-Keyser model. In the lower troposphere, the cyclone's bent-back front and the associated frontal T-bone structure become evident with the cyclone development. Cold Conveyor Belt (CCB) is also well organized over the northern part of the cyclone. During its developing stage, since the CCB dominates just over the Kuroshio Current/Kuroshio Extension, a large amount of moisture is efficiently supplied from the warm current into the CCB. The vapor evaporated from the underlying warm current is transported into the bent-back front by the CCB and converges horizontally in the vicinity of the front. As a result, strong diabatic heating arises over the corresponding moisture convergence area in that vicinity, indicating that the abundant moisture due to the warm current plays a vital role in rapid development of the cyclone through latent heat release processes. Both processes of the moisture transport from the warm current into the cyclone system via the CCB and of the latent heat release around the bent-back front are also confirmed by trajectory analyses. The rapid SLP decrease of the cyclone center can in turn increase the moisture supply from the warm current through enhancement of the CCB. We anticipate that such a feedback process plays a key role in the rapid intensification of the cyclone highlighted in this study.

A penalized framework for distributed lag non-linear models.

PubMed

Gasparrini, Antonio; Scheipl, Fabian; Armstrong, Ben; Kenward, Michael G

2017-09-01

Distributed lag non-linear models (DLNMs) are a modelling tool for describing potentially non-linear and delayed dependencies. Here, we illustrate an extension of the DLNM framework through the use of penalized splines within generalized additive models (GAM). This extension offers built-in model selection procedures and the possibility of accommodating assumptions on the shape of the lag structure through specific penalties. In addition, this framework includes, as special cases, simpler models previously proposed for linear relationships (DLMs). Alternative versions of penalized DLNMs are compared with each other and with the standard unpenalized version in a simulation study. Results show that this penalized extension to the DLNM class provides greater flexibility and improved inferential properties. The framework exploits recent theoretical developments of GAMs and is implemented using efficient routines within freely available software. Real-data applications are illustrated through two reproducible examples in time series and survival analysis. © 2017 The Authors Biometrics published by Wiley Periodicals, Inc. on behalf of International Biometric Society.

Ascent Guidance for a Winged Boost Vehicle. M.S. Thesis

NASA Technical Reports Server (NTRS)

Corvin, Michael Alexander

1988-01-01

The objective of the advanced ascent guidance study was to investigate guidance concepts which could contribute to increased autonomy during ascent operations in a winged boost vehicle such as the proposed Shuttle II. The guidance scheme was required to yield near a full-optimal ascent in the presence of vehicle system and environmental dispersions. The study included consideration of trajectory shaping issues, trajectory design, closed loop and predictive adaptive guidance techniques and control of dynamic pressure by throttling. An extensive ascent vehicle simulation capability was developed for use in the study.

Toward a Principled Sampling Theory for Quasi-Orders

PubMed Central

Ünlü, Ali; Schrepp, Martin

2016-01-01

Quasi-orders, that is, reflexive and transitive binary relations, have numerous applications. In educational theories, the dependencies of mastery among the problems of a test can be modeled by quasi-orders. Methods such as item tree or Boolean analysis that mine for quasi-orders in empirical data are sensitive to the underlying quasi-order structure. These data mining techniques have to be compared based on extensive simulation studies, with unbiased samples of randomly generated quasi-orders at their basis. In this paper, we develop techniques that can provide the required quasi-order samples. We introduce a discrete doubly inductive procedure for incrementally constructing the set of all quasi-orders on a finite item set. A randomization of this deterministic procedure allows us to generate representative samples of random quasi-orders. With an outer level inductive algorithm, we consider the uniform random extensions of the trace quasi-orders to higher dimension. This is combined with an inner level inductive algorithm to correct the extensions that violate the transitivity property. The inner level correction step entails sampling biases. We propose three algorithms for bias correction and investigate them in simulation. It is evident that, on even up to 50 items, the new algorithms create close to representative quasi-order samples within acceptable computing time. Hence, the principled approach is a significant improvement to existing methods that are used to draw quasi-orders uniformly at random but cannot cope with reasonably large item sets. PMID:27965601

Toward a Principled Sampling Theory for Quasi-Orders.

PubMed

Ünlü, Ali; Schrepp, Martin

2016-01-01

Quasi-orders, that is, reflexive and transitive binary relations, have numerous applications. In educational theories, the dependencies of mastery among the problems of a test can be modeled by quasi-orders. Methods such as item tree or Boolean analysis that mine for quasi-orders in empirical data are sensitive to the underlying quasi-order structure. These data mining techniques have to be compared based on extensive simulation studies, with unbiased samples of randomly generated quasi-orders at their basis. In this paper, we develop techniques that can provide the required quasi-order samples. We introduce a discrete doubly inductive procedure for incrementally constructing the set of all quasi-orders on a finite item set. A randomization of this deterministic procedure allows us to generate representative samples of random quasi-orders. With an outer level inductive algorithm, we consider the uniform random extensions of the trace quasi-orders to higher dimension. This is combined with an inner level inductive algorithm to correct the extensions that violate the transitivity property. The inner level correction step entails sampling biases. We propose three algorithms for bias correction and investigate them in simulation. It is evident that, on even up to 50 items, the new algorithms create close to representative quasi-order samples within acceptable computing time. Hence, the principled approach is a significant improvement to existing methods that are used to draw quasi-orders uniformly at random but cannot cope with reasonably large item sets.

Granuloma Inguinale Simulating Squamous Cell Carcinoma.

PubMed

Mani, M Z; Singh, Trilochan; Mathew, Mary

1981-01-01

A case of extensive granuloma inguinale simulating squamous cell carcinoma is described. There was past history of urethritis leading to a urethral fistula. The ulcer healed almost completely within 19 days of receiving streptomycin injections. The patient had associated scabies and presumably also had latent syphillis (His VDRL was reactive in 1:8 dilution). The patient belonged to Madhya Pradesh.

Using FIA data in the Forest Vegetation Simulator

Treesearch

John D. Shaw

2009-01-01

The Forest Vegetation Simulator (FVS) is a national system of forest growth models maintained by the USDA Forest Service. It is the official tool for stand growth projection on National Forest lands, but it is also used widely on other ownerships. Model extensions and post-processors permit FVS users to perform a broad range of functions, including silvicultural...

Evaluation of aqua crop simulation of early season evaporation and water flux in a semiarid environment

USDA-ARS?s Scientific Manuscript database

The AquaCrop model of crop growth, water use, yield and water use efficiency (WUE) is intended for use by extension personnel, farm and irrigation managers, planners and other less advanced users of simulation models in irrigation planning and scheduling. It could be useful in estimating changes in ...

Modeling winter wheat phenological responses to water deficits in the Unified Plant Growth Model (UPGM) component of the spatially distributed Agricultural Ecosystem Services (AgES) model

USDA-ARS?s Scientific Manuscript database

Accurately predicting phenology in crop simulation models is critical for correctly simulating crop production. While extensive work in modeling phenology has focused on the temperature response function (resulting in robust phenology models), limited work on quantifying the phenological responses t...

Evaluation of forest management systems under risk of wildfire

Treesearch

Kari Hyytiainen; Robert G. Haight

2010-01-01

We evaluate the economic efficiency of even- and uneven-aged management systems under risk of wildfire. The management problems are formulated for a mixed-conifer stand and approximations of the optimal solutions are obtained using simulation optimization. The Northern Idaho variant of the Forest Vegetation Simulator and its Fire and Fuels Extension is used to predict...

Simulating ungulate herbivory across forest landscapes: A browsing extension for LANDIS-II

Treesearch

Nathan R. De Jager; Patrick J. Drohan; Brian M. Miranda; Brian R. Sturtevant; Susan L. Stout; Alejandro A. Royo; Eric J. Gustafson; Mark C. Romanski

2017-01-01

Browsing ungulates alter forest productivity and vegetation succession through selective foraging onspecies that often dominate early succession. However, the long-term and large-scale effects of browsing on forest succession are not possible to project without the use of simulation models. To explore the effects of ungulates on succession in a spatially explicit...

Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site

PubMed Central

Stafford, Kate A.; Palmer III, Arthur G.

2014-01-01

Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially of the E. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. In this work, we describe molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states. Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion. Notably, representatives of bacterial, eukaryotic, and retroviral RNases H all exhibit similar active-site rigidity, suggesting that this dynamic feature is only subtly modulated by amino acid sequence and is primarily imposed by the distinctive RNase H protein fold. PMID:25075292

A parametric study of surface roughness and bonding mechanisms of aluminum alloys with epoxies: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Timilsina, Rajendra; Termaath, Stephanie

The marine environment is highly aggressive towards most materials. However, aluminium-magnesium alloys (Al-Mg, specifically, 5xxx series) have exceptionally long service life in such aggressive marine environments. For instance, an Al-Mg alloy, AA5083, is extensively used in naval structures because of its good mechanical strength, formability, seawater corrosion resistance and weldability. However, bonding mechanisms of these alloys with epoxies in a rough surface environment are not fully understood yet. It requires a rigorous investigation at molecular or atomic levels. We performed a molecular dynamics simulation to study an adherend surface preparation and surface bonding mechanisms of Al-Mg alloy (AA5083) with different epoxies by developing several computer models. Various distributions of surface roughness are introduced in the models and performed molecular dynamics simulations. Formation of a beta phase (Al3Mg2) , microstructures, bonding energies at the interface, bonding strengths and durability are investigated. Office of Naval Research.

Data representation for joint kinematics simulation of the lower limb within an educational context.

PubMed

Van Sint Jan, Serge; Hilal, Isam; Salvia, Patrick; Sholukha, Victor; Poulet, Pascal; Kirokoya, Ibrahim; Rooze, Marcel

2003-04-01

Three-dimensional (3D) visualization is becoming increasingly frequent in both qualitative and quantitative biomechanical studies of anatomical structures involving multiple data sources (e.g. morphological data and kinematics data). For many years, this kind of experiment was limited to the use of bi-dimensional images due to a lack of accurate 3D data. However, recent progress in medical imaging and computer graphics has forged new perspectives. Indeed, new techniques allow the development of an interactive interface for the simulation of human motions combining data from both medical imaging (i.e., morphology) and biomechanical studies (i.e., kinematics). Fields of application include medical education, biomechanical research and clinical research. This paper presents an experimental protocol for the development of anatomically realistic joint simulation within a pedagogical context. Results are shown for the lower limb. Extension to other joints is straightforward. This work is part of the Virtual Animation of the Kinematics of the Human project (VAKHUM) (http://www.ulb.ac.be/project/vakhum).

Conformational Heterogeneity of the HIV Envelope Glycan Shield.

PubMed

Yang, Mingjun; Huang, Jing; Simon, Raphael; Wang, Lai-Xi; MacKerell, Alexander D

2017-06-30

To better understand the conformational properties of the glycan shield covering the surface of the HIV gp120/gp41 envelope (Env) trimer, and how the glycan shield impacts the accessibility of the underlying protein surface, we performed enhanced sampling molecular dynamics (MD) simulations of a model glycosylated HIV Env protein and related systems. Our simulation studies revealed a conformationally heterogeneous glycan shield with a network of glycan-glycan interactions more extensive than those observed to date. We found that partial preorganization of the glycans potentially favors binding by established broadly neutralizing antibodies; omission of several specific glycans could increase the accessibility of other glycans or regions of the protein surface to antibody or CD4 receptor binding; the number of glycans that can potentially interact with known antibodies is larger than that observed in experimental studies; and specific glycan conformations can maximize or minimize interactions with individual antibodies. More broadly, the enhanced sampling MD simulations described here provide a valuable tool to guide the engineering of specific Env glycoforms for HIV vaccine design.

Comparative Environmental Performance of Two-Diesel-Fuel Oxygenates: Dibutyl Maleate (DBM) and Triproplyene Glycol Monomethyl Ether (TGME)

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

Layton, D.W.; Marchetti, A.A.

2001-10-01

Many studies have shown that the addition of oxygen bearing compounds to diesel fuel can significantly reduce particulate emissions. To assist in the evaluation of the environmental performance of diesel-fuel oxygenates, we have implemented a suite of diagnostic models for simulating the transport of compounds released to air, water, and soils/groundwater as well as regional landscapes. As a means of studying the comparative performance of DBM and TGME, we conducted a series of simulations for selected environmental media. Benzene and methyl tertiary butyl ether (MTBE) were also addressed because they represent benchmark fuel-related compounds that have been the subject ofmore » extensive environmental measurements and modeling. The simulations showed that DBM and TGME are less mobile in soil because of reduced vapor-phase transport and increased retention on soil particles. The key distinction between these two oxygenates is that DBM is predicted to have a greater potential than TGME for aerobic biodegradation, based on chemical structure.« less

Extension of four-dimensional atmospheric models. [and cloud cover data bank

NASA Technical Reports Server (NTRS)

Fowler, M. G.; Lisa, A. S.; Tung, S. L.

1975-01-01

The cloud data bank, the 4-D atmospheric model, and a set of computer programs designed to simulate meteorological conditions for any location above the earth are described in turns of space vehicle design and simulation of vehicle reentry trajectories. Topics discussed include: the relationship between satellite and surface observed cloud cover using LANDSAT 1 photographs and including the effects of cloud shadows; extension of the 4-D model to the altitude of 52 km; and addition of the u and v wind components to the 4-D model of means and variances at 1 km levels from the surface to 25 km. Results of the cloud cover analysis are presented along with the stratospheric model and the tropospheric wind profiles.

Extension of a hybrid particle-continuum method for a mixture of chemical species

NASA Astrophysics Data System (ADS)

Verhoff, Ashley M.; Boyd, Iain D.

2012-11-01

Due to the physical accuracy and numerical efficiency achieved by analyzing transitional, hypersonic flow fields with hybrid particle-continuum methods, this paper describes a Modular Particle-Continuum (MPC) method and its extension to include multiple chemical species. Considerations that are specific to a hybrid approach for simulating gas mixtures are addressed, including a discussion of the Chapman-Enskog velocity distribution function (VDF) for near-equilibrium flows, and consistent viscosity models for the individual CFD and DSMC modules of the MPC method. Representative results for a hypersonic blunt-body flow are then presented, where the flow field properties, surface properties, and computational performance are compared for simulations employing full CFD, full DSMC, and the MPC method.

GPU accelerated Discrete Element Method (DEM) molecular dynamics for conservative, faceted particle simulations

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

Spellings, Matthew; Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109; Marson, Ryan L.

Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks–Chandler–Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method ismore » a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.« less

Intercomparison of terrestrial carbon fluxes and carbon use efficiency simulated by CMIP5 Earth System Models

NASA Astrophysics Data System (ADS)

Kim, Dongmin; Lee, Myong-In; Jeong, Su-Jong; Im, Jungho; Cha, Dong Hyun; Lee, Sanggyun

2017-12-01

This study compares historical simulations of the terrestrial carbon cycle produced by 10 Earth System Models (ESMs) that participated in the fifth phase of the Coupled Model Intercomparison Project (CMIP5). Using MODIS satellite estimates, this study validates the simulation of gross primary production (GPP), net primary production (NPP), and carbon use efficiency (CUE), which depend on plant function types (PFTs). The models show noticeable deficiencies compared to the MODIS data in the simulation of the spatial patterns of GPP and NPP and large differences among the simulations, although the multi-model ensemble (MME) mean provides a realistic global mean value and spatial distributions. The larger model spreads in GPP and NPP compared to those of surface temperature and precipitation suggest that the differences among simulations in terms of the terrestrial carbon cycle are largely due to uncertainties in the parameterization of terrestrial carbon fluxes by vegetation. The models also exhibit large spatial differences in their simulated CUE values and at locations where the dominant PFT changes, primarily due to differences in the parameterizations. While the MME-simulated CUE values show a strong dependence on surface temperatures, the observed CUE values from MODIS show greater complexity, as well as non-linear sensitivity. This leads to the overall underestimation of CUE using most of the PFTs incorporated into current ESMs. The results of this comparison suggest that more careful and extensive validation is needed to improve the terrestrial carbon cycle in terms of ecosystem-level processes.

Richtmyer-Meshkov flow in elastic solids.

PubMed

Piriz, A R; López Cela, J J; Tahir, N A; Hoffmann, D H H

2006-09-01

Richtmyer-Meshkov flow is studied by means of an analytical model which describes the asymptotic oscillations of a corrugated interface between two perfectly elastic solids after the interaction with a shock wave. The model shows that the flow stability is due to the restoring effect of the elastic force. It provides a simple approximate but still very accurate formula for the oscillation period. It also shows that as it is observed in numerical simulations, the amplitude oscillates around a mean value equal to the post-shock amplitude, and that this is a consequence of the stress free conditions of the material immediately after the shock interaction. Extensive numerical simulations are presented to validate the model results.

Characterizing the Hazard of a Wake Vortex Encounter

NASA Technical Reports Server (NTRS)

Vicroy, Dan D.; Brandon, Jay; Greene, George; Rivers, Robert; Shah, Gautam; Stewart, Eric; Stuever, Robert

1998-01-01

The National Aeronautics and Space Administration (NASA) is conducting research with the goal of enabling safe improvements in the capacity of the nation's air transportation system. The wake vortex upset hazard is an important factor in establishing the minimum safe spacing between aircraft during landing and take-off operations, thus impacting airport capacity. Static and free-flight wind tunnel tests and flight tests have provided an extensive data set for improved understanding of vortex encounter dynamics and simulation. Piloted and batch simulation studies are also ongoing to establish a first-order hazard metric and determine the limits of an operationally acceptable wake induced upset. This paper outlines NASA's research in these areas.

Continuous metabolic and cardiovascular measurements on a monkey subject during a simulated 6-day Spacelab mission

NASA Technical Reports Server (NTRS)

Pace, N.; Rahlmann, D. F.; Mains, R. C.; Kodama, A. M.; Mccutcheon, E. P.

1978-01-01

An adult male pig-tailed monkey (Macaca nemestrina) with surgically implanted biotelemetry unit was inserted into a fiberglass pod system which was installed in a Spacelab mock-up to simulate a 6-day mission during which extensive physiological measurements were obtained. The purpose of the pod was to make possible the study of respiratory gas exchange. Body temperature and selected cardiovascular parameters were recorded continuously for 2.6 days prior to 'launch', 6.3 days during 'flight', and 1.8 days after 'landing'. The results are surveyed, and it is concluded that it is feasible to perform sound physiological experiments on nonhuman primates in the Spacelab environment

Advanced power analysis methodology targeted to the optimization of a digital pixel readout chip design and its critical serial powering system

NASA Astrophysics Data System (ADS)

Marconi, S.; Orfanelli, S.; Karagounis, M.; Hemperek, T.; Christiansen, J.; Placidi, P.

2017-02-01

A dedicated power analysis methodology, based on modern digital design tools and integrated with the VEPIX53 simulation framework developed within RD53 collaboration, is being used to guide vital choices for the design and optimization of the next generation ATLAS and CMS pixel chips and their critical serial powering circuit (shunt-LDO). Power consumption is studied at different stages of the design flow under different operating conditions. Significant effort is put into extensive investigations of dynamic power variations in relation with the decoupling seen by the powering network. Shunt-LDO simulations are also reported to prove the reliability at the system level.

Simulations and observations of cloudtop processes

NASA Technical Reports Server (NTRS)

Siems, S. T.; Bretherton, C. S.; Baker, M. B.

1990-01-01

Turbulent entrainment at zero mean shear stratified interfaces has been studied extensively in the laboratory and theoretically for the classical situation in which density is a passive tracer of the mixing and the turbulent motions producing the entrainment are directed toward the interface. It is the purpose of the numerical simulations and data analysis to investigate these processes and, specifically, to focus on the following questions: (1) Can local cooling below cloudtop play an important role in setting up convective circulations within the cloud, and bringing about entrainment; (2) Can Cloudtop Entrainment Instability (CEI) alone lead to runaway entrainment under geophysically realistic conditions; and (3) What are the important mechanisms of entrainment at cloudtop under zero or low mean shear conditions.

Numerical aerodynamic simulation facility. Preliminary study extension

NASA Technical Reports Server (NTRS)

1978-01-01

The production of an optimized design of key elements of the candidate facility was the primary objective of this report. This was accomplished by effort in the following tasks: (1) to further develop, optimize and describe the function description of the custom hardware; (2) to delineate trade off areas between performance, reliability, availability, serviceability, and programmability; (3) to develop metrics and models for validation of the candidate systems performance; (4) to conduct a functional simulation of the system design; (5) to perform a reliability analysis of the system design; and (6) to develop the software specifications to include a user level high level programming language, a correspondence between the programming language and instruction set and outline the operation system requirements.

Integrative Analysis of Cancer Diagnosis Studies with Composite Penalization

PubMed Central

Liu, Jin; Huang, Jian; Ma, Shuangge

2013-01-01

Summary In cancer diagnosis studies, high-throughput gene profiling has been extensively conducted, searching for genes whose expressions may serve as markers. Data generated from such studies have the “large d, small n” feature, with the number of genes profiled much larger than the sample size. Penalization has been extensively adopted for simultaneous estimation and marker selection. Because of small sample sizes, markers identified from the analysis of single datasets can be unsatisfactory. A cost-effective remedy is to conduct integrative analysis of multiple heterogeneous datasets. In this article, we investigate composite penalization methods for estimation and marker selection in integrative analysis. The proposed methods use the minimax concave penalty (MCP) as the outer penalty. Under the homogeneity model, the ridge penalty is adopted as the inner penalty. Under the heterogeneity model, the Lasso penalty and MCP are adopted as the inner penalty. Effective computational algorithms based on coordinate descent are developed. Numerical studies, including simulation and analysis of practical cancer datasets, show satisfactory performance of the proposed methods. PMID:24578589

XNsim: Internet-Enabled Collaborative Distributed Simulation via an Extensible Network

NASA Technical Reports Server (NTRS)

Novotny, John; Karpov, Igor; Zhang, Chendi; Bedrossian, Nazareth S.

2007-01-01

In this paper, the XNsim approach to achieve Internet-enabled, dynamically scalable collaborative distributed simulation capabilities is presented. With this approach, a complete simulation can be assembled from shared component subsystems written in different formats, that run on different computing platforms, with different sampling rates, in different geographic locations, and over singlelmultiple networks. The subsystems interact securely with each other via the Internet. Furthermore, the simulation topology can be dynamically modified. The distributed simulation uses a combination of hub-and-spoke and peer-topeer network topology. A proof-of-concept demonstrator is also presented. The XNsim demonstrator can be accessed at http://www.jsc.draver.corn/xn that hosts various examples of Internet enabled simulations.

Adaptive Control of a Utility-Scale Wind Turbine Operating in Region 3

NASA Technical Reports Server (NTRS)

Frost, Susan A.; Balas, Mark J.; Wright, Alan D.

2009-01-01

Adaptive control techniques are well suited to nonlinear applications, such as wind turbines, which are difficult to accurately model and which have effects from poorly known operating environments. The turbulent and unpredictable conditions in which wind turbines operate create many challenges for their operation. In this paper, we design an adaptive collective pitch controller for a high-fidelity simulation of a utility scale, variable-speed horizontal axis wind turbine. The objective of the adaptive pitch controller in Region 3 is to regulate generator speed and reject step disturbances. The control objective is accomplished by collectively pitching the turbine blades. We use an extension of the Direct Model Reference Adaptive Control (DMRAC) approach to track a reference point and to reject persistent disturbances. The turbine simulation models the Controls Advanced Research Turbine (CART) of the National Renewable Energy Laboratory in Golden, Colorado. The CART is a utility-scale wind turbine which has a well-developed and extensively verified simulator. The adaptive collective pitch controller for Region 3 was compared in simulations with a bas celliansesical Proportional Integrator (PI) collective pitch controller. In the simulations, the adaptive pitch controller showed improved speed regulation in Region 3 when compared with the baseline PI pitch controller and it demonstrated robustness to modeling errors.

Effect of ski simulator training on kinematic and muscle activation of the lower extremities

PubMed Central

Moon, Jeheon; Koo, Dohoon; Kim, Kitae; Shin, Insik; Kim, Hyeyoung; Kim, Jinhae

2015-01-01

[Purpose] This study aimed to verify the effectiveness of an augmented reality-based ski simulator through analyzing the changes in movement patterns as well as the engagement of major muscles of the lower body. [Subjects] Seven subjects participated in the study. All were national team-level athletes studying at “K” Sports University in Korea who exhibited comparable performance levels and had no record of injuries in the preceding 6 months (Age 23.4 ± 3.8 years; Height 172.6 ± 12.1 cm; Weight 72.3 ± 16.2 kg; Experience 12.3 ± 4.8 years). [Methods] A reality-based ski simulator developed by a Korean manufacturer was used for the study. Three digital video cameras and a wireless electromyography system were used to perform 3-dimensional motion analysis and measure muscle activation level. [Results] Left hip angulation was found to increase as the frequency of the turns increased. Electromyography data revealed that the activation level of the quadriceps group’s extension muscles and the biceps femoris group’s flexing muscles had a crossing pattern. [Conclusion] Sustained training using an augmented reality-based ski simulator resulted in movements that extended the lower body joints, which is thought to contribute to increasing muscle fatigue. PMID:26357449

A computational study of the chemokine receptor CXCR1 bound with interleukin-8

NASA Astrophysics Data System (ADS)

Wang, Yang; Severin Lupala, Cecylia; Wang, Ting; Li, Xuanxuan; Yun, Ji-Hye; Park, Jae-hyun; Jin, Zeyu; Lee, Weontae; Tan, Leihan; Liu, Haiguang

2018-03-01

CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 (IL8) molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCR1-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCR1-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCR1-IL8 binding poses were investigated in detail. Furthermore, the role of the N-terminal of CXCR1 receptor was studied by comparing four complex models differing in the N-terminal sequences. The results indicate that the receptor N-terminal affects the binding of IL8 significantly. With a shorter N-terminal domain, the binding of IL8 to CXCR1 becomes unstable. The homology modeling and simulations also reveal the key receptor-ligand residues involved in the electrostatic interactions known to be vital for complex formation. Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213).

Direct Numerical Simulation of Pebble Bed Flows: Database Development and Investigation of Low-Frequency Temporal Instabilities

DOE PAGES

Fick, Lambert H.; Merzari, Elia; Hassan, Yassin A.

2017-02-20

Computational analyses of fluid flow through packed pebble bed domains using the Reynolds-averaged NavierStokes framework have had limited success in the past. Because of a lack of high-fidelity experimental or computational data, optimization of Reynolds-averaged closure models for these geometries has not been extensively developed. In the present study, direct numerical simulation was employed to develop a high-fidelity database that can be used for optimizing Reynolds-averaged closure models for pebble bed flows. A face-centered cubic domain with periodic boundaries was used. Flow was simulated at a Reynolds number of 9308 and cross-verified by using available quasi-DNS data. During the simulations,more » low-frequency instability modes were observed that affected the stationary solution. Furthermore, these instabilities were investigated by using the method of proper orthogonal decomposition, and a correlation was found between the time-dependent asymmetry of the averaged velocity profile data and the behavior of the highest energy eigenmodes.« less

Modelling and Simulation of Grid Connected SPV System with Active Power Filtering Features

NASA Astrophysics Data System (ADS)

Saroha, Jaipal; Pandove, Gitanjali; Singh, Mukhtiar

2017-09-01

In this paper, the detailed simulation studies for a grid connected solar photovoltaic system (SPV) have been presented. The power electronics devices like DC-DC boost converter and grid interfacing inverter are most important components of proposed system. Here, the DC-DC boost converter is controlled to extract maximum power out of SPV under different irradiation levels, while the grid interfacing inverter is utilized to evacuate the active power and feed it into grid at synchronized voltage and frequency. Moreover, the grid interfacing inverter is also controlled to sort out the issues related to power quality by compensating the reactive power and harmonics current component of nearby load at point of common coupling. Besides, detailed modeling of various component utilized in proposed system is also presented. Finally, extensive simulations have been performed under different irradiation levels with various kinds of load to validate the aforementioned claims. The overall system design and simulation have been performed by using Sim Power System toolbox available in the library of MATLAB.

Turbulence dissipation challenge: particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Roytershteyn, V.; Karimabadi, H.; Omelchenko, Y.; Germaschewski, K.

2015-12-01

We discuss application of three particle in cell (PIC) codes to the problems relevant to turbulence dissipation challenge. VPIC is a fully kinetic code extensively used to study a variety of diverse problems ranging from laboratory plasmas to astrophysics. PSC is a flexible fully kinetic code offering a variety of algorithms that can be advantageous to turbulence simulations, including high order particle shapes, dynamic load balancing, and ability to efficiently run on Graphics Processing Units (GPUs). Finally, HYPERS is a novel hybrid (kinetic ions+fluid electrons) code, which utilizes asynchronous time advance and a number of other advanced algorithms. We present examples drawn both from large-scale turbulence simulations and from the test problems outlined by the turbulence dissipation challenge. Special attention is paid to such issues as the small-scale intermittency of inertial range turbulence, mode content of the sub-proton range of scales, the formation of electron-scale current sheets and the role of magnetic reconnection, as well as numerical challenges of applying PIC codes to simulations of astrophysical turbulence.

Direct Numerical Simulation of Pebble Bed Flows: Database Development and Investigation of Low-Frequency Temporal Instabilities

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

Fick, Lambert H.; Merzari, Elia; Hassan, Yassin A.

Computational analyses of fluid flow through packed pebble bed domains using the Reynolds-averaged NavierStokes framework have had limited success in the past. Because of a lack of high-fidelity experimental or computational data, optimization of Reynolds-averaged closure models for these geometries has not been extensively developed. In the present study, direct numerical simulation was employed to develop a high-fidelity database that can be used for optimizing Reynolds-averaged closure models for pebble bed flows. A face-centered cubic domain with periodic boundaries was used. Flow was simulated at a Reynolds number of 9308 and cross-verified by using available quasi-DNS data. During the simulations,more » low-frequency instability modes were observed that affected the stationary solution. Furthermore, these instabilities were investigated by using the method of proper orthogonal decomposition, and a correlation was found between the time-dependent asymmetry of the averaged velocity profile data and the behavior of the highest energy eigenmodes.« less

Object oriented studies into artificial space debris

NASA Technical Reports Server (NTRS)

Adamson, J. M.; Marshall, G.

1988-01-01

A prototype simulation is being developed under contract to the Royal Aerospace Establishment (RAE), Farnborough, England, to assist in the discrimination of artificial space objects/debris. The methodology undertaken has been to link Object Oriented programming, intelligent knowledge based system (IKBS) techniques and advanced computer technology with numeric analysis to provide a graphical, symbolic simulation. The objective is to provide an additional layer of understanding on top of conventional classification methods. Use is being made of object and rule based knowledge representation, multiple reasoning, truth maintenance and uncertainty. Software tools being used include Knowledge Engineering Environment (KEE) and SymTactics for knowledge representation. Hooks are being developed within the SymTactics framework to incorporate mathematical models describing orbital motion and fragmentation. Penetration and structural analysis can also be incorporated. SymTactics is an Object Oriented discrete event simulation tool built as a domain specific extension to the KEE environment. The tool provides facilities for building, debugging and monitoring dynamic (military) simulations.

A parallel simulated annealing algorithm for standard cell placement on a hypercube computer

NASA Technical Reports Server (NTRS)

Jones, Mark Howard

1987-01-01

A parallel version of a simulated annealing algorithm is presented which is targeted to run on a hypercube computer. A strategy for mapping the cells in a two dimensional area of a chip onto processors in an n-dimensional hypercube is proposed such that both small and large distance moves can be applied. Two types of moves are allowed: cell exchanges and cell displacements. The computation of the cost function in parallel among all the processors in the hypercube is described along with a distributed data structure that needs to be stored in the hypercube to support parallel cost evaluation. A novel tree broadcasting strategy is used extensively in the algorithm for updating cell locations in the parallel environment. Studies on the performance of the algorithm on example industrial circuits show that it is faster and gives better final placement results than the uniprocessor simulated annealing algorithms. An improved uniprocessor algorithm is proposed which is based on the improved results obtained from parallelization of the simulated annealing algorithm.

ASC FY17 Implementation Plan, Rev. 1

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

Hamilton, P. G.

The Stockpile Stewardship Program (SSP) is an integrated technical program for maintaining the safety, surety, and reliability of the U.S. nuclear stockpile. The SSP uses nuclear test data, computational modeling and simulation, and experimental facilities to advance understanding of nuclear weapons. It includes stockpile surveillance, experimental research, development and engineering programs, and an appropriately scaled production capability to support stockpile requirements. This integrated national program requires the continued use of experimental facilities and programs, and the computational capabilities to support these programs. The Advanced Simulation and Computing Program (ASC) is a cornerstone of the SSP, providing simulation capabilities and computationalmore » resources that support annual stockpile assessment and certification, study advanced nuclear weapons design and manufacturing processes, analyze accident scenarios and weapons aging, and provide the tools to enable stockpile Life Extension Programs (LEPs) and the resolution of Significant Finding Investigations (SFIs). This requires a balance of resources, including technical staff, hardware, simulation software, and computer science solutions.« less

Cortical hypometabolism and hypoperfusion in Parkinson's disease is extensive: probably even at early disease stages.

PubMed

Borghammer, Per; Chakravarty, Mallar; Jonsdottir, Kristjana Yr; Sato, Noriko; Matsuda, Hiroshi; Ito, Kengo; Arahata, Yutaka; Kato, Takashi; Gjedde, Albert

2010-05-01

Recent cerebral blood flow (CBF) and glucose consumption (CMRglc) studies of Parkinson's disease (PD) revealed conflicting results. Using simulated data, we previously demonstrated that the often-reported subcortical hypermetabolism in PD could be explained as an artifact of biased global mean (GM) normalization, and that low-magnitude, extensive cortical hypometabolism is best detected by alternative data-driven normalization methods. Thus, we hypothesized that PD is characterized by extensive cortical hypometabolism but no concurrent widespread subcortical hypermetabolism and tested it on three independent samples of PD patients. We compared SPECT CBF images of 32 early-stage and 33 late-stage PD patients with that of 60 matched controls. We also compared PET FDG images from 23 late-stage PD patients with that of 13 controls. Three different normalization methods were compared: (1) GM normalization, (2) cerebellum normalization, (3) reference cluster normalization (Yakushev et al.). We employed standard voxel-based statistics (fMRIstat) and principal component analysis (SSM). Additionally, we performed a meta-analysis of all quantitative CBF and CMRglc studies in the literature to investigate whether the global mean (GM) values in PD are decreased. Voxel-based analysis with GM normalization and the SSM method performed similarly, i.e., both detected decreases in small cortical clusters and concomitant increases in extensive subcortical regions. Cerebellum normalization revealed more widespread cortical decreases but no subcortical increase. In all comparisons, the Yakushev method detected nearly identical patterns of very extensive cortical hypometabolism. Lastly, the meta-analyses demonstrated that global CBF and CMRglc values are decreased in PD. Based on the results, we conclude that PD most likely has widespread cortical hypometabolism, even at early disease stages. In contrast, extensive subcortical hypermetabolism is probably not a feature of PD.

Curve Boxplot: Generalization of Boxplot for Ensembles of Curves.

PubMed

Mirzargar, Mahsa; Whitaker, Ross T; Kirby, Robert M

2014-12-01

In simulation science, computational scientists often study the behavior of their simulations by repeated solutions with variations in parameters and/or boundary values or initial conditions. Through such simulation ensembles, one can try to understand or quantify the variability or uncertainty in a solution as a function of the various inputs or model assumptions. In response to a growing interest in simulation ensembles, the visualization community has developed a suite of methods for allowing users to observe and understand the properties of these ensembles in an efficient and effective manner. An important aspect of visualizing simulations is the analysis of derived features, often represented as points, surfaces, or curves. In this paper, we present a novel, nonparametric method for summarizing ensembles of 2D and 3D curves. We propose an extension of a method from descriptive statistics, data depth, to curves. We also demonstrate a set of rendering and visualization strategies for showing rank statistics of an ensemble of curves, which is a generalization of traditional whisker plots or boxplots to multidimensional curves. Results are presented for applications in neuroimaging, hurricane forecasting and fluid dynamics.

Observers' focus of attention in the simulation of self-perception.

PubMed

Wegner, D M; Finstuen, K

1977-01-01

This research was designed to assess the effects of a manipulation of observers' focus of attention--from a focus on the actor to a focus on the actor's situation--upon observers' attributions of attitude to an actor in a simulation of a forced-compliance cognitive dissonance experiment. Observers induced through empathy instructions to focus attention on the actor's situation inferred less actor attitude positivity than did observers given no specific observational set. In addition, situation-focused observers inferred that the actor's attitude was directly related to reward magnitude, whereas actor-focused observers inferred that the actor's attitude was inversely related to reward magnitude. An extension of self-perception theory, offered as an interpretation of these and other results, suggested that motivation attribution made by actors and observers in dissonance and simulation studies are dependent on focus of attention. The attributions made by actor-focused observers simulate those of objectively self-aware actors and are based upon perceived intrinsic motivation; the attributions of situation-focused observers simulate those of subjectively self-aware actors and are based upon perceived extrinsic motivation.

Radiation dominated acoustophoresis driven by surface acoustic waves.

PubMed

Guo, Jinhong; Kang, Yuejun; Ai, Ye

2015-10-01

Acoustophoresis-based particle manipulation in microfluidics has gained increasing attention in recent years. Despite the fact that experimental studies have been extensively performed to demonstrate this technique for various microfluidic applications, numerical simulation of acoustophoresis driven by surface acoustic waves (SAWs) has still been largely unexplored. In this work, a numerical model taking into account the acoustic-piezoelectric interaction was developed to simulate the generation of a standing surface acoustic wave (SSAW) field and predict the acoustic pressure field in the liquid. Acoustic radiation dominated particle tracing was performed to simulate acoustophoresis of particles with different sizes undergoing a SSAW field. A microfluidic device composed of two interdigital transducers (IDTs) for SAW generation and a microfluidic channel was fabricated for experimental validation. Numerical simulations could well capture the focusing phenomenon of particles to the pressure nodes in the experimental observation. Further comparison of particle trajectories demonstrated considerably quantitative agreement between numerical simulations and experimental results with fitting in the applied voltage. Particle switching was also demonstrated using the fabricated device that could be further developed as an active particle sorting device. Copyright © 2015 Elsevier Inc. All rights reserved.

Local rules simulation of the kinetics of virus capsid self-assembly.

PubMed

Schwartz, R; Shor, P W; Prevelige, P E; Berger, B

1998-12-01

A computer model is described for studying the kinetics of the self-assembly of icosahedral viral capsids. Solution of this problem is crucial to an understanding of the viral life cycle, which currently cannot be adequately addressed through laboratory techniques. The abstract simulation model employed to address this is based on the local rules theory of. Proc. Natl. Acad. Sci. USA. 91:7732-7736). It is shown that the principle of local rules, generalized with a model of kinetics and other extensions, can be used to simulate complicated problems in self-assembly. This approach allows for a computationally tractable molecular dynamics-like simulation of coat protein interactions while retaining many relevant features of capsid self-assembly. Three simple simulation experiments are presented to illustrate the use of this model. These show the dependence of growth and malformation rates on the energetics of binding interactions, the tolerance of errors in binding positions, and the concentration of subunits in the examples. These experiments demonstrate a tradeoff within the model between growth rate and fidelity of assembly for the three parameters. A detailed discussion of the computational model is also provided.

Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Flethcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock- shear- layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

The high latitude ionosphere-magnetosphere transition region: Simulation and data comparison

NASA Technical Reports Server (NTRS)

Wilson, Gordon R.; Horwitz, James L.

1995-01-01

A brief description of the major activities pursued during the last year (March 1994 - February 1995) of this grant are: (1) the development of a 200 km to 1 Re, O(+) H(+) Model; (2) the extension of the E x B convection heating study to include centrifugal effects; (3) the study of electron precipitation effects; (4) the study of wave heating of O(+); and (5) the polar wind acceleration study. A list of both papers published and papers submitted, along with a proposal for next year's study and a copy of the published paper is included.

A comparison of four streamflow record extension techniques

USGS Publications Warehouse

Hirsch, Robert M.

1982-01-01

One approach to developing time series of streamflow, which may be used for simulation and optimization studies of water resources development activities, is to extend an existing gage record in time by exploiting the interstation correlation between the station of interest and some nearby (long-term) base station. Four methods of extension are described, and their properties are explored. The methods are regression (REG), regression plus noise (RPN), and two new methods, maintenance of variance extension types 1 and 2 (MOVE.l, MOVE.2). MOVE.l is equivalent to a method which is widely used in psychology, biometrics, and geomorphology and which has been called by various names, e.g., ‘line of organic correlation,’ ‘reduced major axis,’ ‘unique solution,’ and ‘equivalence line.’ The methods are examined for bias and standard error of estimate of moments and order statistics, and an empirical examination is made of the preservation of historic low-flow characteristics using 50-year-long monthly records from seven streams. The REG and RPN methods are shown to have serious deficiencies as record extension techniques. MOVE.2 is shown to be marginally better than MOVE.l, according to the various comparisons of bias and accuracy.

A Comparison of Four Streamflow Record Extension Techniques

NASA Astrophysics Data System (ADS)

Hirsch, Robert M.

1982-08-01

One approach to developing time series of streamflow, which may be used for simulation and optimization studies of water resources development activities, is to extend an existing gage record in time by exploiting the interstation correlation between the station of interest and some nearby (long-term) base station. Four methods of extension are described, and their properties are explored. The methods are regression (REG), regression plus noise (RPN), and two new methods, maintenance of variance extension types 1 and 2 (MOVE.l, MOVE.2). MOVE.l is equivalent to a method which is widely used in psychology, biometrics, and geomorphology and which has been called by various names, e.g., `line of organic correlation,' `reduced major axis,' `unique solution,' and `equivalence line.' The methods are examined for bias and standard error of estimate of moments and order statistics, and an empirical examination is made of the preservation of historic low-flow characteristics using 50-year-long monthly records from seven streams. The REG and RPN methods are shown to have serious deficiencies as record extension techniques. MOVE.2 is shown to be marginally better than MOVE.l, according to the various comparisons of bias and accuracy.

Finite element modeling of mitral leaflet tissue using a layered shell approximation

PubMed Central

Ratcliffe, Mark B.; Guccione, Julius M.

2012-01-01

The current study presents a finite element model of mitral leaflet tissue, which incorporates the anisotropic material response and approximates the layered structure. First, continuum mechanics and the theory of layered composites are used to develop an analytical representation of membrane stress in the leaflet material. This is done with an existing anisotropic constitutive law from literature. Then, the concept is implemented in a finite element (FE) model by overlapping and merging two layers of transversely isotropic membrane elements in LS-DYNA, which homogenizes the response. The FE model is then used to simulate various biaxial extension tests and out-of-plane pressure loading. Both the analytical and FE model show good agreement with experimental biaxial extension data, and show good mutual agreement. This confirms that the layered composite approximation presented in the current study is able to capture the exponential stiffening seen in both the circumferential and radial directions of mitral leaflets. PMID:22971896

Evaluation of bioenergy crop growth and the impacts of bioenergy crops on streamflow, tile drain flow and nutrient losses in an extensively tile-drained watershed using SWAT.

PubMed

Guo, Tian; Cibin, Raj; Chaubey, Indrajeet; Gitau, Margaret; Arnold, Jeffrey G; Srinivasan, Raghavan; Kiniry, James R; Engel, Bernard A

2018-02-01

Large quantities of biofuel production are expected from bioenergy crops at a national scale to meet US biofuel goals. It is important to study biomass production of bioenergy crops and the impacts of these crops on water quantity and quality to identify environment-friendly and productive biofeedstock systems. SWAT2012 with a new tile drainage routine and improved perennial grass and tree growth simulation was used to model long-term annual biomass yields, streamflow, tile flow, sediment load, and nutrient losses under various bioenergy scenarios in an extensively agricultural watershed in the Midwestern US. Simulated results from bioenergy crop scenarios were compared with those from the baseline. The results showed that simulated annual crop yields were similar to observed county level values for corn and soybeans, and were reasonable for Miscanthus, switchgrass and hybrid poplar. Removal of 38% of corn stover (3.74Mg/ha/yr) with Miscanthus production on highly erodible areas and marginal land (17.49Mg/ha/yr) provided the highest biofeedstock production (279,000Mg/yr). Streamflow, tile flow, erosion and nutrient losses were reduced under bioenergy crop scenarios of bioenergy crops on highly erodible areas and marginal land. Corn stover removal did not result in significant water quality changes. The increase in sediment and nutrient losses under corn stover removal could be offset with the combination of other bioenergy crops. Potential areas for bioenergy crop production when meeting the criteria above were small (10.88km 2 ), thus the ability to produce biomass and improve water quality was not substantial. The study showed that corn stover removal with bioenergy crops both on highly erodible areas and marginal land could provide more biofuel production relative to the baseline, and was beneficial to water quality at the watershed scale, providing guidance for further research on evaluation of bioenergy crop scenarios in a typical extensively tile-drained watershed in the Midwestern U.S. Copyright © 2017 Elsevier B.V. All rights reserved.

A Continuous Labour Supply Model in Microsimulation: A Life-Cycle Modelling Approach with Heterogeneity and Uncertainty Extension

PubMed Central

Li, Jinjing; Sologon, Denisa Maria

2014-01-01

This paper advances a structural inter-temporal model of labour supply that is able to simulate the dynamics of labour supply in a continuous setting and addresses two main drawbacks of most existing models. The first limitation is the inability to incorporate individual heterogeneity as every agent is sharing the same parameters of the utility function. The second one is the strong assumption that individuals make decisions in a world of perfect certainty. Essentially, this paper offers an extension of marginal-utility-of-wealth-constant labour supply functions known as “Frisch functions” under certainty and uncertainty with homogenous and heterogeneous preferences. The lifetime models based on the fixed effect vector decomposition yield the most stable simulation results, under both certain and uncertain future wage assumptions. Due to its improved accuracy and stability, this lifetime labour supply model is particularly suitable for enhancing the performance of the life cycle simulation models, thus providing a better reference for policymaking. PMID:25391021

Charge plasma technique based dopingless accumulation mode junctionless cylindrical surrounding gate MOSFET: analog performance improvement

NASA Astrophysics Data System (ADS)

Trivedi, Nitin; Kumar, Manoj; Haldar, Subhasis; Deswal, S. S.; Gupta, Mridula; Gupta, R. S.

2017-09-01

A charge plasma technique based dopingless (DL) accumulation mode (AM) junctionless (JL) cylindrical surrounding gate (CSG) MOSFET has been proposed and extensively investigated. Proposed device has no physical junction at source to channel and channel to drain interface. The complete silicon pillar has been considered as undoped. The high free electron density or induced N+ region is designed by keeping the work function of source/drain metal contacts lower than the work function of undoped silicon. Thus, its fabrication complexity is drastically reduced by curbing the requirement of high temperature doping techniques. The electrical/analog characteristics for the proposed device has been extensively investigated using the numerical simulation and are compared with conventional junctionless cylindrical surrounding gate (JL-CSG) MOSFET with identical dimensions. For the numerical simulation purpose ATLAS-3D device simulator is used. The results show that the proposed device is more short channel immune to conventional JL-CSG MOSFET and suitable for faster switching applications due to higher I ON/ I OFF ratio.

Recent Progress in Understanding the Shock Response of Ferroelectric Ceramics*

NASA Astrophysics Data System (ADS)

Setchell, Robert E.

2001-06-01

Ferroelectric ceramics exhibit a permanent remanent polarization, and the use of shock depoling of these materials to achieve pulsed sources of electrical power was proposed in the late 1950s. During the following twenty years, extensive studies were conducted to examine the shock response of ferroelectric ceramics primarily based on lead zirconate titanate (PZT). Under limited conditions, relatively simple analytical models were found to adequately describe the observed electrical behavior. In general, however, the studies indicated a complex behavior involving finite-rate depoling kinetics with stress and field dependencies. Dielectric relaxation and shock-induced conductivity were also suggested. Unfortunately, few experimental studies were undertaken over the next twenty years, and the development of more comprehensive models was inhibited. In recent years, a strong interest in advancing numerical simulation capabilities has motivated new experimental studies and corresponding model development. More than seventy gas gun experiments have examined several ferroelectric ceramics, with most experiments on lead zirconate titanate having a Zr:Ti ratio of 95:5 and modified with 2ferroelectric but is near an antiferroelectric phase boundary, and depoling results from a shock-driven phase transition. Experiments have examined unpoled, normally poled, and axially poled PZT 95/5 over broad ranges of shock pressure and peak electric field. The extensive base of new data provides quantitative insights into the stress and field dependencies of depoling kinetics and dielectric properties, and is being actively utilized to develop and refine material response models used in numerical simulations of pulsed power devices.

Modeling of a historical earthquake in Erzincan, Turkey (Ms 7.8, in 1939) using regional seismological information obtained from a recent event

NASA Astrophysics Data System (ADS)

Karimzadeh, Shaghayegh; Askan, Aysegul

2018-04-01

Located within a basin structure, at the conjunction of North East Anatolian, North Anatolian and Ovacik Faults, Erzincan city center (Turkey) is one of the most hazardous regions in the world. Combination of the seismotectonic and geological settings of the region has resulted in series of significant seismic activities including the 1939 (Ms 7.8) as well as the 1992 (Mw = 6.6) earthquakes. The devastative 1939 earthquake occurred in the pre-instrumental era in the region with no available local seismograms. Thus, a limited number of studies exist on that earthquake. However, the 1992 event, despite the sparse local network at that time, has been studied extensively. This study aims to simulate the 1939 Erzincan earthquake using available regional seismic and geological parameters. Despite several uncertainties involved, such an effort to quantitatively model the 1939 earthquake is promising, given the historical reports of extensive damage and fatalities in the area. The results of this study are expressed in terms of anticipated acceleration time histories at certain locations, spatial distribution of selected ground motion parameters and felt intensity maps in the region. Simulated motions are first compared against empirical ground motion prediction equations derived with both local and global datasets. Next, anticipated intensity maps of the 1939 earthquake are obtained using local correlations between peak ground motion parameters and felt intensity values. Comparisons of the estimated intensity distributions with the corresponding observed intensities indicate a reasonable modeling of the 1939 earthquake.

Mathematical modeling of a nickel-cadmium battery

NASA Technical Reports Server (NTRS)

Fan, Deyuan; White, Ralph E.

1991-01-01

Extensions are presented for a mathematical model of an Ni-CD cell (Fan and White, 1991). These extensions consist of intercalation thermodynamics for the nickel electrode and oxygen generation and reduction reactions during charge and overcharge. The simulated results indicate that intercalation may be important in the nickel electrode and that including the oxygen reactions provides a means of predicting the efficiency of the cell on charge and discharge.

Asymmetrical booster ascent guidance and control system design study. Volume 2: SSFS math models - Ascent. [space shuttle development

NASA Technical Reports Server (NTRS)

Williams, F. E.; Lemon, R. S.

1974-01-01

The engineering equations and mathematical models developed for use in the space shuttle functional simulator (SSFS) are presented, and include extensive revisions and additions to earlier documentation. Definitions of coordinate systems used by the SSFS models and coordinate tranformations are given, along with documentation of the flexible body mathematical models. The models were incorporated in the SSFS and are in the checkout stage.

GEE-Smoothing Spline in Semiparametric Model with Correlated Nominal Data

NASA Astrophysics Data System (ADS)

Ibrahim, Noor Akma; Suliadi

2010-11-01

In this paper we propose GEE-Smoothing spline in the estimation of semiparametric models with correlated nominal data. The method can be seen as an extension of parametric generalized estimating equation to semiparametric models. The nonparametric component is estimated using smoothing spline specifically the natural cubic spline. We use profile algorithm in the estimation of both parametric and nonparametric components. The properties of the estimators are evaluated using simulation studies.

Promotion of cooperation by adaptive interaction: The role of heterogeneity in neighborhoods

NASA Astrophysics Data System (ADS)

Han, Xu; Zhao, Xiaowei; Xia, Haoxiang

2018-07-01

Evolution of cooperation in prisoner's dilemma games has been studied extensively in the past decades. Recent studies have investigated the effect of adaptive interaction intensity on spatial prisoner's dilemma, showing that if individuals can adjust their interaction intensity with each opponent at the same extent, cooperation can be promoted in a proper scale. However, the previous studies about adaptive interaction willingness do not consider the heterogeneity of the opponents. In this paper, a simulative model is developed to examine whether and how the interactive diversity influences cooperation in the spatial prisoner's dilemma games, in which individuals consider the corresponding behavior of different opponents. The simulation results show that the proposed mechanism can effectively promote cooperation, and the average payoff of the system can significantly be improved by high interaction intensity between cooperators. In addition, we also show four kinds of different individuals to analyze the evolution progresses. The simulations show that cooperators on the boundary decrease their interaction willingness, which makes the boundary defectors lose their opportunity to participate in the interaction and be invaded by cooperators.

Effect of a rotating propeller on the separation angle of attack

NASA Technical Reports Server (NTRS)

Boldman, D. R.; Iek, C.; Hwang, D. P.; Larkin, M.; Schweiger, P.

1993-01-01

The present study represents an extension of an earlier wind tunnel experiment performed with the P&W 17-in. Advanced Ducted Propeller (ADP) Simulator operating at Mach 0.2. In order to study the effects of a rotating propeller on the inlet flow, data were obtained in the UTRC 10- by 15-Foot Large Subsonic Wind Tunnel with the same hardware and instrumentation, but with the propellar removed. These new tests were performed over a range of flow rates which duplicated flow rates in the powered simulator program. The flow through the inlet was provided by a remotely located vacuum source. A comparison of the results of this flow-through study with the previous data from the powered simulator indicated that in the conventional inlet the propeller produced an increase in the separation angle of attack between 4.0 deg at a specific flow of 22.4 lb/sec-sq ft to 2.7 deg at a higher specific flow of 33.8 lb/sec-sq ft. A similar effect on separation angle of attack was obtained by using stationary blockage rather than a propeller.

Flight Simulator and Training Human Factors Validation

NASA Technical Reports Server (NTRS)

Glaser, Scott T.; Leland, Richard

2009-01-01

Loss of control has been identified as the leading cause of aircraft accidents in recent years. Efforts have been made to better equip pilots to deal with these types of events, commonly referred to as upsets. A major challenge in these endeavors has been recreating the motion environments found in flight as the majority of upsets take place well beyond the normal operating envelope of large aircraft. The Environmental Tectonics Corporation has developed a simulator motion base, called GYROLAB, that is capable of recreating the sustained accelerations, or G-forces, and motions of flight. A two part research study was accomplished that coupled NASA's Generic Transport Model with a GYROLAB device. The goal of the study was to characterize physiological effects of the upset environment and to demonstrate that a sustained motion based simulator can be an effective means for upset recovery training. Two groups of 25 Air Transport Pilots participated in the study. The results showed reliable signs of pilot arousal at specific stages of similar upsets. Further validation also demonstrated that sustained motion technology was successful in improving pilot performance during recovery following an extensive training program using GYROLAB technology.

An Improved Dynamic Model for the Respiratory Response to Exercise

PubMed Central

Serna, Leidy Y.; Mañanas, Miguel A.; Hernández, Alher M.; Rabinovich, Roberto A.

2018-01-01

Respiratory system modeling has been extensively studied in steady-state conditions to simulate sleep disorders, to predict its behavior under ventilatory diseases or stimuli and to simulate its interaction with mechanical ventilation. Nevertheless, the studies focused on the instantaneous response are limited, which restricts its application in clinical practice. The aim of this study is double: firstly, to analyze both dynamic and static responses of two known respiratory models under exercise stimuli by using an incremental exercise stimulus sequence (to analyze the model responses when step inputs are applied) and experimental data (to assess prediction capability of each model). Secondly, to propose changes in the models' structures to improve their transient and stationary responses. The versatility of the resulting model vs. the other two is shown according to the ability to simulate ventilatory stimuli, like exercise, with a proper regulation of the arterial blood gases, suitable constant times and a better adjustment to experimental data. The proposed model adjusts the breathing pattern every respiratory cycle using an optimization criterion based on minimization of work of breathing through regulation of respiratory frequency. PMID:29467674

Deriving Therapies for Children with Primary CNS Tumors Using Pharmacokinetic Modeling and Simulation of Cerebral Microdialysis Data

PubMed Central

Jacus, M.O.; Throm, S.L.; Turner, D.C.; Patel, Y.T.; Freeman, B.B.; Morfouace, M.; Boulos, N.; Stewart, C. F.

2014-01-01

The treatment of children with primary central nervous system (CNS) tumors continues to be a challenge despite recent advances in technology and diagnostics. In this overview, we describe our approach for identifying and evaluating active anticancer drugs through a process that enables rational translation from the lab to the clinic. The preclinical approach we discuss uses tumor subgroup-specific models of pediatric CNS tumors, cerebral microdialysis sampling of tumor extracellular fluid (tECF), and pharmacokinetic modeling and simulation to overcome challenges that currently hinder researchers in this field. This approach involves performing extensive systemic (plasma) and target site (CNS tumor) pharmacokinetic studies. Pharmacokinetic modeling and simulation of the data derived from these studies are then used to inform future decisions regarding drug administration, including dosage and schedule. Here, we also present how our approach was used to examine two FDA approved drugs, simvastatin and pemetrexed, as candidates for new therapies for pediatric CNS tumors. We determined that due to unfavorable pharmacokinetic characteristics and insufficient concentrations in tumor tissue in a mouse model of ependymoma, simvastatin would not be efficacious in further preclinical trials. In contrast to simvastatin, pemetrexed was advanced to preclinical efficacy studies after our studies determined that plasma exposures were similar to those in humans treated at similar tolerable dosages and adequate unbound concentrations were found in tumor tissue of medulloblastoma-bearing mice. Generally speaking, the high clinical failure rates for CNS drug candidates can be partially explained by the fact that therapies are often moved into clinical trials without extensive and rational preclinical studies to optimize the transition. Our approach addresses this limitation by using pharmacokinetic and pharmacodynamic modeling of data generated from appropriate in vivo models to support the rational testing and usage of innovative therapies in children with CNS tumors. PMID:24269626

Rapidly Re-Configurable Flight Simulator Tools for Crew Vehicle Integration Research and Design

NASA Technical Reports Server (NTRS)

Schutte, Paul C.; Trujillo, Anna; Pritchett, Amy R.

2000-01-01

While simulation is a valuable research and design tool, the time and difficulty required to create new simulations (or re-use existing simulations) often limits their application. This report describes the design of the software architecture for the Reconfigurable Flight Simulator (RFS), which provides a robust simulation framework that allows the simulator to fulfill multiple research and development goals. The core of the architecture provides the interface standards for simulation components, registers and initializes components, and handles the communication between simulation components. The simulation components are each a pre-compiled library 'plug-in' module. This modularity allows independent development and sharing of individual simulation components. Additional interfaces can be provided through the use of Object Data/Method Extensions (OD/ME). RFS provides a programmable run-time environment for real-time access and manipulation, and has networking capabilities using the High Level Architecture (HLA).