Computer Simulations to Support Science Instruction and Learning: A critical review of the literature

NASA Astrophysics Data System (ADS)

Smetana, Lara Kathleen; Bell, Randy L.

2012-06-01

Researchers have explored the effectiveness of computer simulations for supporting science teaching and learning during the past four decades. The purpose of this paper is to provide a comprehensive, critical review of the literature on the impact of computer simulations on science teaching and learning, with the goal of summarizing what is currently known and providing guidance for future research. We report on the outcomes of 61 empirical studies dealing with the efficacy of, and implications for, computer simulations in science instruction. The overall findings suggest that simulations can be as effective, and in many ways more effective, than traditional (i.e. lecture-based, textbook-based and/or physical hands-on) instructional practices in promoting science content knowledge, developing process skills, and facilitating conceptual change. As with any other educational tool, the effectiveness of computer simulations is dependent upon the ways in which they are used. Thus, we outline specific research-based guidelines for best practice. Computer simulations are most effective when they (a) are used as supplements; (b) incorporate high-quality support structures; (c) encourage student reflection; and (d) promote cognitive dissonance. Used appropriately, computer simulations involve students in inquiry-based, authentic science explorations. Additionally, as educational technologies continue to evolve, advantages such as flexibility, safety, and efficiency deserve attention.

The National Shipbuilding Research Program, Computer Aided Process Planning for Shipyards

DTIC Science & Technology

1986-08-01

Factory Simulation with Conventional Factory Planning Techniques Financial Justification of State-of-the-Art Investment: A Study Using CAPP I–5 T I T L...and engineer to order.” “Factory Simulation: Approach to Integration of Computer- Based Factory Simulation with Conventional Factory Planning Techniques

Effects of Thinking Style on Design Strategies: Using Bridge Construction Simulation Programs

ERIC Educational Resources Information Center

Sun, Chuen-Tsai; Wang, Dai-Yi; Chang, Yu-Yeh

2013-01-01

Computer simulation users can freely control operational factors and simulation results, repeat processes, make changes, and learn from simulation environment feedback. The focus of this paper is on simulation-based design tools and their effects on student learning processes in a group of 101 Taiwanese senior high school students. Participants…

A direct-execution parallel architecture for the Advanced Continuous Simulation Language (ACSL)

NASA Technical Reports Server (NTRS)

Carroll, Chester C.; Owen, Jeffrey E.

1988-01-01

A direct-execution parallel architecture for the Advanced Continuous Simulation Language (ACSL) is presented which overcomes the traditional disadvantages of simulations executed on a digital computer. The incorporation of parallel processing allows the mapping of simulations into a digital computer to be done in the same inherently parallel manner as they are currently mapped onto an analog computer. The direct-execution format maximizes the efficiency of the executed code since the need for a high level language compiler is eliminated. Resolution is greatly increased over that which is available with an analog computer without the sacrifice in execution speed normally expected with digitial computer simulations. Although this report covers all aspects of the new architecture, key emphasis is placed on the processing element configuration and the microprogramming of the ACLS constructs. The execution times for all ACLS constructs are computed using a model of a processing element based on the AMD 29000 CPU and the AMD 29027 FPU. The increase in execution speed provided by parallel processing is exemplified by comparing the derived execution times of two ACSL programs with the execution times for the same programs executed on a similar sequential architecture.

A configurable distributed high-performance computing framework for satellite's TDI-CCD imaging simulation

NASA Astrophysics Data System (ADS)

Xue, Bo; Mao, Bingjing; Chen, Xiaomei; Ni, Guoqiang

2010-11-01

This paper renders a configurable distributed high performance computing(HPC) framework for TDI-CCD imaging simulation. It uses strategy pattern to adapt multi-algorithms. Thus, this framework help to decrease the simulation time with low expense. Imaging simulation for TDI-CCD mounted on satellite contains four processes: 1) atmosphere leads degradation, 2) optical system leads degradation, 3) electronic system of TDI-CCD leads degradation and re-sampling process, 4) data integration. Process 1) to 3) utilize diversity data-intensity algorithms such as FFT, convolution and LaGrange Interpol etc., which requires powerful CPU. Even uses Intel Xeon X5550 processor, regular series process method takes more than 30 hours for a simulation whose result image size is 1500 * 1462. With literature study, there isn't any mature distributing HPC framework in this field. Here we developed a distribute computing framework for TDI-CCD imaging simulation, which is based on WCF[1], uses Client/Server (C/S) layer and invokes the free CPU resources in LAN. The server pushes the process 1) to 3) tasks to those free computing capacity. Ultimately we rendered the HPC in low cost. In the computing experiment with 4 symmetric nodes and 1 server , this framework reduced about 74% simulation time. Adding more asymmetric nodes to the computing network, the time decreased namely. In conclusion, this framework could provide unlimited computation capacity in condition that the network and task management server are affordable. And this is the brand new HPC solution for TDI-CCD imaging simulation and similar applications.

Accelerating Monte Carlo simulations of photon transport in a voxelized geometry using a massively parallel graphics processing unit.

PubMed

Badal, Andreu; Badano, Aldo

2009-11-01

It is a known fact that Monte Carlo simulations of radiation transport are computationally intensive and may require long computing times. The authors introduce a new paradigm for the acceleration of Monte Carlo simulations: The use of a graphics processing unit (GPU) as the main computing device instead of a central processing unit (CPU). A GPU-based Monte Carlo code that simulates photon transport in a voxelized geometry with the accurate physics models from PENELOPE has been developed using the CUDATM programming model (NVIDIA Corporation, Santa Clara, CA). An outline of the new code and a sample x-ray imaging simulation with an anthropomorphic phantom are presented. A remarkable 27-fold speed up factor was obtained using a GPU compared to a single core CPU. The reported results show that GPUs are currently a good alternative to CPUs for the simulation of radiation transport. Since the performance of GPUs is currently increasing at a faster pace than that of CPUs, the advantages of GPU-based software are likely to be more pronounced in the future.

Extending rule-based methods to model molecular geometry and 3D model resolution.

PubMed

Hoard, Brittany; Jacobson, Bruna; Manavi, Kasra; Tapia, Lydia

2016-08-01

Computational modeling is an important tool for the study of complex biochemical processes associated with cell signaling networks. However, it is challenging to simulate processes that involve hundreds of large molecules due to the high computational cost of such simulations. Rule-based modeling is a method that can be used to simulate these processes with reasonably low computational cost, but traditional rule-based modeling approaches do not include details of molecular geometry. The incorporation of geometry into biochemical models can more accurately capture details of these processes, and may lead to insights into how geometry affects the products that form. Furthermore, geometric rule-based modeling can be used to complement other computational methods that explicitly represent molecular geometry in order to quantify binding site accessibility and steric effects. We propose a novel implementation of rule-based modeling that encodes details of molecular geometry into the rules and binding rates. We demonstrate how rules are constructed according to the molecular curvature. We then perform a study of antigen-antibody aggregation using our proposed method. We simulate the binding of antibody complexes to binding regions of the shrimp allergen Pen a 1 using a previously developed 3D rigid-body Monte Carlo simulation, and we analyze the aggregate sizes. Then, using our novel approach, we optimize a rule-based model according to the geometry of the Pen a 1 molecule and the data from the Monte Carlo simulation. We use the distances between the binding regions of Pen a 1 to optimize the rules and binding rates. We perform this procedure for multiple conformations of Pen a 1 and analyze the impact of conformation and resolution on the optimal rule-based model. We find that the optimized rule-based models provide information about the average steric hindrance between binding regions and the probability that antibodies will bind to these regions. These optimized models quantify the variation in aggregate size that results from differences in molecular geometry and from model resolution.

Parallel Signal Processing and System Simulation using aCe

NASA Technical Reports Server (NTRS)

Dorband, John E.; Aburdene, Maurice F.

2003-01-01

Recently, networked and cluster computation have become very popular for both signal processing and system simulation. A new language is ideally suited for parallel signal processing applications and system simulation since it allows the programmer to explicitly express the computations that can be performed concurrently. In addition, the new C based parallel language (ace C) for architecture-adaptive programming allows programmers to implement algorithms and system simulation applications on parallel architectures by providing them with the assurance that future parallel architectures will be able to run their applications with a minimum of modification. In this paper, we will focus on some fundamental features of ace C and present a signal processing application (FFT).

Computational studies of physical properties of Nb-Si based alloys

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

Ouyang, Lizhi

2015-04-16

The overall goal is to provide physical properties data supplementing experiments for thermodynamic modeling and other simulations such as phase filed simulation for microstructure and continuum simulations for mechanical properties. These predictive computational modeling and simulations may yield insights that can be used to guide materials design, processing, and manufacture. Ultimately, they may lead to usable Nb-Si based alloy which could play an important role in current plight towards greener energy. The main objectives of the proposed projects are: (1) developing a first principles method based supercell approach for calculating thermodynamic and mechanic properties of ordered crystals and disordered latticesmore » including solid solution; (2) application of the supercell approach to Nb-Si base alloy to compute physical properties data that can be used for thermodynamic modeling and other simulations to guide the optimal design of Nb-Si based alloy.« less

A heterogeneous system based on GPU and multi-core CPU for real-time fluid and rigid body simulation

NASA Astrophysics Data System (ADS)

da Silva Junior, José Ricardo; Gonzalez Clua, Esteban W.; Montenegro, Anselmo; Lage, Marcos; Dreux, Marcelo de Andrade; Joselli, Mark; Pagliosa, Paulo A.; Kuryla, Christine Lucille

2012-03-01

Computational fluid dynamics in simulation has become an important field not only for physics and engineering areas but also for simulation, computer graphics, virtual reality and even video game development. Many efficient models have been developed over the years, but when many contact interactions must be processed, most models present difficulties or cannot achieve real-time results when executed. The advent of parallel computing has enabled the development of many strategies for accelerating the simulations. Our work proposes a new system which uses some successful algorithms already proposed, as well as a data structure organisation based on a heterogeneous architecture using CPUs and GPUs, in order to process the simulation of the interaction of fluids and rigid bodies. This successfully results in a two-way interaction between them and their surrounding objects. As far as we know, this is the first work that presents a computational collaborative environment which makes use of two different paradigms of hardware architecture for this specific kind of problem. Since our method achieves real-time results, it is suitable for virtual reality, simulation and video game fluid simulation problems.

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.

RTM user's guide

NASA Technical Reports Server (NTRS)

Claus, Steven J.; Loos, Alfred C.

1989-01-01

RTM is a FORTRAN '77 computer code which simulates the infiltration of textile reinforcements and the kinetics of thermosetting polymer resin systems. The computer code is based on the process simulation model developed by the author. The compaction of dry, woven textile composites is simulated to describe the increase in fiber volume fraction with increasing compaction pressure. Infiltration is assumed to follow D'Arcy's law for Newtonian viscous fluids. The chemical changes which occur in the resin during processing are simulated with a thermo-kinetics model. The computer code is discussed on the basis of the required input data, output files and some comments on how to interpret the results. An example problem is solved and a complete listing is included.

A multi-GPU real-time dose simulation software framework for lung radiotherapy.

PubMed

Santhanam, A P; Min, Y; Neelakkantan, H; Papp, N; Meeks, S L; Kupelian, P A

2012-09-01

Medical simulation frameworks facilitate both the preoperative and postoperative analysis of the patient's pathophysical condition. Of particular importance is the simulation of radiation dose delivery for real-time radiotherapy monitoring and retrospective analyses of the patient's treatment. In this paper, a software framework tailored for the development of simulation-based real-time radiation dose monitoring medical applications is discussed. A multi-GPU-based computational framework coupled with inter-process communication methods is introduced for simulating the radiation dose delivery on a deformable 3D volumetric lung model and its real-time visualization. The model deformation and the corresponding dose calculation are allocated among the GPUs in a task-specific manner and is performed in a pipelined manner. Radiation dose calculations are computed on two different GPU hardware architectures. The integration of this computational framework with a front-end software layer and back-end patient database repository is also discussed. Real-time simulation of the dose delivered is achieved at once every 120 ms using the proposed framework. With a linear increase in the number of GPU cores, the computational time of the simulation was linearly decreased. The inter-process communication time also improved with an increase in the hardware memory. Variations in the delivered dose and computational speedup for variations in the data dimensions are investigated using D70 and D90 as well as gEUD as metrics for a set of 14 patients. Computational speed-up increased with an increase in the beam dimensions when compared with a CPU-based commercial software while the error in the dose calculation was <1%. Our analyses show that the framework applied to deformable lung model-based radiotherapy is an effective tool for performing both real-time and retrospective analyses.

Analysis of the possibilities and limits of the Moldflow method

NASA Astrophysics Data System (ADS)

Brierre, M.

1982-01-01

The Moldflow information and computation service is presented. Moldflow is a computer program and data bank available as a computer aid to dimensioning thermoplastic injection molding equipment and processes. It is based on the simultaneous solution of thermal and rheological equations and is intended to completely simulate the injection process. The Moldflow system is described and algorithms are discussed, based on Moldflow listings.

User's guide to resin infusion simulation program in the FORTRAN language

NASA Technical Reports Server (NTRS)

Weideman, Mark H.; Hammond, Vince H.; Loos, Alfred C.

1992-01-01

RTMCL is a user friendly computer code which simulates the manufacture of fabric composites by the resin infusion process. The computer code is based on the process simulation model described in reference 1. Included in the user's guide is a detailed step by step description of how to run the program and enter and modify the input data set. Sample input and output files are included along with an explanation of the results. Finally, a complete listing of the program is provided.

A Fast Synthetic Aperture Radar Raw Data Simulation Using Cloud Computing.

PubMed

Li, Zhixin; Su, Dandan; Zhu, Haijiang; Li, Wei; Zhang, Fan; Li, Ruirui

2017-01-08

Synthetic Aperture Radar (SAR) raw data simulation is a fundamental problem in radar system design and imaging algorithm research. The growth of surveying swath and resolution results in a significant increase in data volume and simulation period, which can be considered to be a comprehensive data intensive and computing intensive issue. Although several high performance computing (HPC) methods have demonstrated their potential for accelerating simulation, the input/output (I/O) bottleneck of huge raw data has not been eased. In this paper, we propose a cloud computing based SAR raw data simulation algorithm, which employs the MapReduce model to accelerate the raw data computing and the Hadoop distributed file system (HDFS) for fast I/O access. The MapReduce model is designed for the irregular parallel accumulation of raw data simulation, which greatly reduces the parallel efficiency of graphics processing unit (GPU) based simulation methods. In addition, three kinds of optimization strategies are put forward from the aspects of programming model, HDFS configuration and scheduling. The experimental results show that the cloud computing based algorithm achieves 4_ speedup over the baseline serial approach in an 8-node cloud environment, and each optimization strategy can improve about 20%. This work proves that the proposed cloud algorithm is capable of solving the computing intensive and data intensive issues in SAR raw data simulation, and is easily extended to large scale computing to achieve higher acceleration.

Computer Models of Personality: Implications for Measurement

ERIC Educational Resources Information Center

Cranton, P. A.

1976-01-01

Current research on computer models of personality is reviewed and categorized under five headings: (1) models of belief systems; (2) models of interpersonal behavior; (3) models of decision-making processes; (4) prediction models; and (5) theory-based simulations of specific processes. The use of computer models in personality measurement is…

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

Demeure, I.M.

The research presented here is concerned with representation techniques and tools to support the design, prototyping, simulation, and evaluation of message-based parallel, distributed computations. The author describes ParaDiGM-Parallel, Distributed computation Graph Model-a visual representation technique for parallel, message-based distributed computations. ParaDiGM provides several views of a computation depending on the aspect of concern. It is made of two complementary submodels, the DCPG-Distributed Computing Precedence Graph-model, and the PAM-Process Architecture Model-model. DCPGs are precedence graphs used to express the functionality of a computation in terms of tasks, message-passing, and data. PAM graphs are used to represent the partitioning of a computationmore » into schedulable units or processes, and the pattern of communication among those units. There is a natural mapping between the two models. He illustrates the utility of ParaDiGM as a representation technique by applying it to various computations (e.g., an adaptive global optimization algorithm, the client-server model). ParaDiGM representations are concise. They can be used in documenting the design and the implementation of parallel, distributed computations, in describing such computations to colleagues, and in comparing and contrasting various implementations of the same computation. He then describes VISA-VISual Assistant, a software tool to support the design, prototyping, and simulation of message-based parallel, distributed computations. VISA is based on the ParaDiGM model. In particular, it supports the editing of ParaDiGM graphs to describe the computations of interest, and the animation of these graphs to provide visual feedback during simulations. The graphs are supplemented with various attributes, simulation parameters, and interpretations which are procedures that can be executed by VISA.« less

Quantum decision-maker theory and simulation

NASA Astrophysics Data System (ADS)

Zak, Michail; Meyers, Ronald E.; Deacon, Keith S.

2000-07-01

A quantum device simulating the human decision making process is introduced. It consists of quantum recurrent nets generating stochastic processes which represent the motor dynamics, and of classical neural nets describing the evolution of probabilities of these processes which represent the mental dynamics. The autonomy of the decision making process is achieved by a feedback from the mental to motor dynamics which changes the stochastic matrix based upon the probability distribution. This feedback replaces unavailable external information by an internal knowledge- base stored in the mental model in the form of probability distributions. As a result, the coupled motor-mental dynamics is described by a nonlinear version of Markov chains which can decrease entropy without an external source of information. Applications to common sense based decisions as well as to evolutionary games are discussed. An example exhibiting self-organization is computed using quantum computer simulation. Force on force and mutual aircraft engagements using the quantum decision maker dynamics are considered.

Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces

NASA Astrophysics Data System (ADS)

Ferrando, N.; Gosálvez, M. A.; Cerdá, J.; Gadea, R.; Sato, K.

2011-03-01

Presently, dynamic surface-based models are required to contain increasingly larger numbers of points and to propagate them over longer time periods. For large numbers of surface points, the octree data structure can be used as a balance between low memory occupation and relatively rapid access to the stored data. For evolution rules that depend on neighborhood states, extended simulation periods can be obtained by using simplified atomistic propagation models, such as the Cellular Automata (CA). This method, however, has an intrinsic parallel updating nature and the corresponding simulations are highly inefficient when performed on classical Central Processing Units (CPUs), which are designed for the sequential execution of tasks. In this paper, a series of guidelines is presented for the efficient adaptation of octree-based, CA simulations of complex, evolving surfaces into massively parallel computing hardware. A Graphics Processing Unit (GPU) is used as a cost-efficient example of the parallel architectures. For the actual simulations, we consider the surface propagation during anisotropic wet chemical etching of silicon as a computationally challenging process with a wide-spread use in microengineering applications. A continuous CA model that is intrinsically parallel in nature is used for the time evolution. Our study strongly indicates that parallel computations of dynamically evolving surfaces simulated using CA methods are significantly benefited by the incorporation of octrees as support data structures, substantially decreasing the overall computational time and memory usage.

Design of a high-speed digital processing element for parallel simulation

NASA Technical Reports Server (NTRS)

Milner, E. J.; Cwynar, D. S.

1983-01-01

A prototype of a custom designed computer to be used as a processing element in a multiprocessor based jet engine simulator is described. The purpose of the custom design was to give the computer the speed and versatility required to simulate a jet engine in real time. Real time simulations are needed for closed loop testing of digital electronic engine controls. The prototype computer has a microcycle time of 133 nanoseconds. This speed was achieved by: prefetching the next instruction while the current one is executing, transporting data using high speed data busses, and using state of the art components such as a very large scale integration (VLSI) multiplier. Included are discussions of processing element requirements, design philosophy, the architecture of the custom designed processing element, the comprehensive instruction set, the diagnostic support software, and the development status of the custom design.

Modeling cell adhesion and proliferation: a cellular-automata based approach.

PubMed

Vivas, J; Garzón-Alvarado, D; Cerrolaza, M

Cell adhesion is a process that involves the interaction between the cell membrane and another surface, either a cell or a substrate. Unlike experimental tests, computer models can simulate processes and study the result of experiments in a shorter time and lower costs. One of the tools used to simulate biological processes is the cellular automata, which is a dynamic system that is discrete both in space and time. This work describes a computer model based on cellular automata for the adhesion process and cell proliferation to predict the behavior of a cell population in suspension and adhered to a substrate. The values of the simulated system were obtained through experimental tests on fibroblast monolayer cultures. The results allow us to estimate the cells settling time in culture as well as the adhesion and proliferation time. The change in the cells morphology as the adhesion over the contact surface progress was also observed. The formation of the initial link between cell and the substrate of the adhesion was observed after 100 min where the cell on the substrate retains its spherical morphology during the simulation. The cellular automata model developed is, however, a simplified representation of the steps in the adhesion process and the subsequent proliferation. A combined framework of experimental and computational simulation based on cellular automata was proposed to represent the fibroblast adhesion on substrates and changes in a macro-scale observed in the cell during the adhesion process. The approach showed to be simple and efficient.

Some Computer-Based Developments in Sociology.

ERIC Educational Resources Information Center

Heise, David R.; Simmons, Roberta G.

1985-01-01

Discusses several ways in which computers are being used in sociology and how they continue to change this discipline. Areas considered include data collection, data analysis, simulations of social processes based on mathematical models, and problem areas (including standardization concerns, training, and the financing of computing facilities).…

Accelerating Monte Carlo simulations of photon transport in a voxelized geometry using a massively parallel graphics processing unit

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

Badal, Andreu; Badano, Aldo

Purpose: It is a known fact that Monte Carlo simulations of radiation transport are computationally intensive and may require long computing times. The authors introduce a new paradigm for the acceleration of Monte Carlo simulations: The use of a graphics processing unit (GPU) as the main computing device instead of a central processing unit (CPU). Methods: A GPU-based Monte Carlo code that simulates photon transport in a voxelized geometry with the accurate physics models from PENELOPE has been developed using the CUDA programming model (NVIDIA Corporation, Santa Clara, CA). Results: An outline of the new code and a sample x-raymore » imaging simulation with an anthropomorphic phantom are presented. A remarkable 27-fold speed up factor was obtained using a GPU compared to a single core CPU. Conclusions: The reported results show that GPUs are currently a good alternative to CPUs for the simulation of radiation transport. Since the performance of GPUs is currently increasing at a faster pace than that of CPUs, the advantages of GPU-based software are likely to be more pronounced in the future.« less

Adaptive Crack Modeling with Interface Solid Elements for Plain and Fiber Reinforced Concrete Structures.

PubMed

Zhan, Yijian; Meschke, Günther

2017-07-08

The effective analysis of the nonlinear behavior of cement-based engineering structures not only demands physically-reliable models, but also computationally-efficient algorithms. Based on a continuum interface element formulation that is suitable to capture complex cracking phenomena in concrete materials and structures, an adaptive mesh processing technique is proposed for computational simulations of plain and fiber-reinforced concrete structures to progressively disintegrate the initial finite element mesh and to add degenerated solid elements into the interfacial gaps. In comparison with the implementation where the entire mesh is processed prior to the computation, the proposed adaptive cracking model allows simulating the failure behavior of plain and fiber-reinforced concrete structures with remarkably reduced computational expense.

Adaptive Crack Modeling with Interface Solid Elements for Plain and Fiber Reinforced Concrete Structures

PubMed Central

Zhan, Yijian

2017-01-01

The effective analysis of the nonlinear behavior of cement-based engineering structures not only demands physically-reliable models, but also computationally-efficient algorithms. Based on a continuum interface element formulation that is suitable to capture complex cracking phenomena in concrete materials and structures, an adaptive mesh processing technique is proposed for computational simulations of plain and fiber-reinforced concrete structures to progressively disintegrate the initial finite element mesh and to add degenerated solid elements into the interfacial gaps. In comparison with the implementation where the entire mesh is processed prior to the computation, the proposed adaptive cracking model allows simulating the failure behavior of plain and fiber-reinforced concrete structures with remarkably reduced computational expense. PMID:28773130

Improvements to information management systems simulator

NASA Technical Reports Server (NTRS)

Bilek, R. W.

1972-01-01

The performance of personnel in the augmentation and improvement of the interactive IMSIM information management simulation model is summarized. With this augmented model, NASA now has even greater capabilities for the simulation of computer system configurations, data processing loads imposed on these configurations, and executive software to control system operations. Through these simulations, NASA has an extremely cost effective capability for the design and analysis of computer-based data management systems.

The TeraShake Computational Platform for Large-Scale Earthquake Simulations

NASA Astrophysics Data System (ADS)

Cui, Yifeng; Olsen, Kim; Chourasia, Amit; Moore, Reagan; Maechling, Philip; Jordan, Thomas

Geoscientific and computer science researchers with the Southern California Earthquake Center (SCEC) are conducting a large-scale, physics-based, computationally demanding earthquake system science research program with the goal of developing predictive models of earthquake processes. The computational demands of this program continue to increase rapidly as these researchers seek to perform physics-based numerical simulations of earthquake processes for larger meet the needs of this research program, a multiple-institution team coordinated by SCEC has integrated several scientific codes into a numerical modeling-based research tool we call the TeraShake computational platform (TSCP). A central component in the TSCP is a highly scalable earthquake wave propagation simulation program called the TeraShake anelastic wave propagation (TS-AWP) code. In this chapter, we describe how we extended an existing, stand-alone, wellvalidated, finite-difference, anelastic wave propagation modeling code into the highly scalable and widely used TS-AWP and then integrated this code into the TeraShake computational platform that provides end-to-end (initialization to analysis) research capabilities. We also describe the techniques used to enhance the TS-AWP parallel performance on TeraGrid supercomputers, as well as the TeraShake simulations phases including input preparation, run time, data archive management, and visualization. As a result of our efforts to improve its parallel efficiency, the TS-AWP has now shown highly efficient strong scaling on over 40K processors on IBM’s BlueGene/L Watson computer. In addition, the TSCP has developed into a computational system that is useful to many members of the SCEC community for performing large-scale earthquake simulations.

Computer simulation of the metastatic progression.

PubMed

Wedemann, Gero; Bethge, Anja; Haustein, Volker; Schumacher, Udo

2014-01-01

A novel computer model based on a discrete event simulation procedure describes quantitatively the processes underlying the metastatic cascade. Analytical functions describe the size of the primary tumor and the metastases, while a rate function models the intravasation events of the primary tumor and metastases. Events describe the behavior of the malignant cells until the formation of new metastases. The results of the computer simulations are in quantitative agreement with clinical data determined from a patient with hepatocellular carcinoma in the liver. The model provides a more detailed view on the process than a conventional mathematical model. In particular, the implications of interventions on metastasis formation can be calculated.

Efficiency and Accuracy in Thermal Simulation of Powder Bed Fusion of Bulk Metallic Glass

NASA Astrophysics Data System (ADS)

Lindwall, J.; Malmelöv, A.; Lundbäck, A.; Lindgren, L.-E.

2018-05-01

Additive manufacturing by powder bed fusion processes can be utilized to create bulk metallic glass as the process yields considerably high cooling rates. However, there is a risk that reheated material set in layers may become devitrified, i.e., crystallize. Therefore, it is advantageous to simulate the process to fully comprehend it and design it to avoid the aforementioned risk. However, a detailed simulation is computationally demanding. It is necessary to increase the computational speed while maintaining accuracy of the computed temperature field in critical regions. The current study evaluates a few approaches based on temporal reduction to achieve this. It is found that the evaluated approaches save a lot of time and accurately predict the temperature history.

Computational Analysis and Simulation of Empathic Behaviors: a Survey of Empathy Modeling with Behavioral Signal Processing Framework.

PubMed

Xiao, Bo; Imel, Zac E; Georgiou, Panayiotis; Atkins, David C; Narayanan, Shrikanth S

2016-05-01

Empathy is an important psychological process that facilitates human communication and interaction. Enhancement of empathy has profound significance in a range of applications. In this paper, we review emerging directions of research on computational analysis of empathy expression and perception as well as empathic interactions, including their simulation. We summarize the work on empathic expression analysis by the targeted signal modalities (e.g., text, audio, and facial expressions). We categorize empathy simulation studies into theory-based emotion space modeling or application-driven user and context modeling. We summarize challenges in computational study of empathy including conceptual framing and understanding of empathy, data availability, appropriate use and validation of machine learning techniques, and behavior signal processing. Finally, we propose a unified view of empathy computation and offer a series of open problems for future research.

Modelling rollover behaviour of exacavator-based forest machines

Treesearch

M.W. Veal; S.E. Taylor; Robert B. Rummer

2003-01-01

This poster presentation provides results from analytical and computer simulation models of rollover behaviour of hydraulic excavators. These results are being used as input to the operator protective structure standards development process. Results from rigid body mechanics and computer simulation methods agree well with field rollover test data. These results show...

Real-time simulation of a spiking neural network model of the basal ganglia circuitry using general purpose computing on graphics processing units.

PubMed

Igarashi, Jun; Shouno, Osamu; Fukai, Tomoki; Tsujino, Hiroshi

2011-11-01

Real-time simulation of a biologically realistic spiking neural network is necessary for evaluation of its capacity to interact with real environments. However, the real-time simulation of such a neural network is difficult due to its high computational costs that arise from two factors: (1) vast network size and (2) the complicated dynamics of biologically realistic neurons. In order to address these problems, mainly the latter, we chose to use general purpose computing on graphics processing units (GPGPUs) for simulation of such a neural network, taking advantage of the powerful computational capability of a graphics processing unit (GPU). As a target for real-time simulation, we used a model of the basal ganglia that has been developed according to electrophysiological and anatomical knowledge. The model consists of heterogeneous populations of 370 spiking model neurons, including computationally heavy conductance-based models, connected by 11,002 synapses. Simulation of the model has not yet been performed in real-time using a general computing server. By parallelization of the model on the NVIDIA Geforce GTX 280 GPU in data-parallel and task-parallel fashion, faster-than-real-time simulation was robustly realized with only one-third of the GPU's total computational resources. Furthermore, we used the GPU's full computational resources to perform faster-than-real-time simulation of three instances of the basal ganglia model; these instances consisted of 1100 neurons and 33,006 synapses and were synchronized at each calculation step. Finally, we developed software for simultaneous visualization of faster-than-real-time simulation output. These results suggest the potential power of GPGPU techniques in real-time simulation of realistic neural networks. Copyright © 2011 Elsevier Ltd. All rights reserved.

Launch Site Computer Simulation and its Application to Processes

NASA Technical Reports Server (NTRS)

Sham, Michael D.

1995-01-01

This paper provides an overview of computer simulation, the Lockheed developed STS Processing Model, and the application of computer simulation to a wide range of processes. The STS Processing Model is an icon driven model that uses commercial off the shelf software and a Macintosh personal computer. While it usually takes one year to process and launch 8 space shuttles, with the STS Processing Model this process is computer simulated in about 5 minutes. Facilities, orbiters, or ground support equipment can be added or deleted and the impact on launch rate, facility utilization, or other factors measured as desired. This same computer simulation technology can be used to simulate manufacturing, engineering, commercial, or business processes. The technology does not require an 'army' of software engineers to develop and operate, but instead can be used by the layman with only a minimal amount of training. Instead of making changes to a process and realizing the results after the fact, with computer simulation, changes can be made and processes perfected before they are implemented.

Computer simulations in the high school: students' cognitive stages, science process skills and academic achievement in microbiology

NASA Astrophysics Data System (ADS)

Huppert, J.; Michal Lomask, S.; Lazarowitz, R.

2002-08-01

Computer-assisted learning, including simulated experiments, has great potential to address the problem solving process which is a complex activity. It requires a highly structured approach in order to understand the use of simulations as an instructional device. This study is based on a computer simulation program, 'The Growth Curve of Microorganisms', which required tenth grade biology students to use problem solving skills whilst simultaneously manipulating three independent variables in one simulated experiment. The aims were to investigate the computer simulation's impact on students' academic achievement and on their mastery of science process skills in relation to their cognitive stages. The results indicate that the concrete and transition operational students in the experimental group achieved significantly higher academic achievement than their counterparts in the control group. The higher the cognitive operational stage, the higher students' achievement was, except in the control group where students in the concrete and transition operational stages did not differ. Girls achieved equally with the boys in the experimental group. Students' academic achievement may indicate the potential impact a computer simulation program can have, enabling students with low reasoning abilities to cope successfully with learning concepts and principles in science which require high cognitive skills.

[The characteristics of computer simulation of traffic accidents].

PubMed

Zou, Dong-Hua; Liu, Ning-Guo; Chen, Jian-Guo; Jin, Xian-Long; Zhang, Xiao-Yun; Zhang, Jian-Hua; Chen, Yi-Jiu

2008-12-01

To reconstruct the collision process of traffic accident and the injury mode of the victim by computer simulation technology in forensic assessment of traffic accident. Forty actual accidents were reconstructed by stimulation software and high performance computer based on analysis of the trace evidences at the scene, damage of the vehicles and injury of the victims, with 2 cases discussed in details. The reconstruction correlated very well in 28 cases, well in 9 cases, and suboptimal in 3 cases with the above parameters. Accurate reconstruction of the accident would be helpful for assessment of the injury mechanism of the victims. Reconstruction of the collision process of traffic accident and the injury mechanism of the victim by computer simulation is useful in traffic accident assessment.

Graphics processing unit based computation for NDE applications

NASA Astrophysics Data System (ADS)

Nahas, C. A.; Rajagopal, Prabhu; Balasubramaniam, Krishnan; Krishnamurthy, C. V.

2012-05-01

Advances in parallel processing in recent years are helping to improve the cost of numerical simulation. Breakthroughs in Graphical Processing Unit (GPU) based computation now offer the prospect of further drastic improvements. The introduction of 'compute unified device architecture' (CUDA) by NVIDIA (the global technology company based in Santa Clara, California, USA) has made programming GPUs for general purpose computing accessible to the average programmer. Here we use CUDA to develop parallel finite difference schemes as applicable to two problems of interest to NDE community, namely heat diffusion and elastic wave propagation. The implementations are for two-dimensions. Performance improvement of the GPU implementation against serial CPU implementation is then discussed.

About Distributed Simulation-based Optimization of Forming Processes using a Grid Architecture

NASA Astrophysics Data System (ADS)

Grauer, Manfred; Barth, Thomas

2004-06-01

Permanently increasing complexity of products and their manufacturing processes combined with a shorter "time-to-market" leads to more and more use of simulation and optimization software systems for product design. Finding a "good" design of a product implies the solution of computationally expensive optimization problems based on the results of simulation. Due to the computational load caused by the solution of these problems, the requirements on the Information&Telecommunication (IT) infrastructure of an enterprise or research facility are shifting from stand-alone resources towards the integration of software and hardware resources in a distributed environment for high-performance computing. Resources can either comprise software systems, hardware systems, or communication networks. An appropriate IT-infrastructure must provide the means to integrate all these resources and enable their use even across a network to cope with requirements from geographically distributed scenarios, e.g. in computational engineering and/or collaborative engineering. Integrating expert's knowledge into the optimization process is inevitable in order to reduce the complexity caused by the number of design variables and the high dimensionality of the design space. Hence, utilization of knowledge-based systems must be supported by providing data management facilities as a basis for knowledge extraction from product data. In this paper, the focus is put on a distributed problem solving environment (PSE) capable of providing access to a variety of necessary resources and services. A distributed approach integrating simulation and optimization on a network of workstations and cluster systems is presented. For geometry generation the CAD-system CATIA is used which is coupled with the FEM-simulation system INDEED for simulation of sheet-metal forming processes and the problem solving environment OpTiX for distributed optimization.

A Web-based Distributed Voluntary Computing Platform for Large Scale Hydrological Computations

NASA Astrophysics Data System (ADS)

Demir, I.; Agliamzanov, R.

2014-12-01

Distributed volunteer computing can enable researchers and scientist to form large parallel computing environments to utilize the computing power of the millions of computers on the Internet, and use them towards running large scale environmental simulations and models to serve the common good of local communities and the world. Recent developments in web technologies and standards allow client-side scripting languages to run at speeds close to native application, and utilize the power of Graphics Processing Units (GPU). Using a client-side scripting language like JavaScript, we have developed an open distributed computing framework that makes it easy for researchers to write their own hydrologic models, and run them on volunteer computers. Users will easily enable their websites for visitors to volunteer sharing their computer resources to contribute running advanced hydrological models and simulations. Using a web-based system allows users to start volunteering their computational resources within seconds without installing any software. The framework distributes the model simulation to thousands of nodes in small spatial and computational sizes. A relational database system is utilized for managing data connections and queue management for the distributed computing nodes. In this paper, we present a web-based distributed volunteer computing platform to enable large scale hydrological simulations and model runs in an open and integrated environment.

A Fast Synthetic Aperture Radar Raw Data Simulation Using Cloud Computing

PubMed Central

Li, Zhixin; Su, Dandan; Zhu, Haijiang; Li, Wei; Zhang, Fan; Li, Ruirui

2017-01-01

Synthetic Aperture Radar (SAR) raw data simulation is a fundamental problem in radar system design and imaging algorithm research. The growth of surveying swath and resolution results in a significant increase in data volume and simulation period, which can be considered to be a comprehensive data intensive and computing intensive issue. Although several high performance computing (HPC) methods have demonstrated their potential for accelerating simulation, the input/output (I/O) bottleneck of huge raw data has not been eased. In this paper, we propose a cloud computing based SAR raw data simulation algorithm, which employs the MapReduce model to accelerate the raw data computing and the Hadoop distributed file system (HDFS) for fast I/O access. The MapReduce model is designed for the irregular parallel accumulation of raw data simulation, which greatly reduces the parallel efficiency of graphics processing unit (GPU) based simulation methods. In addition, three kinds of optimization strategies are put forward from the aspects of programming model, HDFS configuration and scheduling. The experimental results show that the cloud computing based algorithm achieves 4× speedup over the baseline serial approach in an 8-node cloud environment, and each optimization strategy can improve about 20%. This work proves that the proposed cloud algorithm is capable of solving the computing intensive and data intensive issues in SAR raw data simulation, and is easily extended to large scale computing to achieve higher acceleration. PMID:28075343

Developing Subdomain Allocation Algorithms Based on Spatial and Communicational Constraints to Accelerate Dust Storm Simulation

PubMed Central

Gui, Zhipeng; Yu, Manzhu; Yang, Chaowei; Jiang, Yunfeng; Chen, Songqing; Xia, Jizhe; Huang, Qunying; Liu, Kai; Li, Zhenlong; Hassan, Mohammed Anowarul; Jin, Baoxuan

2016-01-01

Dust storm has serious disastrous impacts on environment, human health, and assets. The developments and applications of dust storm models have contributed significantly to better understand and predict the distribution, intensity and structure of dust storms. However, dust storm simulation is a data and computing intensive process. To improve the computing performance, high performance computing has been widely adopted by dividing the entire study area into multiple subdomains and allocating each subdomain on different computing nodes in a parallel fashion. Inappropriate allocation may introduce imbalanced task loads and unnecessary communications among computing nodes. Therefore, allocation is a key factor that may impact the efficiency of parallel process. An allocation algorithm is expected to consider the computing cost and communication cost for each computing node to minimize total execution time and reduce overall communication cost for the entire simulation. This research introduces three algorithms to optimize the allocation by considering the spatial and communicational constraints: 1) an Integer Linear Programming (ILP) based algorithm from combinational optimization perspective; 2) a K-Means and Kernighan-Lin combined heuristic algorithm (K&K) integrating geometric and coordinate-free methods by merging local and global partitioning; 3) an automatic seeded region growing based geometric and local partitioning algorithm (ASRG). The performance and effectiveness of the three algorithms are compared based on different factors. Further, we adopt the K&K algorithm as the demonstrated algorithm for the experiment of dust model simulation with the non-hydrostatic mesoscale model (NMM-dust) and compared the performance with the MPI default sequential allocation. The results demonstrate that K&K method significantly improves the simulation performance with better subdomain allocation. This method can also be adopted for other relevant atmospheric and numerical modeling. PMID:27044039

Applying GIS and high performance agent-based simulation for managing an Old World Screwworm fly invasion of Australia.

PubMed

Welch, M C; Kwan, P W; Sajeev, A S M

2014-10-01

Agent-based modelling has proven to be a promising approach for developing rich simulations for complex phenomena that provide decision support functions across a broad range of areas including biological, social and agricultural sciences. This paper demonstrates how high performance computing technologies, namely General-Purpose Computing on Graphics Processing Units (GPGPU), and commercial Geographic Information Systems (GIS) can be applied to develop a national scale, agent-based simulation of an incursion of Old World Screwworm fly (OWS fly) into the Australian mainland. The development of this simulation model leverages the combination of massively data-parallel processing capabilities supported by NVidia's Compute Unified Device Architecture (CUDA) and the advanced spatial visualisation capabilities of GIS. These technologies have enabled the implementation of an individual-based, stochastic lifecycle and dispersal algorithm for the OWS fly invasion. The simulation model draws upon a wide range of biological data as input to stochastically determine the reproduction and survival of the OWS fly through the different stages of its lifecycle and dispersal of gravid females. Through this model, a highly efficient computational platform has been developed for studying the effectiveness of control and mitigation strategies and their associated economic impact on livestock industries can be materialised. Copyright © 2014 International Atomic Energy Agency 2014. Published by Elsevier B.V. All rights reserved.

Towards real-time photon Monte Carlo dose calculation in the cloud

NASA Astrophysics Data System (ADS)

Ziegenhein, Peter; Kozin, Igor N.; Kamerling, Cornelis Ph; Oelfke, Uwe

2017-06-01

Near real-time application of Monte Carlo (MC) dose calculation in clinic and research is hindered by the long computational runtimes of established software. Currently, fast MC software solutions are available utilising accelerators such as graphical processing units (GPUs) or clusters based on central processing units (CPUs). Both platforms are expensive in terms of purchase costs and maintenance and, in case of the GPU, provide only limited scalability. In this work we propose a cloud-based MC solution, which offers high scalability of accurate photon dose calculations. The MC simulations run on a private virtual supercomputer that is formed in the cloud. Computational resources can be provisioned dynamically at low cost without upfront investment in expensive hardware. A client-server software solution has been developed which controls the simulations and transports data to and from the cloud efficiently and securely. The client application integrates seamlessly into a treatment planning system. It runs the MC simulation workflow automatically and securely exchanges simulation data with the server side application that controls the virtual supercomputer. Advanced encryption standards were used to add an additional security layer, which encrypts and decrypts patient data on-the-fly at the processor register level. We could show that our cloud-based MC framework enables near real-time dose computation. It delivers excellent linear scaling for high-resolution datasets with absolute runtimes of 1.1 seconds to 10.9 seconds for simulating a clinical prostate and liver case up to 1% statistical uncertainty. The computation runtimes include the transportation of data to and from the cloud as well as process scheduling and synchronisation overhead. Cloud-based MC simulations offer a fast, affordable and easily accessible alternative for near real-time accurate dose calculations to currently used GPU or cluster solutions.

Towards real-time photon Monte Carlo dose calculation in the cloud.

PubMed

Ziegenhein, Peter; Kozin, Igor N; Kamerling, Cornelis Ph; Oelfke, Uwe

2017-06-07

Near real-time application of Monte Carlo (MC) dose calculation in clinic and research is hindered by the long computational runtimes of established software. Currently, fast MC software solutions are available utilising accelerators such as graphical processing units (GPUs) or clusters based on central processing units (CPUs). Both platforms are expensive in terms of purchase costs and maintenance and, in case of the GPU, provide only limited scalability. In this work we propose a cloud-based MC solution, which offers high scalability of accurate photon dose calculations. The MC simulations run on a private virtual supercomputer that is formed in the cloud. Computational resources can be provisioned dynamically at low cost without upfront investment in expensive hardware. A client-server software solution has been developed which controls the simulations and transports data to and from the cloud efficiently and securely. The client application integrates seamlessly into a treatment planning system. It runs the MC simulation workflow automatically and securely exchanges simulation data with the server side application that controls the virtual supercomputer. Advanced encryption standards were used to add an additional security layer, which encrypts and decrypts patient data on-the-fly at the processor register level. We could show that our cloud-based MC framework enables near real-time dose computation. It delivers excellent linear scaling for high-resolution datasets with absolute runtimes of 1.1 seconds to 10.9 seconds for simulating a clinical prostate and liver case up to 1% statistical uncertainty. The computation runtimes include the transportation of data to and from the cloud as well as process scheduling and synchronisation overhead. Cloud-based MC simulations offer a fast, affordable and easily accessible alternative for near real-time accurate dose calculations to currently used GPU or cluster solutions.

Error Estimation and Uncertainty Propagation in Computational Fluid Mechanics

NASA Technical Reports Server (NTRS)

Zhu, J. Z.; He, Guowei; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

Numerical simulation has now become an integral part of engineering design process. Critical design decisions are routinely made based on the simulation results and conclusions. Verification and validation of the reliability of the numerical simulation is therefore vitally important in the engineering design processes. We propose to develop theories and methodologies that can automatically provide quantitative information about the reliability of the numerical simulation by estimating numerical approximation error, computational model induced errors and the uncertainties contained in the mathematical models so that the reliability of the numerical simulation can be verified and validated. We also propose to develop and implement methodologies and techniques that can control the error and uncertainty during the numerical simulation so that the reliability of the numerical simulation can be improved.

A computational model for simulating text comprehension.

PubMed

Lemaire, Benoît; Denhière, Guy; Bellissens, Cédrick; Jhean-Larose, Sandra

2006-11-01

In the present article, we outline the architecture of a computer program for simulating the process by which humans comprehend texts. The program is based on psycholinguistic theories about human memory and text comprehension processes, such as the construction-integration model (Kintsch, 1998), the latent semantic analysis theory of knowledge representation (Landauer & Dumais, 1997), and the predication algorithms (Kintsch, 2001; Lemaire & Bianco, 2003), and it is intended to help psycholinguists investigate the way humans comprehend texts.

GPU-based optical propagation simulator of a laser-processed crystal block for the X'tal cube PET detector.

PubMed

Ogata, Yuma; Ohnishi, Takashi; Moriya, Takahiro; Inadama, Naoko; Nishikido, Fumihiko; Yoshida, Eiji; Murayama, Hideo; Yamaya, Taiga; Haneishi, Hideaki

2014-01-01

The X'tal cube is a next-generation DOI detector for PET that we are developing to offer higher resolution and higher sensitivity than is available with present detectors. It is constructed from a cubic monolithic scintillation crystal and silicon photomultipliers which are coupled on various positions of the six surfaces of the cube. A laser-processing technique is applied to produce 3D optical boundaries composed of micro-cracks inside the monolithic scintillator crystal. The current configuration is based on an empirical trial of a laser-processed boundary. There is room to improve the spatial resolution by optimizing the setting of the laser-processed boundary. In fact, the laser-processing technique has high freedom in setting the parameters of the boundary such as size, pitch, and angle. Computer simulation can effectively optimize such parameters. In this study, to design optical characteristics properly for the laser-processed crystal, we developed a Monte Carlo simulator which can model arbitrary arrangements of laser-processed optical boundaries (LPBs). The optical characteristics of the LPBs were measured by use of a setup with a laser and a photo-diode, and then modeled in the simulator. The accuracy of the simulator was confirmed by comparison of position histograms obtained from the simulation and from experiments with a prototype detector composed of a cubic LYSO monolithic crystal with 6 × 6 × 6 segments and multi-pixel photon counters. Furthermore, the simulator was accelerated by parallel computing with general-purpose computing on a graphics processing unit. The calculation speed was about 400 times faster than that with a CPU.

A meta-analysis of outcomes from the use of computer-simulated experiments in science education

NASA Astrophysics Data System (ADS)

Lejeune, John Van

The purpose of this study was to synthesize the findings from existing research on the effects of computer simulated experiments on students in science education. Results from 40 reports were integrated by the process of meta-analysis to examine the effect of computer-simulated experiments and interactive videodisc simulations on student achievement and attitudes. Findings indicated significant positive differences in both low-level and high-level achievement of students who use computer-simulated experiments and interactive videodisc simulations as compared to students who used more traditional learning activities. No significant differences in retention, student attitudes toward the subject, or toward the educational method were found. Based on the findings of this study, computer-simulated experiments and interactive videodisc simulations should be used to enhance students' learning in science, especially in cases where the use of traditional laboratory activities are expensive, dangerous, or impractical.

Accelerating sino-atrium computer simulations with graphic processing units.

PubMed

Zhang, Hong; Xiao, Zheng; Lin, Shien-fong

2015-01-01

Sino-atrial node cells (SANCs) play a significant role in rhythmic firing. To investigate their role in arrhythmia and interactions with the atrium, computer simulations based on cellular dynamic mathematical models are generally used. However, the large-scale computation usually makes research difficult, given the limited computational power of Central Processing Units (CPUs). In this paper, an accelerating approach with Graphic Processing Units (GPUs) is proposed in a simulation consisting of the SAN tissue and the adjoining atrium. By using the operator splitting method, the computational task was made parallel. Three parallelization strategies were then put forward. The strategy with the shortest running time was further optimized by considering block size, data transfer and partition. The results showed that for a simulation with 500 SANCs and 30 atrial cells, the execution time taken by the non-optimized program decreased 62% with respect to a serial program running on CPU. The execution time decreased by 80% after the program was optimized. The larger the tissue was, the more significant the acceleration became. The results demonstrated the effectiveness of the proposed GPU-accelerating methods and their promising applications in more complicated biological simulations.

Use of mechanistic simulations as a quantitative risk-ranking tool within the quality by design framework.

PubMed

Stocker, Elena; Toschkoff, Gregor; Sacher, Stephan; Khinast, Johannes G

2014-11-20

The purpose of this study is to evaluate the use of computer simulations for generating quantitative knowledge as a basis for risk ranking and mechanistic process understanding, as required by ICH Q9 on quality risk management systems. In this specific publication, the main focus is the demonstration of a risk assessment workflow, including a computer simulation for the generation of mechanistic understanding of active tablet coating in a pan coater. Process parameter screening studies are statistically planned under consideration of impacts on a potentially critical quality attribute, i.e., coating mass uniformity. Based on computer simulation data the process failure mode and effects analysis of the risk factors is performed. This results in a quantitative criticality assessment of process parameters and the risk priority evaluation of failure modes. The factor for a quantitative reassessment of the criticality and risk priority is the coefficient of variation, which represents the coating mass uniformity. The major conclusion drawn from this work is a successful demonstration of the integration of computer simulation in the risk management workflow leading to an objective and quantitative risk assessment. Copyright © 2014. Published by Elsevier B.V.

A Method for Combining Experimentation and Molecular Dynamics Simulation to Improve Cohesive Zone Models for Metallic Microstructures

NASA Technical Reports Server (NTRS)

Hochhalter, J. D.; Glaessgen, E. H.; Ingraffea, A. R.; Aquino, W. A.

2009-01-01

Fracture processes within a material begin at the nanometer length scale at which the formation, propagation, and interaction of fundamental damage mechanisms occur. Physics-based modeling of these atomic processes quickly becomes computationally intractable as the system size increases. Thus, a multiscale modeling method, based on the aggregation of fundamental damage processes occurring at the nanoscale within a cohesive zone model, is under development and will enable computationally feasible and physically meaningful microscale fracture simulation in polycrystalline metals. This method employs atomistic simulation to provide an optimization loop with an initial prediction of a cohesive zone model (CZM). This initial CZM is then applied at the crack front region within a finite element model. The optimization procedure iterates upon the CZM until the finite element model acceptably reproduces the near-crack-front displacement fields obtained from experimental observation. With this approach, a comparison can be made between the original CZM predicted by atomistic simulation and the converged CZM that is based on experimental observation. Comparison of the two CZMs gives insight into how atomistic simulation scales.

Numerical computation of hurricane effects on historic coastal hydrology in Southern Florida

USGS Publications Warehouse

Swain, Eric D.; Krohn, M. Dennis; Langtimm, Catherine A.

2015-01-01

The hindcast simulation estimated hydrologic processes for the 1926 to 1932 period. It shows promise as a simulator in long-term ecological studies to test hypotheses based on theoretical or empirical-based studies at larger landscape scales.

Computing the apparent centroid of radar targets

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

Lee, C.E.

1996-12-31

A high-frequency multibounce radar scattering code was used as a simulation platform for demonstrating an algorithm to compute the ARC of specific radar targets. To illustrate this simulation process, several targets models were used. Simulation results for a sphere model were used to determine the errors of approximation associated with the simulation; verifying the process. The severity of glint induced tracking errors was also illustrated using a model of an F-15 aircraft. It was shown, in a deterministic manner, that the ARC of a target can fall well outside its physical extent. Finally, the apparent radar centroid simulation based onmore » a ray casting procedure is well suited for use on most massively parallel computing platforms and could lead to the development of a near real-time radar tracking simulation for applications such as endgame fuzing, survivability, and vulnerability analyses using specific radar targets and fuze algorithms.« less

A method of computer modelling the lithium-ion batteries aging process based on the experimental characteristics

NASA Astrophysics Data System (ADS)

Czerepicki, A.; Koniak, M.

2017-06-01

The paper presents a method of modelling the processes of aging lithium-ion batteries, its implementation as a computer application and results for battery state estimation. Authors use previously developed behavioural battery model, which was built using battery operating characteristics obtained from the experiment. This model was implemented in the form of a computer program using a database to store battery characteristics. Batteries aging process is a new extended functionality of the model. Algorithm of computer simulation uses a real measurements of battery capacity as a function of the battery charge and discharge cycles number. Simulation allows to take into account the incomplete cycles of charge or discharge battery, which are characteristic for transport powered by electricity. The developed model was used to simulate the battery state estimation for different load profiles, obtained by measuring the movement of the selected means of transport.

Computational Analysis and Simulation of Empathic Behaviors: A Survey of Empathy Modeling with Behavioral Signal Processing Framework

PubMed Central

Xiao, Bo; Imel, Zac E.; Georgiou, Panayiotis; Atkins, David C.; Narayanan, Shrikanth S.

2017-01-01

Empathy is an important psychological process that facilitates human communication and interaction. Enhancement of empathy has profound significance in a range of applications. In this paper, we review emerging directions of research on computational analysis of empathy expression and perception as well as empathic interactions, including their simulation. We summarize the work on empathic expression analysis by the targeted signal modalities (e.g., text, audio, facial expressions). We categorize empathy simulation studies into theory-based emotion space modeling or application-driven user and context modeling. We summarize challenges in computational study of empathy including conceptual framing and understanding of empathy, data availability, appropriate use and validation of machine learning techniques, and behavior signal processing. Finally, we propose a unified view of empathy computation, and offer a series of open problems for future research. PMID:27017830

Automating approximate Bayesian computation by local linear regression.

PubMed

Thornton, Kevin R

2009-07-07

In several biological contexts, parameter inference often relies on computationally-intensive techniques. "Approximate Bayesian Computation", or ABC, methods based on summary statistics have become increasingly popular. A particular flavor of ABC based on using a linear regression to approximate the posterior distribution of the parameters, conditional on the summary statistics, is computationally appealing, yet no standalone tool exists to automate the procedure. Here, I describe a program to implement the method. The software package ABCreg implements the local linear-regression approach to ABC. The advantages are: 1. The code is standalone, and fully-documented. 2. The program will automatically process multiple data sets, and create unique output files for each (which may be processed immediately in R), facilitating the testing of inference procedures on simulated data, or the analysis of multiple data sets. 3. The program implements two different transformation methods for the regression step. 4. Analysis options are controlled on the command line by the user, and the program is designed to output warnings for cases where the regression fails. 5. The program does not depend on any particular simulation machinery (coalescent, forward-time, etc.), and therefore is a general tool for processing the results from any simulation. 6. The code is open-source, and modular.Examples of applying the software to empirical data from Drosophila melanogaster, and testing the procedure on simulated data, are shown. In practice, the ABCreg simplifies implementing ABC based on local-linear regression.

Experiences in teaching of modeling and simulation with emphasize on equation-based and acausal modeling techniques.

PubMed

Kulhánek, Tomáš; Ježek, Filip; Mateják, Marek; Šilar, Jan; Kofránek, Jří

2015-08-01

This work introduces experiences of teaching modeling and simulation for graduate students in the field of biomedical engineering. We emphasize the acausal and object-oriented modeling technique and we have moved from teaching block-oriented tool MATLAB Simulink to acausal and object oriented Modelica language, which can express the structure of the system rather than a process of computation. However, block-oriented approach is allowed in Modelica language too and students have tendency to express the process of computation. Usage of the exemplar acausal domains and approach allows students to understand the modeled problems much deeper. The causality of the computation is derived automatically by the simulation tool.

On Fast Post-Processing of Global Positioning System Simulator Truth Data and Receiver Measurements and Solutions Data

NASA Technical Reports Server (NTRS)

Kizhner, Semion; Day, John H. (Technical Monitor)

2000-01-01

Post-Processing of data related to a Global Positioning System (GPS) simulation is an important activity in qualification of a GPS receiver for space flight. Because a GPS simulator is a critical resource it is desirable to move off the pertinent simulation data from the simulator as soon as a test is completed. The simulator data files are usually moved to a Personal Computer (PC), where the post-processing of the receiver logged measurements and solutions data and simulated data is performed. Typically post-processing is accomplished using PC-based commercial software languages and tools. Because of commercial software systems generality their general-purpose functions are notoriously slow and more than often are the bottleneck problem even for short duration experiments. For example, it may take 8 hours to post-process data from a 6-hour simulation. There is a need to do post-processing faster, especially in order to use the previous test results as feedback for a next simulation setup. This paper demonstrates that a fast software linear interpolation algorithm is applicable to a large class of engineering problems, like GPS simulation data post-processing, where computational time is a critical resource and is one of the most important considerations. An approach is developed that allows to speed-up post-processing by an order of magnitude. It is based on improving the post-processing bottleneck interpolation algorithm using apriori information that is specific to the GPS simulation application. The presented post-processing scheme was used in support of a few successful space flight missions carrying GPS receivers. A future approach to solving the post-processing performance problem using Field Programmable Gate Array (FPGA) technology is described.

Development of capability for microtopography-resolving simulations of hydrologic processes in permafrost affected regions

NASA Astrophysics Data System (ADS)

Painter, S.; Moulton, J. D.; Berndt, M.; Coon, E.; Garimella, R.; Lewis, K. C.; Manzini, G.; Mishra, P.; Travis, B. J.; Wilson, C. J.

2012-12-01

The frozen soils of the Arctic and subarctic regions contain vast amounts of stored organic carbon. This carbon is vulnerable to release to the atmosphere as temperatures warm and permafrost degrades. Understanding the response of the subsurface and surface hydrologic system to degrading permafrost is key to understanding the rate, timing, and chemical form of potential carbon releases to the atmosphere. Simulating the hydrologic system in degrading permafrost regions is challenging because of the potential for topographic evolution and associated drainage network reorganization as permafrost thaws and massive ground ice melts. The critical process models required for simulating hydrology include subsurface thermal hydrology of freezing/thawing soils, thermal processes within ice wedges, mechanical deformation processes, overland flow, and surface energy balances including snow dynamics. A new simulation tool, the Arctic Terrestrial Simulator (ATS), is being developed to simulate these coupled processes. The computational infrastructure must accommodate fully unstructured grids that track evolving topography, allow accurate solutions on distorted grids, provide robust and efficient solutions on highly parallel computer architectures, and enable flexibility in the strategies for coupling among the various processes. The ATS is based on Amanzi (Moulton et al. 2012), an object-oriented multi-process simulator written in C++ that provides much of the necessary computational infrastructure. Status and plans for the ATS including major hydrologic process models and validation strategies will be presented. Highly parallel simulations of overland flow using high-resolution digital elevation maps of polygonal patterned ground landscapes demonstrate the feasibility of the approach. Simulations coupling three-phase subsurface thermal hydrology with a simple thaw-induced subsidence model illustrate the strong feedbacks among the processes. D. Moulton, M. Berndt, M. Day, J. Meza, et al., High-Level Design of Amanzi, the Multi-Process High Performance Computing Simulator, Technical Report ASCEM-HPC-2011-03-1, DOE Environmental Management, 2012.

[Acquiring skills in malignant hyperthermia crisis management: comparison of high-fidelity simulation versus computer-based case study].

PubMed

Mejía, Vilma; Gonzalez, Carlos; Delfino, Alejandro E; Altermatt, Fernando R; Corvetto, Marcia A

The primary purpose of this study was to compare the effect of high fidelity simulation versus a computer-based case solving self-study, in skills acquisition about malignant hyperthermia on first year anesthesiology residents. After institutional ethical committee approval, 31 first year anesthesiology residents were enrolled in this prospective randomized single-blinded study. Participants were randomized to either a High Fidelity Simulation Scenario or a computer-based Case Study about malignant hyperthermia. After the intervention, all subjects' performance in was assessed through a high fidelity simulation scenario using a previously validated assessment rubric. Additionally, knowledge tests and a satisfaction survey were applied. Finally, a semi-structured interview was done to assess self-perception of reasoning process and decision-making. 28 first year residents finished successfully the study. Resident's management skill scores were globally higher in High Fidelity Simulation versus Case Study, however they were significant in 4 of the 8 performance rubric elements: recognize signs and symptoms (p = 0.025), prioritization of initial actions of management (p = 0.003), recognize complications (p = 0.025) and communication (p = 0.025). Average scores from pre- and post-test knowledge questionnaires improved from 74% to 85% in the High Fidelity Simulation group, and decreased from 78% to 75% in the Case Study group (p = 0.032). Regarding the qualitative analysis, there was no difference in factors influencing the student's process of reasoning and decision-making with both teaching strategies. Simulation-based training with a malignant hyperthermia high-fidelity scenario was superior to computer-based case study, improving knowledge and skills in malignant hyperthermia crisis management, with a very good satisfaction level in anesthesia residents. Copyright © 2018 Sociedade Brasileira de Anestesiologia. Publicado por Elsevier Editora Ltda. All rights reserved.

A manifold learning approach to data-driven computational materials and processes

NASA Astrophysics Data System (ADS)

Ibañez, Ruben; Abisset-Chavanne, Emmanuelle; Aguado, Jose Vicente; Gonzalez, David; Cueto, Elias; Duval, Jean Louis; Chinesta, Francisco

2017-10-01

Standard simulation in classical mechanics is based on the use of two very different types of equations. The first one, of axiomatic character, is related to balance laws (momentum, mass, energy, …), whereas the second one consists of models that scientists have extracted from collected, natural or synthetic data. In this work we propose a new method, able to directly link data to computers in order to perform numerical simulations. These simulations will employ universal laws while minimizing the need of explicit, often phenomenological, models. They are based on manifold learning methodologies.

Clinical results of computerized tomography-based simulation with laser patient marking.

PubMed

Ragan, D P; Forman, J D; He, T; Mesina, C F

1996-02-01

Accuracy of a patient treatment portal marking device and computerized tomography (CT) simulation have been clinically tested. A CT-based simulator has been assembled based on a commercial CT scanner. This includes visualization software and a computer-controlled laser drawing device. This laser drawing device is used to transfer the setup, central axis, and/or radiation portals from the CT simulator to the patient for appropriate patient skin marking. A protocol for clinical testing is reported. Twenty-five prospectively, sequentially accessioned patients have been analyzed. The simulation process can be completed in an average time of 62 min. Under many cases, the treatment portals can be designed and the patient marked in one session. Mechanical accuracy of the system was found to be within +/- 1mm. The portal projection accuracy in clinical cases is observed to be better than +/- 1.2 mm. Operating costs are equivalent to the conventional simulation process it replaces. Computed tomography simulation is a clinical accurate substitute for conventional simulation when used with an appropriate patient marking system and digitally reconstructed radiographs. Personnel time spent in CT simulation is equivalent to time in conventional simulation.

A POLLUTION REDUCTION METHODOLOGY FOR CHEMICAL PROCESS SIMULATORS

EPA Science Inventory

A pollution minimization methodology was developed for chemical process design using computer simulation. It is based on a pollution balance that at steady state is used to define a pollution index with units of mass of pollution per mass of products. The pollution balance has be...

Real-Time Monitoring of Scada Based Control System for Filling Process

NASA Astrophysics Data System (ADS)

Soe, Aung Kyaw; Myint, Aung Naing; Latt, Maung Maung; Theingi

2008-10-01

This paper is a design of real-time monitoring for filling system using Supervisory Control and Data Acquisition (SCADA). The monitoring of production process is described in real-time using Visual Basic.Net programming under Visual Studio 2005 software without SCADA software. The software integrators are programmed to get the required information for the configuration screens. Simulation of components is expressed on the computer screen using parallel port between computers and filling devices. The programs of real-time simulation for the filling process from the pure drinking water industry are provided.

Modelling and simulation techniques for membrane biology.

PubMed

Burrage, Kevin; Hancock, John; Leier, André; Nicolau, Dan V

2007-07-01

One of the most important aspects of Computational Cell Biology is the understanding of the complicated dynamical processes that take place on plasma membranes. These processes are often so complicated that purely temporal models cannot always adequately capture the dynamics. On the other hand, spatial models can have large computational overheads. In this article, we review some of these issues with respect to chemistry, membrane microdomains and anomalous diffusion and discuss how to select appropriate modelling and simulation paradigms based on some or all the following aspects: discrete, continuous, stochastic, delayed and complex spatial processes.

Optimal segmentation and packaging process

DOEpatents

Kostelnik, Kevin M.; Meservey, Richard H.; Landon, Mark D.

1999-01-01

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

Simulation and optimization of an experimental membrane wastewater treatment plant using computational intelligence methods.

PubMed

Ludwig, T; Kern, P; Bongards, M; Wolf, C

2011-01-01

The optimization of relaxation and filtration times of submerged microfiltration flat modules in membrane bioreactors used for municipal wastewater treatment is essential for efficient plant operation. However, the optimization and control of such plants and their filtration processes is a challenging problem due to the underlying highly nonlinear and complex processes. This paper presents the use of genetic algorithms for this optimization problem in conjunction with a fully calibrated simulation model, as computational intelligence methods are perfectly suited to the nonconvex multi-objective nature of the optimization problems posed by these complex systems. The simulation model is developed and calibrated using membrane modules from the wastewater simulation software GPS-X based on the Activated Sludge Model No.1 (ASM1). Simulation results have been validated at a technical reference plant. They clearly show that filtration process costs for cleaning and energy can be reduced significantly by intelligent process optimization.

Quantifying uncertainty and computational complexity for pore-scale simulations

NASA Astrophysics Data System (ADS)

Chen, C.; Yuan, Z.; Wang, P.; Yang, X.; Zhenyan, L.

2016-12-01

Pore-scale simulation is an essential tool to understand the complex physical process in many environmental problems, from multi-phase flow in the subsurface to fuel cells. However, in practice, factors such as sample heterogeneity, data sparsity and in general, our insufficient knowledge of the underlying process, render many simulation parameters and hence the prediction results uncertain. Meanwhile, most pore-scale simulations (in particular, direct numerical simulation) incur high computational cost due to finely-resolved spatio-temporal scales, which further limits our data/samples collection. To address those challenges, we propose a novel framework based on the general polynomial chaos (gPC) and build a surrogate model representing the essential features of the underlying system. To be specific, we apply the novel framework to analyze the uncertainties of the system behavior based on a series of pore-scale numerical experiments, such as flow and reactive transport in 2D heterogeneous porous media and 3D packed beds. Comparing with recent pore-scale uncertainty quantification studies using Monte Carlo techniques, our new framework requires fewer number of realizations and hence considerably reduce the overall computational cost, while maintaining the desired accuracy.

Development of IR imaging system simulator

NASA Astrophysics Data System (ADS)

Xiang, Xinglang; He, Guojing; Dong, Weike; Dong, Lu

2017-02-01

To overcome the disadvantages of the tradition semi-physical simulation and injection simulation equipment in the performance evaluation of the infrared imaging system (IRIS), a low-cost and reconfigurable IRIS simulator, which can simulate the realistic physical process of infrared imaging, is proposed to test and evaluate the performance of the IRIS. According to the theoretical simulation framework and the theoretical models of the IRIS, the architecture of the IRIS simulator is constructed. The 3D scenes are generated and the infrared atmospheric transmission effects are simulated using OGRE technology in real-time on the computer. The physical effects of the IRIS are classified as the signal response characteristic, modulation transfer characteristic and noise characteristic, and they are simulated on the single-board signal processing platform based on the core processor FPGA in real-time using high-speed parallel computation method.

Predicting Flows of Rarefied Gases

NASA Technical Reports Server (NTRS)

LeBeau, Gerald J.; Wilmoth, Richard G.

2005-01-01

DSMC Analysis Code (DAC) is a flexible, highly automated, easy-to-use computer program for predicting flows of rarefied gases -- especially flows of upper-atmospheric, propulsion, and vented gases impinging on spacecraft surfaces. DAC implements the direct simulation Monte Carlo (DSMC) method, which is widely recognized as standard for simulating flows at densities so low that the continuum-based equations of computational fluid dynamics are invalid. DAC enables users to model complex surface shapes and boundary conditions quickly and easily. The discretization of a flow field into computational grids is automated, thereby relieving the user of a traditionally time-consuming task while ensuring (1) appropriate refinement of grids throughout the computational domain, (2) determination of optimal settings for temporal discretization and other simulation parameters, and (3) satisfaction of the fundamental constraints of the method. In so doing, DAC ensures an accurate and efficient simulation. In addition, DAC can utilize parallel processing to reduce computation time. The domain decomposition needed for parallel processing is completely automated, and the software employs a dynamic load-balancing mechanism to ensure optimal parallel efficiency throughout the simulation.

Integrated Sensing and Information Processing Theme-Based Redesign of the Undergraduate Electrical and Computer Engineering Curriculum at Duke University

ERIC Educational Resources Information Center

Ybarra, Gary A.; Collins, Leslie M.; Huettel, Lisa G.; Brown, April S.; Coonley, Kip D.; Massoud, Hisham Z.; Board, John A.; Cummer, Steven A.; Choudhury, Romit Roy; Gustafson, Michael R.; Jokerst, Nan M.; Brooke, Martin A.; Willett, Rebecca M.; Kim, Jungsang; Absher, Martha S.

2011-01-01

The field of electrical and computer engineering has evolved significantly in the past two decades. This evolution has broadened the field of ECE, and subfields have seen deep penetration into very specialized areas. Remarkable devices and systems arising from innovative processes, exotic materials, high speed computer simulations, and complex…

A scalable parallel black oil simulator on distributed memory parallel computers

NASA Astrophysics Data System (ADS)

Wang, Kun; Liu, Hui; Chen, Zhangxin

2015-11-01

This paper presents our work on developing a parallel black oil simulator for distributed memory computers based on our in-house parallel platform. The parallel simulator is designed to overcome the performance issues of common simulators that are implemented for personal computers and workstations. The finite difference method is applied to discretize the black oil model. In addition, some advanced techniques are employed to strengthen the robustness and parallel scalability of the simulator, including an inexact Newton method, matrix decoupling methods, and algebraic multigrid methods. A new multi-stage preconditioner is proposed to accelerate the solution of linear systems from the Newton methods. Numerical experiments show that our simulator is scalable and efficient, and is capable of simulating extremely large-scale black oil problems with tens of millions of grid blocks using thousands of MPI processes on parallel computers.

Computing and data processing

NASA Technical Reports Server (NTRS)

Smarr, Larry; Press, William; Arnett, David W.; Cameron, Alastair G. W.; Crutcher, Richard M.; Helfand, David J.; Horowitz, Paul; Kleinmann, Susan G.; Linsky, Jeffrey L.; Madore, Barry F.

1991-01-01

The applications of computers and data processing to astronomy are discussed. Among the topics covered are the emerging national information infrastructure, workstations and supercomputers, supertelescopes, digital astronomy, astrophysics in a numerical laboratory, community software, archiving of ground-based observations, dynamical simulations of complex systems, plasma astrophysics, and the remote control of fourth dimension supercomputers.

High performance transcription factor-DNA docking with GPU computing

PubMed Central

2012-01-01

Background Protein-DNA docking is a very challenging problem in structural bioinformatics and has important implications in a number of applications, such as structure-based prediction of transcription factor binding sites and rational drug design. Protein-DNA docking is very computational demanding due to the high cost of energy calculation and the statistical nature of conformational sampling algorithms. More importantly, experiments show that the docking quality depends on the coverage of the conformational sampling space. It is therefore desirable to accelerate the computation of the docking algorithm, not only to reduce computing time, but also to improve docking quality. Methods In an attempt to accelerate the sampling process and to improve the docking performance, we developed a graphics processing unit (GPU)-based protein-DNA docking algorithm. The algorithm employs a potential-based energy function to describe the binding affinity of a protein-DNA pair, and integrates Monte-Carlo simulation and a simulated annealing method to search through the conformational space. Algorithmic techniques were developed to improve the computation efficiency and scalability on GPU-based high performance computing systems. Results The effectiveness of our approach is tested on a non-redundant set of 75 TF-DNA complexes and a newly developed TF-DNA docking benchmark. We demonstrated that the GPU-based docking algorithm can significantly accelerate the simulation process and thereby improving the chance of finding near-native TF-DNA complex structures. This study also suggests that further improvement in protein-DNA docking research would require efforts from two integral aspects: improvement in computation efficiency and energy function design. Conclusions We present a high performance computing approach for improving the prediction accuracy of protein-DNA docking. The GPU-based docking algorithm accelerates the search of the conformational space and thus increases the chance of finding more near-native structures. To the best of our knowledge, this is the first ad hoc effort of applying GPU or GPU clusters to the protein-DNA docking problem. PMID:22759575

Computer-based simulation training to improve learning outcomes in mannequin-based simulation exercises.

PubMed

Curtin, Lindsay B; Finn, Laura A; Czosnowski, Quinn A; Whitman, Craig B; Cawley, Michael J

2011-08-10

To assess the impact of computer-based simulation on the achievement of student learning outcomes during mannequin-based simulation. Participants were randomly assigned to rapid response teams of 5-6 students and then teams were randomly assigned to either a group that completed either computer-based or mannequin-based simulation cases first. In both simulations, students used their critical thinking skills and selected interventions independent of facilitator input. A predetermined rubric was used to record and assess students' performance in the mannequin-based simulations. Feedback and student performance scores were generated by the software in the computer-based simulations. More of the teams in the group that completed the computer-based simulation before completing the mannequin-based simulation achieved the primary outcome for the exercise, which was survival of the simulated patient (41.2% vs. 5.6%). The majority of students (>90%) recommended the continuation of simulation exercises in the course. Students in both groups felt the computer-based simulation should be completed prior to the mannequin-based simulation. The use of computer-based simulation prior to mannequin-based simulation improved the achievement of learning goals and outcomes. In addition to improving participants' skills, completing the computer-based simulation first may improve participants' confidence during the more real-life setting achieved in the mannequin-based simulation.

Design and implementation of laser target simulator in hardware-in-the-loop simulation system based on LabWindows/CVI and RTX

NASA Astrophysics Data System (ADS)

Tong, Qiujie; Wang, Qianqian; Li, Xiaoyang; Shan, Bin; Cui, Xuntai; Li, Chenyu; Peng, Zhong

2016-11-01

In order to satisfy the requirements of the real-time and generality, a laser target simulator in semi-physical simulation system based on RTX+LabWindows/CVI platform is proposed in this paper. Compared with the upper-lower computers simulation platform architecture used in the most of the real-time system now, this system has better maintainability and portability. This system runs on the Windows platform, using Windows RTX real-time extension subsystem to ensure the real-time performance of the system combining with the reflective memory network to complete some real-time tasks such as calculating the simulation model, transmitting the simulation data, and keeping real-time communication. The real-time tasks of simulation system run under the RTSS process. At the same time, we use the LabWindows/CVI to compile a graphical interface, and complete some non-real-time tasks in the process of simulation such as man-machine interaction, display and storage of the simulation data, which run under the Win32 process. Through the design of RTX shared memory and task scheduling algorithm, the data interaction between the real-time tasks process of RTSS and non-real-time tasks process of Win32 is completed. The experimental results show that this system has the strongly real-time performance, highly stability, and highly simulation accuracy. At the same time, it also has the good performance of human-computer interaction.

Advances in Integrated Computational Materials Engineering "ICME"

NASA Astrophysics Data System (ADS)

Hirsch, Jürgen

The methods of Integrated Computational Materials Engineering that were developed and successfully applied for Aluminium have been constantly improved. The main aspects and recent advances of integrated material and process modeling are simulations of material properties like strength and forming properties and for the specific microstructure evolution during processing (rolling, extrusion, annealing) under the influence of material constitution and process variations through the production process down to the final application. Examples are discussed for the through-process simulation of microstructures and related properties of Aluminium sheet, including DC ingot casting, pre-heating and homogenization, hot and cold rolling, final annealing. New results are included of simulation solution annealing and age hardening of 6xxx alloys for automotive applications. Physically based quantitative descriptions and computer assisted evaluation methods are new ICME methods of integrating new simulation tools also for customer applications, like heat affected zones in welding of age hardening alloys. The aspects of estimating the effect of specific elements due to growing recycling volumes requested also for high end Aluminium products are also discussed, being of special interest in the Aluminium producing industries.

High-performance biocomputing for simulating the spread of contagion over large contact networks

PubMed Central

2012-01-01

Background Many important biological problems can be modeled as contagion diffusion processes over interaction networks. This article shows how the EpiSimdemics interaction-based simulation system can be applied to the general contagion diffusion problem. Two specific problems, computational epidemiology and human immune system modeling, are given as examples. We then show how the graphics processing unit (GPU) within each compute node of a cluster can effectively be used to speed-up the execution of these types of problems. Results We show that a single GPU can accelerate the EpiSimdemics computation kernel by a factor of 6 and the entire application by a factor of 3.3, compared to the execution time on a single core. When 8 CPU cores and 2 GPU devices are utilized, the speed-up of the computational kernel increases to 9.5. When combined with effective techniques for inter-node communication, excellent scalability can be achieved without significant loss of accuracy in the results. Conclusions We show that interaction-based simulation systems can be used to model disparate and highly relevant problems in biology. We also show that offloading some of the work to GPUs in distributed interaction-based simulations can be an effective way to achieve increased intra-node efficiency. PMID:22537298

GPU-based efficient realistic techniques for bleeding and smoke generation in surgical simulators.

PubMed

Halic, Tansel; Sankaranarayanan, Ganesh; De, Suvranu

2010-12-01

In actual surgery, smoke and bleeding due to cauterization processes provide important visual cues to the surgeon, which have been proposed as factors in surgical skill assessment. While several virtual reality (VR)-based surgical simulators have incorporated the effects of bleeding and smoke generation, they are not realistic due to the requirement of real-time performance. To be interactive, visual update must be performed at at least 30 Hz and haptic (touch) information must be refreshed at 1 kHz. Simulation of smoke and bleeding is, therefore, either ignored or simulated using highly simplified techniques, since other computationally intensive processes compete for the available Central Processing Unit (CPU) resources. In this study we developed a novel low-cost method to generate realistic bleeding and smoke in VR-based surgical simulators, which outsources the computations to the graphical processing unit (GPU), thus freeing up the CPU for other time-critical tasks. This method is independent of the complexity of the organ models in the virtual environment. User studies were performed using 20 subjects to determine the visual quality of the simulations compared to real surgical videos. The smoke and bleeding simulation were implemented as part of a laparoscopic adjustable gastric banding (LAGB) simulator. For the bleeding simulation, the original implementation using the shader did not incur noticeable overhead. However, for smoke generation, an input/output (I/O) bottleneck was observed and two different methods were developed to overcome this limitation. Based on our benchmark results, a buffered approach performed better than a pipelined approach and could support up to 15 video streams in real time. Human subject studies showed that the visual realism of the simulations were as good as in real surgery (median rating of 4 on a 5-point Likert scale). Based on the performance results and subject study, both bleeding and smoke simulations were concluded to be efficient, highly realistic and well suited to VR-based surgical simulators. Copyright © 2010 John Wiley & Sons, Ltd.

A brief introduction to computer-intensive methods, with a view towards applications in spatial statistics and stereology.

PubMed

Mattfeldt, Torsten

2011-04-01

Computer-intensive methods may be defined as data analytical procedures involving a huge number of highly repetitive computations. We mention resampling methods with replacement (bootstrap methods), resampling methods without replacement (randomization tests) and simulation methods. The resampling methods are based on simple and robust principles and are largely free from distributional assumptions. Bootstrap methods may be used to compute confidence intervals for a scalar model parameter and for summary statistics from replicated planar point patterns, and for significance tests. For some simple models of planar point processes, point patterns can be simulated by elementary Monte Carlo methods. The simulation of models with more complex interaction properties usually requires more advanced computing methods. In this context, we mention simulation of Gibbs processes with Markov chain Monte Carlo methods using the Metropolis-Hastings algorithm. An alternative to simulations on the basis of a parametric model consists of stochastic reconstruction methods. The basic ideas behind the methods are briefly reviewed and illustrated by simple worked examples in order to encourage novices in the field to use computer-intensive methods. © 2010 The Authors Journal of Microscopy © 2010 Royal Microscopical Society.

Using Business Simulations as Authentic Assessment Tools

ERIC Educational Resources Information Center

Neely, Pat; Tucker, Jan

2012-01-01

New modalities for assessing student learning exist as a result of advances in computer technology. Conventional measurement practices have been transformed into computer based testing. Although current testing replicates assessment processes used in college classrooms, a greater opportunity exists to use computer technology to create authentic…

Analysis and Simulation of a Blue Energy Cycle

DOE PAGES

Sharma, Ms. Ketki; Kim, Yong-Ha; Yiacoumi, Sotira; ...

2016-01-30

The mixing process of fresh water and seawater releases a significant amount of energy and is a potential source of renewable energy. The so called ‘blue energy’ or salinity-gradient energy can be harvested by a device consisting of carbon electrodes immersed in an electrolyte solution, based on the principle of capacitive double layer expansion (CDLE). In this study, we have investigated the feasibility of energy production based on the CDLE principle. Experiments and computer simulations were used to study the process. Mesoporous carbon materials, synthesized at the Oak Ridge National Laboratory, were used as electrode materials in the experiments. Neutronmore » imaging of the blue energy cycle was conducted with cylindrical mesoporous carbon electrodes and 0.5 M lithium chloride as the electrolyte solution. For experiments conducted at 0.6 V and 0.9 V applied potential, a voltage increase of 0.061 V and 0.054 V was observed, respectively. From sequences of neutron images obtained for each step of the blue energy cycle, information on the direction and magnitude of lithium ion transport was obtained. A computer code was developed to simulate the process. Experimental data and computer simulations allowed us to predict energy production.« less

Computer Modeling and Simulation

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

Pronskikh, V. S.

2014-05-09

Verification and validation of computer codes and models used in simulation are two aspects of the scientific practice of high importance and have recently been discussed by philosophers of science. While verification is predominantly associated with the correctness of the way a model is represented by a computer code or algorithm, validation more often refers to model’s relation to the real world and its intended use. It has been argued that because complex simulations are generally not transparent to a practitioner, the Duhem problem can arise for verification and validation due to their entanglement; such an entanglement makes it impossiblemore » to distinguish whether a coding error or model’s general inadequacy to its target should be blamed in the case of the model failure. I argue that in order to disentangle verification and validation, a clear distinction between computer modeling (construction of mathematical computer models of elementary processes) and simulation (construction of models of composite objects and processes by means of numerical experimenting with them) needs to be made. Holding on to that distinction, I propose to relate verification (based on theoretical strategies such as inferences) to modeling and validation, which shares the common epistemology with experimentation, to simulation. To explain reasons of their intermittent entanglement I propose a weberian ideal-typical model of modeling and simulation as roles in practice. I suggest an approach to alleviate the Duhem problem for verification and validation generally applicable in practice and based on differences in epistemic strategies and scopes« less

Simulation-based MDP verification for leading-edge masks

NASA Astrophysics Data System (ADS)

Su, Bo; Syrel, Oleg; Pomerantsev, Michael; Hagiwara, Kazuyuki; Pearman, Ryan; Pang, Leo; Fujimara, Aki

2017-07-01

For IC design starts below the 20nm technology node, the assist features on photomasks shrink well below 60nm and the printed patterns of those features on masks written by VSB eBeam writers start to show a large deviation from the mask designs. Traditional geometry-based fracturing starts to show large errors for those small features. As a result, other mask data preparation (MDP) methods have become available and adopted, such as rule-based Mask Process Correction (MPC), model-based MPC and eventually model-based MDP. The new MDP methods may place shot edges slightly differently from target to compensate for mask process effects, so that the final patterns on a mask are much closer to the design (which can be viewed as the ideal mask), especially for those assist features. Such an alteration generally produces better masks that are closer to the intended mask design. Traditional XOR-based MDP verification cannot detect problems caused by eBeam effects. Much like model-based OPC verification which became a necessity for OPC a decade ago, we see the same trend in MDP today. Simulation-based MDP verification solution requires a GPU-accelerated computational geometry engine with simulation capabilities. To have a meaningful simulation-based mask check, a good mask process model is needed. The TrueModel® system is a field tested physical mask model developed by D2S. The GPU-accelerated D2S Computational Design Platform (CDP) is used to run simulation-based mask check, as well as model-based MDP. In addition to simulation-based checks such as mask EPE or dose margin, geometry-based rules are also available to detect quality issues such as slivers or CD splits. Dose margin related hotspots can also be detected by setting a correct detection threshold. In this paper, we will demonstrate GPU-acceleration for geometry processing, and give examples of mask check results and performance data. GPU-acceleration is necessary to make simulation-based mask MDP verification acceptable.

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

This research is aimed at developing a neiv and advanced simulation framework that will significantly improve the overall efficiency of aerospace systems design and development. This objective will be accomplished through an innovative integration of object-oriented and Web-based technologies ivith both new and proven simulation methodologies. The basic approach involves Ihree major areas of research: Aerospace system and component representation using a hierarchical object-oriented component model which enables the use of multimodels and enforces component interoperability. Collaborative software environment that streamlines the process of developing, sharing and integrating aerospace design and analysis models. . Development of a distributed infrastructure which enables Web-based exchange of models to simplify the collaborative design process, and to support computationally intensive aerospace design and analysis processes. Research for the first year dealt with the design of the basic architecture and supporting infrastructure, an initial implementation of that design, and a demonstration of its application to an example aircraft engine system simulation.

Children's Independent Exploration of a Natural Phenomenon by Using a Pictorial Computer-Based Simulation.

ERIC Educational Resources Information Center

Kangassalo, Marjatta

Using a pictorial computer simulation of a natural phenomenon, children's exploration processes and their construction of conceptual models were examined. The selected natural phenomenon was the variations of sunlight and heat of the sun experienced on the earth in relation to the positions of the earth and sun in space, and the subjects were…

Cellular automata-based modelling and simulation of biofilm structure on multi-core computers.

PubMed

Skoneczny, Szymon

2015-01-01

The article presents a mathematical model of biofilm growth for aerobic biodegradation of a toxic carbonaceous substrate. Modelling of biofilm growth has fundamental significance in numerous processes of biotechnology and mathematical modelling of bioreactors. The process following double-substrate kinetics with substrate inhibition proceeding in a biofilm has not been modelled so far by means of cellular automata. Each process in the model proposed, i.e. diffusion of substrates, uptake of substrates, growth and decay of microorganisms and biofilm detachment, is simulated in a discrete manner. It was shown that for flat biofilm of constant thickness, the results of the presented model agree with those of a continuous model. The primary outcome of the study was to propose a mathematical model of biofilm growth; however a considerable amount of focus was also placed on the development of efficient algorithms for its solution. Two parallel algorithms were created, differing in the way computations are distributed. Computer programs were created using OpenMP Application Programming Interface for C++ programming language. Simulations of biofilm growth were performed on three high-performance computers. Speed-up coefficients of computer programs were compared. Both algorithms enabled a significant reduction of computation time. It is important, inter alia, in modelling and simulation of bioreactor dynamics.

Lagrangian Particle Tracking Simulation for Warm-Rain Processes in Quasi-One-Dimensional Domain

NASA Astrophysics Data System (ADS)

Kunishima, Y.; Onishi, R.

2017-12-01

Conventional cloud simulations are based on the Euler method and compute each microphysics process in a stochastic way assuming infinite numbers of particles within each numerical grid. They therefore cannot provide the Lagrangian statistics of individual particles in cloud microphysics (i.e., aerosol particles, cloud particles, and rain drops) nor discuss the statistical fluctuations due to finite number of particles. We here simulate the entire precipitation process of warm-rain, with tracking individual particles. We use the Lagrangian Cloud Simulator (LCS), which is based on the Euler-Lagrangian framework. In that framework, flow motion and scalar transportation are computed with the Euler method, and particle motion with the Lagrangian one. The LCS tracks particle motions and collision events individually with considering the hydrodynamic interaction between approaching particles with a superposition method, that is, it can directly represent the collisional growth of cloud particles. It is essential for trustworthy collision detection to take account of the hydrodynamic interaction. In this study, we newly developed a stochastic model based on the Twomey cloud condensation nuclei (CCN) activation for the Lagrangian tracking simulation and integrated it into the LCS. Coupling with the Euler computation for water vapour and temperature fields, the initiation and condensational growth of water droplets were computed in the Lagrangian way. We applied the integrated LCS for a kinematic simulation of warm-rain processes in a vertically-elongated domain of, at largest, 0.03×0.03×3000 (m3) with horizontal periodicity. Aerosol particles with a realistic number density, 5×107 (m3), were evenly distributed over the domain at the initial state. Prescribed updraft at the early stage initiated development of a precipitating cloud. We have confirmed that the obtained bulk statistics fairly agree with those from a conventional spectral-bin scheme for a vertical column domain. The centre of the discussion will be the Lagrangian statistics which is collected from the individual behaviour of the tracked particles.

IMPROVING TACONITE PROCESSING PLANT EFFICIENCY BY COMPUTER SIMULATION, Final Report

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

William M. Bond; Salih Ersayin

2007-03-30

This project involved industrial scale testing of a mineral processing simulator to improve the efficiency of a taconite processing plant, namely the Minorca mine. The Concentrator Modeling Center at the Coleraine Minerals Research Laboratory, University of Minnesota Duluth, enhanced the capabilities of available software, Usim Pac, by developing mathematical models needed for accurate simulation of taconite plants. This project provided funding for this technology to prove itself in the industrial environment. As the first step, data representing existing plant conditions were collected by sampling and sample analysis. Data were then balanced and provided a basis for assessing the efficiency ofmore » individual devices and the plant, and also for performing simulations aimed at improving plant efficiency. Performance evaluation served as a guide in developing alternative process strategies for more efficient production. A large number of computer simulations were then performed to quantify the benefits and effects of implementing these alternative schemes. Modification of makeup ball size was selected as the most feasible option for the target performance improvement. This was combined with replacement of existing hydrocyclones with more efficient ones. After plant implementation of these modifications, plant sampling surveys were carried out to validate findings of the simulation-based study. Plant data showed very good agreement with the simulated data, confirming results of simulation. After the implementation of modifications in the plant, several upstream bottlenecks became visible. Despite these bottlenecks limiting full capacity, concentrator energy improvement of 7% was obtained. Further improvements in energy efficiency are expected in the near future. The success of this project demonstrated the feasibility of a simulation-based approach. Currently, the Center provides simulation-based service to all the iron ore mining companies operating in northern Minnesota, and future proposals are pending with non-taconite mineral processing applications.« less

On the upscaling of process-based models in deltaic applications

NASA Astrophysics Data System (ADS)

Li, L.; Storms, J. E. A.; Walstra, D. J. R.

2018-03-01

Process-based numerical models are increasingly used to study the evolution of marine and terrestrial depositional environments. Whilst a detailed description of small-scale processes provides an accurate representation of reality, application on geological timescales is restrained by the associated increase in computational time. In order to reduce the computational time, a number of acceleration methods are combined and evaluated for a schematic supply-driven delta (static base level) and an accommodation-driven delta (variable base level). The performance of the combined acceleration methods is evaluated by comparing the morphological indicators such as distributary channel networking and delta volumes derived from the model predictions for various levels of acceleration. The results of the accelerated models are compared to the outcomes from a series of simulations to capture autogenic variability. Autogenic variability is quantified by re-running identical models on an initial bathymetry with 1 cm added noise. The overall results show that the variability of the accelerated models fall within the autogenic variability range, suggesting that the application of acceleration methods does not significantly affect the simulated delta evolution. The Time-scale compression method (the acceleration method introduced in this paper) results in an increased computational efficiency of 75% without adversely affecting the simulated delta evolution compared to a base case. The combination of the Time-scale compression method with the existing acceleration methods has the potential to extend the application range of process-based models towards geologic timescales.

Computational Models of Laryngeal Aerodynamics: Potentials and Numerical Costs.

PubMed

Sadeghi, Hossein; Kniesburges, Stefan; Kaltenbacher, Manfred; Schützenberger, Anne; Döllinger, Michael

2018-02-07

Human phonation is based on the interaction between tracheal airflow and laryngeal dynamics. This fluid-structure interaction is based on the energy exchange between airflow and vocal folds. Major challenges in analyzing the phonatory process in-vivo are the small dimensions and the poor accessibility of the region of interest. For improved analysis of the phonatory process, numerical simulations of the airflow and the vocal fold dynamics have been suggested. Even though most of the models reproduced the phonatory process fairly well, development of comprehensive larynx models is still a subject of research. In the context of clinical application, physiological accuracy and computational model efficiency are of great interest. In this study, a simple numerical larynx model is introduced that incorporates the laryngeal fluid flow. It is based on a synthetic experimental model with silicone vocal folds. The degree of realism was successively increased in separate computational models and each model was simulated for 10 oscillation cycles. Results show that relevant features of the laryngeal flow field, such as glottal jet deflection, develop even when applying rather simple static models with oscillating flow rates. Including further phonatory components such as vocal fold motion, mucosal wave propagation, and ventricular folds, the simulations show phonatory key features like intraglottal flow separation and increased flow rate in presence of ventricular folds. The simulation time on 100 CPU cores ranged between 25 and 290 hours, currently restricting clinical application of these models. Nevertheless, results show high potential of numerical simulations for better understanding of phonatory process. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Computational Simulation of Thermal and Spattering Phenomena and Microstructure in Selective Laser Melting of Inconel 625

NASA Astrophysics Data System (ADS)

Özel, Tuğrul; Arısoy, Yiğit M.; Criales, Luis E.

Computational modelling of Laser Powder Bed Fusion (L-PBF) processes such as Selective laser Melting (SLM) can reveal information that is hard to obtain or unobtainable by in-situ experimental measurements. A 3D thermal field that is not visible by the thermal camera can be obtained by solving the 3D heat transfer problem. Furthermore, microstructural modelling can be used to predict the quality and mechanical properties of the product. In this paper, a nonlinear 3D Finite Element Method based computational code is developed to simulate the SLM process with different process parameters such as laser power and scan velocity. The code is further improved by utilizing an in-situ thermal camera recording to predict spattering which is in turn included as a stochastic heat loss. Then, thermal gradients extracted from the simulations applied to predict growth directions in the resulting microstructure.

Micromagnetics on high-performance workstation and mobile computational platforms

NASA Astrophysics Data System (ADS)

Fu, S.; Chang, R.; Couture, S.; Menarini, M.; Escobar, M. A.; Kuteifan, M.; Lubarda, M.; Gabay, D.; Lomakin, V.

2015-05-01

The feasibility of using high-performance desktop and embedded mobile computational platforms is presented, including multi-core Intel central processing unit, Nvidia desktop graphics processing units, and Nvidia Jetson TK1 Platform. FastMag finite element method-based micromagnetic simulator is used as a testbed, showing high efficiency on all the platforms. Optimization aspects of improving the performance of the mobile systems are discussed. The high performance, low cost, low power consumption, and rapid performance increase of the embedded mobile systems make them a promising candidate for micromagnetic simulations. Such architectures can be used as standalone systems or can be built as low-power computing clusters.

A simplified computational memory model from information processing.

PubMed

Zhang, Lanhua; Zhang, Dongsheng; Deng, Yuqin; Ding, Xiaoqian; Wang, Yan; Tang, Yiyuan; Sun, Baoliang

2016-11-23

This paper is intended to propose a computational model for memory from the view of information processing. The model, called simplified memory information retrieval network (SMIRN), is a bi-modular hierarchical functional memory network by abstracting memory function and simulating memory information processing. At first meta-memory is defined to express the neuron or brain cortices based on the biology and graph theories, and we develop an intra-modular network with the modeling algorithm by mapping the node and edge, and then the bi-modular network is delineated with intra-modular and inter-modular. At last a polynomial retrieval algorithm is introduced. In this paper we simulate the memory phenomena and functions of memorization and strengthening by information processing algorithms. The theoretical analysis and the simulation results show that the model is in accordance with the memory phenomena from information processing view.

Simulation training tools for nonlethal weapons using gaming environments

NASA Astrophysics Data System (ADS)

Donne, Alexsana; Eagan, Justin; Tse, Gabriel; Vanderslice, Tom; Woods, Jerry

2006-05-01

Modern simulation techniques have a growing role for evaluating new technologies and for developing cost-effective training programs. A mission simulator facilitates the productive exchange of ideas by demonstration of concepts through compellingly realistic computer simulation. Revolutionary advances in 3D simulation technology have made it possible for desktop computers to process strikingly realistic and complex interactions with results depicted in real-time. Computer games now allow for multiple real human players and "artificially intelligent" (AI) simulated robots to play together. Advances in computer processing power have compensated for the inherent intensive calculations required for complex simulation scenarios. The main components of the leading game-engines have been released for user modifications, enabling game enthusiasts and amateur programmers to advance the state-of-the-art in AI and computer simulation technologies. It is now possible to simulate sophisticated and realistic conflict situations in order to evaluate the impact of non-lethal devices as well as conflict resolution procedures using such devices. Simulations can reduce training costs as end users: learn what a device does and doesn't do prior to use, understand responses to the device prior to deployment, determine if the device is appropriate for their situational responses, and train with new devices and techniques before purchasing hardware. This paper will present the status of SARA's mission simulation development activities, based on the Half-Life gameengine, for the purpose of evaluating the latest non-lethal weapon devices, and for developing training tools for such devices.

Creativity in Education: A Standard for Computer-Based Teaching.

ERIC Educational Resources Information Center

Schank, Roger C.; Farrell, Robert

1988-01-01

Discussion of the potential of computers in education focuses on the need for experiential learning and developing creativity in students. Learning processes are explained in light of artificial intelligence research, problems with current uses of computers in education are discussed, and possible solutions using intelligent simulation software…

Physics-based interactive volume manipulation for sharing surgical process.

PubMed

Nakao, Megumi; Minato, Kotaro

2010-05-01

This paper presents a new set of techniques by which surgeons can interactively manipulate patient-specific volumetric models for sharing surgical process. To handle physical interaction between the surgical tools and organs, we propose a simple surface-constraint-based manipulation algorithm to consistently simulate common surgical manipulations such as grasping, holding and retraction. Our computation model is capable of simulating soft-tissue deformation and incision in real time. We also present visualization techniques in order to rapidly visualize time-varying, volumetric information on the deformed image. This paper demonstrates the success of the proposed methods in enabling the simulation of surgical processes, and the ways in which this simulation facilitates preoperative planning and rehearsal.

Multidisciplinary Simulation Acceleration using Multiple Shared-Memory Graphical Processing Units

NASA Astrophysics Data System (ADS)

Kemal, Jonathan Yashar

For purposes of optimizing and analyzing turbomachinery and other designs, the unsteady Favre-averaged flow-field differential equations for an ideal compressible gas can be solved in conjunction with the heat conduction equation. We solve all equations using the finite-volume multiple-grid numerical technique, with the dual time-step scheme used for unsteady simulations. Our numerical solver code targets CUDA-capable Graphical Processing Units (GPUs) produced by NVIDIA. Making use of MPI, our solver can run across networked compute notes, where each MPI process can use either a GPU or a Central Processing Unit (CPU) core for primary solver calculations. We use NVIDIA Tesla C2050/C2070 GPUs based on the Fermi architecture, and compare our resulting performance against Intel Zeon X5690 CPUs. Solver routines converted to CUDA typically run about 10 times faster on a GPU for sufficiently dense computational grids. We used a conjugate cylinder computational grid and ran a turbulent steady flow simulation using 4 increasingly dense computational grids. Our densest computational grid is divided into 13 blocks each containing 1033x1033 grid points, for a total of 13.87 million grid points or 1.07 million grid points per domain block. To obtain overall speedups, we compare the execution time of the solver's iteration loop, including all resource intensive GPU-related memory copies. Comparing the performance of 8 GPUs to that of 8 CPUs, we obtain an overall speedup of about 6.0 when using our densest computational grid. This amounts to an 8-GPU simulation running about 39.5 times faster than running than a single-CPU simulation.

Integration of High-resolution Data for Temporal Bone Surgical Simulations

PubMed Central

Wiet, Gregory J.; Stredney, Don; Powell, Kimerly; Hittle, Brad; Kerwin, Thomas

2016-01-01

Purpose To report on the state of the art in obtaining high-resolution 3D data of the microanatomy of the temporal bone and to process that data for integration into a surgical simulator. Specifically, we report on our experience in this area and discuss the issues involved to further the field. Data Sources Current temporal bone image acquisition and image processing established in the literature as well as in house methodological development. Review Methods We reviewed the current English literature for the techniques used in computer-based temporal bone simulation systems to obtain and process anatomical data for use within the simulation. Search terms included “temporal bone simulation, surgical simulation, temporal bone.” Articles were chosen and reviewed that directly addressed data acquisition and processing/segmentation and enhancement with emphasis given to computer based systems. We present the results from this review in relationship to our approach. Conclusions High-resolution CT imaging (≤100μm voxel resolution), along with unique image processing and rendering algorithms, and structure specific enhancement are needed for high-level training and assessment using temporal bone surgical simulators. Higher resolution clinical scanning and automated processes that run in efficient time frames are needed before these systems can routinely support pre-surgical planning. Additionally, protocols such as that provided in this manuscript need to be disseminated to increase the number and variety of virtual temporal bones available for training and performance assessment. PMID:26762105

Solving probability reasoning based on DNA strand displacement and probability modules.

PubMed

Zhang, Qiang; Wang, Xiaobiao; Wang, Xiaojun; Zhou, Changjun

2017-12-01

In computation biology, DNA strand displacement technology is used to simulate the computation process and has shown strong computing ability. Most researchers use it to solve logic problems, but it is only rarely used in probabilistic reasoning. To process probabilistic reasoning, a conditional probability derivation model and total probability model based on DNA strand displacement were established in this paper. The models were assessed through the game "read your mind." It has been shown to enable the application of probabilistic reasoning in genetic diagnosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

An innovative computationally efficient hydromechanical coupling approach for fault reactivation in geological subsurface utilization

NASA Astrophysics Data System (ADS)

Adams, M.; Kempka, T.; Chabab, E.; Ziegler, M.

2018-02-01

Estimating the efficiency and sustainability of geological subsurface utilization, i.e., Carbon Capture and Storage (CCS) requires an integrated risk assessment approach, considering the occurring coupled processes, beside others, the potential reactivation of existing faults. In this context, hydraulic and mechanical parameter uncertainties as well as different injection rates have to be considered and quantified to elaborate reliable environmental impact assessments. Consequently, the required sensitivity analyses consume significant computational time due to the high number of realizations that have to be carried out. Due to the high computational costs of two-way coupled simulations in large-scale 3D multiphase fluid flow systems, these are not applicable for the purpose of uncertainty and risk assessments. Hence, an innovative semi-analytical hydromechanical coupling approach for hydraulic fault reactivation will be introduced. This approach determines the void ratio evolution in representative fault elements using one preliminary base simulation, considering one model geometry and one set of hydromechanical parameters. The void ratio development is then approximated and related to one reference pressure at the base of the fault. The parametrization of the resulting functions is then directly implemented into a multiphase fluid flow simulator to carry out the semi-analytical coupling for the simulation of hydromechanical processes. Hereby, the iterative parameter exchange between the multiphase and mechanical simulators is omitted, since the update of porosity and permeability is controlled by one reference pore pressure at the fault base. The suggested procedure is capable to reduce the computational time required by coupled hydromechanical simulations of a multitude of injection rates by a factor of up to 15.

Optimal segmentation and packaging process

DOEpatents

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

1999-08-10

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

Marcus canonical integral for non-Gaussian processes and its computation: pathwise simulation and tau-leaping algorithm.

PubMed

Li, Tiejun; Min, Bin; Wang, Zhiming

2013-03-14

The stochastic integral ensuring the Newton-Leibnitz chain rule is essential in stochastic energetics. Marcus canonical integral has this property and can be understood as the Wong-Zakai type smoothing limit when the driving process is non-Gaussian. However, this important concept seems not well-known for physicists. In this paper, we discuss Marcus integral for non-Gaussian processes and its computation in the context of stochastic energetics. We give a comprehensive introduction to Marcus integral and compare three equivalent definitions in the literature. We introduce the exact pathwise simulation algorithm and give the error analysis. We show how to compute the thermodynamic quantities based on the pathwise simulation algorithm. We highlight the information hidden in the Marcus mapping, which plays the key role in determining thermodynamic quantities. We further propose the tau-leaping algorithm, which advance the process with deterministic time steps when tau-leaping condition is satisfied. The numerical experiments and its efficiency analysis show that it is very promising.

A Computer Simulation of Bacterial Growth During Food-Processing

DTIC Science & Technology

1974-11-01

1 AD A TECHNICAL REPORT A COMPUTER SIMULATION OF BACTERIAL GROWTH DURING FOOD PROCESSING =r= by Edward W. Ross, Jr. Approved for public...COMPUTER SIMULATION OF BACTERIAL GROWTH DURING FOOD - PROCESSING Edward W. Ross, Jr. Army Natick Laboratories Natick, Massachusetts Novembe...CATALOG NUMBER 4. TITLE fand SubtKUJ "A Computer Sinulatlon of Bacterial Growth During Food - Processing " 5. TYPE OF REPORT A PERIOD COVERED 6

Improving Students’ Science Process Skills through Simple Computer Simulations on Linear Motion Conceptions

NASA Astrophysics Data System (ADS)

Siahaan, P.; Suryani, A.; Kaniawati, I.; Suhendi, E.; Samsudin, A.

2017-02-01

The purpose of this research is to identify the development of students’ science process skills (SPS) on linear motion concept by utilizing simple computer simulation. In order to simplify the learning process, the concept is able to be divided into three sub-concepts: 1) the definition of motion, 2) the uniform linear motion and 3) the uniformly accelerated motion. This research was administered via pre-experimental method with one group pretest-posttest design. The respondents which were involved in this research were 23 students of seventh grade in one of junior high schools in Bandung City. The improving process of students’ science process skill is examined based on normalized gain analysis from pretest and posttest scores for all sub-concepts. The result of this research shows that students’ science process skills are dramatically improved by 47% (moderate) on observation skill; 43% (moderate) on summarizing skill, 70% (high) on prediction skill, 44% (moderate) on communication skill and 49% (moderate) on classification skill. These results clarify that the utilizing simple computer simulations in physics learning is be able to improve overall science skills at moderate level.

Computer and laboratory simulation of interactions between spacecraft surfaces and charged-particle environments

NASA Technical Reports Server (NTRS)

Stevens, N. J.

1979-01-01

Cases where the charged-particle environment acts on the spacecraft (e.g., spacecraft charging phenomena) and cases where a system on the spacecraft causes the interaction (e.g., high voltage space power systems) are considered. Both categories were studied in ground simulation facilities to understand the processes involved and to measure the pertinent parameters. Computer simulations are based on the NASA Charging Analyzer Program (NASCAP) code. Analytical models are developed in this code and verified against the experimental data. Extrapolation from the small test samples to space conditions are made with this code. Typical results from laboratory and computer simulations are presented for both types of interactions. Extrapolations from these simulations to performance in space environments are discussed.

Task-based image quality assessment in radiation therapy: initial characterization and demonstration with CT simulation images

NASA Astrophysics Data System (ADS)

Dolly, Steven R.; Anastasio, Mark A.; Yu, Lifeng; Li, Hua

2017-03-01

In current radiation therapy practice, image quality is still assessed subjectively or by utilizing physically-based metrics. Recently, a methodology for objective task-based image quality (IQ) assessment in radiation therapy was proposed by Barrett et al.1 In this work, we present a comprehensive implementation and evaluation of this new IQ assessment methodology. A modular simulation framework was designed to perform an automated, computer-simulated end-to-end radiation therapy treatment. A fully simulated framework was created that utilizes new learning-based stochastic object models (SOM) to obtain known organ boundaries, generates a set of images directly from the numerical phantoms created with the SOM, and automates the image segmentation and treatment planning steps of a radiation therapy work ow. By use of this computational framework, therapeutic operating characteristic (TOC) curves can be computed and the area under the TOC curve (AUTOC) can be employed as a figure-of-merit to guide optimization of different components of the treatment planning process. The developed computational framework is employed to optimize X-ray CT pre-treatment imaging. We demonstrate that use of the radiation therapy-based-based IQ measures lead to different imaging parameters than obtained by use of physical-based measures.

Automated recognition of helium speech. Phase I: Investigation of microprocessor based analysis/synthesis system

NASA Astrophysics Data System (ADS)

Jelinek, H. J.

1986-01-01

This is the Final Report of Electronic Design Associates on its Phase I SBIR project. The purpose of this project is to develop a method for correcting helium speech, as experienced in diver-surface communication. The goal of the Phase I study was to design, prototype, and evaluate a real time helium speech corrector system based upon digital signal processing techniques. The general approach was to develop hardware (an IBM PC board) to digitize helium speech and software (a LAMBDA computer based simulation) to translate the speech. As planned in the study proposal, this initial prototype may now be used to assess expected performance from a self contained real time system which uses an identical algorithm. The Final Report details the work carried out to produce the prototype system. Four major project tasks were: a signal processing scheme for converting helium speech to normal sounding speech was generated. The signal processing scheme was simulated on a general purpose (LAMDA) computer. Actual helium speech was supplied to the simulation and the converted speech was generated. An IBM-PC based 14 bit data Input/Output board was designed and built. A bibliography of references on speech processing was generated.

Comparative Implementation of High Performance Computing for Power System Dynamic Simulations

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

Jin, Shuangshuang; Huang, Zhenyu; Diao, Ruisheng

Dynamic simulation for transient stability assessment is one of the most important, but intensive, computations for power system planning and operation. Present commercial software is mainly designed for sequential computation to run a single simulation, which is very time consuming with a single processer. The application of High Performance Computing (HPC) to dynamic simulations is very promising in accelerating the computing process by parallelizing its kernel algorithms while maintaining the same level of computation accuracy. This paper describes the comparative implementation of four parallel dynamic simulation schemes in two state-of-the-art HPC environments: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP).more » These implementations serve to match the application with dedicated multi-processor computing hardware and maximize the utilization and benefits of HPC during the development process.« less

Range Process Simulation Tool

NASA Technical Reports Server (NTRS)

Phillips, Dave; Haas, William; Barth, Tim; Benjamin, Perakath; Graul, Michael; Bagatourova, Olga

2005-01-01

Range Process Simulation Tool (RPST) is a computer program that assists managers in rapidly predicting and quantitatively assessing the operational effects of proposed technological additions to, and/or upgrades of, complex facilities and engineering systems such as the Eastern Test Range. Originally designed for application to space transportation systems, RPST is also suitable for assessing effects of proposed changes in industrial facilities and large organizations. RPST follows a model-based approach that includes finite-capacity schedule analysis and discrete-event process simulation. A component-based, scalable, open architecture makes RPST easily and rapidly tailorable for diverse applications. Specific RPST functions include: (1) definition of analysis objectives and performance metrics; (2) selection of process templates from a processtemplate library; (3) configuration of process models for detailed simulation and schedule analysis; (4) design of operations- analysis experiments; (5) schedule and simulation-based process analysis; and (6) optimization of performance by use of genetic algorithms and simulated annealing. The main benefits afforded by RPST are provision of information that can be used to reduce costs of operation and maintenance, and the capability for affordable, accurate, and reliable prediction and exploration of the consequences of many alternative proposed decisions.

Module-based multiscale simulation of angiogenesis in skeletal muscle

PubMed Central

2011-01-01

Background Mathematical modeling of angiogenesis has been gaining momentum as a means to shed new light on the biological complexity underlying blood vessel growth. A variety of computational models have been developed, each focusing on different aspects of the angiogenesis process and occurring at different biological scales, ranging from the molecular to the tissue levels. Integration of models at different scales is a challenging and currently unsolved problem. Results We present an object-oriented module-based computational integration strategy to build a multiscale model of angiogenesis that links currently available models. As an example case, we use this approach to integrate modules representing microvascular blood flow, oxygen transport, vascular endothelial growth factor transport and endothelial cell behavior (sensing, migration and proliferation). Modeling methodologies in these modules include algebraic equations, partial differential equations and agent-based models with complex logical rules. We apply this integrated model to simulate exercise-induced angiogenesis in skeletal muscle. The simulation results compare capillary growth patterns between different exercise conditions for a single bout of exercise. Results demonstrate how the computational infrastructure can effectively integrate multiple modules by coordinating their connectivity and data exchange. Model parameterization offers simulation flexibility and a platform for performing sensitivity analysis. Conclusions This systems biology strategy can be applied to larger scale integration of computational models of angiogenesis in skeletal muscle, or other complex processes in other tissues under physiological and pathological conditions. PMID:21463529

Advantages of Computer Simulation in Enhancing Students' Learning about Landform Evolution: A Case Study Using the Grand Canyon

ERIC Educational Resources Information Center

Luo, Wei; Pelletier, Jon; Duffin, Kirk; Ormand, Carol; Hung, Wei-chen; Shernoff, David J.; Zhai, Xiaoming; Iverson, Ellen; Whalley, Kyle; Gallaher, Courtney; Furness, Walter

2016-01-01

The long geological time needed for landform development and evolution poses a challenge for understanding and appreciating the processes involved. The Web-based Interactive Landform Simulation Model--Grand Canyon (WILSIM-GC, http://serc.carleton.edu/landform/) is an educational tool designed to help students better understand such processes,…

Computational simulation of the creep-rupture process in filamentary composite materials

NASA Technical Reports Server (NTRS)

Slattery, Kerry T.; Hackett, Robert M.

1991-01-01

A computational simulation of the internal damage accumulation which causes the creep-rupture phenomenon in filamentary composite materials is developed. The creep-rupture process involves complex interactions between several damage mechanisms. A statistically-based computational simulation using a time-differencing approach is employed to model these progressive interactions. The finite element method is used to calculate the internal stresses. The fibers are modeled as a series of bar elements which are connected transversely by matrix elements. Flaws are distributed randomly throughout the elements in the model. Load is applied, and the properties of the individual elements are updated at the end of each time step as a function of the stress history. The simulation is continued until failure occurs. Several cases, with different initial flaw dispersions, are run to establish a statistical distribution of the time-to-failure. The calculations are performed on a supercomputer. The simulation results compare favorably with the results of creep-rupture experiments conducted at the Lawrence Livermore National Laboratory.

Real-time computing platform for spiking neurons (RT-spike).

PubMed

Ros, Eduardo; Ortigosa, Eva M; Agís, Rodrigo; Carrillo, Richard; Arnold, Michael

2006-07-01

A computing platform is described for simulating arbitrary networks of spiking neurons in real time. A hybrid computing scheme is adopted that uses both software and hardware components to manage the tradeoff between flexibility and computational power; the neuron model is implemented in hardware and the network model and the learning are implemented in software. The incremental transition of the software components into hardware is supported. We focus on a spike response model (SRM) for a neuron where the synapses are modeled as input-driven conductances. The temporal dynamics of the synaptic integration process are modeled with a synaptic time constant that results in a gradual injection of charge. This type of model is computationally expensive and is not easily amenable to existing software-based event-driven approaches. As an alternative we have designed an efficient time-based computing architecture in hardware, where the different stages of the neuron model are processed in parallel. Further improvements occur by computing multiple neurons in parallel using multiple processing units. This design is tested using reconfigurable hardware and its scalability and performance evaluated. Our overall goal is to investigate biologically realistic models for the real-time control of robots operating within closed action-perception loops, and so we evaluate the performance of the system on simulating a model of the cerebellum where the emulation of the temporal dynamics of the synaptic integration process is important.

GPU-based Efficient Realistic Techniques for Bleeding and Smoke Generation in Surgical Simulators

PubMed Central

Halic, Tansel; Sankaranarayanan, Ganesh; De, Suvranu

2010-01-01

Background In actual surgery, smoke and bleeding due to cautery processes, provide important visual cues to the surgeon which have been proposed as factors in surgical skill assessment. While several virtual reality (VR)-based surgical simulators have incorporated effects of bleeding and smoke generation, they are not realistic due to the requirement of real time performance. To be interactive, visual update must be performed at least 30 Hz and haptic (touch) information must be refreshed at 1 kHz. Simulation of smoke and bleeding is, therefore, either ignored or simulated using highly simplified techniques since other computationally intensive processes compete for the available CPU resources. Methods In this work, we develop a novel low-cost method to generate realistic bleeding and smoke in VR-based surgical simulators which outsources the computations to the graphical processing unit (GPU), thus freeing up the CPU for other time-critical tasks. This method is independent of the complexity of the organ models in the virtual environment. User studies were performed using 20 subjects to determine the visual quality of the simulations compared to real surgical videos. Results The smoke and bleeding simulation were implemented as part of a Laparoscopic Adjustable Gastric Banding (LAGB) simulator. For the bleeding simulation, the original implementation using the shader did not incur in noticeable overhead. However, for smoke generation, an I/O (Input/Output) bottleneck was observed and two different methods were developed to overcome this limitation. Based on our benchmark results, a buffered approach performed better than a pipelined approach and could support up to 15 video streams in real time. Human subject studies showed that the visual realism of the simulations were as good as in real surgery (median rating of 4 on a 5-point Likert scale). Conclusions Based on the performance results and subject study, both bleeding and smoke simulations were concluded to be efficient, highly realistic and well suited in VR-based surgical simulators. PMID:20878651

Fast Photon Monte Carlo for Water Cherenkov Detectors

NASA Astrophysics Data System (ADS)

Latorre, Anthony; Seibert, Stanley

2012-03-01

We present Chroma, a high performance optical photon simulation for large particle physics detectors, such as the water Cerenkov far detector option for LBNE. This software takes advantage of the CUDA parallel computing platform to propagate photons using modern graphics processing units. In a computer model of a 200 kiloton water Cerenkov detector with 29,000 photomultiplier tubes, Chroma can propagate 2.5 million photons per second, around 200 times faster than the same simulation with Geant4. Chroma uses a surface based approach to modeling geometry which offers many benefits over a solid based modelling approach which is used in other simulations like Geant4.

Tree-Structured Digital Organisms Model

NASA Astrophysics Data System (ADS)

Suzuki, Teruhiko; Nobesawa, Shiho; Tahara, Ikuo

Tierra and Avida are well-known models of digital organisms. They describe a life process as a sequence of computation codes. A linear sequence model may not be the only way to describe a digital organism, though it is very simple for a computer-based model. Thus we propose a new digital organism model based on a tree structure, which is rather similar to the generic programming. With our model, a life process is a combination of various functions, as if life in the real world is. This implies that our model can easily describe the hierarchical structure of life, and it can simulate evolutionary computation through mutual interaction of functions. We verified our model by simulations that our model can be regarded as a digital organism model according to its definitions. Our model even succeeded in creating species such as viruses and parasites.

Real-Time Visualization of an HPF-based CFD Simulation

NASA Technical Reports Server (NTRS)

Kremenetsky, Mark; Vaziri, Arsi; Haimes, Robert; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

Current time-dependent CFD simulations produce very large multi-dimensional data sets at each time step. The visual analysis of computational results are traditionally performed by post processing the static data on graphics workstations. We present results from an alternate approach in which we analyze the simulation data in situ on each processing node at the time of simulation. The locally analyzed results, usually more economical and in a reduced form, are then combined and sent back for visualization on a graphics workstation.

Automated Classification of Phonological Errors in Aphasic Language

PubMed Central

Ahuja, Sanjeev B.; Reggia, James A.; Berndt, Rita S.

1984-01-01

Using heuristically-guided state space search, a prototype program has been developed to simulate and classify phonemic errors occurring in the speech of neurologically-impaired patients. Simulations are based on an interchangeable rule/operator set of elementary errors which represent a theory of phonemic processing faults. This work introduces and evaluates a novel approach to error simulation and classification, it provides a prototype simulation tool for neurolinguistic research, and it forms the initial phase of a larger research effort involving computer modelling of neurolinguistic processes.

Structurally Integrated Coatings for Wear and Corrosion (SICWC): Arc Lamp, InfraRed (IR) Thermal Processing

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

Mackiewicz-Ludtka, G.; Sebright, J.

2007-12-15

The primary goal of this Cooperative Research and Development Agreement (CRADA) betwe1311 UT-Battelle (Contractor) and Caterpillar Inc. (Participant) was to develop the plasma arc lamp (PAL), infrared (IR) thermal processing technology 1.) to enhance surface coating performance by improving the interfacial bond strength between selected coatings and substrates; and 2.) to extend this technology base for transitioning of the arc lamp processing to the industrial Participant. Completion of the following three key technical tasks (described below) was necessary in order to accomplish this goal. First, thermophysical property data sets were successfully determined for composite coatings applied to 1010 steel substrates,more » with a more limited data set successfully measured for free-standing coatings. These data are necessary for the computer modeling simulations and parametric studies to; A.) simulate PAL IR processing, facilitating the development of the initial processing parameters; and B.) help develop a better understanding of the basic PAL IR fusing process fundamentals, including predicting the influence of melt pool stirring and heat tnmsfar characteristics introduced during plasma arc lamp infrared (IR) processing; Second, a methodology and a set of procedures were successfully developed and the plasma arc lamp (PAL) power profiles were successfully mapped as a function of PAL power level for the ORNL PAL. The latter data also are necessary input for the computer model to accurately simulate PAL processing during process modeling simulations, and to facilitate a better understand of the fusing process fundamentals. Third, several computer modeling codes have been evaluated as to their capabilities and accuracy in being able to capture and simulate convective mixing that may occur during PAL thermal processing. The results from these evaluation efforts are summarized in this report. The intention of this project was to extend the technology base and provide for transitioning of the arc lamp processing to the industrial Participant.« less

Hybrid neuro-heuristic methodology for simulation and control of dynamic systems over time interval.

PubMed

Woźniak, Marcin; Połap, Dawid

2017-09-01

Simulation and positioning are very important aspects of computer aided engineering. To process these two, we can apply traditional methods or intelligent techniques. The difference between them is in the way they process information. In the first case, to simulate an object in a particular state of action, we need to perform an entire process to read values of parameters. It is not very convenient for objects for which simulation takes a long time, i.e. when mathematical calculations are complicated. In the second case, an intelligent solution can efficiently help on devoted way of simulation, which enables us to simulate the object only in a situation that is necessary for a development process. We would like to present research results on developed intelligent simulation and control model of electric drive engine vehicle. For a dedicated simulation method based on intelligent computation, where evolutionary strategy is simulating the states of the dynamic model, an intelligent system based on devoted neural network is introduced to control co-working modules while motion is in time interval. Presented experimental results show implemented solution in situation when a vehicle transports things over area with many obstacles, what provokes sudden changes in stability that may lead to destruction of load. Therefore, applied neural network controller prevents the load from destruction by positioning characteristics like pressure, acceleration, and stiffness voltage to absorb the adverse changes of the ground. Copyright © 2017 Elsevier Ltd. All rights reserved.

Argonne simulation framework for intelligent transportation systems

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

Ewing, T.; Doss, E.; Hanebutte, U.

1996-04-01

A simulation framework has been developed which defines a high-level architecture for a large-scale, comprehensive, scalable simulation of an Intelligent Transportation System (ITS). The simulator is designed to run on parallel computers and distributed (networked) computer systems; however, a version for a stand alone workstation is also available. The ITS simulator includes an Expert Driver Model (EDM) of instrumented ``smart`` vehicles with in-vehicle navigation units. The EDM is capable of performing optimal route planning and communicating with Traffic Management Centers (TMC). A dynamic road map data base is sued for optimum route planning, where the data is updated periodically tomore » reflect any changes in road or weather conditions. The TMC has probe vehicle tracking capabilities (display position and attributes of instrumented vehicles), and can provide 2-way interaction with traffic to provide advisories and link times. Both the in-vehicle navigation module and the TMC feature detailed graphical user interfaces that includes human-factors studies to support safety and operational research. Realistic modeling of variations of the posted driving speed are based on human factor studies that take into consideration weather, road conditions, driver`s personality and behavior and vehicle type. The simulator has been developed on a distributed system of networked UNIX computers, but is designed to run on ANL`s IBM SP-X parallel computer system for large scale problems. A novel feature of the developed simulator is that vehicles will be represented by autonomous computer processes, each with a behavior model which performs independent route selection and reacts to external traffic events much like real vehicles. Vehicle processes interact with each other and with ITS components by exchanging messages. With this approach, one will be able to take advantage of emerging massively parallel processor (MPP) systems.« less

Simulation framework for intelligent transportation systems

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

Ewing, T.; Doss, E.; Hanebutte, U.

1996-10-01

A simulation framework has been developed for a large-scale, comprehensive, scaleable simulation of an Intelligent Transportation System (ITS). The simulator is designed for running on parallel computers and distributed (networked) computer systems, but can run on standalone workstations for smaller simulations. The simulator currently models instrumented smart vehicles with in-vehicle navigation units capable of optimal route planning and Traffic Management Centers (TMC). The TMC has probe vehicle tracking capabilities (display position and attributes of instrumented vehicles), and can provide two-way interaction with traffic to provide advisories and link times. Both the in-vehicle navigation module and the TMC feature detailed graphicalmore » user interfaces to support human-factors studies. Realistic modeling of variations of the posted driving speed are based on human factors studies that take into consideration weather, road conditions, driver personality and behavior, and vehicle type. The prototype has been developed on a distributed system of networked UNIX computers but is designed to run on parallel computers, such as ANL`s IBM SP-2, for large-scale problems. A novel feature of the approach is that vehicles are represented by autonomous computer processes which exchange messages with other processes. The vehicles have a behavior model which governs route selection and driving behavior, and can react to external traffic events much like real vehicles. With this approach, the simulation is scaleable to take advantage of emerging massively parallel processor (MPP) systems.« less

A simplified computational memory model from information processing

PubMed Central

Zhang, Lanhua; Zhang, Dongsheng; Deng, Yuqin; Ding, Xiaoqian; Wang, Yan; Tang, Yiyuan; Sun, Baoliang

2016-01-01

This paper is intended to propose a computational model for memory from the view of information processing. The model, called simplified memory information retrieval network (SMIRN), is a bi-modular hierarchical functional memory network by abstracting memory function and simulating memory information processing. At first meta-memory is defined to express the neuron or brain cortices based on the biology and graph theories, and we develop an intra-modular network with the modeling algorithm by mapping the node and edge, and then the bi-modular network is delineated with intra-modular and inter-modular. At last a polynomial retrieval algorithm is introduced. In this paper we simulate the memory phenomena and functions of memorization and strengthening by information processing algorithms. The theoretical analysis and the simulation results show that the model is in accordance with the memory phenomena from information processing view. PMID:27876847

Time Warp Operating System, Version 2.5.1

NASA Technical Reports Server (NTRS)

Bellenot, Steven F.; Gieselman, John S.; Hawley, Lawrence R.; Peterson, Judy; Presley, Matthew T.; Reiher, Peter L.; Springer, Paul L.; Tupman, John R.; Wedel, John J., Jr.; Wieland, Frederick P.;

3D numerical simulation of transient processes in hydraulic turbines

NASA Astrophysics Data System (ADS)

Cherny, S.; Chirkov, D.; Bannikov, D.; Lapin, V.; Skorospelov, V.; Eshkunova, I.; Avdushenko, A.

2010-08-01

An approach for numerical simulation of 3D hydraulic turbine flows in transient operating regimes is presented. The method is based on a coupled solution of incompressible RANS equations, runner rotation equation, and water hammer equations. The issue of setting appropriate boundary conditions is considered in detail. As an illustration, the simulation results for runaway process are presented. The evolution of vortex structure and its effect on computed runaway traces are analyzed.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Möckel, M.; Wiedemann, C.; Flegel, S.; Gelhaus, J.; Vörsmann, P.; Klinkrad, H.; Krag, H.

2011-07-01

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction to OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Moeckel, Marek; Wiedemann, Carsten; Flegel, Sven Kevin; Gelhaus, Johannes; Klinkrad, Heiner; Krag, Holger; Voersmann, Peter

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction of OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Efficient coarse simulation of a growing avascular tumor

PubMed Central

Kavousanakis, Michail E.; Liu, Ping; Boudouvis, Andreas G.; Lowengrub, John; Kevrekidis, Ioannis G.

2013-01-01

The subject of this work is the development and implementation of algorithms which accelerate the simulation of early stage tumor growth models. Among the different computational approaches used for the simulation of tumor progression, discrete stochastic models (e.g., cellular automata) have been widely used to describe processes occurring at the cell and subcell scales (e.g., cell-cell interactions and signaling processes). To describe macroscopic characteristics (e.g., morphology) of growing tumors, large numbers of interacting cells must be simulated. However, the high computational demands of stochastic models make the simulation of large-scale systems impractical. Alternatively, continuum models, which can describe behavior at the tumor scale, often rely on phenomenological assumptions in place of rigorous upscaling of microscopic models. This limits their predictive power. In this work, we circumvent the derivation of closed macroscopic equations for the growing cancer cell populations; instead, we construct, based on the so-called “equation-free” framework, a computational superstructure, which wraps around the individual-based cell-level simulator and accelerates the computations required for the study of the long-time behavior of systems involving many interacting cells. The microscopic model, e.g., a cellular automaton, which simulates the evolution of cancer cell populations, is executed for relatively short time intervals, at the end of which coarse-scale information is obtained. These coarse variables evolve on slower time scales than each individual cell in the population, enabling the application of forward projection schemes, which extrapolate their values at later times. This technique is referred to as coarse projective integration. Increasing the ratio of projection times to microscopic simulator execution times enhances the computational savings. Crucial accuracy issues arising for growing tumors with radial symmetry are addressed by applying the coarse projective integration scheme in a cotraveling (cogrowing) frame. As a proof of principle, we demonstrate that the application of this scheme yields highly accurate solutions, while preserving the computational savings of coarse projective integration. PMID:22587128

Fast simulation of Proton Induced X-Ray Emission Tomography using CUDA

NASA Astrophysics Data System (ADS)

Beasley, D. G.; Marques, A. C.; Alves, L. C.; da Silva, R. C.

2013-07-01

A new 3D Proton Induced X-Ray Emission Tomography (PIXE-T) and Scanning Transmission Ion Microscopy Tomography (STIM-T) simulation software has been developed in Java and uses NVIDIA™ Common Unified Device Architecture (CUDA) to calculate the X-ray attenuation for large detector areas. A challenge with PIXE-T is to get sufficient counts while retaining a small beam spot size. Therefore a high geometric efficiency is required. However, as the detector solid angle increases the calculations required for accurate reconstruction of the data increase substantially. To overcome this limitation, the CUDA parallel computing platform was used which enables general purpose programming of NVIDIA graphics processing units (GPUs) to perform computations traditionally handled by the central processing unit (CPU). For simulation performance evaluation, the results of a CPU- and a CUDA-based simulation of a phantom are presented. Furthermore, a comparison with the simulation code in the PIXE-Tomography reconstruction software DISRA (A. Sakellariou, D.N. Jamieson, G.J.F. Legge, 2001) is also shown. Compared to a CPU implementation, the CUDA based simulation is approximately 30× faster.

OpenSimulator Interoperability with DRDC Simulation Tools: Compatibility Study

DTIC Science & Technology

2014-09-01

into two components: (1) backend data services consisting of user accounts, login service, assets, and inventory; and (2) the simulator server which...components are combined into a single OpenSimulator process. In grid mode, the two components are separated, placing the backend services into a ROBUST... mobile devices. Potential points of compatibility between Unity and OpenSimulator include: a Unity-based desktop computer OpenSimulator viewer; a

Development of an Output-based Adaptive Method for Multi-Dimensional Euler and Navier-Stokes Simulations

NASA Technical Reports Server (NTRS)

Darmofal, David L.

2003-01-01

The use of computational simulations in the prediction of complex aerodynamic flows is becoming increasingly prevalent in the design process within the aerospace industry. Continuing advancements in both computing technology and algorithmic development are ultimately leading to attempts at simulating ever-larger, more complex problems. However, by increasing the reliance on computational simulations in the design cycle, we must also increase the accuracy of these simulations in order to maintain or improve the reliability arid safety of the resulting aircraft. At the same time, large-scale computational simulations must be made more affordable so that their potential benefits can be fully realized within the design cycle. Thus, a continuing need exists for increasing the accuracy and efficiency of computational algorithms such that computational fluid dynamics can become a viable tool in the design of more reliable, safer aircraft. The objective of this research was the development of an error estimation and grid adaptive strategy for reducing simulation errors in integral outputs (functionals) such as lift or drag from from multi-dimensional Euler and Navier-Stokes simulations. In this final report, we summarize our work during this grant.

Projective simulation for artificial intelligence

NASA Astrophysics Data System (ADS)

Briegel, Hans J.; de Las Cuevas, Gemma

2012-05-01

We propose a model of a learning agent whose interaction with the environment is governed by a simulation-based projection, which allows the agent to project itself into future situations before it takes real action. Projective simulation is based on a random walk through a network of clips, which are elementary patches of episodic memory. The network of clips changes dynamically, both due to new perceptual input and due to certain compositional principles of the simulation process. During simulation, the clips are screened for specific features which trigger factual action of the agent. The scheme is different from other, computational, notions of simulation, and it provides a new element in an embodied cognitive science approach to intelligent action and learning. Our model provides a natural route for generalization to quantum-mechanical operation and connects the fields of reinforcement learning and quantum computation.

Projective simulation for artificial intelligence

PubMed Central

Briegel, Hans J.; De las Cuevas, Gemma

2012-01-01

We propose a model of a learning agent whose interaction with the environment is governed by a simulation-based projection, which allows the agent to project itself into future situations before it takes real action. Projective simulation is based on a random walk through a network of clips, which are elementary patches of episodic memory. The network of clips changes dynamically, both due to new perceptual input and due to certain compositional principles of the simulation process. During simulation, the clips are screened for specific features which trigger factual action of the agent. The scheme is different from other, computational, notions of simulation, and it provides a new element in an embodied cognitive science approach to intelligent action and learning. Our model provides a natural route for generalization to quantum-mechanical operation and connects the fields of reinforcement learning and quantum computation. PMID:22590690

Computational Materials Science and Chemistry: Accelerating Discovery and Innovation through Simulation-Based Engineering and Science

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

Crabtree, George; Glotzer, Sharon; McCurdy, Bill

This report is based on a SC Workshop on Computational Materials Science and Chemistry for Innovation on July 26-27, 2010, to assess the potential of state-of-the-art computer simulations to accelerate understanding and discovery in materials science and chemistry, with a focus on potential impacts in energy technologies and innovation. The urgent demand for new energy technologies has greatly exceeded the capabilities of today's materials and chemical processes. To convert sunlight to fuel, efficiently store energy, or enable a new generation of energy production and utilization technologies requires the development of new materials and processes of unprecedented functionality and performance. Newmore » materials and processes are critical pacing elements for progress in advanced energy systems and virtually all industrial technologies. Over the past two decades, the United States has developed and deployed the world's most powerful collection of tools for the synthesis, processing, characterization, and simulation and modeling of materials and chemical systems at the nanoscale, dimensions of a few atoms to a few hundred atoms across. These tools, which include world-leading x-ray and neutron sources, nanoscale science facilities, and high-performance computers, provide an unprecedented view of the atomic-scale structure and dynamics of materials and the molecular-scale basis of chemical processes. For the first time in history, we are able to synthesize, characterize, and model materials and chemical behavior at the length scale where this behavior is controlled. This ability is transformational for the discovery process and, as a result, confers a significant competitive advantage. Perhaps the most spectacular increase in capability has been demonstrated in high performance computing. Over the past decade, computational power has increased by a factor of a million due to advances in hardware and software. This rate of improvement, which shows no sign of abating, has enabled the development of computer simulations and models of unprecedented fidelity. We are at the threshold of a new era where the integrated synthesis, characterization, and modeling of complex materials and chemical processes will transform our ability to understand and design new materials and chemistries with predictive power. In turn, this predictive capability will transform technological innovation by accelerating the development and deployment of new materials and processes in products and manufacturing. Harnessing the potential of computational science and engineering for the discovery and development of materials and chemical processes is essential to maintaining leadership in these foundational fields that underpin energy technologies and industrial competitiveness. Capitalizing on the opportunities presented by simulation-based engineering and science in materials and chemistry will require an integration of experimental capabilities with theoretical and computational modeling; the development of a robust and sustainable infrastructure to support the development and deployment of advanced computational models; and the assembly of a community of scientists and engineers to implement this integration and infrastructure. This community must extend to industry, where incorporating predictive materials science and chemistry into design tools can accelerate the product development cycle and drive economic competitiveness. The confluence of new theories, new materials synthesis capabilities, and new computer platforms has created an unprecedented opportunity to implement a "materials-by-design" paradigm with wide-ranging benefits in technological innovation and scientific discovery. The Workshop on Computational Materials Science and Chemistry for Innovation was convened in Bethesda, Maryland, on July 26-27, 2010. Sponsored by the Department of Energy (DOE) Offices of Advanced Scientific Computing Research and Basic Energy Sciences, the workshop brought together 160 experts in materials science, chemistry, and computational science representing more than 65 universities, laboratories, and industries, and four agencies. The workshop examined seven foundational challenge areas in materials science and chemistry: materials for extreme conditions, self-assembly, light harvesting, chemical reactions, designer fluids, thin films and interfaces, and electronic structure. Each of these challenge areas is critical to the development of advanced energy systems, and each can be accelerated by the integrated application of predictive capability with theory and experiment. The workshop concluded that emerging capabilities in predictive modeling and simulation have the potential to revolutionize the development of new materials and chemical processes. Coupled with world-leading materials characterization and nanoscale science facilities, this predictive capability provides the foundation for an innovation ecosystem that can accelerate the discovery, development, and deployment of new technologies, including advanced energy systems. Delivering on the promise of this innovation ecosystem requires the following: Integration of synthesis, processing, characterization, theory, and simulation and modeling. Many of the newly established Energy Frontier Research Centers and Energy Hubs are exploiting this integration. Achieving/strengthening predictive capability in foundational challenge areas. Predictive capability in the seven foundational challenge areas described in this report is critical to the development of advanced energy technologies. Developing validated computational approaches that span vast differences in time and length scales. This fundamental computational challenge crosscuts all of the foundational challenge areas. Similarly challenging is coupling of analytical data from multiple instruments and techniques that are required to link these length and time scales. Experimental validation and quantification of uncertainty in simulation and modeling. Uncertainty quantification becomes increasingly challenging as simulations become more complex. Robust and sustainable computational infrastructure, including software and applications. For modeling and simulation, software equals infrastructure. To validate the computational tools, software is critical infrastructure that effectively translates huge arrays of experimental data into useful scientific understanding. An integrated approach for managing this infrastructure is essential. Efficient transfer and incorporation of simulation-based engineering and science in industry. Strategies for bridging the gap between research and industrial applications and for widespread industry adoption of integrated computational materials engineering are needed.« less

Simulation-Based Approach for Site-Specific Optimization of Hydrokinetic Turbine Arrays

NASA Astrophysics Data System (ADS)

Sotiropoulos, F.; Chawdhary, S.; Yang, X.; Khosronejad, A.; Angelidis, D.

2014-12-01

A simulation-based approach has been developed to enable site-specific optimization of tidal and current turbine arrays in real-life waterways. The computational code is based on the St. Anthony Falls Laboratory Virtual StreamLab (VSL3D), which is able to carry out high-fidelity simulations of turbulent flow and sediment transport processes in rivers and streams taking into account the arbitrary geometrical complexity characterizing natural waterways. The computational framework can be used either in turbine-resolving mode, to take into account all geometrical details of the turbine, or with the turbines parameterized as actuator disks or actuator lines. Locally refined grids are employed to dramatically increase the resolution of the simulation and enable efficient simulations of multi-turbine arrays. Turbine/sediment interactions are simulated using the coupled hydro-morphodynamic module of VSL3D. The predictive capabilities of the resulting computational framework will be demonstrated by applying it to simulate turbulent flow past a tri-frame configuration of hydrokinetic turbines in a rigid-bed turbulent open channel flow as well as turbines mounted on mobile bed open channels to investigate turbine/sediment interactions. The utility of the simulation-based approach for guiding the optimal development of turbine arrays in real-life waterways will also be discussed and demonstrated. This work was supported by NSF grant IIP-1318201. Simulations were carried out at the Minnesota Supercomputing Institute.

[The history of development of evolutionary methods in St. Petersburg school of computer simulation in biology].

PubMed

Menshutkin, V V; Kazanskiĭ, A B; Levchenko, V F

2010-01-01

The history of rise and development of evolutionary methods in Saint Petersburg school of biological modelling is traced and analyzed. Some pioneering works in simulation of ecological and evolutionary processes, performed in St.-Petersburg school became an exemplary ones for many followers in Russia and abroad. The individual-based approach became the crucial point in the history of the school as an adequate instrument for construction of models of biological evolution. This approach is natural for simulation of the evolution of life-history parameters and adaptive processes in populations and communities. In some cases simulated evolutionary process was used for solving a reverse problem, i. e., for estimation of uncertain life-history parameters of population. Evolutionary computations is one more aspect of this approach application in great many fields. The problems and vistas of ecological and evolutionary modelling in general are discussed.

Data flow modeling techniques

NASA Technical Reports Server (NTRS)

Kavi, K. M.

1984-01-01

There have been a number of simulation packages developed for the purpose of designing, testing and validating computer systems, digital systems and software systems. Complex analytical tools based on Markov and semi-Markov processes have been designed to estimate the reliability and performance of simulated systems. Petri nets have received wide acceptance for modeling complex and highly parallel computers. In this research data flow models for computer systems are investigated. Data flow models can be used to simulate both software and hardware in a uniform manner. Data flow simulation techniques provide the computer systems designer with a CAD environment which enables highly parallel complex systems to be defined, evaluated at all levels and finally implemented in either hardware or software. Inherent in data flow concept is the hierarchical handling of complex systems. In this paper we will describe how data flow can be used to model computer system.

Computer-aided system design

NASA Technical Reports Server (NTRS)

Walker, Carrie K.

1991-01-01

A technique has been developed for combining features of a systems architecture design and assessment tool and a software development tool. This technique reduces simulation development time and expands simulation detail. The Architecture Design and Assessment System (ADAS), developed at the Research Triangle Institute, is a set of computer-assisted engineering tools for the design and analysis of computer systems. The ADAS system is based on directed graph concepts and supports the synthesis and analysis of software algorithms mapped to candidate hardware implementations. Greater simulation detail is provided by the ADAS functional simulator. With the functional simulator, programs written in either Ada or C can be used to provide a detailed description of graph nodes. A Computer-Aided Software Engineering tool developed at the Charles Stark Draper Laboratory (CSDL CASE) automatically generates Ada or C code from engineering block diagram specifications designed with an interactive graphical interface. A technique to use the tools together has been developed, which further automates the design process.

Spaceborne computer executive routine functional design specification. Volume 2: Computer executive design for space station/base

NASA Technical Reports Server (NTRS)

Kennedy, J. R.; Fitzpatrick, W. S.

1971-01-01

The computer executive functional system design concepts derived from study of the Space Station/Base are presented. Information Management System hardware configuration as directly influencing the executive design is reviewed. The hardware configuration and generic executive design requirements are considered in detail in a previous report (System Configuration and Executive Requirements Specifications for Reusable Shuttle and Space Station/Base, 9/25/70). This report defines basic system primitives and delineates processes and process control. Supervisor states are considered for describing basic multiprogramming and multiprocessing systems. A high-level computer executive including control of scheduling, allocation of resources, system interactions, and real-time supervisory functions is defined. The description is oriented to provide a baseline for a functional simulation of the computer executive system.

Adaptive quantum computation in changing environments using projective simulation

NASA Astrophysics Data System (ADS)

Tiersch, M.; Ganahl, E. J.; Briegel, H. J.

2015-08-01

Quantum information processing devices need to be robust and stable against external noise and internal imperfections to ensure correct operation. In a setting of measurement-based quantum computation, we explore how an intelligent agent endowed with a projective simulator can act as controller to adapt measurement directions to an external stray field of unknown magnitude in a fixed direction. We assess the agent’s learning behavior in static and time-varying fields and explore composition strategies in the projective simulator to improve the agent’s performance. We demonstrate the applicability by correcting for stray fields in a measurement-based algorithm for Grover’s search. Thereby, we lay out a path for adaptive controllers based on intelligent agents for quantum information tasks.

Adaptive quantum computation in changing environments using projective simulation

PubMed Central

Tiersch, M.; Ganahl, E. J.; Briegel, H. J.

2015-01-01

Quantum information processing devices need to be robust and stable against external noise and internal imperfections to ensure correct operation. In a setting of measurement-based quantum computation, we explore how an intelligent agent endowed with a projective simulator can act as controller to adapt measurement directions to an external stray field of unknown magnitude in a fixed direction. We assess the agent’s learning behavior in static and time-varying fields and explore composition strategies in the projective simulator to improve the agent’s performance. We demonstrate the applicability by correcting for stray fields in a measurement-based algorithm for Grover’s search. Thereby, we lay out a path for adaptive controllers based on intelligent agents for quantum information tasks. PMID:26260263

Accelerating population balance-Monte Carlo simulation for coagulation dynamics from the Markov jump model, stochastic algorithm and GPU parallel computing

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

Xu, Zuwei; Zhao, Haibo, E-mail: klinsmannzhb@163.com; Zheng, Chuguang

2015-01-15

This paper proposes a comprehensive framework for accelerating population balance-Monte Carlo (PBMC) simulation of particle coagulation dynamics. By combining Markov jump model, weighted majorant kernel and GPU (graphics processing unit) parallel computing, a significant gain in computational efficiency is achieved. The Markov jump model constructs a coagulation-rule matrix of differentially-weighted simulation particles, so as to capture the time evolution of particle size distribution with low statistical noise over the full size range and as far as possible to reduce the number of time loopings. Here three coagulation rules are highlighted and it is found that constructing appropriate coagulation rule providesmore » a route to attain the compromise between accuracy and cost of PBMC methods. Further, in order to avoid double looping over all simulation particles when considering the two-particle events (typically, particle coagulation), the weighted majorant kernel is introduced to estimate the maximum coagulation rates being used for acceptance–rejection processes by single-looping over all particles, and meanwhile the mean time-step of coagulation event is estimated by summing the coagulation kernels of rejected and accepted particle pairs. The computational load of these fast differentially-weighted PBMC simulations (based on the Markov jump model) is reduced greatly to be proportional to the number of simulation particles in a zero-dimensional system (single cell). Finally, for a spatially inhomogeneous multi-dimensional (multi-cell) simulation, the proposed fast PBMC is performed in each cell, and multiple cells are parallel processed by multi-cores on a GPU that can implement the massively threaded data-parallel tasks to obtain remarkable speedup ratio (comparing with CPU computation, the speedup ratio of GPU parallel computing is as high as 200 in a case of 100 cells with 10 000 simulation particles per cell). These accelerating approaches of PBMC are demonstrated in a physically realistic Brownian coagulation case. The computational accuracy is validated with benchmark solution of discrete-sectional method. The simulation results show that the comprehensive approach can attain very favorable improvement in cost without sacrificing computational accuracy.« less

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

Sharma, Ms. Ketki; Kim, Yong-Ha; Yiacoumi, Sotira

The mixing process of fresh water and seawater releases a significant amount of energy and is a potential source of renewable energy. The so called ‘blue energy’ or salinity-gradient energy can be harvested by a device consisting of carbon electrodes immersed in an electrolyte solution, based on the principle of capacitive double layer expansion (CDLE). In this study, we have investigated the feasibility of energy production based on the CDLE principle. Experiments and computer simulations were used to study the process. Mesoporous carbon materials, synthesized at the Oak Ridge National Laboratory, were used as electrode materials in the experiments. Neutronmore » imaging of the blue energy cycle was conducted with cylindrical mesoporous carbon electrodes and 0.5 M lithium chloride as the electrolyte solution. For experiments conducted at 0.6 V and 0.9 V applied potential, a voltage increase of 0.061 V and 0.054 V was observed, respectively. From sequences of neutron images obtained for each step of the blue energy cycle, information on the direction and magnitude of lithium ion transport was obtained. A computer code was developed to simulate the process. Experimental data and computer simulations allowed us to predict energy production.« less

GPU-based prompt gamma ray imaging from boron neutron capture therapy.

PubMed

Yoon, Do-Kun; Jung, Joo-Young; Jo Hong, Key; Sil Lee, Keum; Suk Suh, Tae

2015-01-01

The purpose of this research is to perform the fast reconstruction of a prompt gamma ray image using a graphics processing unit (GPU) computation from boron neutron capture therapy (BNCT) simulations. To evaluate the accuracy of the reconstructed image, a phantom including four boron uptake regions (BURs) was used in the simulation. After the Monte Carlo simulation of the BNCT, the modified ordered subset expectation maximization reconstruction algorithm using the GPU computation was used to reconstruct the images with fewer projections. The computation times for image reconstruction were compared between the GPU and the central processing unit (CPU). Also, the accuracy of the reconstructed image was evaluated by a receiver operating characteristic (ROC) curve analysis. The image reconstruction time using the GPU was 196 times faster than the conventional reconstruction time using the CPU. For the four BURs, the area under curve values from the ROC curve were 0.6726 (A-region), 0.6890 (B-region), 0.7384 (C-region), and 0.8009 (D-region). The tomographic image using the prompt gamma ray event from the BNCT simulation was acquired using the GPU computation in order to perform a fast reconstruction during treatment. The authors verified the feasibility of the prompt gamma ray image reconstruction using the GPU computation for BNCT simulations.

Simulating the decentralized processes of the human immune system in a virtual anatomy model.

PubMed

Sarpe, Vladimir; Jacob, Christian

2013-01-01

Many physiological processes within the human body can be perceived and modeled as large systems of interacting particles or swarming agents. The complex processes of the human immune system prove to be challenging to capture and illustrate without proper reference to the spatial distribution of immune-related organs and systems. Our work focuses on physical aspects of immune system processes, which we implement through swarms of agents. This is our first prototype for integrating different immune processes into one comprehensive virtual physiology simulation. Using agent-based methodology and a 3-dimensional modeling and visualization environment (LINDSAY Composer), we present an agent-based simulation of the decentralized processes in the human immune system. The agents in our model - such as immune cells, viruses and cytokines - interact through simulated physics in two different, compartmentalized and decentralized 3-dimensional environments namely, (1) within the tissue and (2) inside a lymph node. While the two environments are separated and perform their computations asynchronously, an abstract form of communication is allowed in order to replicate the exchange, transportation and interaction of immune system agents between these sites. The distribution of simulated processes, that can communicate across multiple, local CPUs or through a network of machines, provides a starting point to build decentralized systems that replicate larger-scale processes within the human body, thus creating integrated simulations with other physiological systems, such as the circulatory, endocrine, or nervous system. Ultimately, this system integration across scales is our goal for the LINDSAY Virtual Human project. Our current immune system simulations extend our previous work on agent-based simulations by introducing advanced visualizations within the context of a virtual human anatomy model. We also demonstrate how to distribute a collection of connected simulations over a network of computers. As a future endeavour, we plan to use parameter tuning techniques on our model to further enhance its biological credibility. We consider these in silico experiments and their associated modeling and optimization techniques as essential components in further enhancing our capabilities of simulating a whole-body, decentralized immune system, to be used both for medical education and research as well as for virtual studies in immunoinformatics.

Mechanisms of Developmental Change in Infant Categorization

ERIC Educational Resources Information Center

Westermann, Gert; Mareschal, Denis

2012-01-01

Computational models are tools for testing mechanistic theories of learning and development. Formal models allow us to instantiate theories of cognitive development in computer simulations. Model behavior can then be compared to real performance. Connectionist models, loosely based on neural information processing, have been successful in…

Streaming parallel GPU acceleration of large-scale filter-based spiking neural networks.

PubMed

Slażyński, Leszek; Bohte, Sander

2012-01-01

The arrival of graphics processing (GPU) cards suitable for massively parallel computing promises affordable large-scale neural network simulation previously only available at supercomputing facilities. While the raw numbers suggest that GPUs may outperform CPUs by at least an order of magnitude, the challenge is to develop fine-grained parallel algorithms to fully exploit the particulars of GPUs. Computation in a neural network is inherently parallel and thus a natural match for GPU architectures: given inputs, the internal state for each neuron can be updated in parallel. We show that for filter-based spiking neurons, like the Spike Response Model, the additive nature of membrane potential dynamics enables additional update parallelism. This also reduces the accumulation of numerical errors when using single precision computation, the native precision of GPUs. We further show that optimizing simulation algorithms and data structures to the GPU's architecture has a large pay-off: for example, matching iterative neural updating to the memory architecture of the GPU speeds up this simulation step by a factor of three to five. With such optimizations, we can simulate in better-than-realtime plausible spiking neural networks of up to 50 000 neurons, processing over 35 million spiking events per second.

A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations

DOE PAGES

Scheibe, Timothy D.; Yang, Xiaofan; Chen, Xingyuan; ...

2015-06-01

Extensive research efforts have been invested in reducing model errors to improve the predictive ability of biogeochemical earth and environmental system simulators, with applications ranging from contaminant transport and remediation to impacts of biogeochemical elemental cycling (e.g., carbon and nitrogen) on local ecosystems and regional to global climate. While the bulk of this research has focused on improving model parameterizations in the face of observational limitations, the more challenging type of model error/uncertainty to identify and quantify is model structural error which arises from incorrect mathematical representations of (or failure to consider) important physical, chemical, or biological processes, properties, ormore » system states in model formulations. While improved process understanding can be achieved through scientific study, such understanding is usually developed at small scales. Process-based numerical models are typically designed for a particular characteristic length and time scale. For application-relevant scales, it is generally necessary to introduce approximations and empirical parameterizations to describe complex systems or processes. This single-scale approach has been the best available to date because of limited understanding of process coupling combined with practical limitations on system characterization and computation. While computational power is increasing significantly and our understanding of biological and environmental processes at fundamental scales is accelerating, using this information to advance our knowledge of the larger system behavior requires the development of multiscale simulators. Accordingly there has been much recent interest in novel multiscale methods in which microscale and macroscale models are explicitly coupled in a single hybrid multiscale simulation. A limited number of hybrid multiscale simulations have been developed for biogeochemical earth systems, but they mostly utilize application-specific and sometimes ad-hoc approaches for model coupling. We are developing a generalized approach to hierarchical model coupling designed for high-performance computational systems, based on the Swift computing workflow framework. In this presentation we will describe the generalized approach and provide two use cases: 1) simulation of a mixing-controlled biogeochemical reaction coupling pore- and continuum-scale models, and 2) simulation of biogeochemical impacts of groundwater – river water interactions coupling fine- and coarse-grid model representations. This generalized framework can be customized for use with any pair of linked models (microscale and macroscale) with minimal intrusiveness to the at-scale simulators. It combines a set of python scripts with the Swift workflow environment to execute a complex multiscale simulation utilizing an approach similar to the well-known Heterogeneous Multiscale Method. User customization is facilitated through user-provided input and output file templates and processing function scripts, and execution within a high-performance computing environment is handled by Swift, such that minimal to no user modification of at-scale codes is required.« less

Benchmark tests for a Formula SAE Student car prototyping

NASA Astrophysics Data System (ADS)

Mariasiu, Florin

2011-12-01

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

Computational simulation of laser heat processing of materials

NASA Astrophysics Data System (ADS)

Shankar, Vijaya; Gnanamuthu, Daniel

1987-04-01

A computational model simulating the laser heat treatment of AISI 4140 steel plates with a CW CO2 laser beam has been developed on the basis of the three-dimensional, time-dependent heat equation (subject to the appropriate boundary conditions). The solution method is based on Newton iteration applied to a triple-approximate factorized form of the equation. The method is implicit and time-accurate; the maintenance of time-accuracy in the numerical formulation is noted to be critical for the simulation of finite length workpieces with a finite laser beam dwell time.

Image Understanding Architecture

DTIC Science & Technology

1991-09-01

architecture to support real-time, knowledge -based image understanding , and develop the software support environment that will be needed to utilize...NUMBER OF PAGES Image Understanding Architecture, Knowledge -Based Vision, AI Real-Time Computer Vision, Software Simulator, Parallel Processor IL PRICE... information . In addition to sensory and knowledge -based processing it is useful to introduce a level of symbolic processing. Thus, vision researchers

New method of processing heat treatment experiments with numerical simulation support

NASA Astrophysics Data System (ADS)

Kik, T.; Moravec, J.; Novakova, I.

2017-08-01

In this work, benefits of combining modern software for numerical simulations of welding processes with laboratory research was described. Proposed new method of processing heat treatment experiments leading to obtaining relevant input data for numerical simulations of heat treatment of large parts was presented. It is now possible, by using experiments on small tested samples, to simulate cooling conditions comparable with cooling of bigger parts. Results from this method of testing makes current boundary conditions during real cooling process more accurate, but also can be used for improvement of software databases and optimization of a computational models. The point is to precise the computation of temperature fields for large scale hardening parts based on new method of temperature dependence determination of the heat transfer coefficient into hardening media for the particular material, defined maximal thickness of processed part and cooling conditions. In the paper we will also present an example of the comparison standard and modified (according to newly suggested methodology) heat transfer coefficient data’s and theirs influence on the simulation results. It shows how even the small changes influence mainly on distribution of temperature, metallurgical phases, hardness and stresses distribution. By this experiment it is also possible to obtain not only input data and data enabling optimization of computational model but at the same time also verification data. The greatest advantage of described method is independence of used cooling media type.

Numerical simulation of disperse particle flows on a graphics processing unit

NASA Astrophysics Data System (ADS)

Sierakowski, Adam J.

In both nature and technology, we commonly encounter solid particles being carried within fluid flows, from dust storms to sediment erosion and from food processing to energy generation. The motion of uncountably many particles in highly dynamic flow environments characterizes the tremendous complexity of such phenomena. While methods exist for the full-scale numerical simulation of such systems, current computational capabilities require the simplification of the numerical task with significant approximation using closure models widely recognized as insufficient. There is therefore a fundamental need for the investigation of the underlying physical processes governing these disperse particle flows. In the present work, we develop a new tool based on the Physalis method for the first-principles numerical simulation of thousands of particles (a small fraction of an entire disperse particle flow system) in order to assist in the search for new reduced-order closure models. We discuss numerous enhancements to the efficiency and stability of the Physalis method, which introduces the influence of spherical particles to a fixed-grid incompressible Navier-Stokes flow solver using a local analytic solution to the flow equations. Our first-principles investigation demands the modeling of unresolved length and time scales associated with particle collisions. We introduce a collision model alongside Physalis, incorporating lubrication effects and proposing a new nonlinearly damped Hertzian contact model. By reproducing experimental studies from the literature, we document extensive validation of the methods. We discuss the implementation of our methods for massively parallel computation using a graphics processing unit (GPU). We combine Eulerian grid-based algorithms with Lagrangian particle-based algorithms to achieve computational throughput up to 90 times faster than the legacy implementation of Physalis for a single central processing unit. By avoiding all data communication between the GPU and the host system during the simulation, we utilize with great efficacy the GPU hardware with which many high performance computing systems are currently equipped. We conclude by looking forward to the future of Physalis with multi-GPU parallelization in order to perform resolved disperse flow simulations of more than 100,000 particles and further advance the development of reduced-order closure models.

The management submodel of the Wind Erosion Prediction System

USDA-ARS?s Scientific Manuscript database

The Wind Erosion Prediction System (WEPS) is a process-based, daily time-step, computer model that predicts soil erosion via simulation of the physical processes controlling wind erosion. WEPS is comprised of several individual modules (submodels) that reflect different sets of physical processes, ...

FINAL REPORT FOR VERIFICATION OF THE METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFPPT)

EPA Science Inventory

The United States Environmental Protection Agency (USEPA) has prepared a computer process simulation package for the metal finishing industry that enables users to predict process outputs based upon process inputs and other operating conditions. This report documents the developm...

Design and Application of Interactive Simulations in Problem-Solving in University-Level Physics Education

ERIC Educational Resources Information Center

Ceberio, Mikel; Almudí, José Manuel; Franco, Ángel

2016-01-01

In recent years, interactive computer simulations have been progressively integrated in the teaching of the sciences and have contributed significant improvements in the teaching-learning process. Practicing problem-solving is a key factor in science and engineering education. The aim of this study was to design simulation-based problem-solving…

Performance evaluation of GPU parallelization, space-time adaptive algorithms, and their combination for simulating cardiac electrophysiology.

PubMed

Sachetto Oliveira, Rafael; Martins Rocha, Bernardo; Burgarelli, Denise; Meira, Wagner; Constantinides, Christakis; Weber Dos Santos, Rodrigo

2018-02-01

The use of computer models as a tool for the study and understanding of the complex phenomena of cardiac electrophysiology has attained increased importance nowadays. At the same time, the increased complexity of the biophysical processes translates into complex computational and mathematical models. To speed up cardiac simulations and to allow more precise and realistic uses, 2 different techniques have been traditionally exploited: parallel computing and sophisticated numerical methods. In this work, we combine a modern parallel computing technique based on multicore and graphics processing units (GPUs) and a sophisticated numerical method based on a new space-time adaptive algorithm. We evaluate each technique alone and in different combinations: multicore and GPU, multicore and GPU and space adaptivity, multicore and GPU and space adaptivity and time adaptivity. All the techniques and combinations were evaluated under different scenarios: 3D simulations on slabs, 3D simulations on a ventricular mouse mesh, ie, complex geometry, sinus-rhythm, and arrhythmic conditions. Our results suggest that multicore and GPU accelerate the simulations by an approximate factor of 33×, whereas the speedups attained by the space-time adaptive algorithms were approximately 48. Nevertheless, by combining all the techniques, we obtained speedups that ranged between 165 and 498. The tested methods were able to reduce the execution time of a simulation by more than 498× for a complex cellular model in a slab geometry and by 165× in a realistic heart geometry simulating spiral waves. The proposed methods will allow faster and more realistic simulations in a feasible time with no significant loss of accuracy. Copyright © 2017 John Wiley & Sons, Ltd.

Multi-resolution simulation of focused ultrasound propagation through ovine skull from a single-element transducer

NASA Astrophysics Data System (ADS)

Yoon, Kyungho; Lee, Wonhye; Croce, Phillip; Cammalleri, Amanda; Yoo, Seung-Schik

2018-05-01

Transcranial focused ultrasound (tFUS) is emerging as a non-invasive brain stimulation modality. Complicated interactions between acoustic pressure waves and osseous tissue introduce many challenges in the accurate targeting of an acoustic focus through the cranium. Image-guidance accompanied by a numerical simulation is desired to predict the intracranial acoustic propagation through the skull; however, such simulations typically demand heavy computation, which warrants an expedited processing method to provide on-site feedback for the user in guiding the acoustic focus to a particular brain region. In this paper, we present a multi-resolution simulation method based on the finite-difference time-domain formulation to model the transcranial propagation of acoustic waves from a single-element transducer (250 kHz). The multi-resolution approach improved computational efficiency by providing the flexibility in adjusting the spatial resolution. The simulation was also accelerated by utilizing parallelized computation through the graphic processing unit. To evaluate the accuracy of the method, we measured the actual acoustic fields through ex vivo sheep skulls with different sonication incident angles. The measured acoustic fields were compared to the simulation results in terms of focal location, dimensions, and pressure levels. The computational efficiency of the presented method was also assessed by comparing simulation speeds at various combinations of resolution grid settings. The multi-resolution grids consisting of 0.5 and 1.0 mm resolutions gave acceptable accuracy (under 3 mm in terms of focal position and dimension, less than 5% difference in peak pressure ratio) with a speed compatible with semi real-time user feedback (within 30 s). The proposed multi-resolution approach may serve as a novel tool for simulation-based guidance for tFUS applications.

Multi-resolution simulation of focused ultrasound propagation through ovine skull from a single-element transducer.

PubMed

Yoon, Kyungho; Lee, Wonhye; Croce, Phillip; Cammalleri, Amanda; Yoo, Seung-Schik

2018-05-10

Transcranial focused ultrasound (tFUS) is emerging as a non-invasive brain stimulation modality. Complicated interactions between acoustic pressure waves and osseous tissue introduce many challenges in the accurate targeting of an acoustic focus through the cranium. Image-guidance accompanied by a numerical simulation is desired to predict the intracranial acoustic propagation through the skull; however, such simulations typically demand heavy computation, which warrants an expedited processing method to provide on-site feedback for the user in guiding the acoustic focus to a particular brain region. In this paper, we present a multi-resolution simulation method based on the finite-difference time-domain formulation to model the transcranial propagation of acoustic waves from a single-element transducer (250 kHz). The multi-resolution approach improved computational efficiency by providing the flexibility in adjusting the spatial resolution. The simulation was also accelerated by utilizing parallelized computation through the graphic processing unit. To evaluate the accuracy of the method, we measured the actual acoustic fields through ex vivo sheep skulls with different sonication incident angles. The measured acoustic fields were compared to the simulation results in terms of focal location, dimensions, and pressure levels. The computational efficiency of the presented method was also assessed by comparing simulation speeds at various combinations of resolution grid settings. The multi-resolution grids consisting of 0.5 and 1.0 mm resolutions gave acceptable accuracy (under 3 mm in terms of focal position and dimension, less than 5% difference in peak pressure ratio) with a speed compatible with semi real-time user feedback (within 30 s). The proposed multi-resolution approach may serve as a novel tool for simulation-based guidance for tFUS applications.

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience

PubMed Central

Stockton, David B.; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project. PMID:26528175

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience.

PubMed

Stockton, David B; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project.

Reduced order model based on principal component analysis for process simulation and optimization

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

Lang, Y.; Malacina, A.; Biegler, L.

2009-01-01

It is well-known that distributed parameter computational fluid dynamics (CFD) models provide more accurate results than conventional, lumped-parameter unit operation models used in process simulation. Consequently, the use of CFD models in process/equipment co-simulation offers the potential to optimize overall plant performance with respect to complex thermal and fluid flow phenomena. Because solving CFD models is time-consuming compared to the overall process simulation, we consider the development of fast reduced order models (ROMs) based on CFD results to closely approximate the high-fidelity equipment models in the co-simulation. By considering process equipment items with complicated geometries and detailed thermodynamic property models,more » this study proposes a strategy to develop ROMs based on principal component analysis (PCA). Taking advantage of commercial process simulation and CFD software (for example, Aspen Plus and FLUENT), we are able to develop systematic CFD-based ROMs for equipment models in an efficient manner. In particular, we show that the validity of the ROM is more robust within well-sampled input domain and the CPU time is significantly reduced. Typically, it takes at most several CPU seconds to evaluate the ROM compared to several CPU hours or more to solve the CFD model. Two case studies, involving two power plant equipment examples, are described and demonstrate the benefits of using our proposed ROM methodology for process simulation and optimization.« less

Optimization of Multi-Fidelity Computer Experiments via the EQIE Criterion

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

He, Xu; Tuo, Rui; Jeff Wu, C. F.

Computer experiments based on mathematical models are powerful tools for understanding physical processes. This article addresses the problem of kriging-based optimization for deterministic computer experiments with tunable accuracy. Our approach is to use multi- delity computer experiments with increasing accuracy levels and a nonstationary Gaussian process model. We propose an optimization scheme that sequentially adds new computer runs by following two criteria. The first criterion, called EQI, scores candidate inputs with given level of accuracy, and the second criterion, called EQIE, scores candidate combinations of inputs and accuracy. Here, from simulation results and a real example using finite element analysis,more » our method out-performs the expected improvement (EI) criterion which works for single-accuracy experiments.« less

Optimization of Multi-Fidelity Computer Experiments via the EQIE Criterion

DOE PAGES

He, Xu; Tuo, Rui; Jeff Wu, C. F.

2017-01-31

Computer experiments based on mathematical models are powerful tools for understanding physical processes. This article addresses the problem of kriging-based optimization for deterministic computer experiments with tunable accuracy. Our approach is to use multi- delity computer experiments with increasing accuracy levels and a nonstationary Gaussian process model. We propose an optimization scheme that sequentially adds new computer runs by following two criteria. The first criterion, called EQI, scores candidate inputs with given level of accuracy, and the second criterion, called EQIE, scores candidate combinations of inputs and accuracy. Here, from simulation results and a real example using finite element analysis,more » our method out-performs the expected improvement (EI) criterion which works for single-accuracy experiments.« less

Three dimensional geometric modeling of processing-tomatoes

USDA-ARS?s Scientific Manuscript database

Characterizing tomato geometries with different shapes and sizes would facilitate the design of tomato processing equipments and promote computer-based engineering simulations. This research sought to develop a three-dimensional geometric model that can describe the morphological attributes of proce...

Towards inverse modeling of turbidity currents: The inverse lock-exchange problem

NASA Astrophysics Data System (ADS)

Lesshafft, Lutz; Meiburg, Eckart; Kneller, Ben; Marsden, Alison

2011-04-01

A new approach is introduced for turbidite modeling, leveraging the potential of computational fluid dynamics methods to simulate the flow processes that led to turbidite formation. The practical use of numerical flow simulation for the purpose of turbidite modeling so far is hindered by the need to specify parameters and initial flow conditions that are a priori unknown. The present study proposes a method to determine optimal simulation parameters via an automated optimization process. An iterative procedure matches deposit predictions from successive flow simulations against available localized reference data, as in practice may be obtained from well logs, and aims at convergence towards the best-fit scenario. The final result is a prediction of the entire deposit thickness and local grain size distribution. The optimization strategy is based on a derivative-free, surrogate-based technique. Direct numerical simulations are performed to compute the flow dynamics. A proof of concept is successfully conducted for the simple test case of a two-dimensional lock-exchange turbidity current. The optimization approach is demonstrated to accurately retrieve the initial conditions used in a reference calculation.

Virtual Observation System for Earth System Model: An Application to ACME Land Model Simulations

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

Wang, Dali; Yuan, Fengming; Hernandez, Benjamin

Investigating and evaluating physical-chemical-biological processes within an Earth system model (EMS) can be very challenging due to the complexity of both model design and software implementation. A virtual observation system (VOS) is presented to enable interactive observation of these processes during system simulation. Based on advance computing technologies, such as compiler-based software analysis, automatic code instrumentation, and high-performance data transport, the VOS provides run-time observation capability, in-situ data analytics for Earth system model simulation, model behavior adjustment opportunities through simulation steering. A VOS for a terrestrial land model simulation within the Accelerated Climate Modeling for Energy model is also presentedmore » to demonstrate the implementation details and system innovations.« less

Virtual Observation System for Earth System Model: An Application to ACME Land Model Simulations

DOE PAGES

Wang, Dali; Yuan, Fengming; Hernandez, Benjamin; ...

2017-01-01

Investigating and evaluating physical-chemical-biological processes within an Earth system model (EMS) can be very challenging due to the complexity of both model design and software implementation. A virtual observation system (VOS) is presented to enable interactive observation of these processes during system simulation. Based on advance computing technologies, such as compiler-based software analysis, automatic code instrumentation, and high-performance data transport, the VOS provides run-time observation capability, in-situ data analytics for Earth system model simulation, model behavior adjustment opportunities through simulation steering. A VOS for a terrestrial land model simulation within the Accelerated Climate Modeling for Energy model is also presentedmore » to demonstrate the implementation details and system innovations.« less

The Numerical Propulsion System Simulation: A Multidisciplinary Design System for Aerospace Vehicles

NASA Technical Reports Server (NTRS)

Lytle, John K.

1999-01-01

Advances in computational technology and in physics-based modeling are making large scale, detailed simulations of complex systems possible within the design environment. For example, the integration of computing, communications, and aerodynamics has reduced the time required to analyze ma or propulsion system components from days and weeks to minutes and hours. This breakthrough has enabled the detailed simulation of major propulsion system components to become a routine part of design process and to provide the designer with critical information about the components early in the design process. This paper describes the development of the Numerical Propulsion System Simulation (NPSS), a multidisciplinary system of analysis tools that is focussed on extending the simulation capability from components to the full system. This will provide the product developer with a "virtual wind tunnel" that will reduce the number of hardware builds and tests required during the development of advanced aerospace propulsion systems.

Parallelization of a Fully-Distributed Hydrologic Model using Sub-basin Partitioning

NASA Astrophysics Data System (ADS)

Vivoni, E. R.; Mniszewski, S.; Fasel, P.; Springer, E.; Ivanov, V. Y.; Bras, R. L.

2005-12-01

A primary obstacle towards advances in watershed simulations has been the limited computational capacity available to most models. The growing trend of model complexity, data availability and physical representation has not been matched by adequate developments in computational efficiency. This situation has created a serious bottleneck which limits existing distributed hydrologic models to small domains and short simulations. In this study, we present novel developments in the parallelization of a fully-distributed hydrologic model. Our work is based on the TIN-based Real-time Integrated Basin Simulator (tRIBS), which provides continuous hydrologic simulation using a multiple resolution representation of complex terrain based on a triangulated irregular network (TIN). While the use of TINs reduces computational demand, the sequential version of the model is currently limited over large basins (>10,000 km2) and long simulation periods (>1 year). To address this, a parallel MPI-based version of the tRIBS model has been implemented and tested using high performance computing resources at Los Alamos National Laboratory. Our approach utilizes domain decomposition based on sub-basin partitioning of the watershed. A stream reach graph based on the channel network structure is used to guide the sub-basin partitioning. Individual sub-basins or sub-graphs of sub-basins are assigned to separate processors to carry out internal hydrologic computations (e.g. rainfall-runoff transformation). Routed streamflow from each sub-basin forms the major hydrologic data exchange along the stream reach graph. Individual sub-basins also share subsurface hydrologic fluxes across adjacent boundaries. We demonstrate how the sub-basin partitioning provides computational feasibility and efficiency for a set of test watersheds in northeastern Oklahoma. We compare the performance of the sequential and parallelized versions to highlight the efficiency gained as the number of processors increases. We also discuss how the coupled use of TINs and parallel processing can lead to feasible long-term simulations in regional watersheds while preserving basin properties at high-resolution.

Computer simulation of the human respiratory system for educational purposes.

PubMed

Botsis, Taxiarhis; Halkiotis, Stelios-Chris; Kourlaba, Georgia

2004-01-01

The main objective of this study was the development of a computer simulation system for the human respiratory system, in order to educate students of nursing. This approach was based on existing mathematical models and on our own constructed specific functions. For the development of this educational tool the appropriate software packages were used according to the special demands of this process. This system is called ReSim (Respiratory Simulation) and consists of two parts: the first part deals with pulmonary volumes and the second one represents the mechanical behavior of lungs. The target group evaluated ReSim. The outcomes of the evaluation process were positive and helped us realize the system characteristics that needed improvements. Our basic conclusion is that the extended use of such systems supports the educational process and offers new potential for learning.

Uncertainty-based simulation-optimization using Gaussian process emulation: Application to coastal groundwater management

NASA Astrophysics Data System (ADS)

Rajabi, Mohammad Mahdi; Ketabchi, Hamed

2017-12-01

Combined simulation-optimization (S/O) schemes have long been recognized as a valuable tool in coastal groundwater management (CGM). However, previous applications have mostly relied on deterministic seawater intrusion (SWI) simulations. This is a questionable simplification, knowing that SWI models are inevitably prone to epistemic and aleatory uncertainty, and hence a management strategy obtained through S/O without consideration of uncertainty may result in significantly different real-world outcomes than expected. However, two key issues have hindered the use of uncertainty-based S/O schemes in CGM, which are addressed in this paper. The first issue is how to solve the computational challenges resulting from the need to perform massive numbers of simulations. The second issue is how the management problem is formulated in presence of uncertainty. We propose the use of Gaussian process (GP) emulation as a valuable tool in solving the computational challenges of uncertainty-based S/O in CGM. We apply GP emulation to the case study of Kish Island (located in the Persian Gulf) using an uncertainty-based S/O algorithm which relies on continuous ant colony optimization and Monte Carlo simulation. In doing so, we show that GP emulation can provide an acceptable level of accuracy, with no bias and low statistical dispersion, while tremendously reducing the computational time. Moreover, five new formulations for uncertainty-based S/O are presented based on concepts such as energy distances, prediction intervals and probabilities of SWI occurrence. We analyze the proposed formulations with respect to their resulting optimized solutions, the sensitivity of the solutions to the intended reliability levels, and the variations resulting from repeated optimization runs.

Rupture Dynamics and Seismic Radiation on Rough Faults for Simulation-Based PSHA

NASA Astrophysics Data System (ADS)

Mai, P. M.; Galis, M.; Thingbaijam, K. K. S.; Vyas, J. C.; Dunham, E. M.

2017-12-01

Simulation-based ground-motion predictions may augment PSHA studies in data-poor regions or provide additional shaking estimations, incl. seismic waveforms, for critical facilities. Validation and calibration of such simulation approaches, based on observations and GMPE's, is important for engineering applications, while seismologists push to include the precise physics of the earthquake rupture process and seismic wave propagation in 3D heterogeneous Earth. Geological faults comprise both large-scale segmentation and small-scale roughness that determine the dynamics of the earthquake rupture process and its radiated seismic wavefield. We investigate how different parameterizations of fractal fault roughness affect the rupture evolution and resulting near-fault ground motions. Rupture incoherence induced by fault roughness generates realistic ω-2 decay for high-frequency displacement amplitude spectra. Waveform characteristics and GMPE-based comparisons corroborate that these rough-fault rupture simulations generate realistic synthetic seismogram for subsequent engineering application. Since dynamic rupture simulations are computationally expensive, we develop kinematic approximations that emulate the observed dynamics. Simplifying the rough-fault geometry, we find that perturbations in local moment tensor orientation are important, while perturbations in local source location are not. Thus, a planar fault can be assumed if the local strike, dip, and rake are maintained. The dynamic rake angle variations are anti-correlated with local dip angles. Based on a dynamically consistent Yoffe source-time function, we show that the seismic wavefield of the approximated kinematic rupture well reproduces the seismic radiation of the full dynamic source process. Our findings provide an innovative pseudo-dynamic source characterization that captures fault roughness effects on rupture dynamics. Including the correlations between kinematic source parameters, we present a new pseudo-dynamic rupture modeling approach for computing broadband ground-motion time-histories for simulation-based PSHA

Hafnium transistor process design for neural interfacing.

PubMed

Parent, David W; Basham, Eric J

2009-01-01

A design methodology is presented that uses 1-D process simulations of Metal Insulator Semiconductor (MIS) structures to design the threshold voltage of hafnium oxide based transistors used for neural recording. The methodology is comprised of 1-D analytical equations for threshold voltage specification, and doping profiles, and 1-D MIS Technical Computer Aided Design (TCAD) to design a process to implement a specific threshold voltage, which minimized simulation time. The process was then verified with a 2-D process/electrical TCAD simulation. Hafnium oxide films (HfO) were grown and characterized for dielectric constant and fixed oxide charge for various annealing temperatures, two important design variables in threshold voltage design.

Final Report Collaborative Project. Improving the Representation of Coastal and Estuarine Processes in Earth System Models

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

Bryan, Frank; Dennis, John; MacCready, Parker

This project aimed to improve long term global climate simulations by resolving and enhancing the representation of the processes involved in the cycling of freshwater through estuaries and coastal regions. This was a collaborative multi-institution project consisting of physical oceanographers, climate model developers, and computational scientists. It specifically targeted the DOE objectives of advancing simulation and predictive capability of climate models through improvements in resolution and physical process representation. The main computational objectives were: 1. To develop computationally efficient, but physically based, parameterizations of estuary and continental shelf mixing processes for use in an Earth System Model (CESM). 2. Tomore » develop a two-way nested regional modeling framework in order to dynamically downscale the climate response of particular coastal ocean regions and to upscale the impact of the regional coastal processes to the global climate in an Earth System Model (CESM). 3. To develop computational infrastructure to enhance the efficiency of data transfer between specific sources and destinations, i.e., a point-to-point communication capability, (used in objective 1) within POP, the ocean component of CESM.« less

Physical Processes and Applications of the Monte Carlo Radiative Energy Deposition (MRED) Code

NASA Astrophysics Data System (ADS)

Reed, Robert A.; Weller, Robert A.; Mendenhall, Marcus H.; Fleetwood, Daniel M.; Warren, Kevin M.; Sierawski, Brian D.; King, Michael P.; Schrimpf, Ronald D.; Auden, Elizabeth C.

2015-08-01

MRED is a Python-language scriptable computer application that simulates radiation transport. It is the computational engine for the on-line tool CRÈME-MC. MRED is based on c++ code from Geant4 with additional Fortran components to simulate electron transport and nuclear reactions with high precision. We provide a detailed description of the structure of MRED and the implementation of the simulation of physical processes used to simulate radiation effects in electronic devices and circuits. Extensive discussion and references are provided that illustrate the validation of models used to implement specific simulations of relevant physical processes. Several applications of MRED are summarized that demonstrate its ability to predict and describe basic physical phenomena associated with irradiation of electronic circuits and devices. These include effects from single particle radiation (including both direct ionization and indirect ionization effects), dose enhancement effects, and displacement damage effects. MRED simulations have also helped to identify new single event upset mechanisms not previously observed by experiment, but since confirmed, including upsets due to muons and energetic electrons.

Reduced order surrogate modelling (ROSM) of high dimensional deterministic simulations

NASA Astrophysics Data System (ADS)

Mitry, Mina

Often, computationally expensive engineering simulations can prohibit the engineering design process. As a result, designers may turn to a less computationally demanding approximate, or surrogate, model to facilitate their design process. However, owing to the the curse of dimensionality, classical surrogate models become too computationally expensive for high dimensional data. To address this limitation of classical methods, we develop linear and non-linear Reduced Order Surrogate Modelling (ROSM) techniques. Two algorithms are presented, which are based on a combination of linear/kernel principal component analysis and radial basis functions. These algorithms are applied to subsonic and transonic aerodynamic data, as well as a model for a chemical spill in a channel. The results of this thesis show that ROSM can provide a significant computational benefit over classical surrogate modelling, sometimes at the expense of a minor loss in accuracy.

Dynamic modelling of an adsorption storage tank using a hybrid approach combining computational fluid dynamics and process simulation

USGS Publications Warehouse

Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.

2004-01-01

A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.

Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

PubMed Central

Wang, Qing; Xue, Tuo; Song, Chunnian; Wang, Yan; Chen, Guangju

2016-01-01

Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35). The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD) variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg) presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes. PMID:27171075

Representing the work of medical protocols for organizational simulation.

PubMed Central

Fridsma, D. B.

1998-01-01

Developing and implementing patient care protocols within a specific organizational setting requires knowledge of the protocol, the organization, and the way in which the organization does its work. Computer-based simulation tools have been used in many industries to provide managers with prospective insight into problems of work process and organization design mismatch. Many of these simulation tools are designed for well-understood routine work processes in which there are few contingent tasks. In this paper, we describe theoretic that make it possible to simulate medical protocols using an information-processing theory framework. These simulations will allow medical administrators to test different protocol and organizational designs before actually using them within a particular clinical setting. PMID:9929231

Three-dimensional photoacoustic tomography based on graphics-processing-unit-accelerated finite element method.

PubMed

Peng, Kuan; He, Ling; Zhu, Ziqiang; Tang, Jingtian; Xiao, Jiaying

2013-12-01

Compared with commonly used analytical reconstruction methods, the frequency-domain finite element method (FEM) based approach has proven to be an accurate and flexible algorithm for photoacoustic tomography. However, the FEM-based algorithm is computationally demanding, especially for three-dimensional cases. To enhance the algorithm's efficiency, in this work a parallel computational strategy is implemented in the framework of the FEM-based reconstruction algorithm using a graphic-processing-unit parallel frame named the "compute unified device architecture." A series of simulation experiments is carried out to test the accuracy and accelerating effect of the improved method. The results obtained indicate that the parallel calculation does not change the accuracy of the reconstruction algorithm, while its computational cost is significantly reduced by a factor of 38.9 with a GTX 580 graphics card using the improved method.

On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods

PubMed Central

Lee, Anthony; Yau, Christopher; Giles, Michael B.; Doucet, Arnaud; Holmes, Christopher C.

2011-01-01

We present a case-study on the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods. Graphics cards, containing multiple Graphics Processing Units (GPUs), are self-contained parallel computational devices that can be housed in conventional desktop and laptop computers and can be thought of as prototypes of the next generation of many-core processors. For certain classes of population-based Monte Carlo algorithms they offer massively parallel simulation, with the added advantage over conventional distributed multi-core processors that they are cheap, easily accessible, easy to maintain, easy to code, dedicated local devices with low power consumption. On a canonical set of stochastic simulation examples including population-based Markov chain Monte Carlo methods and Sequential Monte Carlo methods, we nd speedups from 35 to 500 fold over conventional single-threaded computer code. Our findings suggest that GPUs have the potential to facilitate the growth of statistical modelling into complex data rich domains through the availability of cheap and accessible many-core computation. We believe the speedup we observe should motivate wider use of parallelizable simulation methods and greater methodological attention to their design. PMID:22003276

The transesophageal echocardiography simulator based on computed tomography images.

PubMed

Piórkowski, Adam; Kempny, Aleksander

2013-02-01

Simulators are a new tool in education in many fields, including medicine, where they greatly improve familiarity with medical procedures, reduce costs, and, importantly, cause no harm to patients. This is so in the case of transesophageal echocardiography (TEE), in which the use of a simulator facilitates spatial orientation and helps in case studies. The aim of the project described in this paper is to simulate an examination by TEE. This research makes use of available computed tomography data to simulate the corresponding echocardiographic view. This paper describes the essential characteristics that distinguish these two modalities and the key principles of the wave phenomena that should be considered in the simulation process, taking into account the conditions specific to the echocardiography. The construction of the CT2TEE (Web-based TEE simulator) is also presented. The considerations include ray-tracing and ray-casting techniques in the context of ultrasound beam and artifact simulation. An important aspect of the interaction with the user is raised.

GAPD: a GPU-accelerated atom-based polychromatic diffraction simulation code.

PubMed

E, J C; Wang, L; Chen, S; Zhang, Y Y; Luo, S N

2018-03-01

GAPD, a graphics-processing-unit (GPU)-accelerated atom-based polychromatic diffraction simulation code for direct, kinematics-based, simulations of X-ray/electron diffraction of large-scale atomic systems with mono-/polychromatic beams and arbitrary plane detector geometries, is presented. This code implements GPU parallel computation via both real- and reciprocal-space decompositions. With GAPD, direct simulations are performed of the reciprocal lattice node of ultralarge systems (∼5 billion atoms) and diffraction patterns of single-crystal and polycrystalline configurations with mono- and polychromatic X-ray beams (including synchrotron undulator sources), and validation, benchmark and application cases are presented.

Progress in Unsteady Turbopump Flow Simulations

NASA Technical Reports Server (NTRS)

Kiris, Cetin C.; Chan, William; Kwak, Dochan; Williams, Robert

2002-01-01

This viewgraph presentation discusses unsteady flow simulations for a turbopump intended for a reusable launch vehicle (RLV). The simulation process makes use of computational grids and parallel processing. The architecture of the parallel computers used is discussed, as is the scripting of turbopump simulations.

75 FR 75961 - Notice of Implementation of the Wind Erosion Prediction System for Soil Erodibility System...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-07

... Wind Erosion Prediction System for Soil Erodibility System Calculations for the Natural Resources... Erosion Prediction System (WEPS) for soil erodibility system calculations scheduled for implementation for... computer model is a process-based, daily time-step computer model that predicts soil erosion via simulation...

The Modeling of Human Intelligence in the Computer as Demonstrated in the Game of DIPLOMAT.

ERIC Educational Resources Information Center

Collins, James Edward; Paulsen, Thomas Dean

An attempt was made to develop human-like behavior in the computer. A theory of the human learning process was described. A computer game was presented which simulated the human capabilities of reasoning and learning. The program was required to make intelligent decisions based on past experiences and critical analysis of the present situation.…

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

NASA Astrophysics Data System (ADS)

Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

2014-01-01

Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers

PubMed Central

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation. PMID:28239346

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers.

PubMed

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation.

Benefits of computer screen-based simulation in learning cardiac arrest procedures.

PubMed

Bonnetain, Elodie; Boucheix, Jean-Michel; Hamet, Maël; Freysz, Marc

2010-07-01

What is the best way to train medical students early so that they acquire basic skills in cardiopulmonary resuscitation as effectively as possible? Studies have shown the benefits of high-fidelity patient simulators, but have also demonstrated their limits. New computer screen-based multimedia simulators have fewer constraints than high-fidelity patient simulators. In this area, as yet, there has been no research on the effectiveness of transfer of learning from a computer screen-based simulator to more realistic situations such as those encountered with high-fidelity patient simulators. We tested the benefits of learning cardiac arrest procedures using a multimedia computer screen-based simulator in 28 Year 2 medical students. Just before the end of the traditional resuscitation course, we compared two groups. An experiment group (EG) was first asked to learn to perform the appropriate procedures in a cardiac arrest scenario (CA1) in the computer screen-based learning environment and was then tested on a high-fidelity patient simulator in another cardiac arrest simulation (CA2). While the EG was learning to perform CA1 procedures in the computer screen-based learning environment, a control group (CG) actively continued to learn cardiac arrest procedures using practical exercises in a traditional class environment. Both groups were given the same amount of practice, exercises and trials. The CG was then also tested on the high-fidelity patient simulator for CA2, after which it was asked to perform CA1 using the computer screen-based simulator. Performances with both simulators were scored on a precise 23-point scale. On the test on a high-fidelity patient simulator, the EG trained with a multimedia computer screen-based simulator performed significantly better than the CG trained with traditional exercises and practice (16.21 versus 11.13 of 23 possible points, respectively; p<0.001). Computer screen-based simulation appears to be effective in preparing learners to use high-fidelity patient simulators, which present simulations that are closer to real-life situations.

Space-filling designs for computer experiments: A review

DOE PAGES

Joseph, V. Roshan

2016-01-29

Improving the quality of a product/process using a computer simulator is a much less expensive option than the real physical testing. However, simulation using computationally intensive computer models can be time consuming and therefore, directly doing the optimization on the computer simulator can be infeasible. Experimental design and statistical modeling techniques can be used for overcoming this problem. This article reviews experimental designs known as space-filling designs that are suitable for computer simulations. In the review, a special emphasis is given for a recently developed space-filling design called maximum projection design. Furthermore, its advantages are illustrated using a simulation conductedmore » for optimizing a milling process.« less

Space-filling designs for computer experiments: A review

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

Joseph, V. Roshan

Improving the quality of a product/process using a computer simulator is a much less expensive option than the real physical testing. However, simulation using computationally intensive computer models can be time consuming and therefore, directly doing the optimization on the computer simulator can be infeasible. Experimental design and statistical modeling techniques can be used for overcoming this problem. This article reviews experimental designs known as space-filling designs that are suitable for computer simulations. In the review, a special emphasis is given for a recently developed space-filling design called maximum projection design. Furthermore, its advantages are illustrated using a simulation conductedmore » for optimizing a milling process.« less

Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

PubMed

Hafner, Jürgen

2010-09-29

During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

The Numerical Propulsion System Simulation: An Overview

NASA Technical Reports Server (NTRS)

Lytle, John K.

2000-01-01

Advances in computational technology and in physics-based modeling are making large-scale, detailed simulations of complex systems possible within the design environment. For example, the integration of computing, communications, and aerodynamics has reduced the time required to analyze major propulsion system components from days and weeks to minutes and hours. This breakthrough has enabled the detailed simulation of major propulsion system components to become a routine part of designing systems, providing the designer with critical information about the components early in the design process. This paper describes the development of the numerical propulsion system simulation (NPSS), a modular and extensible framework for the integration of multicomponent and multidisciplinary analysis tools using geographically distributed resources such as computing platforms, data bases, and people. The analysis is currently focused on large-scale modeling of complete aircraft engines. This will provide the product developer with a "virtual wind tunnel" that will reduce the number of hardware builds and tests required during the development of advanced aerospace propulsion systems.

Advanced reliability modeling of fault-tolerant computer-based systems

NASA Technical Reports Server (NTRS)

Bavuso, S. J.

1982-01-01

Two methodologies for the reliability assessment of fault tolerant digital computer based systems are discussed. The computer-aided reliability estimation 3 (CARE 3) and gate logic software simulation (GLOSS) are assessment technologies that were developed to mitigate a serious weakness in the design and evaluation process of ultrareliable digital systems. The weak link is based on the unavailability of a sufficiently powerful modeling technique for comparing the stochastic attributes of one system against others. Some of the more interesting attributes are reliability, system survival, safety, and mission success.

Parallel implementation of the particle simulation method with dynamic load balancing: Toward realistic geodynamical simulation

NASA Astrophysics Data System (ADS)

Furuichi, M.; Nishiura, D.

2015-12-01

Fully Lagrangian methods such as Smoothed Particle Hydrodynamics (SPH) and Discrete Element Method (DEM) have been widely used to solve the continuum and particles motions in the computational geodynamics field. These mesh-free methods are suitable for the problems with the complex geometry and boundary. In addition, their Lagrangian nature allows non-diffusive advection useful for tracking history dependent properties (e.g. rheology) of the material. These potential advantages over the mesh-based methods offer effective numerical applications to the geophysical flow and tectonic processes, which are for example, tsunami with free surface and floating body, magma intrusion with fracture of rock, and shear zone pattern generation of granular deformation. In order to investigate such geodynamical problems with the particle based methods, over millions to billion particles are required for the realistic simulation. Parallel computing is therefore important for handling such huge computational cost. An efficient parallel implementation of SPH and DEM methods is however known to be difficult especially for the distributed-memory architecture. Lagrangian methods inherently show workload imbalance problem for parallelization with the fixed domain in space, because particles move around and workloads change during the simulation. Therefore dynamic load balance is key technique to perform the large scale SPH and DEM simulation. In this work, we present the parallel implementation technique of SPH and DEM method utilizing dynamic load balancing algorithms toward the high resolution simulation over large domain using the massively parallel super computer system. Our method utilizes the imbalances of the executed time of each MPI process as the nonlinear term of parallel domain decomposition and minimizes them with the Newton like iteration method. In order to perform flexible domain decomposition in space, the slice-grid algorithm is used. Numerical tests show that our approach is suitable for solving the particles with different calculation costs (e.g. boundary particles) as well as the heterogeneous computer architecture. We analyze the parallel efficiency and scalability on the super computer systems (K-computer, Earth simulator 3, etc.).

Simulating complex intracellular processes using object-oriented computational modelling.

PubMed

Johnson, Colin G; Goldman, Jacki P; Gullick, William J

2004-11-01

The aim of this paper is to give an overview of computer modelling and simulation in cellular biology, in particular as applied to complex biochemical processes within the cell. This is illustrated by the use of the techniques of object-oriented modelling, where the computer is used to construct abstractions of objects in the domain being modelled, and these objects then interact within the computer to simulate the system and allow emergent properties to be observed. The paper also discusses the role of computer simulation in understanding complexity in biological systems, and the kinds of information which can be obtained about biology via simulation.

Wall Shear Stress Distribution in a Patient-Specific Cerebral Aneurysm Model using Reduced Order Modeling

NASA Astrophysics Data System (ADS)

Han, Suyue; Chang, Gary Han; Schirmer, Clemens; Modarres-Sadeghi, Yahya

2016-11-01

We construct a reduced-order model (ROM) to study the Wall Shear Stress (WSS) distributions in image-based patient-specific aneurysms models. The magnitude of WSS has been shown to be a critical factor in growth and rupture of human aneurysms. We start the process by running a training case using Computational Fluid Dynamics (CFD) simulation with time-varying flow parameters, such that these parameters cover the range of parameters of interest. The method of snapshot Proper Orthogonal Decomposition (POD) is utilized to construct the reduced-order bases using the training CFD simulation. The resulting ROM enables us to study the flow patterns and the WSS distributions over a range of system parameters computationally very efficiently with a relatively small number of modes. This enables comprehensive analysis of the model system across a range of physiological conditions without the need to re-compute the simulation for small changes in the system parameters.

GPU-based prompt gamma ray imaging from boron neutron capture therapy

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

Yoon, Do-Kun; Jung, Joo-Young; Suk Suh, Tae, E-mail: suhsanta@catholic.ac.kr

Purpose: The purpose of this research is to perform the fast reconstruction of a prompt gamma ray image using a graphics processing unit (GPU) computation from boron neutron capture therapy (BNCT) simulations. Methods: To evaluate the accuracy of the reconstructed image, a phantom including four boron uptake regions (BURs) was used in the simulation. After the Monte Carlo simulation of the BNCT, the modified ordered subset expectation maximization reconstruction algorithm using the GPU computation was used to reconstruct the images with fewer projections. The computation times for image reconstruction were compared between the GPU and the central processing unit (CPU).more » Also, the accuracy of the reconstructed image was evaluated by a receiver operating characteristic (ROC) curve analysis. Results: The image reconstruction time using the GPU was 196 times faster than the conventional reconstruction time using the CPU. For the four BURs, the area under curve values from the ROC curve were 0.6726 (A-region), 0.6890 (B-region), 0.7384 (C-region), and 0.8009 (D-region). Conclusions: The tomographic image using the prompt gamma ray event from the BNCT simulation was acquired using the GPU computation in order to perform a fast reconstruction during treatment. The authors verified the feasibility of the prompt gamma ray image reconstruction using the GPU computation for BNCT simulations.« less

TU-FG-BRB-07: GPU-Based Prompt Gamma Ray Imaging From Boron Neutron Capture Therapy

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

Kim, S; Suh, T; Yoon, D

Purpose: The purpose of this research is to perform the fast reconstruction of a prompt gamma ray image using a graphics processing unit (GPU) computation from boron neutron capture therapy (BNCT) simulations. Methods: To evaluate the accuracy of the reconstructed image, a phantom including four boron uptake regions (BURs) was used in the simulation. After the Monte Carlo simulation of the BNCT, the modified ordered subset expectation maximization reconstruction algorithm using the GPU computation was used to reconstruct the images with fewer projections. The computation times for image reconstruction were compared between the GPU and the central processing unit (CPU).more » Also, the accuracy of the reconstructed image was evaluated by a receiver operating characteristic (ROC) curve analysis. Results: The image reconstruction time using the GPU was 196 times faster than the conventional reconstruction time using the CPU. For the four BURs, the area under curve values from the ROC curve were 0.6726 (A-region), 0.6890 (B-region), 0.7384 (C-region), and 0.8009 (D-region). Conclusion: The tomographic image using the prompt gamma ray event from the BNCT simulation was acquired using the GPU computation in order to perform a fast reconstruction during treatment. The authors verified the feasibility of the prompt gamma ray reconstruction using the GPU computation for BNCT simulations.« less

Energy efficient hybrid computing systems using spin devices

NASA Astrophysics Data System (ADS)

Sharad, Mrigank

Emerging spin-devices like magnetic tunnel junctions (MTJ's), spin-valves and domain wall magnets (DWM) have opened new avenues for spin-based logic design. This work explored potential computing applications which can exploit such devices for higher energy-efficiency and performance. The proposed applications involve hybrid design schemes, where charge-based devices supplement the spin-devices, to gain large benefits at the system level. As an example, lateral spin valves (LSV) involve switching of nanomagnets using spin-polarized current injection through a metallic channel such as Cu. Such spin-torque based devices possess several interesting properties that can be exploited for ultra-low power computation. Analog characteristic of spin current facilitate non-Boolean computation like majority evaluation that can be used to model a neuron. The magneto-metallic neurons can operate at ultra-low terminal voltage of ˜20mV, thereby resulting in small computation power. Moreover, since nano-magnets inherently act as memory elements, these devices can facilitate integration of logic and memory in interesting ways. The spin based neurons can be integrated with CMOS and other emerging devices leading to different classes of neuromorphic/non-Von-Neumann architectures. The spin-based designs involve `mixed-mode' processing and hence can provide very compact and ultra-low energy solutions for complex computation blocks, both digital as well as analog. Such low-power, hybrid designs can be suitable for various data processing applications like cognitive computing, associative memory, and currentmode on-chip global interconnects. Simulation results for these applications based on device-circuit co-simulation framework predict more than ˜100x improvement in computation energy as compared to state of the art CMOS design, for optimal spin-device parameters.

A Computer-Based Simulation of an Acid-Base Titration

ERIC Educational Resources Information Center

Boblick, John M.

1971-01-01

Reviews the advantages of computer simulated environments for experiments, referring in particular to acid-base titrations. Includes pre-lab instructions and a sample computer printout of a student's use of an acid-base simulation. Ten references. (PR)

Study on efficiency of time computation in x-ray imaging simulation base on Monte Carlo algorithm using graphics processing unit

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

Setiani, Tia Dwi, E-mail: tiadwisetiani@gmail.com; Suprijadi; Nuclear Physics and Biophysics Reaserch Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung Jalan Ganesha 10 Bandung, 40132

Monte Carlo (MC) is one of the powerful techniques for simulation in x-ray imaging. MC method can simulate the radiation transport within matter with high accuracy and provides a natural way to simulate radiation transport in complex systems. One of the codes based on MC algorithm that are widely used for radiographic images simulation is MC-GPU, a codes developed by Andrea Basal. This study was aimed to investigate the time computation of x-ray imaging simulation in GPU (Graphics Processing Unit) compared to a standard CPU (Central Processing Unit). Furthermore, the effect of physical parameters to the quality of radiographic imagesmore » and the comparison of image quality resulted from simulation in the GPU and CPU are evaluated in this paper. The simulations were run in CPU which was simulated in serial condition, and in two GPU with 384 cores and 2304 cores. In simulation using GPU, each cores calculates one photon, so, a large number of photon were calculated simultaneously. Results show that the time simulations on GPU were significantly accelerated compared to CPU. The simulations on the 2304 core of GPU were performed about 64 -114 times faster than on CPU, while the simulation on the 384 core of GPU were performed about 20 – 31 times faster than in a single core of CPU. Another result shows that optimum quality of images from the simulation was gained at the history start from 10{sup 8} and the energy from 60 Kev to 90 Kev. Analyzed by statistical approach, the quality of GPU and CPU images are relatively the same.« less

BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes.

PubMed

Gao, Junhui; Li, Li; Wu, Xiaolin; Wei, Dong-Qing

2012-03-01

BioNetSim, a Petri net-based software for modeling and simulating biochemistry processes, is developed, whose design and implement are presented in this paper, including logic construction, real-time access to KEGG (Kyoto Encyclopedia of Genes and Genomes), and BioModel database. Furthermore, glycolysis is simulated as an example of its application. BioNetSim is a helpful tool for researchers to download data, model biological network, and simulate complicated biochemistry processes. Gene regulatory networks, metabolic pathways, signaling pathways, and kinetics of cell interaction are all available in BioNetSim, which makes modeling more efficient and effective. Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction. Moreover, it shows several powerful predominances. (1) It creates models in database. (2) It realizes the real-time access to KEGG and BioModel and transfers data to Petri net. (3) It provides qualitative analysis, such as computation of constants. (4) It generates graphs for tracing the concentration of every molecule during the simulation processes.

A mathematical model and computational framework for three-dimensional chondrocyte cell growth in a porous tissue scaffold placed inside a bi-directional flow perfusion bioreactor.

PubMed

Shakhawath Hossain, Md; Bergstrom, D J; Chen, X B

2015-12-01

The in vitro chondrocyte cell culture for cartilage tissue regeneration in a perfusion bioreactor is a complex process. Mathematical modeling and computational simulation can provide important insights into the culture process, which would be helpful for selecting culture conditions to improve the quality of the developed tissue constructs. However, simulation of the cell culture process is a challenging task due to the complicated interaction between the cells and local fluid flow and nutrient transport inside the complex porous scaffolds. In this study, a mathematical model and computational framework has been developed to simulate the three-dimensional (3D) cell growth in a porous scaffold placed inside a bi-directional flow perfusion bioreactor. The model was developed by taking into account the two-way coupling between the cell growth and local flow field and associated glucose concentration, and then used to perform a resolved-scale simulation based on the lattice Boltzmann method (LBM). The simulation predicts the local shear stress, glucose concentration, and 3D cell growth inside the porous scaffold for a period of 30 days of cell culture. The predicted cell growth rate was in good overall agreement with the experimental results available in the literature. This study demonstrates that the bi-directional flow perfusion culture system can enhance the homogeneity of the cell growth inside the scaffold. The model and computational framework developed is capable of providing significant insight into the culture process, thus providing a powerful tool for the design and optimization of the cell culture process. © 2015 Wiley Periodicals, Inc.

Computational modeling of residual stress formation during the electron beam melting process for Inconel 718

DOE PAGES

Prabhakar, P.; Sames, William J.; Dehoff, Ryan R.; ...

2015-03-28

Here, a computational modeling approach to simulate residual stress formation during the electron beam melting (EBM) process within the additive manufacturing (AM) technologies for Inconel 718 is presented in this paper. The EBM process has demonstrated a high potential to fabricate components with complex geometries, but the resulting components are influenced by the thermal cycles observed during the manufacturing process. When processing nickel based superalloys, very high temperatures (approx. 1000 °C) are observed in the powder bed, base plate, and build. These high temperatures, when combined with substrate adherence, can result in warping of the base plate and affect themore » final component by causing defects. It is important to have an understanding of the thermo-mechanical response of the entire system, that is, its mechanical behavior towards thermal loading occurring during the EBM process prior to manufacturing a component. Therefore, computational models to predict the response of the system during the EBM process will aid in eliminating the undesired process conditions, a priori, in order to fabricate the optimum component. Such a comprehensive computational modeling approach is demonstrated to analyze warping of the base plate, stress and plastic strain accumulation within the material, and thermal cycles in the system during different stages of the EBM process.« less

The AgESGUI geospatial simulation system for environmental model application and evaluation

USDA-ARS?s Scientific Manuscript database

Practical decision making in spatially-distributed environmental assessment and management is increasingly being based on environmental process-based models linked to geographical information systems (GIS). Furthermore, powerful computers and Internet-accessible assessment tools are providing much g...

A synthetic design environment for ship design

NASA Technical Reports Server (NTRS)

Chipman, Richard R.

1995-01-01

Rapid advances in computer science and information system technology have made possible the creation of synthetic design environments (SDE) which use virtual prototypes to increase the efficiency and agility of the design process. This next generation of computer-based design tools will rely heavily on simulation and advanced visualization techniques to enable integrated product and process teams to concurrently conceptualize, design, and test a product and its fabrication processes. This paper summarizes a successful demonstration of the feasibility of using a simulation based design environment in the shipbuilding industry. As computer science and information science technologies have evolved, there have been many attempts to apply and integrate the new capabilities into systems for the improvement of the process of design. We see the benefits of those efforts in the abundance of highly reliable, technologically complex products and services in the modern marketplace. Furthermore, the computer-based technologies have been so cost effective that the improvements embodied in modern products have been accompanied by lowered costs. Today the state-of-the-art in computerized design has advanced so dramatically that the focus is no longer on merely improving design methodology; rather the goal is to revolutionize the entire process by which complex products are conceived, designed, fabricated, tested, deployed, operated, maintained, refurbished and eventually decommissioned. By concurrently addressing all life-cycle issues, the basic decision making process within an enterprise will be improved dramatically, leading to new levels of quality, innovation, efficiency, and customer responsiveness. By integrating functions and people with an enterprise, such systems will change the fundamental way American industries are organized, creating companies that are more competitive, creative, and productive.

gpuSPHASE-A shared memory caching implementation for 2D SPH using CUDA

NASA Astrophysics Data System (ADS)

Winkler, Daniel; Meister, Michael; Rezavand, Massoud; Rauch, Wolfgang

2017-04-01

Smoothed particle hydrodynamics (SPH) is a meshless Lagrangian method that has been successfully applied to computational fluid dynamics (CFD), solid mechanics and many other multi-physics problems. Using the method to solve transport phenomena in process engineering requires the simulation of several days to weeks of physical time. Based on the high computational demand of CFD such simulations in 3D need a computation time of years so that a reduction to a 2D domain is inevitable. In this paper gpuSPHASE, a new open-source 2D SPH solver implementation for graphics devices, is developed. It is optimized for simulations that must be executed with thousands of frames per second to be computed in reasonable time. A novel caching algorithm for Compute Unified Device Architecture (CUDA) shared memory is proposed and implemented. The software is validated and the performance is evaluated for the well established dambreak test case.

On the Use of Computers for Teaching Fluid Mechanics

NASA Technical Reports Server (NTRS)

Benson, Thomas J.

1994-01-01

Several approaches for improving the teaching of basic fluid mechanics using computers are presented. There are two objectives to these approaches: to increase the involvement of the student in the learning process and to present information to the student in a variety of forms. Items discussed include: the preparation of educational videos using the results of computational fluid dynamics (CFD) calculations, the analysis of CFD flow solutions using workstation based post-processing graphics packages, and the development of workstation or personal computer based simulators which behave like desk top wind tunnels. Examples of these approaches are presented along with observations from working with undergraduate co-ops. Possible problems in the implementation of these approaches as well as solutions to these problems are also discussed.

Quasi-static earthquake cycle simulation based on nonlinear viscoelastic finite element analyses

NASA Astrophysics Data System (ADS)

Agata, R.; Ichimura, T.; Hyodo, M.; Barbot, S.; Hori, T.

2017-12-01

To explain earthquake generation processes, simulation methods of earthquake cycles have been studied. For such simulations, the combination of the rate- and state-dependent friction law at the fault plane and the boundary integral method based on Green's function in an elastic half space is widely used (e.g. Hori 2009; Barbot et al. 2012). In this approach, stress change around the fault plane due to crustal deformation can be computed analytically, while the effects of complex physics such as mantle rheology and gravity are generally not taken into account. To consider such effects, we seek to develop an earthquake cycle simulation combining crustal deformation computation based on the finite element (FE) method with the rate- and state-dependent friction law. Since the drawback of this approach is the computational cost associated with obtaining numerical solutions, we adopt a recently developed fast and scalable FE solver (Ichimura et al. 2016), which assumes use of supercomputers, to solve the problem in a realistic time. As in the previous approach, we solve the governing equations consisting of the rate- and state-dependent friction law. In solving the equations, we compute stress changes along the fault plane due to crustal deformation using FE simulation, instead of computing them by superimposing slip response function as in the previous approach. In stress change computation, we take into account nonlinear viscoelastic deformation in the asthenosphere. In the presentation, we will show simulation results in a normative three-dimensional problem, where a circular-shaped velocity-weakening area is set in a square-shaped fault plane. The results with and without nonlinear viscosity in the asthenosphere will be compared. We also plan to apply the developed code to simulate the post-earthquake deformation of a megathrust earthquake, such as the 2011 Tohoku earthquake. Acknowledgment: The results were obtained using the K computer at the RIKEN (Proposal number hp160221).

New Approaches to the Computer Simulation of Amorphous Alloys: A Review.

PubMed

Valladares, Ariel A; Díaz-Celaya, Juan A; Galván-Colín, Jonathan; Mejía-Mendoza, Luis M; Reyes-Retana, José A; Valladares, Renela M; Valladares, Alexander; Alvarez-Ramirez, Fernando; Qu, Dongdong; Shen, Jun

2011-04-13

In this work we review our new methods to computer generate amorphous atomic topologies of several binary alloys: SiH, SiN, CN; binary systems based on group IV elements like SiC; the GeSe 2 chalcogenide; aluminum-based systems: AlN and AlSi, and the CuZr amorphous alloy. We use an ab initio approach based on density functionals and computationally thermally-randomized periodically-continued cells with at least 108 atoms. The computational thermal process to generate the amorphous alloys is the undermelt-quench approach, or one of its variants, that consists in linearly heating the samples to just below their melting (or liquidus) temperatures, and then linearly cooling them afterwards. These processes are carried out from initial crystalline conditions using short and long time steps. We find that a step four-times the default time step is adequate for most of the simulations. Radial distribution functions (partial and total) are calculated and compared whenever possible with experimental results, and the agreement is very good. For some materials we report studies of the effect of the topological disorder on their electronic and vibrational densities of states and on their optical properties.

New Approaches to the Computer Simulation of Amorphous Alloys: A Review

PubMed Central

Valladares, Ariel A.; Díaz-Celaya, Juan A.; Galván-Colín, Jonathan; Mejía-Mendoza, Luis M.; Reyes-Retana, José A.; Valladares, Renela M.; Valladares, Alexander; Alvarez-Ramirez, Fernando; Qu, Dongdong; Shen, Jun

2011-01-01

In this work we review our new methods to computer generate amorphous atomic topologies of several binary alloys: SiH, SiN, CN; binary systems based on group IV elements like SiC; the GeSe2 chalcogenide; aluminum-based systems: AlN and AlSi, and the CuZr amorphous alloy. We use an ab initio approach based on density functionals and computationally thermally-randomized periodically-continued cells with at least 108 atoms. The computational thermal process to generate the amorphous alloys is the undermelt-quench approach, or one of its variants, that consists in linearly heating the samples to just below their melting (or liquidus) temperatures, and then linearly cooling them afterwards. These processes are carried out from initial crystalline conditions using short and long time steps. We find that a step four-times the default time step is adequate for most of the simulations. Radial distribution functions (partial and total) are calculated and compared whenever possible with experimental results, and the agreement is very good. For some materials we report studies of the effect of the topological disorder on their electronic and vibrational densities of states and on their optical properties. PMID:28879948

Development of computer-aided design system of elastic sensitive elements of automatic metering devices

NASA Astrophysics Data System (ADS)

Kalinkina, M. E.; Kozlov, A. S.; Labkovskaia, R. I.; Pirozhnikova, O. I.; Tkalich, V. L.; Shmakov, N. A.

2018-05-01

The object of research is the element base of devices of control and automation systems, including in its composition annular elastic sensitive elements, methods of their modeling, calculation algorithms and software complexes for automation of their design processes. The article is devoted to the development of the computer-aided design system of elastic sensitive elements used in weight- and force-measuring automation devices. Based on the mathematical modeling of deformation processes in a solid, as well as the results of static and dynamic analysis, the calculation of elastic elements is given using the capabilities of modern software systems based on numerical simulation. In the course of the simulation, the model was a divided hexagonal grid of finite elements with a maximum size not exceeding 2.5 mm. The results of modal and dynamic analysis are presented in this article.

Tools for 3D scientific visualization in computational aerodynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

The purpose is to describe the tools and techniques in use at the NASA Ames Research Center for performing visualization of computational aerodynamics, for example visualization of flow fields from computer simulations of fluid dynamics about vehicles such as the Space Shuttle. The hardware used for visualization is a high-performance graphics workstation connected to a super computer with a high speed channel. At present, the workstation is a Silicon Graphics IRIS 3130, the supercomputer is a CRAY2, and the high speed channel is a hyperchannel. The three techniques used for visualization are post-processing, tracking, and steering. Post-processing analysis is done after the simulation. Tracking analysis is done during a simulation but is not interactive, whereas steering analysis involves modifying the simulation interactively during the simulation. Using post-processing methods, a flow simulation is executed on a supercomputer and, after the simulation is complete, the results of the simulation are processed for viewing. The software in use and under development at NASA Ames Research Center for performing these types of tasks in computational aerodynamics is described. Workstation performance issues, benchmarking, and high-performance networks for this purpose are also discussed as well as descriptions of other hardware for digital video and film recording.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

Two key areas of crucial importance to the computer-based simulation of large space structures are discussed. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area involves massively parallel computers.

3D simulations of early blood vessel formation

NASA Astrophysics Data System (ADS)

Cavalli, F.; Gamba, A.; Naldi, G.; Semplice, M.; Valdembri, D.; Serini, G.

2007-08-01

Blood vessel networks form by spontaneous aggregation of individual cells migrating toward vascularization sites (vasculogenesis). A successful theoretical model of two-dimensional experimental vasculogenesis has been recently proposed, showing the relevance of percolation concepts and of cell cross-talk (chemotactic autocrine loop) to the understanding of this self-aggregation process. Here we study the natural 3D extension of the computational model proposed earlier, which is relevant for the investigation of the genuinely three-dimensional process of vasculogenesis in vertebrate embryos. The computational model is based on a multidimensional Burgers equation coupled with a reaction diffusion equation for a chemotactic factor and a mass conservation law. The numerical approximation of the computational model is obtained by high order relaxed schemes. Space and time discretization are performed by using TVD schemes and, respectively, IMEX schemes. Due to the computational costs of realistic simulations, we have implemented the numerical algorithm on a cluster for parallel computation. Starting from initial conditions mimicking the experimentally observed ones, numerical simulations produce network-like structures qualitatively similar to those observed in the early stages of in vivo vasculogenesis. We develop the computation of critical percolative indices as a robust measure of the network geometry as a first step towards the comparison of computational and experimental data.

Efficient scatter model for simulation of ultrasound images from computed tomography data

NASA Astrophysics Data System (ADS)

D'Amato, J. P.; Lo Vercio, L.; Rubi, P.; Fernandez Vera, E.; Barbuzza, R.; Del Fresno, M.; Larrabide, I.

2015-12-01

Background and motivation: Real-time ultrasound simulation refers to the process of computationally creating fully synthetic ultrasound images instantly. Due to the high value of specialized low cost training for healthcare professionals, there is a growing interest in the use of this technology and the development of high fidelity systems that simulate the acquisitions of echographic images. The objective is to create an efficient and reproducible simulator that can run either on notebooks or desktops using low cost devices. Materials and methods: We present an interactive ultrasound simulator based on CT data. This simulator is based on ray-casting and provides real-time interaction capabilities. The simulation of scattering that is coherent with the transducer position in real time is also introduced. Such noise is produced using a simplified model of multiplicative noise and convolution with point spread functions (PSF) tailored for this purpose. Results: The computational efficiency of scattering maps generation was revised with an improved performance. This allowed a more efficient simulation of coherent scattering in the synthetic echographic images while providing highly realistic result. We describe some quality and performance metrics to validate these results, where a performance of up to 55fps was achieved. Conclusion: The proposed technique for real-time scattering modeling provides realistic yet computationally efficient scatter distributions. The error between the original image and the simulated scattering image was compared for the proposed method and the state-of-the-art, showing negligible differences in its distribution.

Discrete State Change Model of Manufacturing Quality to Aid Assembly Process Design

NASA Astrophysics Data System (ADS)

Koga, Tsuyoshi; Aoyama, Kazuhiro

This paper proposes a representation model of the quality state change in an assembly process that can be used in a computer-aided process design system. In order to formalize the state change of the manufacturing quality in the assembly process, the functions, operations, and quality changes in the assembly process are represented as a network model that can simulate discrete events. This paper also develops a design method for the assembly process. The design method calculates the space of quality state change and outputs a better assembly process (better operations and better sequences) that can be used to obtain the intended quality state of the final product. A computational redesigning algorithm of the assembly process that considers the manufacturing quality is developed. The proposed method can be used to design an improved manufacturing process by simulating the quality state change. A prototype system for planning an assembly process is implemented and applied to the design of an auto-breaker assembly process. The result of the design example indicates that the proposed assembly process planning method outputs a better manufacturing scenario based on the simulation of the quality state change.

3D simulation of floral oil storage in the scopa of South American insects

NASA Astrophysics Data System (ADS)

Ruettgers, Alexander; Griebel, Michael; Pastrik, Lars; Schmied, Heiko; Wittmann, Dieter; Scherrieble, Andreas; Dinkelmann, Albrecht; Stegmaier, Thomas; InstituteNumerical Simulation Team; Institute of Crop Science; Resource Conservation Team; Institute of Textile Technology; Process Engineering Team

2014-11-01

Several species of bees in South America possess structures to store and transport floral oils. By using closely spaced hairs at their back legs, the so called scopa, these bees can absorb and release oil droplets without loss. The high efficiency of this process is a matter of ongoing research. Basing on recent x-ray microtomography scans from the scopa of these bees at the Institute of Textile Technology and Process Engineering Denkendorf, we build a three-dimensional computer model. Using NaSt3DGPF, a two-phase flow solver developed at the Institute for Numerical Simulation of the University of Bonn, we perform massively parallel flow simulations with the complex micro-CT data. In this talk, we discuss the results of our simulations and the transfer of the x-ray measurement into a computer model. This research was funded under GR 1144/18-1 by the Deutsche Forschungsgemeinschaft (DFG).

Computational Modeling and Simulations of Bioparticle Internalization Through Clathrin-mediated Endocytosis

NASA Astrophysics Data System (ADS)

Deng, Hua; Dutta, Prashanta; Liu, Jin

2016-11-01

Clathrin-mediated endocytosis (CME) is one of the most important endocytic pathways for the internalization of bioparticles at lipid membrane of cells, which plays crucial roles in fundamental understanding of viral infections and interacellular/transcelluar targeted drug delivery. During CME, highly dynamic clathrin-coated pit (CCP), formed by the growth of ordered clathrin lattices, is the key scaffolding component that drives the deformation of plasma membrane. Experimental studies have shown that CCP alone can provide sufficient membrane curvature for facilitating membrane invagination. However, currently there is no computational model that could couple cargo receptor binding with membrane invagination process, nor simulations of the dynamic growing process of CCP. We develop a stochastic computational model for the clathrin-mediated endocytosis based on Metropolis Monte Carlo simulations. In our model, the energetic costs of bending membrane and CCP are linked with antigen-antibody interactions. The assembly of clathrin lattices is a dynamic process that correlates with antigen-antibody bond formation. This model helps study the membrane deformation and the effects of CCP during functionalized bioparticles internalization through CME. This work is supported by NSF Grants: CBET-1250107 and CBET-1604211.

Model-based verification and validation of the SMAP uplink processes

NASA Astrophysics Data System (ADS)

Khan, M. O.; Dubos, G. F.; Tirona, J.; Standley, S.

Model-Based Systems Engineering (MBSE) is being used increasingly within the spacecraft design community because of its benefits when compared to document-based approaches. As the complexity of projects expands dramatically with continually increasing computational power and technology infusion, the time and effort needed for verification and validation (V& V) increases geometrically. Using simulation to perform design validation with system-level models earlier in the life cycle stands to bridge the gap between design of the system (based on system-level requirements) and verifying those requirements/validating the system as a whole. This case study stands as an example of how a project can validate a system-level design earlier in the project life cycle than traditional V& V processes by using simulation on a system model. Specifically, this paper describes how simulation was added to a system model of the Soil Moisture Active-Passive (SMAP) mission's uplink process. Also discussed are the advantages and disadvantages of the methods employed and the lessons learned; which are intended to benefit future model-based and simulation-based development efforts.

An earth imaging camera simulation using wide-scale construction of reflectance surfaces

NASA Astrophysics Data System (ADS)

Murthy, Kiran; Chau, Alexandra H.; Amin, Minesh B.; Robinson, M. Dirk

2013-10-01

Developing and testing advanced ground-based image processing systems for earth-observing remote sensing applications presents a unique challenge that requires advanced imagery simulation capabilities. This paper presents an earth-imaging multispectral framing camera simulation system called PayloadSim (PaySim) capable of generating terabytes of photorealistic simulated imagery. PaySim leverages previous work in 3-D scene-based image simulation, adding a novel method for automatically and efficiently constructing 3-D reflectance scenes by draping tiled orthorectified imagery over a geo-registered Digital Elevation Map (DEM). PaySim's modeling chain is presented in detail, with emphasis given to the techniques used to achieve computational efficiency. These techniques as well as cluster deployment of the simulator have enabled tuning and robust testing of image processing algorithms, and production of realistic sample data for customer-driven image product development. Examples of simulated imagery of Skybox's first imaging satellite are shown.

An Analysis of Collaborative Problem-Solving Activities Mediated by Individual-Based and Collaborative Computer Simulations

ERIC Educational Resources Information Center

Chang, C.-J.; Chang, M.-H.; Liu, C.-C.; Chiu, B.-C.; Fan Chiang, S.-H.; Wen, C.-T.; Hwang, F.-K.; Chao, P.-Y.; Chen, Y.-L.; Chai, C.-S.

2017-01-01

Researchers have indicated that the collaborative problem-solving space afforded by the collaborative systems significantly impact the problem-solving process. However, recent investigations into collaborative simulations, which allow a group of students to jointly manipulate a problem in a shared problem space, have yielded divergent results…

Calibration of the APEX model to simulate management practice effects on runoff, sediment, and phosphorus loss

USDA-ARS?s Scientific Manuscript database

Process-based computer models have been proposed as a tool to generate data for phosphorus-index assessment and development. Although models are commonly used to simulate phosphorus (P) loss from agriculture using managements that are different from the calibration data, this use of models has not ...

A resilient and efficient CFD framework: Statistical learning tools for multi-fidelity and heterogeneous information fusion

NASA Astrophysics Data System (ADS)

Lee, Seungjoon; Kevrekidis, Ioannis G.; Karniadakis, George Em

2017-09-01

Exascale-level simulations require fault-resilient algorithms that are robust against repeated and expected software and/or hardware failures during computations, which may render the simulation results unsatisfactory. If each processor can share some global information about the simulation from a coarse, limited accuracy but relatively costless auxiliary simulator we can effectively fill-in the missing spatial data at the required times by a statistical learning technique - multi-level Gaussian process regression, on the fly; this has been demonstrated in previous work [1]. Based on the previous work, we also employ another (nonlinear) statistical learning technique, Diffusion Maps, that detects computational redundancy in time and hence accelerate the simulation by projective time integration, giving the overall computation a "patch dynamics" flavor. Furthermore, we are now able to perform information fusion with multi-fidelity and heterogeneous data (including stochastic data). Finally, we set the foundations of a new framework in CFD, called patch simulation, that combines information fusion techniques from, in principle, multiple fidelity and resolution simulations (and even experiments) with a new adaptive timestep refinement technique. We present two benchmark problems (the heat equation and the Navier-Stokes equations) to demonstrate the new capability that statistical learning tools can bring to traditional scientific computing algorithms. For each problem, we rely on heterogeneous and multi-fidelity data, either from a coarse simulation of the same equation or from a stochastic, particle-based, more "microscopic" simulation. We consider, as such "auxiliary" models, a Monte Carlo random walk for the heat equation and a dissipative particle dynamics (DPD) model for the Navier-Stokes equations. More broadly, in this paper we demonstrate the symbiotic and synergistic combination of statistical learning, domain decomposition, and scientific computing in exascale simulations.

plasmaFoam: An OpenFOAM framework for computational plasma physics and chemistry

NASA Astrophysics Data System (ADS)

Venkattraman, Ayyaswamy; Verma, Abhishek Kumar

2016-09-01

As emphasized in the 2012 Roadmap for low temperature plasmas (LTP), scientific computing has emerged as an essential tool for the investigation and prediction of the fundamental physical and chemical processes associated with these systems. While several in-house and commercial codes exist, with each having its own advantages and disadvantages, a common framework that can be developed by researchers from all over the world will likely accelerate the impact of computational studies on advances in low-temperature plasma physics and chemistry. In this regard, we present a finite volume computational toolbox to perform high-fidelity simulations of LTP systems. This framework, primarily based on the OpenFOAM solver suite, allows us to enhance our understanding of multiscale plasma phenomenon by performing massively parallel, three-dimensional simulations on unstructured meshes using well-established high performance computing tools that are widely used in the computational fluid dynamics community. In this talk, we will present preliminary results obtained using the OpenFOAM-based solver suite with benchmark three-dimensional simulations of microplasma devices including both dielectric and plasma regions. We will also discuss the future outlook for the solver suite.

DEM Based Modeling: Grid or TIN? The Answer Depends

NASA Astrophysics Data System (ADS)

Ogden, F. L.; Moreno, H. A.

2015-12-01

The availability of petascale supercomputing power has enabled process-based hydrological simulations on large watersheds and two-way coupling with mesoscale atmospheric models. Of course with increasing watershed scale come corresponding increases in watershed complexity, including wide ranging water management infrastructure and objectives, and ever increasing demands for forcing data. Simulations of large watersheds using grid-based models apply a fixed resolution over the entire watershed. In large watersheds, this means an enormous number of grids, or coarsening of the grid resolution to reduce memory requirements. One alternative to grid-based methods is the triangular irregular network (TIN) approach. TINs provide the flexibility of variable resolution, which allows optimization of computational resources by providing high resolution where necessary and low resolution elsewhere. TINs also increase required effort in model setup, parameter estimation, and coupling with forcing data which are often gridded. This presentation discusses the costs and benefits of the use of TINs compared to grid-based methods, in the context of large watershed simulations within the traditional gridded WRF-HYDRO framework and the new TIN-based ADHydro high performance computing watershed simulator.

Computing biological functions using BioΨ, a formal description of biological processes based on elementary bricks of actions

PubMed Central

Pérès, Sabine; Felicori, Liza; Rialle, Stéphanie; Jobard, Elodie; Molina, Franck

2010-01-01

Motivation: In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes. Results: We present a formalism that uses the BioΨ concepts to model biological processes from molecular details to networks. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure–function relationships, etc.). We illustrate its application with two examples: the functional comparison of proteases and the functional description of the glycolysis network. This computational approach is compatible with detailed biological knowledge and can be applied to different kinds of systems of simulation. Availability: www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/ Contact: sabine.peres@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20448138

Nonlinear relaxation algorithms for circuit simulation

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

Saleh, R.A.

Circuit simulation is an important Computer-Aided Design (CAD) tool in the design of Integrated Circuits (IC). However, the standard techniques used in programs such as SPICE result in very long computer-run times when applied to large problems. In order to reduce the overall run time, a number of new approaches to circuit simulation were developed and are described. These methods are based on nonlinear relaxation techniques and exploit the relative inactivity of large circuits. Simple waveform-processing techniques are described to determine the maximum possible speed improvement that can be obtained by exploiting this property of large circuits. Three simulation algorithmsmore » are described, two of which are based on the Iterated Timing Analysis (ITA) method and a third based on the Waveform-Relaxation Newton (WRN) method. New programs that incorporate these techniques were developed and used to simulate a variety of industrial circuits. The results from these simulations are provided. The techniques are shown to be much faster than the standard approach. In addition, a number of parallel aspects of these algorithms are described, and a general space-time model of parallel-task scheduling is developed.« less

Image formation simulation for computer-aided inspection planning of machine vision systems

NASA Astrophysics Data System (ADS)

Irgenfried, Stephan; Bergmann, Stephan; Mohammadikaji, Mahsa; Beyerer, Jürgen; Dachsbacher, Carsten; Wörn, Heinz

2017-06-01

In this work, a simulation toolset for Computer Aided Inspection Planning (CAIP) of systems for automated optical inspection (AOI) is presented along with a versatile two-robot-setup for verification of simulation and system planning results. The toolset helps to narrow down the large design space of optical inspection systems in interaction with a system expert. The image formation taking place in optical inspection systems is simulated using GPU-based real time graphics and high quality off-line-rendering. The simulation pipeline allows a stepwise optimization of the system, from fast evaluation of surface patch visibility based on real time graphics up to evaluation of image processing results based on off-line global illumination calculation. A focus of this work is on the dependency of simulation quality on measuring, modeling and parameterizing the optical surface properties of the object to be inspected. The applicability to real world problems is demonstrated by taking the example of planning a 3D laser scanner application. Qualitative and quantitative comparison results of synthetic and real images are presented.

The Learning Effects of Computer Simulations in Science Education

ERIC Educational Resources Information Center

Rutten, Nico; van Joolingen, Wouter R.; van der Veen, Jan T.

2012-01-01

This article reviews the (quasi)experimental research of the past decade on the learning effects of computer simulations in science education. The focus is on two questions: how use of computer simulations can enhance traditional education, and how computer simulations are best used in order to improve learning processes and outcomes. We report on…

CAD-centric Computation Management System for a Virtual TBM

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

Ramakanth Munipalli; K.Y. Szema; P.Y. Huang

HyPerComp Inc. in research collaboration with TEXCEL has set out to build a Virtual Test Blanket Module (VTBM) computational system to address the need in contemporary fusion research for simulating the integrated behavior of the blanket, divertor and plasma facing components in a fusion environment. Physical phenomena to be considered in a VTBM will include fluid flow, heat transfer, mass transfer, neutronics, structural mechanics and electromagnetics. We seek to integrate well established (third-party) simulation software in various disciplines mentioned above. The integrated modeling process will enable user groups to interoperate using a common modeling platform at various stages of themore » analysis. Since CAD is at the core of the simulation (as opposed to computational meshes which are different for each problem,) VTBM will have a well developed CAD interface, governing CAD model editing, cleanup, parameter extraction, model deformation (based on simulation,) CAD-based data interpolation. In Phase-I, we built the CAD-hub of the proposed VTBM and demonstrated its use in modeling a liquid breeder blanket module with coupled MHD and structural mechanics using HIMAG and ANSYS. A complete graphical user interface of the VTBM was created, which will form the foundation of any future development. Conservative data interpolation via CAD (as opposed to mesh-based transfer), the regeneration of CAD models based upon computed deflections, are among the other highlights of phase-I activity.« less

A laparoscopy-based method for BRDF estimation from in vivo human liver.

PubMed

Nunes, A L P; Maciel, A; Cavazzola, L T; Walter, M

2017-01-01

While improved visual realism is known to enhance training effectiveness in virtual surgery simulators, the advances on realistic rendering for these simulators is slower than similar simulations for man-made scenes. One of the main reasons for this is that in vivo data is hard to gather and process. In this paper, we propose the analysis of videolaparoscopy data to compute the Bidirectional Reflectance Distribution Function (BRDF) of living organs as an input to physically based rendering algorithms. From the interplay between light and organic matter recorded in video images, we propose the definition of a process capable of establishing the BRDF for inside-the-body organic surfaces. We present a case study around the liver with patient-specific rendering under global illumination. Results show that despite the limited range of motion allowed within the body, the computed BRDF presents a high-coverage of the sampled regions and produces plausible renderings. Copyright © 2016 Elsevier B.V. All rights reserved.

Computer-based simulation training in emergency medicine designed in the light of malpractice cases.

PubMed

Karakuş, Akan; Duran, Latif; Yavuz, Yücel; Altintop, Levent; Calişkan, Fatih

2014-07-27

Using computer-based simulation systems in medical education is becoming more and more common. Although the benefits of practicing with these systems in medical education have been demonstrated, advantages of using computer-based simulation in emergency medicine education are less validated. The aim of the present study was to assess the success rates of final year medical students in doing emergency medical treatment and evaluating the effectiveness of computer-based simulation training in improving final year medical students' knowledge. Twenty four Students trained with computer-based simulation and completed at least 4 hours of simulation-based education between the dates Feb 1, 2010 - May 1, 2010. Also a control group (traditionally trained, n =24) was chosen. After the end of training, students completed an examination about 5 randomized medical simulation cases. In 5 cases, an average of 3.9 correct medical approaches carried out by computer-based simulation trained students, an average of 2.8 correct medical approaches carried out by traditionally trained group (t = 3.90, p < 0.005). We found that the success of students trained with simulation training in cases which required complicated medical approach, was statistically higher than the ones who didn't take simulation training (p ≤ 0.05). Computer-based simulation training would be significantly effective in learning of medical treatment algorithms. We thought that these programs can improve the success rate of students especially in doing adequate medical approach to complex emergency cases.

Cost efficient CFD simulations: Proper selection of domain partitioning strategies

NASA Astrophysics Data System (ADS)

Haddadi, Bahram; Jordan, Christian; Harasek, Michael

2017-10-01

Computational Fluid Dynamics (CFD) is one of the most powerful simulation methods, which is used for temporally and spatially resolved solutions of fluid flow, heat transfer, mass transfer, etc. One of the challenges of Computational Fluid Dynamics is the extreme hardware demand. Nowadays super-computers (e.g. High Performance Computing, HPC) featuring multiple CPU cores are applied for solving-the simulation domain is split into partitions for each core. Some of the different methods for partitioning are investigated in this paper. As a practical example, a new open source based solver was utilized for simulating packed bed adsorption, a common separation method within the field of thermal process engineering. Adsorption can for example be applied for removal of trace gases from a gas stream or pure gases production like Hydrogen. For comparing the performance of the partitioning methods, a 60 million cell mesh for a packed bed of spherical adsorbents was created; one second of the adsorption process was simulated. Different partitioning methods available in OpenFOAM® (Scotch, Simple, and Hierarchical) have been used with different numbers of sub-domains. The effect of the different methods and number of processor cores on the simulation speedup and also energy consumption were investigated for two different hardware infrastructures (Vienna Scientific Clusters VSC 2 and VSC 3). As a general recommendation an optimum number of cells per processor core was calculated. Optimized simulation speed, lower energy consumption and consequently the cost effects are reported here.

Interactive Design Strategy for a Multi-Functional PAMAM Dendrimer-Based Nano-Therapeutic Using Computational Models and Experimental Analysis

PubMed Central

Lee, Inhan; Williams, Christopher R.; Athey, Brian D.; Baker, James R.

2010-01-01

Molecular dynamics simulations of nano-therapeutics as a final product and of all intermediates in the process of generating a multi-functional nano-therapeutic based on a poly(amidoamine) (PAMAM) dendrimer were performed along with chemical analyses of each of them. The actual structures of the dendrimers were predicted, based on potentiometric titration, gel permeation chromatography, and NMR. The chemical analyses determined the numbers of functional molecules, based on the actual structure of the dendrimer. Molecular dynamics simulations calculated the configurations of the intermediates and the radial distributions of functional molecules, based on their numbers. This interactive process between the simulation results and the chemical analyses provided a further strategy to design the next reaction steps and to gain insight into the products at each chemical reaction step. PMID:20700476

Radiation damage of biomolecules (RADAM) database development: current status

NASA Astrophysics Data System (ADS)

Denifl, S.; Garcia, G.; Huber, B. A.; Marinković, B. P.; Mason, N.; Postler, J.; Rabus, H.; Rixon, G.; Solov'yov, A. V.; Suraud, E.; Yakubovich, A. V.

2013-06-01

Ion beam therapy offers the possibility of excellent dose localization for treatment of malignant tumours, minimizing radiation damage in normal tissue, while maximizing cell killing within the tumour. However, as the underlying dependent physical, chemical and biological processes are too complex to treat them on a purely analytical level, most of our current and future understanding will rely on computer simulations, based on mathematical equations, algorithms and last, but not least, on the available atomic and molecular data. The viability of the simulated output and the success of any computer simulation will be determined by these data, which are treated as the input variables in each computer simulation performed. The radiation research community lacks a complete database for the cross sections of all the different processes involved in ion beam induced damage: ionization and excitation cross sections for ions with liquid water and biological molecules, all the possible electron - medium interactions, dielectric response data, electron attachment to biomolecules etc. In this paper we discuss current progress in the creation of such a database, outline the roadmap of the project and review plans for the exploitation of such a database in future simulations.

LASSIE: simulating large-scale models of biochemical systems on GPUs.

PubMed

Tangherloni, Andrea; Nobile, Marco S; Besozzi, Daniela; Mauri, Giancarlo; Cazzaniga, Paolo

2017-05-10

Mathematical modeling and in silico analysis are widely acknowledged as complementary tools to biological laboratory methods, to achieve a thorough understanding of emergent behaviors of cellular processes in both physiological and perturbed conditions. Though, the simulation of large-scale models-consisting in hundreds or thousands of reactions and molecular species-can rapidly overtake the capabilities of Central Processing Units (CPUs). The purpose of this work is to exploit alternative high-performance computing solutions, such as Graphics Processing Units (GPUs), to allow the investigation of these models at reduced computational costs. LASSIE is a "black-box" GPU-accelerated deterministic simulator, specifically designed for large-scale models and not requiring any expertise in mathematical modeling, simulation algorithms or GPU programming. Given a reaction-based model of a cellular process, LASSIE automatically generates the corresponding system of Ordinary Differential Equations (ODEs), assuming mass-action kinetics. The numerical solution of the ODEs is obtained by automatically switching between the Runge-Kutta-Fehlberg method in the absence of stiffness, and the Backward Differentiation Formulae of first order in presence of stiffness. The computational performance of LASSIE are assessed using a set of randomly generated synthetic reaction-based models of increasing size, ranging from 64 to 8192 reactions and species, and compared to a CPU-implementation of the LSODA numerical integration algorithm. LASSIE adopts a novel fine-grained parallelization strategy to distribute on the GPU cores all the calculations required to solve the system of ODEs. By virtue of this implementation, LASSIE achieves up to 92× speed-up with respect to LSODA, therefore reducing the running time from approximately 1 month down to 8 h to simulate models consisting in, for instance, four thousands of reactions and species. Notably, thanks to its smaller memory footprint, LASSIE is able to perform fast simulations of even larger models, whereby the tested CPU-implementation of LSODA failed to reach termination. LASSIE is therefore expected to make an important breakthrough in Systems Biology applications, for the execution of faster and in-depth computational analyses of large-scale models of complex biological systems.

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

DOE PAGES

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; ...

2017-06-09

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of “KMC stiffness” (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps / cpu-time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order tomore » achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events -- allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm designed for use in achieving and simulating steady-state conditions in KMC simulations. Lastly, as shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.« less

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; Savara, Aditya

2017-10-01

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of "KMC stiffness" (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps/CPU time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order to achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events-allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm is designed for use in achieving and simulating steady-state conditions in KMC simulations. As shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.

Computational Biochemistry-Enzyme Mechanisms Explored.

PubMed

Culka, Martin; Gisdon, Florian J; Ullmann, G Matthias

2017-01-01

Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Computational biochemistry aims at creation of a computational model of an enzyme in order to explain microscopic details of the catalytic process and reproduce or predict macroscopic experimental findings. Results of such computations are in part complementary to experimental data and provide an explanation of a biochemical process at the microscopic level. In order to evaluate the mechanism of an enzyme, a structural model is constructed which can be analyzed by several theoretical approaches. Several simulation methods can and should be combined to get a reliable picture of the process of interest. Furthermore, abstract models of biological systems can be constructed combining computational and experimental data. In this review, we discuss structural computational models of enzymatic systems. We first discuss various models to simulate enzyme catalysis. Furthermore, we review various approaches how to characterize the enzyme mechanism both qualitatively and quantitatively using different modeling approaches. © 2017 Elsevier Inc. All rights reserved.

AMITIS: A 3D GPU-Based Hybrid-PIC Model for Space and Plasma Physics

NASA Astrophysics Data System (ADS)

Fatemi, Shahab; Poppe, Andrew R.; Delory, Gregory T.; Farrell, William M.

2017-05-01

We have developed, for the first time, an advanced modeling infrastructure in space simulations (AMITIS) with an embedded three-dimensional self-consistent grid-based hybrid model of plasma (kinetic ions and fluid electrons) that runs entirely on graphics processing units (GPUs). The model uses NVIDIA GPUs and their associated parallel computing platform, CUDA, developed for general purpose processing on GPUs. The model uses a single CPU-GPU pair, where the CPU transfers data between the system and GPU memory, executes CUDA kernels, and writes simulation outputs on the disk. All computations, including moving particles, calculating macroscopic properties of particles on a grid, and solving hybrid model equations are processed on a single GPU. We explain various computing kernels within AMITIS and compare their performance with an already existing well-tested hybrid model of plasma that runs in parallel using multi-CPU platforms. We show that AMITIS runs ∼10 times faster than the parallel CPU-based hybrid model. We also introduce an implicit solver for computation of Faraday’s Equation, resulting in an explicit-implicit scheme for the hybrid model equation. We show that the proposed scheme is stable and accurate. We examine the AMITIS energy conservation and show that the energy is conserved with an error < 0.2% after 500,000 timesteps, even when a very low number of particles per cell is used.

Exploring the Use of Computer Simulations in Unraveling Research and Development Governance Problems

NASA Technical Reports Server (NTRS)

Balaban, Mariusz A.; Hester, Patrick T.

2012-01-01

Understanding Research and Development (R&D) enterprise relationships and processes at a governance level is not a simple task, but valuable decision-making insight and evaluation capabilities can be gained from their exploration through computer simulations. This paper discusses current Modeling and Simulation (M&S) methods, addressing their applicability to R&D enterprise governance. Specifically, the authors analyze advantages and disadvantages of the four methodologies used most often by M&S practitioners: System Dynamics (SO), Discrete Event Simulation (DES), Agent Based Modeling (ABM), and formal Analytic Methods (AM) for modeling systems at the governance level. Moreover, the paper describes nesting models using a multi-method approach. Guidance is provided to those seeking to employ modeling techniques in an R&D enterprise for the purposes of understanding enterprise governance. Further, an example is modeled and explored for potential insight. The paper concludes with recommendations regarding opportunities for concentration of future work in modeling and simulating R&D governance relationships and processes.

Petascale turbulence simulation using a highly parallel fast multipole method on GPUs

NASA Astrophysics Data System (ADS)

Yokota, Rio; Barba, L. A.; Narumi, Tetsu; Yasuoka, Kenji

2013-03-01

This paper reports large-scale direct numerical simulations of homogeneous-isotropic fluid turbulence, achieving sustained performance of 1.08 petaflop/s on GPU hardware using single precision. The simulations use a vortex particle method to solve the Navier-Stokes equations, with a highly parallel fast multipole method (FMM) as numerical engine, and match the current record in mesh size for this application, a cube of 40963 computational points solved with a spectral method. The standard numerical approach used in this field is the pseudo-spectral method, relying on the FFT algorithm as the numerical engine. The particle-based simulations presented in this paper quantitatively match the kinetic energy spectrum obtained with a pseudo-spectral method, using a trusted code. In terms of parallel performance, weak scaling results show the FMM-based vortex method achieving 74% parallel efficiency on 4096 processes (one GPU per MPI process, 3 GPUs per node of the TSUBAME-2.0 system). The FFT-based spectral method is able to achieve just 14% parallel efficiency on the same number of MPI processes (using only CPU cores), due to the all-to-all communication pattern of the FFT algorithm. The calculation time for one time step was 108 s for the vortex method and 154 s for the spectral method, under these conditions. Computing with 69 billion particles, this work exceeds by an order of magnitude the largest vortex-method calculations to date.

Viscoelastic Finite Difference Modeling Using Graphics Processing Units

NASA Astrophysics Data System (ADS)

Fabien-Ouellet, G.; Gloaguen, E.; Giroux, B.

2014-12-01

Full waveform seismic modeling requires a huge amount of computing power that still challenges today's technology. This limits the applicability of powerful processing approaches in seismic exploration like full-waveform inversion. This paper explores the use of Graphics Processing Units (GPU) to compute a time based finite-difference solution to the viscoelastic wave equation. The aim is to investigate whether the adoption of the GPU technology is susceptible to reduce significantly the computing time of simulations. The code presented herein is based on the freely accessible software of Bohlen (2002) in 2D provided under a General Public License (GNU) licence. This implementation is based on a second order centred differences scheme to approximate time differences and staggered grid schemes with centred difference of order 2, 4, 6, 8, and 12 for spatial derivatives. The code is fully parallel and is written using the Message Passing Interface (MPI), and it thus supports simulations of vast seismic models on a cluster of CPUs. To port the code from Bohlen (2002) on GPUs, the OpenCl framework was chosen for its ability to work on both CPUs and GPUs and its adoption by most of GPU manufacturers. In our implementation, OpenCL works in conjunction with MPI, which allows computations on a cluster of GPU for large-scale model simulations. We tested our code for model sizes between 1002 and 60002 elements. Comparison shows a decrease in computation time of more than two orders of magnitude between the GPU implementation run on a AMD Radeon HD 7950 and the CPU implementation run on a 2.26 GHz Intel Xeon Quad-Core. The speed-up varies depending on the order of the finite difference approximation and generally increases for higher orders. Increasing speed-ups are also obtained for increasing model size, which can be explained by kernel overheads and delays introduced by memory transfers to and from the GPU through the PCI-E bus. Those tests indicate that the GPU memory size and the slow memory transfers are the limiting factors of our GPU implementation. Those results show the benefits of using GPUs instead of CPUs for time based finite-difference seismic simulations. The reductions in computation time and in hardware costs are significant and open the door for new approaches in seismic inversion.

Analytical simulation and PROFAT II: a new methodology and a computer automated tool for fault tree analysis in chemical process industries.

PubMed

Khan, F I; Abbasi, S A

2000-07-10

Fault tree analysis (FTA) is based on constructing a hypothetical tree of base events (initiating events) branching into numerous other sub-events, propagating the fault and eventually leading to the top event (accident). It has been a powerful technique used traditionally in identifying hazards in nuclear installations and power industries. As the systematic articulation of the fault tree is associated with assigning probabilities to each fault, the exercise is also sometimes called probabilistic risk assessment. But powerful as this technique is, it is also very cumbersome and costly, limiting its area of application. We have developed a new algorithm based on analytical simulation (named as AS-II), which makes the application of FTA simpler, quicker, and cheaper; thus opening up the possibility of its wider use in risk assessment in chemical process industries. Based on the methodology we have developed a computer-automated tool. The details are presented in this paper.

On Fast Post-Processing of Global Positioning System Simulator Truth Data and Receiver Measurements and Solutions Data

NASA Technical Reports Server (NTRS)

Kizhner, Semion; Day, John H. (Technical Monitor)

2000-01-01

Post-processing of data, related to a GPS receiver test in a GPS simulator and test facility, is an important step towards qualifying a receiver for space flight. Although the GPS simulator provides all the parameters needed to analyze a simulation, as well as excellent analysis tools on the simulator workstation, post-processing is not a GPS simulator or receiver function alone, and it must be planned as a separate pre-flight test program requirement. A GPS simulator is a critical resource, and it is desirable to move off the pertinent test data from the simulator as soon as a test is completed. The receiver and simulator databases are used to extract the test data files for postprocessing. These files are then usually moved from the simulator and receiver systems to a personal computer (PC) platform, where post-processing is done typically using PC-based commercial software languages and tools. Because of commercial software systems generality their functions are notoriously slow and more than often are the bottleneck even for short duration simulator-based tests. There is a need to do post-processing faster and within an hour after test completion, including all required operations on the simulator and receiver to prepare and move off the post-processing files. This is especially significant in order to use the previous test feedback for the next simulation setup or to run near back-to-back simulation scenarios. Solving the post-processing timing problem is critical for a pre-flight test program success. Towards this goal an approach was developed that allows to speed-up post-processing by an order of a magnitude. It is based on improving the post-processing bottleneck function algorithm using a priory information that is specific to a GPS simulation application and using only the necessary volume of truth data. The presented postprocessing scheme was used in support of a few successful space flight missions carrying GPS receivers.

Computational Modeling of Tissue Self-Assembly

NASA Astrophysics Data System (ADS)

Neagu, Adrian; Kosztin, Ioan; Jakab, Karoly; Barz, Bogdan; Neagu, Monica; Jamison, Richard; Forgacs, Gabor

As a theoretical framework for understanding the self-assembly of living cells into tissues, Steinberg proposed the differential adhesion hypothesis (DAH) according to which a specific cell type possesses a specific adhesion apparatus that combined with cell motility leads to cell assemblies of various cell types in the lowest adhesive energy state. Experimental and theoretical efforts of four decades turned the DAH into a fundamental principle of developmental biology that has been validated both in vitro and in vivo. Based on computational models of cell sorting, we have developed a DAH-based lattice model for tissues in interaction with their environment and simulated biological self-assembly using the Monte Carlo method. The present brief review highlights results on specific morphogenetic processes with relevance to tissue engineering applications. Our own work is presented on the background of several decades of theoretical efforts aimed to model morphogenesis in living tissues. Simulations of systems involving about 105 cells have been performed on high-end personal computers with CPU times of the order of days. Studied processes include cell sorting, cell sheet formation, and the development of endothelialized tubes from rings made of spheroids of two randomly intermixed cell types, when the medium in the interior of the tube was different from the external one. We conclude by noting that computer simulations based on mathematical models of living tissues yield useful guidelines for laboratory work and can catalyze the emergence of innovative technologies in tissue engineering.

An efficient and scalable deformable model for virtual reality-based medical applications.

PubMed

Choi, Kup-Sze; Sun, Hanqiu; Heng, Pheng-Ann

2004-09-01

Modeling of tissue deformation is of great importance to virtual reality (VR)-based medical simulations. Considerable effort has been dedicated to the development of interactively deformable virtual tissues. In this paper, an efficient and scalable deformable model is presented for virtual-reality-based medical applications. It considers deformation as a localized force transmittal process which is governed by algorithms based on breadth-first search (BFS). The computational speed is scalable to facilitate real-time interaction by adjusting the penetration depth. Simulated annealing (SA) algorithms are developed to optimize the model parameters by using the reference data generated with the linear static finite element method (FEM). The mechanical behavior and timing performance of the model have been evaluated. The model has been applied to simulate the typical behavior of living tissues and anisotropic materials. Integration with a haptic device has also been achieved on a generic personal computer (PC) platform. The proposed technique provides a feasible solution for VR-based medical simulations and has the potential for multi-user collaborative work in virtual environment.

The framework for simulation of bioinspired security mechanisms against network infrastructure attacks.

PubMed

Shorov, Andrey; Kotenko, Igor

2014-01-01

The paper outlines a bioinspired approach named "network nervous system" and methods of simulation of infrastructure attacks and protection mechanisms based on this approach. The protection mechanisms based on this approach consist of distributed procedures of information collection and processing, which coordinate the activities of the main devices of a computer network, identify attacks, and determine necessary countermeasures. Attacks and protection mechanisms are specified as structural models using a set-theoretic approach. An environment for simulation of protection mechanisms based on the biological metaphor is considered; the experiments demonstrating the effectiveness of the protection mechanisms are described.

Massively parallel simulator of optical coherence tomography of inhomogeneous turbid media.

PubMed

Malektaji, Siavash; Lima, Ivan T; Escobar I, Mauricio R; Sherif, Sherif S

2017-10-01

An accurate and practical simulator for Optical Coherence Tomography (OCT) could be an important tool to study the underlying physical phenomena in OCT such as multiple light scattering. Recently, many researchers have investigated simulation of OCT of turbid media, e.g., tissue, using Monte Carlo methods. The main drawback of these earlier simulators is the long computational time required to produce accurate results. We developed a massively parallel simulator of OCT of inhomogeneous turbid media that obtains both Class I diffusive reflectivity, due to ballistic and quasi-ballistic scattered photons, and Class II diffusive reflectivity due to multiply scattered photons. This Monte Carlo-based simulator is implemented on graphic processing units (GPUs), using the Compute Unified Device Architecture (CUDA) platform and programming model, to exploit the parallel nature of propagation of photons in tissue. It models an arbitrary shaped sample medium as a tetrahedron-based mesh and uses an advanced importance sampling scheme. This new simulator speeds up simulations of OCT of inhomogeneous turbid media by about two orders of magnitude. To demonstrate this result, we have compared the computation times of our new parallel simulator and its serial counterpart using two samples of inhomogeneous turbid media. We have shown that our parallel implementation reduced simulation time of OCT of the first sample medium from 407 min to 92 min by using a single GPU card, to 12 min by using 8 GPU cards and to 7 min by using 16 GPU cards. For the second sample medium, the OCT simulation time was reduced from 209 h to 35.6 h by using a single GPU card, and to 4.65 h by using 8 GPU cards, and to only 2 h by using 16 GPU cards. Therefore our new parallel simulator is considerably more practical to use than its central processing unit (CPU)-based counterpart. Our new parallel OCT simulator could be a practical tool to study the different physical phenomena underlying OCT, or to design OCT systems with improved performance. Copyright © 2017 Elsevier B.V. All rights reserved.

On the Development of a Computing Infrastructure that Facilitates IPPD from a Decision-Based Design Perspective

NASA Technical Reports Server (NTRS)

Hale, Mark A.; Craig, James I.; Mistree, Farrokh; Schrage, Daniel P.

1995-01-01

Integrated Product and Process Development (IPPD) embodies the simultaneous application of both system and quality engineering methods throughout an iterative design process. The use of IPPD results in the time-conscious, cost-saving development of engineering systems. Georgia Tech has proposed the development of an Integrated Design Engineering Simulator that will merge Integrated Product and Process Development with interdisciplinary analysis techniques and state-of-the-art computational technologies. To implement IPPD, a Decision-Based Design perspective is encapsulated in an approach that focuses on the role of the human designer in product development. The approach has two parts and is outlined in this paper. First, an architecture, called DREAMS, is being developed that facilitates design from a decision-based perspective. Second, a supporting computing infrastructure, called IMAGE, is being designed. The current status of development is given and future directions are outlined.

Computer-Assisted Face Processing Instruction Improves Emotion Recognition, Mentalizing, and Social Skills in Students with ASD

ERIC Educational Resources Information Center

Rice, Linda Marie; Wall, Carla Anne; Fogel, Adam; Shic, Frederick

2015-01-01

This study examined the extent to which a computer-based social skills intervention called "FaceSay"™ was associated with improvements in affect recognition, mentalizing, and social skills of school-aged children with Autism Spectrum Disorder (ASD). "FaceSay"™ offers students simulated practice with eye gaze, joint attention,…

A demonstrative model of a lunar base simulation on a personal computer

NASA Technical Reports Server (NTRS)

1985-01-01

The initial demonstration model of a lunar base simulation is described. This initial model was developed on the personal computer level to demonstrate feasibility and technique before proceeding to a larger computer-based model. Lotus Symphony Version 1.1 software was used to base the demonstration model on an personal computer with an MS-DOS operating system. The personal computer-based model determined the applicability of lunar base modeling techniques developed at an LSPI/NASA workshop. In addition, the personnal computer-based demonstration model defined a modeling structure that could be employed on a larger, more comprehensive VAX-based lunar base simulation. Refinement of this personal computer model and the development of a VAX-based model is planned in the near future.

Temporal acceleration of spatially distributed kinetic Monte Carlo simulations

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

Chatterjee, Abhijit; Vlachos, Dionisios G.

The computational intensity of kinetic Monte Carlo (KMC) simulation is a major impediment in simulating large length and time scales. In recent work, an approximate method for KMC simulation of spatially uniform systems, termed the binomial {tau}-leap method, was introduced [A. Chatterjee, D.G. Vlachos, M.A. Katsoulakis, Binomial distribution based {tau}-leap accelerated stochastic simulation, J. Chem. Phys. 122 (2005) 024112], where molecular bundles instead of individual processes are executed over coarse-grained time increments. This temporal coarse-graining can lead to significant computational savings but its generalization to spatially lattice KMC simulation has not been realized yet. Here we extend the binomial {tau}-leapmore » method to lattice KMC simulations by combining it with spatially adaptive coarse-graining. Absolute stability and computational speed-up analyses for spatial systems along with simulations provide insights into the conditions where accuracy and substantial acceleration of the new spatio-temporal coarse-graining method are ensured. Model systems demonstrate that the r-time increment criterion of Chatterjee et al. obeys the absolute stability limit for values of r up to near 1.« less

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

McCoy, Michel; Archer, Bill; Hendrickson, Bruce

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 resource, including technical staff, hardware, simulation software, and computer science solutions. ASC is now focused on increasing predictive capabilities in a three-dimensional (3D) simulation environment while maintaining support to the SSP. The program continues to improve its unique tools for solving progressively more difficult stockpile problems (sufficient resolution, dimensionality, and scientific details), and quantifying critical margins and uncertainties. Resolving each issue requires increasingly difficult analyses because the aging process has progressively moved the stockpile further away from the original test base. Where possible, the program also enables the use of high performance computing (HPC) and simulation tools to address broader national security needs, such as foreign nuclear weapon assessments and counter nuclear terrorism.« less

Acceleration techniques for dependability simulation. M.S. Thesis

NASA Technical Reports Server (NTRS)

Barnette, James David

1995-01-01

As computer systems increase in complexity, the need to project system performance from the earliest design and development stages increases. We have to employ simulation for detailed dependability studies of large systems. However, as the complexity of the simulation model increases, the time required to obtain statistically significant results also increases. This paper discusses an approach that is application independent and can be readily applied to any process-based simulation model. Topics include background on classical discrete event simulation and techniques for random variate generation and statistics gathering to support simulation.

Exact simulation of max-stable processes.

PubMed

Dombry, Clément; Engelke, Sebastian; Oesting, Marco

2016-06-01

Max-stable processes play an important role as models for spatial extreme events. Their complex structure as the pointwise maximum over an infinite number of random functions makes their simulation difficult. Algorithms based on finite approximations are often inexact and computationally inefficient. We present a new algorithm for exact simulation of a max-stable process at a finite number of locations. It relies on the idea of simulating only the extremal functions, that is, those functions in the construction of a max-stable process that effectively contribute to the pointwise maximum. We further generalize the algorithm by Dieker & Mikosch (2015) for Brown-Resnick processes and use it for exact simulation via the spectral measure. We study the complexity of both algorithms, prove that our new approach via extremal functions is always more efficient, and provide closed-form expressions for their implementation that cover most popular models for max-stable processes and multivariate extreme value distributions. For simulation on dense grids, an adaptive design of the extremal function algorithm is proposed.

Effects of Topography-based Subgrid Structures on Land Surface Modeling

NASA Astrophysics Data System (ADS)

Tesfa, T. K.; Ruby, L.; Brunke, M.; Thornton, P. E.; Zeng, X.; Ghan, S. J.

2017-12-01

Topography has major control on land surface processes through its influence on atmospheric forcing, soil and vegetation properties, network topology and drainage area. Consequently, accurate climate and land surface simulations in mountainous regions cannot be achieved without considering the effects of topographic spatial heterogeneity. To test a computationally less expensive hyper-resolution land surface modeling approach, we developed topography-based landunits within a hierarchical subgrid spatial structure to improve representation of land surface processes in the ACME Land Model (ALM) with minimal increase in computational demand, while improving the ability to capture the spatial heterogeneity of atmospheric forcing and land cover influenced by topography. This study focuses on evaluation of the impacts of the new spatial structures on modeling land surface processes. As a first step, we compare ALM simulations with and without subgrid topography and driven by grid cell mean atmospheric forcing to isolate the impacts of the subgrid topography on the simulated land surface states and fluxes. Recognizing that subgrid topography also has important effects on atmospheric processes that control temperature, radiation, and precipitation, methods are being developed to downscale atmospheric forcings. Hence in the second step, the impacts of the subgrid topographic structure on land surface modeling will be evaluated by including spatial downscaling of the atmospheric forcings. Preliminary results on the atmospheric downscaling and the effects of the new spatial structures on the ALM simulations will be presented.

MEqTrees Telescope and Radio-sky Simulations and CPU Benchmarking

NASA Astrophysics Data System (ADS)

Shanmugha Sundaram, G. A.

2009-09-01

MEqTrees is a Python-based implementation of the classical Measurement Equation, wherein the various 2×2 Jones matrices are parametrized representations in the spatial and sky domains for any generic radio telescope. Customized simulations of radio-source sky models and corrupt Jones terms are demonstrated based on a policy framework, with performance estimates derived for array configurations, ``dirty''-map residuals and processing power requirements for such computations on conventional platforms.

Bayesian experimental design for models with intractable likelihoods.

PubMed

Drovandi, Christopher C; Pettitt, Anthony N

2013-12-01

In this paper we present a methodology for designing experiments for efficiently estimating the parameters of models with computationally intractable likelihoods. The approach combines a commonly used methodology for robust experimental design, based on Markov chain Monte Carlo sampling, with approximate Bayesian computation (ABC) to ensure that no likelihood evaluations are required. The utility function considered for precise parameter estimation is based upon the precision of the ABC posterior distribution, which we form efficiently via the ABC rejection algorithm based on pre-computed model simulations. Our focus is on stochastic models and, in particular, we investigate the methodology for Markov process models of epidemics and macroparasite population evolution. The macroparasite example involves a multivariate process and we assess the loss of information from not observing all variables. © 2013, The International Biometric Society.

Strategies for Large Scale Implementation of a Multiscale, Multiprocess Integrated Hydrologic Model

NASA Astrophysics Data System (ADS)

Kumar, M.; Duffy, C.

2006-05-01

Distributed models simulate hydrologic state variables in space and time while taking into account the heterogeneities in terrain, surface, subsurface properties and meteorological forcings. Computational cost and complexity associated with these model increases with its tendency to accurately simulate the large number of interacting physical processes at fine spatio-temporal resolution in a large basin. A hydrologic model run on a coarse spatial discretization of the watershed with limited number of physical processes needs lesser computational load. But this negatively affects the accuracy of model results and restricts physical realization of the problem. So it is imperative to have an integrated modeling strategy (a) which can be universally applied at various scales in order to study the tradeoffs between computational complexity (determined by spatio- temporal resolution), accuracy and predictive uncertainty in relation to various approximations of physical processes (b) which can be applied at adaptively different spatial scales in the same domain by taking into account the local heterogeneity of topography and hydrogeologic variables c) which is flexible enough to incorporate different number and approximation of process equations depending on model purpose and computational constraint. An efficient implementation of this strategy becomes all the more important for Great Salt Lake river basin which is relatively large (~89000 sq. km) and complex in terms of hydrologic and geomorphic conditions. Also the types and the time scales of hydrologic processes which are dominant in different parts of basin are different. Part of snow melt runoff generated in the Uinta Mountains infiltrates and contributes as base flow to the Great Salt Lake over a time scale of decades to centuries. The adaptive strategy helps capture the steep topographic and climatic gradient along the Wasatch front. Here we present the aforesaid modeling strategy along with an associated hydrologic modeling framework which facilitates a seamless, computationally efficient and accurate integration of the process model with the data model. The flexibility of this framework leads to implementation of multiscale, multiresolution, adaptive refinement/de-refinement and nested modeling simulations with least computational burden. However, performing these simulations and related calibration of these models over a large basin at higher spatio- temporal resolutions is computationally intensive and requires use of increasing computing power. With the advent of parallel processing architectures, high computing performance can be achieved by parallelization of existing serial integrated-hydrologic-model code. This translates to running the same model simulation on a network of large number of processors thereby reducing the time needed to obtain solution. The paper also discusses the implementation of the integrated model on parallel processors. Also will be discussed the mapping of the problem on multi-processor environment, method to incorporate coupling between hydrologic processes using interprocessor communication models, model data structure and parallel numerical algorithms to obtain high performance.

An evaluation of noise reduction algorithms for particle-based fluid simulations in multi-scale applications

NASA Astrophysics Data System (ADS)

Zimoń, M. J.; Prosser, R.; Emerson, D. R.; Borg, M. K.; Bray, D. J.; Grinberg, L.; Reese, J. M.

2016-11-01

Filtering of particle-based simulation data can lead to reduced computational costs and enable more efficient information transfer in multi-scale modelling. This paper compares the effectiveness of various signal processing methods to reduce numerical noise and capture the structures of nano-flow systems. In addition, a novel combination of these algorithms is introduced, showing the potential of hybrid strategies to improve further the de-noising performance for time-dependent measurements. The methods were tested on velocity and density fields, obtained from simulations performed with molecular dynamics and dissipative particle dynamics. Comparisons between the algorithms are given in terms of performance, quality of the results and sensitivity to the choice of input parameters. The results provide useful insights on strategies for the analysis of particle-based data and the reduction of computational costs in obtaining ensemble solutions.

Development of a Web Based Simulating System for Earthquake Modeling on the Grid

NASA Astrophysics Data System (ADS)

Seber, D.; Youn, C.; Kaiser, T.

2007-12-01

Existing cyberinfrastructure-based information, data and computational networks now allow development of state- of-the-art, user-friendly simulation environments that democratize access to high-end computational environments and provide new research opportunities for many research and educational communities. Within the Geosciences cyberinfrastructure network, GEON, we have developed the SYNSEIS (SYNthetic SEISmogram) toolkit to enable efficient computations of 2D and 3D seismic waveforms for a variety of research purposes especially for helping to analyze the EarthScope's USArray seismic data in a speedy and efficient environment. The underlying simulation software in SYNSEIS is a finite difference code, E3D, developed by LLNL (S. Larsen). The code is embedded within the SYNSEIS portlet environment and it is used by our toolkit to simulate seismic waveforms of earthquakes at regional distances (<1000km). Architecturally, SYNSEIS uses both Web Service and Grid computing resources in a portal-based work environment and has a built in access mechanism to connect to national supercomputer centers as well as to a dedicated, small-scale compute cluster for its runs. Even though Grid computing is well-established in many computing communities, its use among domain scientists still is not trivial because of multiple levels of complexities encountered. We grid-enabled E3D using our own dialect XML inputs that include geological models that are accessible through standard Web services within the GEON network. The XML inputs for this application contain structural geometries, source parameters, seismic velocity, density, attenuation values, number of time steps to compute, and number of stations. By enabling a portal based access to a such computational environment coupled with its dynamic user interface we enable a large user community to take advantage of such high end calculations in their research and educational activities. Our system can be used to promote an efficient and effective modeling environment to help scientists as well as educators in their daily activities and speed up the scientific discovery process.

Data-Informed Large-Eddy Simulation of Coastal Land-Air-Sea Interactions

NASA Astrophysics Data System (ADS)

Calderer, A.; Hao, X.; Fernando, H. J.; Sotiropoulos, F.; Shen, L.

2016-12-01

The study of atmospheric flows in coastal areas has not been fully addressed due to the complex processes emerging from the land-air-sea interactions, e.g., abrupt change in land topography, strong current shear, wave shoaling, and depth-limited wave breaking. The available computational tools that have been applied to study such littoral regions are mostly based on open-ocean assumptions, which most times do not lead to reliable solutions. The goal of the present study is to better understand some of these near-shore processes, employing the advanced computational tools, developed in our research group. Our computational framework combines a large-eddy simulation (LES) flow solver for atmospheric flows, a sharp-interface immersed boundary method that can deal with real complex topographies (Calderer et al., J. Comp. Physics 2014), and a phase-resolved, depth-dependent, wave model (Yang and Shen, J. Comp. Physics 2011). Using real measured data taken in the FRF station in Duck, North Carolina, we validate and demonstrate the predictive capabilities of the present computational framework, which are shown to be in overall good agreement with the measured data under different wind-wave scenarios. We also analyse the effects of some of the complex processes captured by our simulation tools.

An Introduction to the BFS Method and Its Use to Model Binary NiAl Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Noebe, Ronald D.; Ferrante, J.; Amador, C.

1998-01-01

We introduce the Bozzolo-Ferrante-Smith (BFS) method for alloys as a computationally efficient tool for aiding in the process of alloy design. An intuitive description of the BFS method is provided, followed by a formal discussion of its implementation. The method is applied to the study of the defect structure of NiAl binary alloys. The groundwork is laid for a detailed progression to higher order NiAl-based alloys linking theoretical calculations and computer simulations based on the BFS method and experimental work validating each step of the alloy design process.

Breaking Lander-Waterman’s Coverage Bound

PubMed Central

Nashta-ali, Damoun; Motahari, Seyed Abolfazl; Hosseinkhalaj, Babak

2016-01-01

Lander-Waterman’s coverage bound establishes the total number of reads required to cover the whole genome of size G bases. In fact, their bound is a direct consequence of the well-known solution to the coupon collector’s problem which proves that for such genome, the total number of bases to be sequenced should be O(G ln G). Although the result leads to a tight bound, it is based on a tacit assumption that the set of reads are first collected through a sequencing process and then are processed through a computation process, i.e., there are two different machines: one for sequencing and one for processing. In this paper, we present a significant improvement compared to Lander-Waterman’s result and prove that by combining the sequencing and computing processes, one can re-sequence the whole genome with as low as O(G) sequenced bases in total. Our approach also dramatically reduces the required computational power for the combined process. Simulation results are performed on real genomes with different sequencing error rates. The results support our theory predicting the log G improvement on coverage bound and corresponding reduction in the total number of bases required to be sequenced. PMID:27806058

Numerical simulation of transonic compressor under circumferential inlet distortion and rotor/stator interference using harmonic balance method

NASA Astrophysics Data System (ADS)

Wang, Ziwei; Jiang, Xiong; Chen, Ti; Hao, Yan; Qiu, Min

2018-05-01

Simulating the unsteady flow of compressor under circumferential inlet distortion and rotor/stator interference would need full-annulus grid with a dual time method. This process is time consuming and needs a large amount of computational resources. Harmonic balance method simulates the unsteady flow in compressor on single passage grid with a series of steady simulations. This will largely increase the computational efficiency in comparison with the dual time method. However, most simulations with harmonic balance method are conducted on the flow under either circumferential inlet distortion or rotor/stator interference. Based on an in-house CFD code, the harmonic balance method is applied in the simulation of flow in the NASA Stage 35 under both circumferential inlet distortion and rotor/stator interference. As the unsteady flow is influenced by two different unsteady disturbances, it leads to the computational instability. The instability can be avoided by coupling the harmonic balance method with an optimizing algorithm. The computational result of harmonic balance method is compared with the result of full-annulus simulation. It denotes that, the harmonic balance method simulates the flow under circumferential inlet distortion and rotor/stator interference as precise as the full-annulus simulation with a speed-up of about 8 times.

Polymerization and Structure of Bio-Based Plastics: A Computer Simulation

NASA Astrophysics Data System (ADS)

Khot, Shrikant N.; Wool, Richard P.

2001-03-01

We recently examined several hundred chemical pathways to convert chemically functionalized plant oil triglycerides, monoglycerides and reactive diluents into high performance plastics with a broad range of properties (US Patent No. 6,121,398). The resulting polymers had linear, branched, light- and highly-crosslinked chain architectures and could be used as pressure sensitive adhesives, elastomers and high performance rigid thermoset composite resins. To optimize the molecular design and minimize the number of chemical trials in this system with excess degrees of freedom, we developed a computer simulation of the free radical polymerization process. The triglyceride structure, degree of chemical substitution, mole fractions, fatty acid distribution function, and reaction kinetic parameters were used as initial inputs on a 3d lattice simulation. The evolution of the network fractal structure was computed and used to measure crosslink density, dangling ends, degree of reaction and defects in the lattice. The molecular connectivity was used to determine strength via a vector percolation model of fracture. The simulation permitted the optimal design of new bio-based materials with respect to monomer selection, cure reaction conditions and desired properties. Supported by the National Science Foundation

pWeb: A High-Performance, Parallel-Computing Framework for Web-Browser-Based Medical Simulation.

PubMed

Halic, Tansel; Ahn, Woojin; De, Suvranu

2014-01-01

This work presents a pWeb - a new language and compiler for parallelization of client-side compute intensive web applications such as surgical simulations. The recently introduced HTML5 standard has enabled creating unprecedented applications on the web. Low performance of the web browser, however, remains the bottleneck of computationally intensive applications including visualization of complex scenes, real time physical simulations and image processing compared to native ones. The new proposed language is built upon web workers for multithreaded programming in HTML5. The language provides fundamental functionalities of parallel programming languages as well as the fork/join parallel model which is not supported by web workers. The language compiler automatically generates an equivalent parallel script that complies with the HTML5 standard. A case study on realistic rendering for surgical simulations demonstrates enhanced performance with a compact set of instructions.

Probabilistic simulation of concurrent engineering of propulsion systems

NASA Technical Reports Server (NTRS)

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

1993-01-01

Technology readiness and the available infrastructure is assessed for timely computational simulation of concurrent engineering for propulsion systems. Results for initial coupled multidisciplinary, fabrication-process, and system simulators are presented including uncertainties inherent in various facets of engineering processes. An approach is outlined for computationally formalizing the concurrent engineering process from cradle-to-grave via discipline dedicated workstations linked with a common database.

Hybrid Quantum-Classical Approach to Quantum Optimal Control.

PubMed

Li, Jun; Yang, Xiaodong; Peng, Xinhua; Sun, Chang-Pu

2017-04-14

A central challenge in quantum computing is to identify more computational problems for which utilization of quantum resources can offer significant speedup. Here, we propose a hybrid quantum-classical scheme to tackle the quantum optimal control problem. We show that the most computationally demanding part of gradient-based algorithms, namely, computing the fitness function and its gradient for a control input, can be accomplished by the process of evolution and measurement on a quantum simulator. By posing queries to and receiving answers from the quantum simulator, classical computing devices update the control parameters until an optimal control solution is found. To demonstrate the quantum-classical scheme in experiment, we use a seven-qubit nuclear magnetic resonance system, on which we have succeeded in optimizing state preparation without involving classical computation of the large Hilbert space evolution.

Implementation of Lean System on Erbium Doped Fibre Amplifier Manufacturing Process to Reduce Production Time

NASA Astrophysics Data System (ADS)

Maneechote, T.; Luangpaiboon, P.

2010-10-01

A manufacturing process of erbium doped fibre amplifiers is complicated. It needs to meet the customers' requirements under a present economic status that products need to be shipped to customers as soon as possible after purchasing orders. This research aims to study and improve processes and production lines of erbium doped fibre amplifiers using lean manufacturing systems via an application of computer simulation. Three scenarios of lean tooled box systems are selected via the expert system. Firstly, the production schedule based on shipment date is combined with a first in first out control system. The second scenario focuses on a designed flow process plant layout. Finally, the previous flow process plant layout combines with production schedule based on shipment date including the first in first out control systems. The computer simulation with the limited data via an expected value is used to observe the performance of all scenarios. The most preferable resulted lean tooled box systems from a computer simulation are selected to implement in the real process of a production of erbium doped fibre amplifiers. A comparison is carried out to determine the actual performance measures via an analysis of variance of the response or the production time per unit achieved in each scenario. The goodness of an adequacy of the linear statistical model via experimental errors or residuals is also performed to check the normality, constant variance and independence of the residuals. The results show that a hybrid scenario of lean manufacturing system with the first in first out control and flow process plant lay out statistically leads to better performance in terms of the mean and variance of production times.

Uses of Computer Simulation Models in Ag-Research and Everyday Life

USDA-ARS?s Scientific Manuscript database

When the news media talks about models they could be talking about role models, fashion models, conceptual models like the auto industry uses, or computer simulation models. A computer simulation model is a computer code that attempts to imitate the processes and functions of certain systems. There ...

Physical Principle for Generation of Randomness

NASA Technical Reports Server (NTRS)

Zak, Michail

2009-01-01

A physical principle (more precisely, a principle that incorporates mathematical models used in physics) has been conceived as the basis of a method of generating randomness in Monte Carlo simulations. The principle eliminates the need for conventional random-number generators. The Monte Carlo simulation method is among the most powerful computational methods for solving high-dimensional problems in physics, chemistry, economics, and information processing. The Monte Carlo simulation method is especially effective for solving problems in which computational complexity increases exponentially with dimensionality. The main advantage of the Monte Carlo simulation method over other methods is that the demand on computational resources becomes independent of dimensionality. As augmented by the present principle, the Monte Carlo simulation method becomes an even more powerful computational method that is especially useful for solving problems associated with dynamics of fluids, planning, scheduling, and combinatorial optimization. The present principle is based on coupling of dynamical equations with the corresponding Liouville equation. The randomness is generated by non-Lipschitz instability of dynamics triggered and controlled by feedback from the Liouville equation. (In non-Lipschitz dynamics, the derivatives of solutions of the dynamical equations are not required to be bounded.)

Displaying Computer Simulations Of Physical Phenomena

NASA Technical Reports Server (NTRS)

Watson, Val

1991-01-01

Paper discusses computer simulation as means of experiencing and learning to understand physical phenomena. Covers both present simulation capabilities and major advances expected in near future. Visual, aural, tactile, and kinesthetic effects used to teach such physical sciences as dynamics of fluids. Recommends classrooms in universities, government, and industry be linked to advanced computing centers so computer simulations integrated into education process.

Modelling and Simulation as a Recognizing Method in Education

ERIC Educational Resources Information Center

Stoffa, Veronika

2004-01-01

Computer animation-simulation models of complex processes and events, which are the method of instruction, can be an effective didactic device. Gaining deeper knowledge about objects modelled helps to plan simulation experiments oriented on processes and events researched. Animation experiments realized on multimedia computers can aid easier…

SAGRAD: A Program for Neural Network Training with Simulated Annealing and the Conjugate Gradient Method.

PubMed

Bernal, Javier; Torres-Jimenez, Jose

2015-01-01

SAGRAD (Simulated Annealing GRADient), a Fortran 77 program for computing neural networks for classification using batch learning, is discussed. Neural network training in SAGRAD is based on a combination of simulated annealing and Møller's scaled conjugate gradient algorithm, the latter a variation of the traditional conjugate gradient method, better suited for the nonquadratic nature of neural networks. Different aspects of the implementation of the training process in SAGRAD are discussed, such as the efficient computation of gradients and multiplication of vectors by Hessian matrices that are required by Møller's algorithm; the (re)initialization of weights with simulated annealing required to (re)start Møller's algorithm the first time and each time thereafter that it shows insufficient progress in reaching a possibly local minimum; and the use of simulated annealing when Møller's algorithm, after possibly making considerable progress, becomes stuck at a local minimum or flat area of weight space. Outlines of the scaled conjugate gradient algorithm, the simulated annealing procedure and the training process used in SAGRAD are presented together with results from running SAGRAD on two examples of training data.

A multilevel-skin neighbor list algorithm for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Chenglong; Zhao, Mingcan; Hou, Chaofeng; Ge, Wei

2018-01-01

Searching of the interaction pairs and organization of the interaction processes are important steps in molecular dynamics (MD) algorithms and are critical to the overall efficiency of the simulation. Neighbor lists are widely used for these steps, where thicker skin can reduce the frequency of list updating but is discounted by more computation in distance check for the particle pairs. In this paper, we propose a new neighbor-list-based algorithm with a precisely designed multilevel skin which can reduce unnecessary computation on inter-particle distances. The performance advantages over traditional methods are then analyzed against the main simulation parameters on Intel CPUs and MICs (many integrated cores), and are clearly demonstrated. The algorithm can be generalized for various discrete simulations using neighbor lists.

Computational study on UV curing characteristics in nanoimprint lithography: Stochastic simulation

NASA Astrophysics Data System (ADS)

Koyama, Masanori; Shirai, Masamitsu; Kawata, Hiroaki; Hirai, Yoshihiko; Yasuda, Masaaki

2017-06-01

A computational simulation model of UV curing in nanoimprint lithography based on a simplified stochastic approach is proposed. The activated unit reacts with a randomly selected monomer within a critical reaction radius. Cluster units are chained to each other. Then, another monomer is activated and the next chain reaction occurs. This process is repeated until a virgin monomer disappears within the reaction radius or until the activated monomers react with each other. The simulation model well describes the basic UV curing characteristics, such as the molecular weight distributions of the reacted monomers and the effect of the initiator concentration on the conversion ratio. The effects of film thickness on UV curing characteristics are also studied by the simulation.

Seafloor identification in sonar imagery via simulations of Helmholtz equations and discrete optimization

NASA Astrophysics Data System (ADS)

Engquist, Björn; Frederick, Christina; Huynh, Quyen; Zhou, Haomin

2017-06-01

We present a multiscale approach for identifying features in ocean beds by solving inverse problems in high frequency seafloor acoustics. The setting is based on Sound Navigation And Ranging (SONAR) imaging used in scientific, commercial, and military applications. The forward model incorporates multiscale simulations, by coupling Helmholtz equations and geometrical optics for a wide range of spatial scales in the seafloor geometry. This allows for detailed recovery of seafloor parameters including material type. Simulated backscattered data is generated using numerical microlocal analysis techniques. In order to lower the computational cost of the large-scale simulations in the inversion process, we take advantage of a pre-computed library of representative acoustic responses from various seafloor parameterizations.

A Rural Community's Involvement in the Design and Usability Testing of a Computer-Based Informed Consent Process for the Personalized Medicine Research Project

PubMed Central

Mahnke, Andrea N; Plasek, Joseph M; Hoffman, David G; Partridge, Nathan S; Foth, Wendy S; Waudby, Carol J; Rasmussen, Luke V; McManus, Valerie D; McCarty, Catherine A

2014-01-01

Many informed consent studies demonstrate that research subjects poorly retain and understand information in written consent documents. Previous research in multimedia consent is mixed in terms of success for improving participants’ understanding, satisfaction, and retention. This failure may be due to a lack of a community-centered design approach to building the interventions. The goal of this study was to gather information from the community to determine the best way to undertake the consent process. Community perceptions regarding different computer-based consenting approaches were evaluated, and a computer-based consent was developed and tested. A second goal was to evaluate whether participants make truly informed decisions to participate in research. Simulations of an informed consent process were videotaped to document the process. Focus groups were conducted to determine community attitudes towards a computer-based informed consent process. Hybrid focus groups were conducted to determine the most acceptable hardware device. Usability testing was conducted on a computer-based consent prototype using a touch-screen kiosk. Based on feedback, a computer-based consent was developed. Representative study participants were able to easily complete the consent, and all were able to correctly answer the comprehension check questions. Community involvement in developing a computer-based consent proved valuable for a population-based genetic study. These findings may translate to other types of informed consents, such as genetic clinical trials consents. A computer-based consent may serve to better communicate consistent, clear, accurate, and complete information regarding the risks and benefits of study participation. Additional analysis is necessary to measure the level of comprehension of the check-question answers by larger numbers of participants. The next step will involve contacting participants to measure whether understanding of what they consented to is retained over time. PMID:24273095

A rural community's involvement in the design and usability testing of a computer-based informed consent process for the Personalized Medicine Research Project.

PubMed

Mahnke, Andrea N; Plasek, Joseph M; Hoffman, David G; Partridge, Nathan S; Foth, Wendy S; Waudby, Carol J; Rasmussen, Luke V; McManus, Valerie D; McCarty, Catherine A

2014-01-01

Many informed consent studies demonstrate that research subjects poorly retain and understand information in written consent documents. Previous research in multimedia consent is mixed in terms of success for improving participants' understanding, satisfaction, and retention. This failure may be due to a lack of a community-centered design approach to building the interventions. The goal of this study was to gather information from the community to determine the best way to undertake the consent process. Community perceptions regarding different computer-based consenting approaches were evaluated, and a computer-based consent was developed and tested. A second goal was to evaluate whether participants make truly informed decisions to participate in research. Simulations of an informed consent process were videotaped to document the process. Focus groups were conducted to determine community attitudes towards a computer-based informed consent process. Hybrid focus groups were conducted to determine the most acceptable hardware device. Usability testing was conducted on a computer-based consent prototype using a touch-screen kiosk. Based on feedback, a computer-based consent was developed. Representative study participants were able to easily complete the consent, and all were able to correctly answer the comprehension check questions. Community involvement in developing a computer-based consent proved valuable for a population-based genetic study. These findings may translate to other types of informed consents, including those for trials involving treatment of genetic disorders. A computer-based consent may serve to better communicate consistent, clear, accurate, and complete information regarding the risks and benefits of study participation. Additional analysis is necessary to measure the level of comprehension of the check-question answers by larger numbers of participants. The next step will involve contacting participants to measure whether understanding of what they consented to is retained over time. © 2013 Wiley Periodicals, Inc.

Learning and evolution in bacterial taxis: an operational amplifier circuit modeling the computational dynamics of the prokaryotic 'two component system' protein network.

PubMed

Di Paola, Vieri; Marijuán, Pedro C; Lahoz-Beltra, Rafael

2004-01-01

Adaptive behavior in unicellular organisms (i.e., bacteria) depends on highly organized networks of proteins governing purposefully the myriad of molecular processes occurring within the cellular system. For instance, bacteria are able to explore the environment within which they develop by utilizing the motility of their flagellar system as well as a sophisticated biochemical navigation system that samples the environmental conditions surrounding the cell, searching for nutrients or moving away from toxic substances or dangerous physical conditions. In this paper we discuss how proteins of the intervening signal transduction network could be modeled as artificial neurons, simulating the dynamical aspects of the bacterial taxis. The model is based on the assumption that, in some important aspects, proteins can be considered as processing elements or McCulloch-Pitts artificial neurons that transfer and process information from the bacterium's membrane surface to the flagellar motor. This simulation of bacterial taxis has been carried out on a hardware realization of a McCulloch-Pitts artificial neuron using an operational amplifier. Based on the behavior of the operational amplifier we produce a model of the interaction between CheY and FliM, elements of the prokaryotic two component system controlling chemotaxis, as well as a simulation of learning and evolution processes in bacterial taxis. On the one side, our simulation results indicate that, computationally, these protein 'switches' are similar to McCulloch-Pitts artificial neurons, suggesting a bridge between evolution and learning in dynamical systems at cellular and molecular levels and the evolutive hardware approach. On the other side, important protein 'tactilizing' properties are not tapped by the model, and this suggests further complexity steps to explore in the approach to biological molecular computing.

Technical Note: Approximate Bayesian parameterization of a process-based tropical forest model

NASA Astrophysics Data System (ADS)

Hartig, F.; Dislich, C.; Wiegand, T.; Huth, A.

2014-02-01

Inverse parameter estimation of process-based models is a long-standing problem in many scientific disciplines. A key question for inverse parameter estimation is how to define the metric that quantifies how well model predictions fit to the data. This metric can be expressed by general cost or objective functions, but statistical inversion methods require a particular metric, the probability of observing the data given the model parameters, known as the likelihood. For technical and computational reasons, likelihoods for process-based stochastic models are usually based on general assumptions about variability in the observed data, and not on the stochasticity generated by the model. Only in recent years have new methods become available that allow the generation of likelihoods directly from stochastic simulations. Previous applications of these approximate Bayesian methods have concentrated on relatively simple models. Here, we report on the application of a simulation-based likelihood approximation for FORMIND, a parameter-rich individual-based model of tropical forest dynamics. We show that approximate Bayesian inference, based on a parametric likelihood approximation placed in a conventional Markov chain Monte Carlo (MCMC) sampler, performs well in retrieving known parameter values from virtual inventory data generated by the forest model. We analyze the results of the parameter estimation, examine its sensitivity to the choice and aggregation of model outputs and observed data (summary statistics), and demonstrate the application of this method by fitting the FORMIND model to field data from an Ecuadorian tropical forest. Finally, we discuss how this approach differs from approximate Bayesian computation (ABC), another method commonly used to generate simulation-based likelihood approximations. Our results demonstrate that simulation-based inference, which offers considerable conceptual advantages over more traditional methods for inverse parameter estimation, can be successfully applied to process-based models of high complexity. The methodology is particularly suitable for heterogeneous and complex data structures and can easily be adjusted to other model types, including most stochastic population and individual-based models. Our study therefore provides a blueprint for a fairly general approach to parameter estimation of stochastic process-based models.

Optimal fabrication processes for unidirectional metal-matrix composites: A computational simulation

NASA Technical Reports Server (NTRS)

Saravanos, D. A.; Murthy, P. L. N.; Morel, M.

1990-01-01

A method is proposed for optimizing the fabrication process of unidirectional metal matrix composites. The temperature and pressure histories are optimized such that the residual microstresses of the composite at the end of the fabrication process are minimized and the material integrity throughout the process is ensured. The response of the composite during the fabrication is simulated based on a nonlinear micromechanics theory. The optimal fabrication problem is formulated and solved with non-linear programming. Application cases regarding the optimization of the fabrication cool-down phases of unidirectional ultra-high modulus graphite/copper and silicon carbide/titanium composites are presented.

Optimal fabrication processes for unidirectional metal-matrix composites - A computational simulation

NASA Technical Reports Server (NTRS)

Saravanos, D. A.; Murthy, P. L. N.; Morel, M.

1990-01-01

A method is proposed for optimizing the fabrication process of unidirectional metal matrix composites. The temperature and pressure histories are optimized such that the residual microstresses of the composite at the end of the fabrication process are minimized and the material integrity throughout the process is ensured. The response of the composite during the fabrication is simulated based on a nonlinear micromechanics theory. The optimal fabrication problem is formulated and solved with nonlinear programming. Application cases regarding the optimization of the fabrication cool-down phases of unidirectional ultra-high modulus graphite/copper and silicon carbide/titanium composites are presented.

The ReaxFF reactive force-field: Development, applications, and future directions

DOE PAGES

Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; ...

2016-03-04

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFFmore » method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less

Estimation of in-situ bioremediation system cost using a hybrid Extreme Learning Machine (ELM)-particle swarm optimization approach

NASA Astrophysics Data System (ADS)

Yadav, Basant; Ch, Sudheer; Mathur, Shashi; Adamowski, Jan

2016-12-01

In-situ bioremediation is the most common groundwater remediation procedure used for treating organically contaminated sites. A simulation-optimization approach, which incorporates a simulation model for groundwaterflow and transport processes within an optimization program, could help engineers in designing a remediation system that best satisfies management objectives as well as regulatory constraints. In-situ bioremediation is a highly complex, non-linear process and the modelling of such a complex system requires significant computational exertion. Soft computing techniques have a flexible mathematical structure which can generalize complex nonlinear processes. In in-situ bioremediation management, a physically-based model is used for the simulation and the simulated data is utilized by the optimization model to optimize the remediation cost. The recalling of simulator to satisfy the constraints is an extremely tedious and time consuming process and thus there is need for a simulator which can reduce the computational burden. This study presents a simulation-optimization approach to achieve an accurate and cost effective in-situ bioremediation system design for groundwater contaminated with BTEX (Benzene, Toluene, Ethylbenzene, and Xylenes) compounds. In this study, the Extreme Learning Machine (ELM) is used as a proxy simulator to replace BIOPLUME III for the simulation. The selection of ELM is done by a comparative analysis with Artificial Neural Network (ANN) and Support Vector Machine (SVM) as they were successfully used in previous studies of in-situ bioremediation system design. Further, a single-objective optimization problem is solved by a coupled Extreme Learning Machine (ELM)-Particle Swarm Optimization (PSO) technique to achieve the minimum cost for the in-situ bioremediation system design. The results indicate that ELM is a faster and more accurate proxy simulator than ANN and SVM. The total cost obtained by the ELM-PSO approach is held to a minimum while successfully satisfying all the regulatory constraints of the contaminated site.

Physical and Mathematical Questions on Signal Processing in Multibase Phase Direction Finders

NASA Astrophysics Data System (ADS)

Denisov, V. P.; Dubinin, D. V.; Meshcheryakov, A. A.

2018-02-01

Questions on improving the accuracy of multiple-base phase direction finders by rejecting anomalously large errors in the process of resolving the measurement ambiguities are considered. A physical basis is derived and calculated relationships characterizing the efficiency of the proposed solutions are obtained. Results of a computer simulation of a three-base direction finder are analyzed, along with field measurements of a three-base direction finder along near-ground paths.

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.

Computer vision camera with embedded FPGA processing

NASA Astrophysics Data System (ADS)

Lecerf, Antoine; Ouellet, Denis; Arias-Estrada, Miguel

2000-03-01

Traditional computer vision is based on a camera-computer system in which the image understanding algorithms are embedded in the computer. To circumvent the computational load of vision algorithms, low-level processing and imaging hardware can be integrated in a single compact module where a dedicated architecture is implemented. This paper presents a Computer Vision Camera based on an open architecture implemented in an FPGA. The system is targeted to real-time computer vision tasks where low level processing and feature extraction tasks can be implemented in the FPGA device. The camera integrates a CMOS image sensor, an FPGA device, two memory banks, and an embedded PC for communication and control tasks. The FPGA device is a medium size one equivalent to 25,000 logic gates. The device is connected to two high speed memory banks, an IS interface, and an imager interface. The camera can be accessed for architecture programming, data transfer, and control through an Ethernet link from a remote computer. A hardware architecture can be defined in a Hardware Description Language (like VHDL), simulated and synthesized into digital structures that can be programmed into the FPGA and tested on the camera. The architecture of a classical multi-scale edge detection algorithm based on a Laplacian of Gaussian convolution has been developed to show the capabilities of the system.

Parallel discrete-event simulation of FCFS stochastic queueing networks

NASA Technical Reports Server (NTRS)

Nicol, David M.

1988-01-01

Physical systems are inherently parallel. Intuition suggests that simulations of these systems may be amenable to parallel execution. The parallel execution of a discrete-event simulation requires careful synchronization of processes in order to ensure the execution's correctness; this synchronization can degrade performance. Largely negative results were recently reported in a study which used a well-known synchronization method on queueing network simulations. Discussed here is a synchronization method (appointments), which has proven itself to be effective on simulations of FCFS queueing networks. The key concept behind appointments is the provision of lookahead. Lookahead is a prediction on a processor's future behavior, based on an analysis of the processor's simulation state. It is shown how lookahead can be computed for FCFS queueing network simulations, give performance data that demonstrates the method's effectiveness under moderate to heavy loads, and discuss performance tradeoffs between the quality of lookahead, and the cost of computing lookahead.

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

PubMed

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

2012-06-22

Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development. In this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

Dependence of Snowmelt Simulations on Scaling of the Forcing Processes (Invited)

NASA Astrophysics Data System (ADS)

Winstral, A. H.; Marks, D. G.; Gurney, R. J.

2009-12-01

The spatial organization and scaling relationships of snow distribution in mountain environs is ultimately dependent on the controlling processes. These processes include interactions between weather, topography, vegetation, snow state, and seasonally-dependent radiation inputs. In large scale snow modeling it is vital to know these dependencies to obtain accurate predictions while reducing computational costs. This study examined the scaling characteristics of the forcing processes and the dependency of distributed snowmelt simulations to their scaling. A base model simulation characterized these processes with 10m resolution over a 14.0 km2 basin with an elevation range of 1474 - 2244 masl. Each of the major processes affecting snow accumulation and melt - precipitation, wind speed, solar radiation, thermal radiation, temperature, and vapor pressure - were independently degraded to 1 km resolution. Seasonal and event-specific results were analyzed. Results indicated that scale effects on melt vary by process and weather conditions. The dependence of melt simulations on the scaling of solar radiation fluxes also had a seasonal component. These process-based scaling characteristics should remain static through time as they are based on physical considerations. As such, these results not only provide guidance for current modeling efforts, but are also well suited to predicting how potential climate changes will affect the heterogeneity of mountain snow distributions.

Method for distributed agent-based non-expert simulation of manufacturing process behavior

DOEpatents

Ivezic, Nenad; Potok, Thomas E.

2004-11-30

A method for distributed agent based non-expert simulation of manufacturing process behavior on a single-processor computer comprises the steps of: object modeling a manufacturing technique having a plurality of processes; associating a distributed agent with each the process; and, programming each the agent to respond to discrete events corresponding to the manufacturing technique, wherein each discrete event triggers a programmed response. The method can further comprise the step of transmitting the discrete events to each agent in a message loop. In addition, the programming step comprises the step of conditioning each agent to respond to a discrete event selected from the group consisting of a clock tick message, a resources received message, and a request for output production message.

Quantitative 3-D Imaging, Segmentation and Feature Extraction of the Respiratory System in Small Mammals for Computational Biophysics Simulations

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

Trease, Lynn L.; Trease, Harold E.; Fowler, John

2007-03-15

One of the critical steps toward performing computational biology simulations, using mesh based integration methods, is in using topologically faithful geometry derived from experimental digital image data as the basis for generating the computational meshes. Digital image data representations contain both the topology of the geometric features and experimental field data distributions. The geometric features that need to be captured from the digital image data are three-dimensional, therefore the process and tools we have developed work with volumetric image data represented as data-cubes. This allows us to take advantage of 2D curvature information during the segmentation and feature extraction process.more » The process is basically: 1) segmenting to isolate and enhance the contrast of the features that we wish to extract and reconstruct, 2) extracting the geometry of the features in an isosurfacing technique, and 3) building the computational mesh using the extracted feature geometry. “Quantitative” image reconstruction and feature extraction is done for the purpose of generating computational meshes, not just for producing graphics "screen" quality images. For example, the surface geometry that we extract must represent a closed water-tight surface.« less

The Role of Computer Simulation in Nanoporous Metals—A Review

PubMed Central

Xia, Re; Wu, Run Ni; Liu, Yi Lun; Sun, Xiao Yu

2015-01-01

Nanoporous metals (NPMs) have proven to be all-round candidates in versatile and diverse applications. In this decade, interest has grown in the fabrication, characterization and applications of these intriguing materials. Most existing reviews focus on the experimental and theoretical works rather than the numerical simulation. Actually, with numerous experiments and theory analysis, studies based on computer simulation, which may model complex microstructure in more realistic ways, play a key role in understanding and predicting the behaviors of NPMs. In this review, we present a comprehensive overview of the computer simulations of NPMs, which are prepared through chemical dealloying. Firstly, we summarize the various simulation approaches to preparation, processing, and the basic physical and chemical properties of NPMs. In this part, the emphasis is attached to works involving dealloying, coarsening and mechanical properties. Then, we conclude with the latest progress as well as the future challenges in simulation studies. We believe that highlighting the importance of simulations will help to better understand the properties of novel materials and help with new scientific research on these materials. PMID:28793491

Scalable and massively parallel Monte Carlo photon transport simulations for heterogeneous computing platforms

NASA Astrophysics Data System (ADS)

Yu, Leiming; Nina-Paravecino, Fanny; Kaeli, David; Fang, Qianqian

2018-01-01

We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing Language framework, this research extends our existing graphics processing unit (GPU)-accelerated MC technique to a highly scalable vendor-independent heterogeneous computing environment, achieving significantly improved performance and software portability. A number of parallel computing techniques are investigated to achieve portable performance over a wide range of computing hardware. Furthermore, multiple thread-level and device-level load-balancing strategies are developed to obtain efficient simulations using multiple central processing units and GPUs.

An efficient surrogate-based simulation-optimization method for calibrating a regional MODFLOW model

NASA Astrophysics Data System (ADS)

Chen, Mingjie; Izady, Azizallah; Abdalla, Osman A.

2017-01-01

Simulation-optimization method entails a large number of model simulations, which is computationally intensive or even prohibitive if the model simulation is extremely time-consuming. Statistical models have been examined as a surrogate of the high-fidelity physical model during simulation-optimization process to tackle this problem. Among them, Multivariate Adaptive Regression Splines (MARS), a non-parametric adaptive regression method, is superior in overcoming problems of high-dimensions and discontinuities of the data. Furthermore, the stability and accuracy of MARS model can be improved by bootstrap aggregating methods, namely, bagging. In this paper, Bagging MARS (BMARS) method is integrated to a surrogate-based simulation-optimization framework to calibrate a three-dimensional MODFLOW model, which is developed to simulate the groundwater flow in an arid hardrock-alluvium region in northwestern Oman. The physical MODFLOW model is surrogated by the statistical model developed using BMARS algorithm. The surrogate model, which is fitted and validated using training dataset generated by the physical model, can approximate solutions rapidly. An efficient Sobol' method is employed to calculate global sensitivities of head outputs to input parameters, which are used to analyze their importance for the model outputs spatiotemporally. Only sensitive parameters are included in the calibration process to further improve the computational efficiency. Normalized root mean square error (NRMSE) between measured and simulated heads at observation wells is used as the objective function to be minimized during optimization. The reasonable history match between the simulated and observed heads demonstrated feasibility of this high-efficient calibration framework.

Prediction of SFL Interruption Performance from the Results of Arc Simulation during High-Current Phase

NASA Astrophysics Data System (ADS)

Lee, Jong-Chul; Lee, Won-Ho; Kim, Woun-Jea

2015-09-01

The design and development procedures of SF6 gas circuit breakers are still largely based on trial and error through testing although the development costs go higher every year. The computation cannot cover the testing satisfactorily because all the real processes arc not taken into account. But the knowledge of the arc behavior and the prediction of the thermal-flow inside the interrupters by numerical simulations are more useful than those by experiments due to the difficulties to obtain physical quantities experimentally and the reduction of computational costs in recent years. In this paper, in order to get further information into the interruption process of a SF6 self-blast interrupter, which is based on a combination of thermal expansion and the arc rotation principle, gas flow simulations with a CFD-arc modeling are performed during the whole switching process such as high-current period, pre-current zero period, and current-zero period. Through the complete work, the pressure-rise and the ramp of the pressure inside the chamber before current zero as well as the post-arc current after current zero should be a good criterion to predict the short-line fault interruption performance of interrupters.

Computer-Assisted Face Processing Instruction Improves Emotion Recognition, Mentalizing, and Social Skills in Students with ASD.

PubMed

Rice, Linda Marie; Wall, Carla Anne; Fogel, Adam; Shic, Frederick

2015-07-01

This study examined the extent to which a computer-based social skills intervention called FaceSay was associated with improvements in affect recognition, mentalizing, and social skills of school-aged children with Autism Spectrum Disorder (ASD). FaceSay offers students simulated practice with eye gaze, joint attention, and facial recognition skills. This randomized control trial included school-aged children meeting educational criteria for autism (N = 31). Results demonstrated that participants who received the intervention improved their affect recognition and mentalizing skills, as well as their social skills. These findings suggest that, by targeting face-processing skills, computer-based interventions may produce changes in broader cognitive and social-skills domains in a cost- and time-efficient manner.

Brian hears: online auditory processing using vectorization over channels.

PubMed

Fontaine, Bertrand; Goodman, Dan F M; Benichoux, Victor; Brette, Romain

2011-01-01

The human cochlea includes about 3000 inner hair cells which filter sounds at frequencies between 20 Hz and 20 kHz. This massively parallel frequency analysis is reflected in models of auditory processing, which are often based on banks of filters. However, existing implementations do not exploit this parallelism. Here we propose algorithms to simulate these models by vectorizing computation over frequency channels, which are implemented in "Brian Hears," a library for the spiking neural network simulator package "Brian." This approach allows us to use high-level programming languages such as Python, because with vectorized operations, the computational cost of interpretation represents a small fraction of the total cost. This makes it possible to define and simulate complex models in a simple way, while all previous implementations were model-specific. In addition, we show that these algorithms can be naturally parallelized using graphics processing units, yielding substantial speed improvements. We demonstrate these algorithms with several state-of-the-art cochlear models, and show that they compare favorably with existing, less flexible, implementations.

Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors.

PubMed

Zhmurov, A; Dima, R I; Kholodov, Y; Barsegov, V

2010-11-01

Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a C(α)-based coarse-grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics processing units (SOP-GPU program). We assessed the computational performance of an end-to-end application of the program, where all the steps of the algorithm are running on a GPU, by profiling the simulation time and memory usage for a number of test systems. The ∼90-fold computational speedup on a GPU, compared with an optimized central processing unit program, enabled us to follow the dynamics in the centisecond timescale, and to obtain the force-extension profiles using experimental pulling speeds (v(f) = 1-10 μm/s) employed in atomic force microscopy and in optical tweezers-based dynamic force spectroscopy. We found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10-fold increase in v(f). This implies that, to resolve accurately the free energy landscape and to relate the results of single-molecule experiments in vitro and in silico, molecular simulations should be carried out under the experimentally relevant force loads. This can be accomplished in reasonable wall-clock time for biomolecules of size as large as 10(5) residues using the SOP-GPU package. © 2010 Wiley-Liss, Inc.

Numerical propulsion system simulation: An interdisciplinary approach

NASA Technical Reports Server (NTRS)

Nichols, Lester D.; Chamis, Christos C.

1991-01-01

The tremendous progress being made in computational engineering and the rapid growth in computing power that is resulting from parallel processing now make it feasible to consider the use of computer simulations to gain insights into the complex interactions in aerospace propulsion systems and to evaluate new concepts early in the design process before a commitment to hardware is made. Described here is a NASA initiative to develop a Numerical Propulsion System Simulation (NPSS) capability.

Numerical propulsion system simulation - An interdisciplinary approach

NASA Technical Reports Server (NTRS)

Nichols, Lester D.; Chamis, Christos C.

1991-01-01

The tremendous progress being made in computational engineering and the rapid growth in computing power that is resulting from parallel processing now make it feasible to consider the use of computer simulations to gain insights into the complex interactions in aerospace propulsion systems and to evaluate new concepts early in the design process before a commitment to hardware is made. Described here is a NASA initiative to develop a Numerical Propulsion System Simulation (NPSS) capability.

Massively Parallel Processing for Fast and Accurate Stamping Simulations

NASA Astrophysics Data System (ADS)

Gress, Jeffrey J.; Xu, Siguang; Joshi, Ramesh; Wang, Chuan-tao; Paul, Sabu

2005-08-01

The competitive automotive market drives automotive manufacturers to speed up the vehicle development cycles and reduce the lead-time. Fast tooling development is one of the key areas to support fast and short vehicle development programs (VDP). In the past ten years, the stamping simulation has become the most effective validation tool in predicting and resolving all potential formability and quality problems before the dies are physically made. The stamping simulation and formability analysis has become an critical business segment in GM math-based die engineering process. As the simulation becomes as one of the major production tools in engineering factory, the simulation speed and accuracy are the two of the most important measures for stamping simulation technology. The speed and time-in-system of forming analysis becomes an even more critical to support the fast VDP and tooling readiness. Since 1997, General Motors Die Center has been working jointly with our software vendor to develop and implement a parallel version of simulation software for mass production analysis applications. By 2001, this technology was matured in the form of distributed memory processing (DMP) of draw die simulations in a networked distributed memory computing environment. In 2004, this technology was refined to massively parallel processing (MPP) and extended to line die forming analysis (draw, trim, flange, and associated spring-back) running on a dedicated computing environment. The evolution of this technology and the insight gained through the implementation of DM0P/MPP technology as well as performance benchmarks are discussed in this publication.

Numerical Simulations for Distribution Characteristics of Internal Forces on Segments of Tunnel Linings

NASA Astrophysics Data System (ADS)

Li, Shouju; Shangguan, Zichang; Cao, Lijuan

A procedure based on FEM is proposed to simulate interaction between concrete segments of tunnel linings and soils. The beam element named as Beam 3 in ANSYS software was used to simulate segments. The ground loss induced from shield tunneling and segment installing processes is simulated in finite element analysis. The distributions of bending moment, axial force and shear force on segments were computed by FEM. The commutated internal forces on segments will be used to design reinforced bars on shield linings. Numerically simulated ground settlements agree with observed values.

DEVELOPMENT AND USE OF COMPUTER-AIDED PROCESS ENGINEERING TOOLS FOR POLLUTION PREVENTION

EPA Science Inventory

The use of Computer-Aided Process Engineering (CAPE) and process simulation tools has become established industry practice to predict simulation software, new opportunities are available for the creation of a wide range of ancillary tools that can be used from within multiple sim...

Gaussian process regression of chirplet decomposed ultrasonic B-scans of a simulated design case

NASA Astrophysics Data System (ADS)

Wertz, John; Homa, Laura; Welter, John; Sparkman, Daniel; Aldrin, John

2018-04-01

The US Air Force seeks to implement damage tolerant lifecycle management of composite structures. Nondestructive characterization of damage is a key input to this framework. One approach to characterization is model-based inversion of the ultrasonic response from damage features; however, the computational expense of modeling the ultrasonic waves within composites is a major hurdle to implementation. A surrogate forward model with sufficient accuracy and greater computational efficiency is therefore critical to enabling model-based inversion and damage characterization. In this work, a surrogate model is developed on the simulated ultrasonic response from delamination-like structures placed at different locations within a representative composite layup. The resulting B-scans are decomposed via the chirplet transform, and a Gaussian process model is trained on the chirplet parameters. The quality of the surrogate is tested by comparing the B-scan for a delamination configuration not represented within the training data set. The estimated B-scan has a maximum error of ˜15% for an estimated reduction in computational runtime of ˜95% for 200 function calls. This considerable reduction in computational expense makes full 3D characterization of impact damage tractable.

Remote detection of carbon monoxide by FTIR for simulating field detection in industrial process

NASA Astrophysics Data System (ADS)

Gao, Qiankun; Liu, Wenqing; Zhang, Yujun; Gao, Mingguang; Xu, Liang; Li, Xiangxian; Jin, Ling

2016-10-01

In order to monitor carbon monoxide in industrial production, we developed a passive gas radiation measurement system based on Fourier transform infrared spectroscopy and carried out infrared radiation measurement experiment of carbon monoxide detection in simulated industrial production environment by this system. The principle, condition, device and data processing method of the experiment are introduced in this paper. In order to solve the problem of light path jitter in the actual industrial field, we simulated the noise in the industrial environment. We combine the advantages of MATHEMATICA software in the aspects of graph processing and symbolic computation to data processing to improve the signal noise ratio and noise suppression. Based on the HITRAN database, the nonlinear least square fitting method was used to calculate the concentration of the CO spectra before and after the data processing. By comparing the calculated concentration, the data processed by MATHEMATICA is reliable and necessary in the industrial production environment.

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

Zitney, S.E.

This paper highlights the use of the CAPE-OPEN (CO) standard interfaces in the Advanced Process Engineering Co-Simulator (APECS) developed at the National Energy Technology Laboratory (NETL). The APECS system uses the CO unit operation, thermodynamic, and reaction interfaces to provide its plug-and-play co-simulation capabilities, including the integration of process simulation with computational fluid dynamics (CFD) simulation. APECS also relies heavily on the use of a CO COM/CORBA bridge for running process/CFD co-simulations on multiple operating systems. For process optimization in the face of multiple and some time conflicting objectives, APECS offers stochastic modeling and multi-objective optimization capabilities developed to complymore » with the CO software standard. At NETL, system analysts are applying APECS to a wide variety of advanced power generation systems, ranging from small fuel cell systems to commercial-scale power plants including the coal-fired, gasification-based FutureGen power and hydrogen production plant.« less

Novel Image Encryption based on Quantum Walks

PubMed Central

Yang, Yu-Guang; Pan, Qing-Xiang; Sun, Si-Jia; Xu, Peng

2015-01-01

Quantum computation has achieved a tremendous success during the last decades. In this paper, we investigate the potential application of a famous quantum computation model, i.e., quantum walks (QW) in image encryption. It is found that QW can serve as an excellent key generator thanks to its inherent nonlinear chaotic dynamic behavior. Furthermore, we construct a novel QW-based image encryption algorithm. Simulations and performance comparisons show that the proposal is secure enough for image encryption and outperforms prior works. It also opens the door towards introducing quantum computation into image encryption and promotes the convergence between quantum computation and image processing. PMID:25586889

A Computer Simulation of Community Pharmacy Practice for Educational Use.

PubMed

Bindoff, Ivan; Ling, Tristan; Bereznicki, Luke; Westbury, Juanita; Chalmers, Leanne; Peterson, Gregory; Ollington, Robert

2014-11-15

To provide a computer-based learning method for pharmacy practice that is as effective as paper-based scenarios, but more engaging and less labor-intensive. We developed a flexible and customizable computer simulation of community pharmacy. Using it, the students would be able to work through scenarios which encapsulate the entirety of a patient presentation. We compared the traditional paper-based teaching method to our computer-based approach using equivalent scenarios. The paper-based group had 2 tutors while the computer group had none. Both groups were given a prescenario and postscenario clinical knowledge quiz and survey. Students in the computer-based group had generally greater improvements in their clinical knowledge score, and third-year students using the computer-based method also showed more improvements in history taking and counseling competencies. Third-year students also found the simulation fun and engaging. Our simulation of community pharmacy provided an educational experience as effective as the paper-based alternative, despite the lack of a human tutor.

Construction of multi-functional open modulized Matlab simulation toolbox for imaging ladar system

NASA Astrophysics Data System (ADS)

Wu, Long; Zhao, Yuan; Tang, Meng; He, Jiang; Zhang, Yong

2011-06-01

Ladar system simulation is to simulate the ladar models using computer simulation technology in order to predict the performance of the ladar system. This paper presents the developments of laser imaging radar simulation for domestic and overseas studies and the studies of computer simulation on ladar system with different application requests. The LadarSim and FOI-LadarSIM simulation facilities of Utah State University and Swedish Defence Research Agency are introduced in details. This paper presents the low level of simulation scale, un-unified design and applications of domestic researches in imaging ladar system simulation, which are mostly to achieve simple function simulation based on ranging equations for ladar systems. Design of laser imaging radar simulation with open and modularized structure is proposed to design unified modules for ladar system, laser emitter, atmosphere models, target models, signal receiver, parameters setting and system controller. Unified Matlab toolbox and standard control modules have been built with regulated input and output of the functions, and the communication protocols between hardware modules. A simulation based on ICCD gain-modulated imaging ladar system for a space shuttle is made based on the toolbox. The simulation result shows that the models and parameter settings of the Matlab toolbox are able to simulate the actual detection process precisely. The unified control module and pre-defined parameter settings simplify the simulation of imaging ladar detection. Its open structures enable the toolbox to be modified for specialized requests. The modulization gives simulations flexibility.

Fast Numerical Simulation of Focused Ultrasound Treatments During Respiratory Motion With Discontinuous Motion Boundaries.

PubMed

Schwenke, Michael; Georgii, Joachim; Preusser, Tobias

2017-07-01

Focused ultrasound (FUS) is rapidly gaining clinical acceptance for several target tissues in the human body. Yet, treating liver targets is not clinically applied due to a high complexity of the procedure (noninvasiveness, target motion, complex anatomy, blood cooling effects, shielding by ribs, and limited image-based monitoring). To reduce the complexity, numerical FUS simulations can be utilized for both treatment planning and execution. These use-cases demand highly accurate and computationally efficient simulations. We propose a numerical method for the simulation of abdominal FUS treatments during respiratory motion of the organs and target. Especially, a novel approach is proposed to simulate the heating during motion by solving Pennes' bioheat equation in a computational reference space, i.e., the equation is mathematically transformed to the reference. The approach allows for motion discontinuities, e.g., the sliding of the liver along the abdominal wall. Implementing the solver completely on the graphics processing unit and combining it with an atlas-based ultrasound simulation approach yields a simulation performance faster than real time (less than 50-s computing time for 100 s of treatment time) on a modern off-the-shelf laptop. The simulation method is incorporated into a treatment planning demonstration application that allows to simulate real patient cases including respiratory motion. The high performance of the presented simulation method opens the door to clinical applications. The methods bear the potential to enable the application of FUS for moving organs.

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.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Potential application of artificial concepts to aerodynamic simulation

NASA Technical Reports Server (NTRS)

Kutler, P.; Mehta, U. B.; Andrews, A.

1984-01-01

The concept of artificial intelligence as it applies to computational fluid dynamics simulation is investigated. How expert systems can be adapted to speed the numerical aerodynamic simulation process is also examined. A proposed expert grid generation system is briefly described which, given flow parameters, configuration geometry, and simulation constraints, uses knowledge about the discretization process to determine grid point coordinates, computational surface information, and zonal interface parameters.

Using Agent Base Models to Optimize Large Scale Network for Large System Inventories

NASA Technical Reports Server (NTRS)

Shameldin, Ramez Ahmed; Bowling, Shannon R.

2010-01-01

The aim of this paper is to use Agent Base Models (ABM) to optimize large scale network handling capabilities for large system inventories and to implement strategies for the purpose of reducing capital expenses. The models used in this paper either use computational algorithms or procedure implementations developed by Matlab to simulate agent based models in a principal programming language and mathematical theory using clusters, these clusters work as a high performance computational performance to run the program in parallel computational. In both cases, a model is defined as compilation of a set of structures and processes assumed to underlie the behavior of a network system.

Automatic mathematical modeling for real time simulation system

NASA Technical Reports Server (NTRS)

Wang, Caroline; Purinton, Steve

1988-01-01

A methodology for automatic mathematical modeling and generating simulation models is described. The models will be verified by running in a test environment using standard profiles with the results compared against known results. The major objective is to create a user friendly environment for engineers to design, maintain, and verify their model and also automatically convert the mathematical model into conventional code for conventional computation. A demonstration program was designed for modeling the Space Shuttle Main Engine Simulation. It is written in LISP and MACSYMA and runs on a Symbolic 3670 Lisp Machine. The program provides a very friendly and well organized environment for engineers to build a knowledge base for base equations and general information. It contains an initial set of component process elements for the Space Shuttle Main Engine Simulation and a questionnaire that allows the engineer to answer a set of questions to specify a particular model. The system is then able to automatically generate the model and FORTRAN code. The future goal which is under construction is to download the FORTRAN code to VAX/VMS system for conventional computation. The SSME mathematical model will be verified in a test environment and the solution compared with the real data profile. The use of artificial intelligence techniques has shown that the process of the simulation modeling can be simplified.

Computational fluid dynamics uses in fluid dynamics/aerodynamics education

NASA Technical Reports Server (NTRS)

Holst, Terry L.

1994-01-01

The field of computational fluid dynamics (CFD) has advanced to the point where it can now be used for the purpose of fluid dynamics physics education. Because of the tremendous wealth of information available from numerical simulation, certain fundamental concepts can be efficiently communicated using an interactive graphical interrogation of the appropriate numerical simulation data base. In other situations, a large amount of aerodynamic information can be communicated to the student by interactive use of simple CFD tools on a workstation or even in a personal computer environment. The emphasis in this presentation is to discuss ideas for how this process might be implemented. Specific examples, taken from previous publications, will be used to highlight the presentation.

A Micro-Level Data-Calibrated Agent-Based Model: The Synergy between Microsimulation and Agent-Based Modeling.

PubMed

Singh, Karandeep; Ahn, Chang-Won; Paik, Euihyun; Bae, Jang Won; Lee, Chun-Hee

2018-01-01

Artificial life (ALife) examines systems related to natural life, its processes, and its evolution, using simulations with computer models, robotics, and biochemistry. In this article, we focus on the computer modeling, or "soft," aspects of ALife and prepare a framework for scientists and modelers to be able to support such experiments. The framework is designed and built to be a parallel as well as distributed agent-based modeling environment, and does not require end users to have expertise in parallel or distributed computing. Furthermore, we use this framework to implement a hybrid model using microsimulation and agent-based modeling techniques to generate an artificial society. We leverage this artificial society to simulate and analyze population dynamics using Korean population census data. The agents in this model derive their decisional behaviors from real data (microsimulation feature) and interact among themselves (agent-based modeling feature) to proceed in the simulation. The behaviors, interactions, and social scenarios of the agents are varied to perform an analysis of population dynamics. We also estimate the future cost of pension policies based on the future population structure of the artificial society. The proposed framework and model demonstrates how ALife techniques can be used by researchers in relation to social issues and policies.

Development of mpi_EPIC model for global agroecosystem modeling

DOE PAGES

Kang, Shujiang; Wang, Dali; Jeff A. Nichols; ...

2014-12-31

Models that address policy-maker concerns about multi-scale effects of food and bioenergy production systems are computationally demanding. We integrated the message passing interface algorithm into the process-based EPIC model to accelerate computation of ecosystem effects. Simulation performance was further enhanced by applying the Vampir framework. When this enhanced mpi_EPIC model was tested, total execution time for a global 30-year simulation of a switchgrass cropping system was shortened to less than 0.5 hours on a supercomputer. The results illustrate that mpi_EPIC using parallel design can balance simulation workloads and facilitate large-scale, high-resolution analysis of agricultural production systems, management alternatives and environmentalmore » effects.« less

ASME V\\&V challenge problem: Surrogate-based V&V

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

Beghini, Lauren L.; Hough, Patricia D.

2015-12-18

The process of verification and validation can be resource intensive. From the computational model perspective, the resource demand typically arises from long simulation run times on multiple cores coupled with the need to characterize and propagate uncertainties. In addition, predictive computations performed for safety and reliability analyses have similar resource requirements. For this reason, there is a tradeoff between the time required to complete the requisite studies and the fidelity or accuracy of the results that can be obtained. At a high level, our approach is cast within a validation hierarchy that provides a framework in which we perform sensitivitymore » analysis, model calibration, model validation, and prediction. The evidence gathered as part of these activities is mapped into the Predictive Capability Maturity Model to assess credibility of the model used for the reliability predictions. With regard to specific technical aspects of our analysis, we employ surrogate-based methods, primarily based on polynomial chaos expansions and Gaussian processes, for model calibration, sensitivity analysis, and uncertainty quantification in order to reduce the number of simulations that must be done. The goal is to tip the tradeoff balance to improving accuracy without increasing the computational demands.« less

An empirical analysis of the distribution of overshoots in a stationary Gaussian stochastic process

NASA Technical Reports Server (NTRS)

Carter, M. C.; Madison, M. W.

1973-01-01

The frequency distribution of overshoots in a stationary Gaussian stochastic process is analyzed. The primary processes involved in this analysis are computer simulation and statistical estimation. Computer simulation is used to simulate stationary Gaussian stochastic processes that have selected autocorrelation functions. An analysis of the simulation results reveals a frequency distribution for overshoots with a functional dependence on the mean and variance of the process. Statistical estimation is then used to estimate the mean and variance of a process. It is shown that for an autocorrelation function, the mean and the variance for the number of overshoots, a frequency distribution for overshoots can be estimated.

The Framework for Simulation of Bioinspired Security Mechanisms against Network Infrastructure Attacks

PubMed Central

Kotenko, Igor

2014-01-01

The paper outlines a bioinspired approach named “network nervous system" and methods of simulation of infrastructure attacks and protection mechanisms based on this approach. The protection mechanisms based on this approach consist of distributed prosedures of information collection and processing, which coordinate the activities of the main devices of a computer network, identify attacks, and determine nessesary countermeasures. Attacks and protection mechanisms are specified as structural models using a set-theoretic approach. An environment for simulation of protection mechanisms based on the biological metaphor is considered; the experiments demonstrating the effectiveness of the protection mechanisms are described. PMID:25254229

TOWARDS A MULTI-SCALE AGENT-BASED PROGRAMMING LANGUAGE METHODOLOGY

PubMed Central

Somogyi, Endre; Hagar, Amit; Glazier, James A.

2017-01-01

Living tissues are dynamic, heterogeneous compositions of objects, including molecules, cells and extra-cellular materials, which interact via chemical, mechanical and electrical process and reorganize via transformation, birth, death and migration processes. Current programming language have difficulty describing the dynamics of tissues because: 1: Dynamic sets of objects participate simultaneously in multiple processes, 2: Processes may be either continuous or discrete, and their activity may be conditional, 3: Objects and processes form complex, heterogeneous relationships and structures, 4: Objects and processes may be hierarchically composed, 5: Processes may create, destroy and transform objects and processes. Some modeling languages support these concepts, but most cannot translate models into executable simulations. We present a new hybrid executable modeling language paradigm, the Continuous Concurrent Object Process Methodology (CCOPM) which naturally expresses tissue models, enabling users to visually create agent-based models of tissues, and also allows computer simulation of these models. PMID:29282379

TOWARDS A MULTI-SCALE AGENT-BASED PROGRAMMING LANGUAGE METHODOLOGY.

PubMed

Somogyi, Endre; Hagar, Amit; Glazier, James A

2016-12-01

Living tissues are dynamic, heterogeneous compositions of objects , including molecules, cells and extra-cellular materials, which interact via chemical, mechanical and electrical process and reorganize via transformation, birth, death and migration processes . Current programming language have difficulty describing the dynamics of tissues because: 1: Dynamic sets of objects participate simultaneously in multiple processes, 2: Processes may be either continuous or discrete, and their activity may be conditional, 3: Objects and processes form complex, heterogeneous relationships and structures, 4: Objects and processes may be hierarchically composed, 5: Processes may create, destroy and transform objects and processes. Some modeling languages support these concepts, but most cannot translate models into executable simulations. We present a new hybrid executable modeling language paradigm, the Continuous Concurrent Object Process Methodology ( CCOPM ) which naturally expresses tissue models, enabling users to visually create agent-based models of tissues, and also allows computer simulation of these models.

A new computational growth model for sea urchin skeletons.

PubMed

Zachos, Louis G

2009-08-07

A new computational model has been developed to simulate growth of regular sea urchin skeletons. The model incorporates the processes of plate addition and individual plate growth into a composite model of whole-body (somatic) growth. A simple developmental model based on hypothetical morphogens underlies the assumptions used to define the simulated growth processes. The data model is based on a Delaunay triangulation of plate growth center points, using the dual Voronoi polygons to define plate topologies. A spherical frame of reference is used for growth calculations, with affine deformation of the sphere (based on a Young-Laplace membrane model) to result in an urchin-like three-dimensional form. The model verifies that the patterns of coronal plates in general meet the criteria of Voronoi polygonalization, that a morphogen/threshold inhibition model for plate addition results in the alternating plate addition pattern characteristic of sea urchins, and that application of the Bertalanffy growth model to individual plates results in simulated somatic growth that approximates that seen in living urchins. The model suggests avenues of research that could explain some of the distinctions between modern sea urchins and the much more disparate groups of forms that characterized the Paleozoic Era.

Reference Computational Meshing Strategy for Computational Fluid Dynamics Simulation of Departure from Nucleate BoilingReference Computational Meshing Strategy for Computational Fluid Dynamics Simulation of Departure from Nucleate Boiling

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

Pointer, William David

The objective of this effort is to establish a strategy and process for generation of suitable computational mesh for computational fluid dynamics simulations of departure from nucleate boiling in a 5 by 5 fuel rod assembly held in place by PWR mixing vane spacer grids. This mesh generation process will support ongoing efforts to develop, demonstrate and validate advanced multi-phase computational fluid dynamics methods that enable more robust identification of dryout conditions and DNB occurrence.Building upon prior efforts and experience, multiple computational meshes were developed using the native mesh generation capabilities of the commercial CFD code STAR-CCM+. These meshes weremore » used to simulate two test cases from the Westinghouse 5 by 5 rod bundle facility. The sensitivity of predicted quantities of interest to the mesh resolution was then established using two evaluation methods, the Grid Convergence Index method and the Least Squares method. This evaluation suggests that the Least Squares method can reliably establish the uncertainty associated with local parameters such as vector velocity components at a point in the domain or surface averaged quantities such as outlet velocity magnitude. However, neither method is suitable for characterization of uncertainty in global extrema such as peak fuel surface temperature, primarily because such parameters are not necessarily associated with a fixed point in space. This shortcoming is significant because the current generation algorithm for identification of DNB event conditions relies on identification of such global extrema. Ongoing efforts to identify DNB based on local surface conditions will address this challenge« less

MOOSE: A parallel computational framework for coupled systems of nonlinear equations.

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

Derek Gaston; Chris Newman; Glen Hansen

Systems of coupled, nonlinear partial differential equations (PDEs) often arise in simulation of nuclear processes. MOOSE: Multiphysics Object Oriented Simulation Environment, a parallel computational framework targeted at the solution of such systems, is presented. As opposed to traditional data-flow oriented computational frameworks, MOOSE is instead founded on the mathematical principle of Jacobian-free Newton-Krylov (JFNK) solution methods. Utilizing the mathematical structure present in JFNK, physics expressions are modularized into `Kernels,'' allowing for rapid production of new simulation tools. In addition, systems are solved implicitly and fully coupled, employing physics based preconditioning, which provides great flexibility even with large variance in timemore » scales. A summary of the mathematics, an overview of the structure of MOOSE, and several representative solutions from applications built on the framework are presented.« less

Shorebird Migration Patterns in Response to Climate Change: A Modeling Approach

NASA Technical Reports Server (NTRS)

Smith, James A.

2010-01-01

The availability of satellite remote sensing observations at multiple spatial and temporal scales, coupled with advances in climate modeling and information technologies offer new opportunities for the application of mechanistic models to predict how continental scale bird migration patterns may change in response to environmental change. In earlier studies, we explored the phenotypic plasticity of a migratory population of Pectoral sandpipers by simulating the movement patterns of an ensemble of 10,000 individual birds in response to changes in stopover locations as an indicator of the impacts of wetland loss and inter-annual variability on the fitness of migratory shorebirds. We used an individual based, biophysical migration model, driven by remotely sensed land surface data, climate data, and biological field data. Mean stop-over durations and stop-over frequency with latitude predicted from our model for nominal cases were consistent with results reported in the literature and available field data. In this study, we take advantage of new computing capabilities enabled by recent GP-GPU computing paradigms and commodity hardware (general purchase computing on graphics processing units). Several aspects of our individual based (agent modeling) approach lend themselves well to GP-GPU computing. We have been able to allocate compute-intensive tasks to the graphics processing units, and now simulate ensembles of 400,000 birds at varying spatial resolutions along the central North American flyway. We are incorporating additional, species specific, mechanistic processes to better reflect the processes underlying bird phenotypic plasticity responses to different climate change scenarios in the central U.S.

Traffic Flow Density Distribution Based on FEM

NASA Astrophysics Data System (ADS)

Ma, Jing; Cui, Jianming

In analysis of normal traffic flow, it usually uses the static or dynamic model to numerical analyze based on fluid mechanics. However, in such handling process, the problem of massive modeling and data handling exist, and the accuracy is not high. Finite Element Method (FEM) is a production which is developed from the combination of a modern mathematics, mathematics and computer technology, and it has been widely applied in various domain such as engineering. Based on existing theory of traffic flow, ITS and the development of FEM, a simulation theory of the FEM that solves the problems existing in traffic flow is put forward. Based on this theory, using the existing Finite Element Analysis (FEA) software, the traffic flow is simulated analyzed with fluid mechanics and the dynamics. Massive data processing problem of manually modeling and numerical analysis is solved, and the authenticity of simulation is enhanced.

Itô and Stratonovich integrals on compound renewal processes: the normal/Poisson case

NASA Astrophysics Data System (ADS)

Germano, Guido; Politi, Mauro; Scalas, Enrico; Schilling, René L.

2010-06-01

Continuous-time random walks, or compound renewal processes, are pure-jump stochastic processes with several applications in insurance, finance, economics and physics. Based on heuristic considerations, a definition is given for stochastic integrals driven by continuous-time random walks, which includes the Itô and Stratonovich cases. It is then shown how the definition can be used to compute these two stochastic integrals by means of Monte Carlo simulations. Our example is based on the normal compound Poisson process, which in the diffusive limit converges to the Wiener process.

Towards data warehousing and mining of protein unfolding simulation data.

PubMed

Berrar, Daniel; Stahl, Frederic; Silva, Candida; Rodrigues, J Rui; Brito, Rui M M; Dubitzky, Werner

2005-10-01

The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

Cryotherapy simulator for localized prostate cancer.

PubMed

Hahn, James K; Manyak, Michael J; Jin, Ge; Kim, Dongho; Rewcastle, John; Kim, Sunil; Walsh, Raymond J

2002-01-01

Cryotherapy is a treatment modality that uses a technique to selectively freeze tissue and thereby cause controlled tissue destruction. The procedure involves placement of multiple small diameter probes through the perineum into the prostate tissue at selected spatial intervals. Transrectal ultrasound is used to properly position the cylindrical probes before activation of the liquid Argon cooling element, which lowers the tissue temperature below -40 degrees Centigrade. Tissue effect is monitored by transrectal ultrasound changes as well as thermocouples placed in the tissue. The computer-based cryotherapy simulation system mimics the major surgical steps involved in the procedure. The simulated real-time ultrasound display is generated from 3-D ultrasound datasets where the interaction of the ultrasound with the instruments as well as the frozen tissue is simulated by image processing. The thermal and mechanical simulations of the tissue are done using a modified finite-difference/finite-element method optimized for real-time performance. The simulator developed is a part of a comprehensive training program, including a computer-based learning system and hands-on training program with a proctor, designed to familiarize the physician with the technique and equipment involved.

Simulating Technology Processes to Foster Learning.

ERIC Educational Resources Information Center

Krumholtz, Nira

1998-01-01

Based on a spiral model of technology evolution, elementary students used LOGO computer software to become both developers and users of technology. The computerized environment enabled 87% to reach intuitive understanding of physical concepts; 24% expressed more formal scientific understanding. (SK)

Knowledge Based Cloud FE Simulation of Sheet Metal Forming Processes.

PubMed

Zhou, Du; Yuan, Xi; Gao, Haoxiang; Wang, Ailing; Liu, Jun; El Fakir, Omer; Politis, Denis J; Wang, Liliang; Lin, Jianguo

2016-12-13

The use of Finite Element (FE) simulation software to adequately predict the outcome of sheet metal forming processes is crucial to enhancing the efficiency and lowering the development time of such processes, whilst reducing costs involved in trial-and-error prototyping. Recent focus on the substitution of steel components with aluminum alloy alternatives in the automotive and aerospace sectors has increased the need to simulate the forming behavior of such alloys for ever more complex component geometries. However these alloys, and in particular their high strength variants, exhibit limited formability at room temperature, and high temperature manufacturing technologies have been developed to form them. Consequently, advanced constitutive models are required to reflect the associated temperature and strain rate effects. Simulating such behavior is computationally very expensive using conventional FE simulation techniques. This paper presents a novel Knowledge Based Cloud FE (KBC-FE) simulation technique that combines advanced material and friction models with conventional FE simulations in an efficient manner thus enhancing the capability of commercial simulation software packages. The application of these methods is demonstrated through two example case studies, namely: the prediction of a material's forming limit under hot stamping conditions, and the tool life prediction under multi-cycle loading conditions.

Knowledge Based Cloud FE Simulation of Sheet Metal Forming Processes

PubMed Central

Zhou, Du; Yuan, Xi; Gao, Haoxiang; Wang, Ailing; Liu, Jun; El Fakir, Omer; Politis, Denis J.; Wang, Liliang; Lin, Jianguo

2016-01-01

The use of Finite Element (FE) simulation software to adequately predict the outcome of sheet metal forming processes is crucial to enhancing the efficiency and lowering the development time of such processes, whilst reducing costs involved in trial-and-error prototyping. Recent focus on the substitution of steel components with aluminum alloy alternatives in the automotive and aerospace sectors has increased the need to simulate the forming behavior of such alloys for ever more complex component geometries. However these alloys, and in particular their high strength variants, exhibit limited formability at room temperature, and high temperature manufacturing technologies have been developed to form them. Consequently, advanced constitutive models are required to reflect the associated temperature and strain rate effects. Simulating such behavior is computationally very expensive using conventional FE simulation techniques. This paper presents a novel Knowledge Based Cloud FE (KBC-FE) simulation technique that combines advanced material and friction models with conventional FE simulations in an efficient manner thus enhancing the capability of commercial simulation software packages. The application of these methods is demonstrated through two example case studies, namely: the prediction of a material's forming limit under hot stamping conditions, and the tool life prediction under multi-cycle loading conditions. PMID:28060298

Using Model Replication to Improve the Reliability of Agent-Based Models

NASA Astrophysics Data System (ADS)

Zhong, Wei; Kim, Yushim

The basic presupposition of model replication activities for a computational model such as an agent-based model (ABM) is that, as a robust and reliable tool, it must be replicable in other computing settings. This assumption has recently gained attention in the community of artificial society and simulation due to the challenges of model verification and validation. Illustrating the replication of an ABM representing fraudulent behavior in a public service delivery system originally developed in the Java-based MASON toolkit for NetLogo by a different author, this paper exemplifies how model replication exercises provide unique opportunities for model verification and validation process. At the same time, it helps accumulate best practices and patterns of model replication and contributes to the agenda of developing a standard methodological protocol for agent-based social simulation.

Technology CAD for integrated circuit fabrication technology development and technology transfer

NASA Astrophysics Data System (ADS)

Saha, Samar

2003-07-01

In this paper systematic simulation-based methodologies for integrated circuit (IC) manufacturing technology development and technology transfer are presented. In technology development, technology computer-aided design (TCAD) tools are used to optimize the device and process parameters to develop a new generation of IC manufacturing technology by reverse engineering from the target product specifications. While in technology transfer to manufacturing co-location, TCAD is used for process centering with respect to high-volume manufacturing equipment of the target manufacturing equipment of the target manufacturing facility. A quantitative model is developed to demonstrate the potential benefits of the simulation-based methodology in reducing the cycle time and cost of typical technology development and technology transfer projects over the traditional practices. The strategy for predictive simulation to improve the effectiveness of a TCAD-based project, is also discussed.

System Diagnostic Builder - A rule generation tool for expert systems that do intelligent data evaluation. [applied to Shuttle Mission Simulator

NASA Technical Reports Server (NTRS)

Nieten, Joseph; Burke, Roger

1993-01-01

Consideration is given to the System Diagnostic Builder (SDB), an automated knowledge acquisition tool using state-of-the-art AI technologies. The SDB employs an inductive machine learning technique to generate rules from data sets that are classified by a subject matter expert. Thus, data are captured from the subject system, classified, and used to drive the rule generation process. These rule bases are used to represent the observable behavior of the subject system, and to represent knowledge about this system. The knowledge bases captured from the Shuttle Mission Simulator can be used as black box simulations by the Intelligent Computer Aided Training devices. The SDB can also be used to construct knowledge bases for the process control industry, such as chemical production or oil and gas production.

Accelerating Dust Storm Simulation by Balancing Task Allocation in Parallel Computing Environment

NASA Astrophysics Data System (ADS)

Gui, Z.; Yang, C.; XIA, J.; Huang, Q.; YU, M.

2013-12-01

Dust storm has serious negative impacts on environment, human health, and assets. The continuing global climate change has increased the frequency and intensity of dust storm in the past decades. To better understand and predict the distribution, intensity and structure of dust storm, a series of dust storm models have been developed, such as Dust Regional Atmospheric Model (DREAM), the NMM meteorological module (NMM-dust) and Chinese Unified Atmospheric Chemistry Environment for Dust (CUACE/Dust). The developments and applications of these models have contributed significantly to both scientific research and our daily life. However, dust storm simulation is a data and computing intensive process. Normally, a simulation for a single dust storm event may take several days or hours to run. It seriously impacts the timeliness of prediction and potential applications. To speed up the process, high performance computing is widely adopted. By partitioning a large study area into small subdomains according to their geographic location and executing them on different computing nodes in a parallel fashion, the computing performance can be significantly improved. Since spatiotemporal correlations exist in the geophysical process of dust storm simulation, each subdomain allocated to a node need to communicate with other geographically adjacent subdomains to exchange data. Inappropriate allocations may introduce imbalance task loads and unnecessary communications among computing nodes. Therefore, task allocation method is the key factor, which may impact the feasibility of the paralleling. The allocation algorithm needs to carefully leverage the computing cost and communication cost for each computing node to minimize total execution time and reduce overall communication cost for the entire system. This presentation introduces two algorithms for such allocation and compares them with evenly distributed allocation method. Specifically, 1) In order to get optimized solutions, a quadratic programming based modeling method is proposed. This algorithm performs well with small amount of computing tasks. However, its efficiency decreases significantly as the subdomain number and computing node number increase. 2) To compensate performance decreasing for large scale tasks, a K-Means clustering based algorithm is introduced. Instead of dedicating to get optimized solutions, this method can get relatively good feasible solutions within acceptable time. However, it may introduce imbalance communication for nodes or node-isolated subdomains. This research shows both two algorithms have their own strength and weakness for task allocation. A combination of the two algorithms is under study to obtain a better performance. Keywords: Scheduling; Parallel Computing; Load Balance; Optimization; Cost Model

User's guide to the Reliability Estimation System Testbed (REST)

NASA Technical Reports Server (NTRS)

Nicol, David M.; Palumbo, Daniel L.; Rifkin, Adam

1992-01-01

The Reliability Estimation System Testbed is an X-window based reliability modeling tool that was created to explore the use of the Reliability Modeling Language (RML). RML was defined to support several reliability analysis techniques including modularization, graphical representation, Failure Mode Effects Simulation (FMES), and parallel processing. These techniques are most useful in modeling large systems. Using modularization, an analyst can create reliability models for individual system components. The modules can be tested separately and then combined to compute the total system reliability. Because a one-to-one relationship can be established between system components and the reliability modules, a graphical user interface may be used to describe the system model. RML was designed to permit message passing between modules. This feature enables reliability modeling based on a run time simulation of the system wide effects of a component's failure modes. The use of failure modes effects simulation enhances the analyst's ability to correctly express system behavior when using the modularization approach to reliability modeling. To alleviate the computation bottleneck often found in large reliability models, REST was designed to take advantage of parallel processing on hypercube processors.

Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks

PubMed Central

Walpole, J.; Chappell, J.C.; Cluceru, J.G.; Mac Gabhann, F.; Bautch, V.L.; Peirce, S. M.

2015-01-01

Many biological processes are controlled by both deterministic and stochastic influences. However, efforts to model these systems often rely on either purely stochastic or purely rule-based methods. To better understand the balance between stochasticity and determinism in biological processes a computational approach that incorporates both influences may afford additional insight into underlying biological mechanisms that give rise to emergent system properties. We apply a combined approach to the simulation and study of angiogenesis, the growth of new blood vessels from existing networks. This complex multicellular process begins with selection of an initiating endothelial cell, or tip cell, which sprouts from the parent vessels in response to stimulation by exogenous cues. We have constructed an agent-based model of sprouting angiogenesis to evaluate endothelial cell sprout initiation frequency and location, and we have experimentally validated it using high-resolution time-lapse confocal microscopy. ABM simulations were then compared to a Monte Carlo model, revealing that purely stochastic simulations could not generate sprout locations as accurately as the rule-informed agent-based model. These findings support the use of rule-based approaches for modeling the complex mechanisms underlying sprouting angiogenesis over purely stochastic methods. PMID:26158406

Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks.

PubMed

Walpole, J; Chappell, J C; Cluceru, J G; Mac Gabhann, F; Bautch, V L; Peirce, S M

2015-09-01

Many biological processes are controlled by both deterministic and stochastic influences. However, efforts to model these systems often rely on either purely stochastic or purely rule-based methods. To better understand the balance between stochasticity and determinism in biological processes a computational approach that incorporates both influences may afford additional insight into underlying biological mechanisms that give rise to emergent system properties. We apply a combined approach to the simulation and study of angiogenesis, the growth of new blood vessels from existing networks. This complex multicellular process begins with selection of an initiating endothelial cell, or tip cell, which sprouts from the parent vessels in response to stimulation by exogenous cues. We have constructed an agent-based model of sprouting angiogenesis to evaluate endothelial cell sprout initiation frequency and location, and we have experimentally validated it using high-resolution time-lapse confocal microscopy. ABM simulations were then compared to a Monte Carlo model, revealing that purely stochastic simulations could not generate sprout locations as accurately as the rule-informed agent-based model. These findings support the use of rule-based approaches for modeling the complex mechanisms underlying sprouting angiogenesis over purely stochastic methods.

The Effects of Inquiry-Based Computer Simulation with Cooperative Learning on Scientific Thinking and Conceptual Understanding of Gas Laws

ERIC Educational Resources Information Center

Abdullah, Sopiah; Shariff, Adilah

2008-01-01

The purpose of the study was to investigate the effects of inquiry-based computer simulation with heterogeneous-ability cooperative learning (HACL) and inquiry-based computer simulation with friendship cooperative learning (FCL) on (a) scientific reasoning (SR) and (b) conceptual understanding (CU) among Form Four students in Malaysian Smart…

GPU-based Green's function simulations of shear waves generated by an applied acoustic radiation force in elastic and viscoelastic models.

PubMed

Yang, Yiqun; Urban, Matthew W; McGough, Robert J

2018-05-15

Shear wave calculations induced by an acoustic radiation force are very time-consuming on desktop computers, and high-performance graphics processing units (GPUs) achieve dramatic reductions in the computation time for these simulations. The acoustic radiation force is calculated using the fast near field method and the angular spectrum approach, and then the shear waves are calculated in parallel with Green's functions on a GPU. This combination enables rapid evaluation of shear waves for push beams with different spatial samplings and for apertures with different f/#. Relative to shear wave simulations that evaluate the same algorithm on an Intel i7 desktop computer, a high performance nVidia GPU reduces the time required for these calculations by a factor of 45 and 700 when applied to elastic and viscoelastic shear wave simulation models, respectively. These GPU-accelerated simulations also compared to measurements in different viscoelastic phantoms, and the results are similar. For parametric evaluations and for comparisons with measured shear wave data, shear wave simulations with the Green's function approach are ideally suited for high-performance GPUs.

Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.

PubMed

Arenas, Miguel

2015-04-01

NGS technologies present a fast and cheap generation of genomic data. Nevertheless, ancestral genome inference is not so straightforward due to complex evolutionary processes acting on this material such as inversions, translocations, and other genome rearrangements that, in addition to their implicit complexity, can co-occur and confound ancestral inferences. Recently, models of genome evolution that accommodate such complex genomic events are emerging. This letter explores these novel evolutionary models and proposes their incorporation into robust statistical approaches based on computer simulations, such as approximate Bayesian computation, that may produce a more realistic evolutionary analysis of genomic data. Advantages and pitfalls in using these analytical methods are discussed. Potential applications of these ancestral genomic inferences are also pointed out.

Numerical simulation of hot-melt extrusion processes for amorphous solid dispersions using model-based melt viscosity.

PubMed

Bochmann, Esther S; Steffens, Kristina E; Gryczke, Andreas; Wagner, Karl G

2018-03-01

Simulation of HME processes is a valuable tool for increased process understanding and ease of scale-up. However, the experimental determination of all required input parameters is tedious, namely the melt rheology of the amorphous solid dispersion (ASD) in question. Hence, a procedure to simplify the application of hot-melt extrusion (HME) simulation for forming amorphous solid dispersions (ASD) is presented. The commercial 1D simulation software Ludovic ® was used to conduct (i) simulations using a full experimental data set of all input variables including melt rheology and (ii) simulations using model-based melt viscosity data based on the ASDs glass transition and the physical properties of polymeric matrix only. Both types of HME computation were further compared to experimental HME results. Variation in physical properties (e.g. heat capacity, density) and several process characteristics of HME (residence time distribution, energy consumption) among the simulations and experiments were evaluated. The model-based melt viscosity was calculated by using the glass transition temperature (T g ) of the investigated blend and the melt viscosity of the polymeric matrix by means of a T g -viscosity correlation. The results of measured melt viscosity and model-based melt viscosity were similar with only few exceptions, leading to similar HME simulation outcomes. At the end, the experimental effort prior to HME simulation could be minimized and the procedure enables a good starting point for rational development of ASDs by means of HME. As model excipients, Vinylpyrrolidone-vinyl acetate copolymer (COP) in combination with various APIs (carbamazepine, dipyridamole, indomethacin, and ibuprofen) or polyethylene glycol (PEG 1500) as plasticizer were used to form the ASDs. Copyright © 2017 Elsevier B.V. All rights reserved.

Numerical Propulsion System Simulation: An Overview

NASA Technical Reports Server (NTRS)

Lytle, John K.

2000-01-01

The cost of implementing new technology in aerospace propulsion systems is becoming prohibitively expensive and time consuming. One of the main contributors to the high cost and lengthy time is the need to perform many large-scale hardware tests and the inability to integrate all appropriate subsystems early in the design process. The NASA Glenn Research Center is developing the technologies required to enable simulations of full aerospace propulsion systems in sufficient detail to resolve critical design issues early in the design process before hardware is built. This concept, called the Numerical Propulsion System Simulation (NPSS), is focused on the integration of multiple disciplines such as aerodynamics, structures and heat transfer with computing and communication technologies to capture complex physical processes in a timely and cost-effective manner. The vision for NPSS, as illustrated, is to be a "numerical test cell" that enables full engine simulation overnight on cost-effective computing platforms. There are several key elements within NPSS that are required to achieve this capability: 1) clear data interfaces through the development and/or use of data exchange standards, 2) modular and flexible program construction through the use of object-oriented programming, 3) integrated multiple fidelity analysis (zooming) techniques that capture the appropriate physics at the appropriate fidelity for the engine systems, 4) multidisciplinary coupling techniques and finally 5) high performance parallel and distributed computing. The current state of development in these five area focuses on air breathing gas turbine engines and is reported in this paper. However, many of the technologies are generic and can be readily applied to rocket based systems and combined cycles currently being considered for low-cost access-to-space applications. Recent accomplishments include: (1) the development of an industry-standard engine cycle analysis program and plug 'n play architecture, called NPSS Version 1, (2) A full engine simulation that combines a 3D low-pressure subsystem with a 0D high pressure core simulation. This demonstrates the ability to integrate analyses at different levels of detail and to aerodynamically couple components, the fan/booster and low-pressure turbine, through a 3D computational fluid dynamics simulation. (3) Simulation of all of the turbomachinery in a modern turbofan engine on parallel computing platform for rapid and cost-effective execution. This capability can also be used to generate full compressor map, requiring both design and off-design simulation. (4) Three levels of coupling characterize the multidisciplinary analysis under NPSS: loosely coupled, process coupled and tightly coupled. The loosely coupled and process coupled approaches require a common geometry definition to link CAD to analysis tools. The tightly coupled approach is currently validating the use of arbitrary Lagrangian/Eulerian formulation for rotating turbomachinery. The validation includes both centrifugal and axial compression systems. The results of the validation will be reported in the paper. (5) The demonstration of significant computing cost/performance reduction for turbine engine applications using PC clusters. The NPSS Project is supported under the NASA High Performance Computing and Communications Program.

Integration of scheduling and discrete event simulation systems to improve production flow planning

NASA Astrophysics Data System (ADS)

Krenczyk, D.; Paprocka, I.; Kempa, W. M.; Grabowik, C.; Kalinowski, K.

2016-08-01

The increased availability of data and computer-aided technologies such as MRPI/II, ERP and MES system, allowing producers to be more adaptive to market dynamics and to improve production scheduling. Integration of production scheduling and computer modelling, simulation and visualization systems can be useful in the analysis of production system constraints related to the efficiency of manufacturing systems. A integration methodology based on semi-automatic model generation method for eliminating problems associated with complexity of the model and labour-intensive and time-consuming process of simulation model creation is proposed. Data mapping and data transformation techniques for the proposed method have been applied. This approach has been illustrated through examples of practical implementation of the proposed method using KbRS scheduling system and Enterprise Dynamics simulation system.

1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time.

PubMed

Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M; Queisser, Gillian

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator-which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics.

New Computer Simulations of Macular Neural Functioning

NASA Technical Reports Server (NTRS)

Ross, Muriel D.; Doshay, D.; Linton, S.; Parnas, B.; Montgomery, K.; Chimento, T.

1994-01-01

We use high performance graphics workstations and supercomputers to study the functional significance of the three-dimensional (3-D) organization of gravity sensors. These sensors have a prototypic architecture foreshadowing more complex systems. Scaled-down simulations run on a Silicon Graphics workstation and scaled-up, 3-D versions run on a Cray Y-MP supercomputer. A semi-automated method of reconstruction of neural tissue from serial sections studied in a transmission electron microscope has been developed to eliminate tedious conventional photography. The reconstructions use a mesh as a step in generating a neural surface for visualization. Two meshes are required to model calyx surfaces. The meshes are connected and the resulting prisms represent the cytoplasm and the bounding membranes. A finite volume analysis method is employed to simulate voltage changes along the calyx in response to synapse activation on the calyx or on calyceal processes. The finite volume method insures that charge is conserved at the calyx-process junction. These and other models indicate that efferent processes act as voltage followers, and that the morphology of some afferent processes affects their functioning. In a final application, morphological information is symbolically represented in three dimensions in a computer. The possible functioning of the connectivities is tested using mathematical interpretations of physiological parameters taken from the literature. Symbolic, 3-D simulations are in progress to probe the functional significance of the connectivities. This research is expected to advance computer-based studies of macular functioning and of synaptic plasticity.

Decoherence and Noise in Spin-based Solid State Quantum Computers. Approximation-Free Numerical Simulations

DTIC Science & Technology

2007-07-21

the spin coherent states P-representation", Conference on Quantum Computations and Many- Body Systems, February 2006, Key West, FL 9. B. N. Harmon...solid-state spin-based qubit systems was the focus of our project. Since decoherence is a complex many- body non-equilibrium process, and its...representation of the density matrix, see Sec. 3 below). This work prompted J. Taylor from the experimental group of C. Marcus and M. Lukin (funded by

Computer Aided Drug Design: Success and Limitations.

PubMed

Baig, Mohammad Hassan; Ahmad, Khurshid; Roy, Sudeep; Ashraf, Jalaluddin Mohammad; Adil, Mohd; Siddiqui, Mohammad Haris; Khan, Saif; Kamal, Mohammad Amjad; Provazník, Ivo; Choi, Inho

2016-01-01

Over the last few decades, computer-aided drug design has emerged as a powerful technique playing a crucial role in the development of new drug molecules. Structure-based drug design and ligand-based drug design are two methods commonly used in computer-aided drug design. In this article, we discuss the theory behind both methods, as well as their successful applications and limitations. To accomplish this, we reviewed structure based and ligand based virtual screening processes. Molecular dynamics simulation, which has become one of the most influential tool for prediction of the conformation of small molecules and changes in their conformation within the biological target, has also been taken into account. Finally, we discuss the principles and concepts of molecular docking, pharmacophores and other methods used in computer-aided drug design.

Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer.

PubMed

Golas, Ewa I; Czaplewski, Cezary

2014-09-01

This work theoretically investigates the mechanical properties of a novel silk-derived biopolymer as polymerized in silico from sericin and elastin-like monomers. Molecular Dynamics simulations and Steered Molecular Dynamics were the principal computational methods used, the latter of which applies an external force onto the system and thereby enables an observation of its response to stress. The models explored herein are single-molecule approximations, and primarily serve as tools in a rational design process for the preliminary assessment of properties in a new material candidate. © 2014 Wiley Periodicals, Inc.

Emotion-affected decision making in human simulation.

PubMed

Zhao, Y; Kang, J; Wright, D K

2006-01-01

Human modelling is an interdisciplinary research field. The topic, emotion-affected decision making, was originally a cognitive psychology issue, but is now recognized as an important research direction for both computer science and biomedical modelling. The main aim of this paper is to attempt to bridge the gap between psychology and bioengineering in emotion-affected decision making. The work is based on Ortony's theory of emotions and bounded rationality theory, and attempts to connect the emotion process with decision making. A computational emotion model is proposed, and the initial framework of this model in virtual human simulation within the platform of Virtools is presented.

Agent-based modeling and systems dynamics model reproduction.

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

North, M. J.; Macal, C. M.

2009-01-01

Reproducibility is a pillar of the scientific endeavour. We view computer simulations as laboratories for electronic experimentation and therefore as tools for science. Recent studies have addressed model reproduction and found it to be surprisingly difficult to replicate published findings. There have been enough failed simulation replications to raise the question, 'can computer models be fully replicated?' This paper answers in the affirmative by reporting on a successful reproduction study using Mathematica, Repast and Swarm for the Beer Game supply chain model. The reproduction process was valuable because it demonstrated the original result's robustness across modelling methodologies and implementation environments.

[Clinical and communication simulation workshop for fellows in gastroenterology: the trainees' perspective].

PubMed

Lang, Alon; Melzer, Ehud; Bar-Meir, Simon; Eliakim, Rami; Ziv, Amitai

2006-11-01

The continuing development in computer-based medical simulators provides an ideal platform for simulator-assisted training programs for medical trainees. Computer-based endoscopic simulators provide a virtual reality environment for training endoscopic procedures. This study illustrates the use of a comprehensive training model combining the use of endoscopic simulators with simulated (actor) patients (SP). To evaluate the effectiveness of a comprehensive simulation workshop from the trainee perspective. Four case studies were developed with emphasis on communication skills. Three workshops with 10 fellows in each were conducted. During each workshop the trainees spent half of the time in SP case studies and the remaining half working with computerized endoscopic simulators with continuous guidance by an expert endoscopist. Questionnaires were completed by the fellows at the end of the workshop. Seventy percent of the fellows felt that the endoscopic simulator was close or very close to reality for gastroscopy and 63% for colonoscopy. Eighty eight percent thought the close guidance was important for the learning process with the simulator. Eighty percent felt that the case studies were an important learning experience for risk management. Further evaluation of multi-modality simulation workshops in gastroenterologist training is needed to identify how best to incorporate this form of instruction into training for gastroenterologists.

A high performance computing framework for physics-based modeling and simulation of military ground vehicles

NASA Astrophysics Data System (ADS)

Negrut, Dan; Lamb, David; Gorsich, David

2011-06-01

This paper describes a software infrastructure made up of tools and libraries designed to assist developers in implementing computational dynamics applications running on heterogeneous and distributed computing environments. Together, these tools and libraries compose a so called Heterogeneous Computing Template (HCT). The heterogeneous and distributed computing hardware infrastructure is assumed herein to be made up of a combination of CPUs and Graphics Processing Units (GPUs). The computational dynamics applications targeted to execute on such a hardware topology include many-body dynamics, smoothed-particle hydrodynamics (SPH) fluid simulation, and fluid-solid interaction analysis. The underlying theme of the solution approach embraced by HCT is that of partitioning the domain of interest into a number of subdomains that are each managed by a separate core/accelerator (CPU/GPU) pair. Five components at the core of HCT enable the envisioned distributed computing approach to large-scale dynamical system simulation: (a) the ability to partition the problem according to the one-to-one mapping; i.e., spatial subdivision, discussed above (pre-processing); (b) a protocol for passing data between any two co-processors; (c) algorithms for element proximity computation; and (d) the ability to carry out post-processing in a distributed fashion. In this contribution the components (a) and (b) of the HCT are demonstrated via the example of the Discrete Element Method (DEM) for rigid body dynamics with friction and contact. The collision detection task required in frictional-contact dynamics (task (c) above), is shown to benefit on the GPU of a two order of magnitude gain in efficiency when compared to traditional sequential implementations. Note: Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not imply its endorsement, recommendation, or favoring by the United States Army. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Army, and shall not be used for advertising or product endorsement purposes.

Development of an E-Prime Based Computer Simulation of an Interactive Human Rights Violation Negotiation Script (Developpement d’un Programme de Simulation par Ordinateur Fonde sur le Logiciel E Prime pour la Negociation Interactive en cas de Violation des Droits de la Personne)

DTIC Science & Technology

2010-12-01

Base ( CFB ) Kingston. The computer simulation developed in this project is intended to be used for future research and as a possible training platform...DRDC Toronto No. CR 2010-055 Development of an E-Prime based computer simulation of an interactive Human Rights Violation negotiation script...Abstract This report describes the method of developing an E-Prime computer simulation of an interactive Human Rights Violation (HRV) negotiation. An

Improving the Computational Effort of Set-Inversion-Based Prandial Insulin Delivery for Its Integration in Insulin Pumps

PubMed Central

León-Vargas, Fabian; Calm, Remei; Bondia, Jorge; Vehí, Josep

2012-01-01

Objective Set-inversion-based prandial insulin delivery is a new model-based bolus advisor for postprandial glucose control in type 1 diabetes mellitus (T1DM). It automatically coordinates the values of basal–bolus insulin to be infused during the postprandial period so as to achieve some predefined control objectives. However, the method requires an excessive computation time to compute the solution set of feasible insulin profiles, which impedes its integration into an insulin pump. In this work, a new algorithm is presented, which reduces computation time significantly and enables the integration of this new bolus advisor into current processing features of smart insulin pumps. Methods A new strategy was implemented that focused on finding the combined basal–bolus solution of interest rather than an extensive search of the feasible set of solutions. Analysis of interval simulations, inclusion of physiological assumptions, and search domain contractions were used. Data from six real patients with T1DM were used to compare the performance between the optimized and the conventional computations. Results In all cases, the optimized version yielded the basal–bolus combination recommended by the conventional method and in only 0.032% of the computation time. Simulations show that the mean number of iterations for the optimized computation requires approximately 3.59 s at 20 MHz processing power, in line with current features of smart pumps. Conclusions A computationally efficient method for basal–bolus coordination in postprandial glucose control has been presented and tested. The results indicate that an embedded algorithm within smart insulin pumps is now feasible. Nonetheless, we acknowledge that a clinical trial will be needed in order to justify this claim. PMID:23294789

The impact of 14nm photomask variability and uncertainty on computational lithography solutions

NASA Astrophysics Data System (ADS)

Sturtevant, John; Tejnil, Edita; Buck, Peter D.; Schulze, Steffen; Kalk, Franklin; Nakagawa, Kent; Ning, Guoxiang; Ackmann, Paul; Gans, Fritz; Buergel, Christian

2013-09-01

Computational lithography solutions rely upon accurate process models to faithfully represent the imaging system output for a defined set of process and design inputs. These models rely upon the accurate representation of multiple parameters associated with the scanner and the photomask. Many input variables for simulation are based upon designed or recipe-requested values or independent measurements. It is known, however, that certain measurement methodologies, while precise, can have significant inaccuracies. Additionally, there are known errors associated with the representation of certain system parameters. With shrinking total CD control budgets, appropriate accounting for all sources of error becomes more important, and the cumulative consequence of input errors to the computational lithography model can become significant. In this work, we examine via simulation, the impact of errors in the representation of photomask properties including CD bias, corner rounding, refractive index, thickness, and sidewall angle. The factors that are most critical to be accurately represented in the model are cataloged. CD bias values are based on state of the art mask manufacturing data and other variables changes are speculated, highlighting the need for improved metrology and communication between mask and OPC model experts. The simulations are done by ignoring the wafer photoresist model, and show the sensitivity of predictions to various model inputs associated with the mask. It is shown that the wafer simulations are very dependent upon the 1D/2D representation of the mask and for 3D, that the mask sidewall angle is a very sensitive factor influencing simulated wafer CD results.

Integrating interactive computational modeling in biology curricula.

PubMed

Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

2015-03-01

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Algorithms for Autonomous GPS Orbit Determination and Formation Flying: Investigation of Initialization Approaches and Orbit Determination for HEO

NASA Technical Reports Server (NTRS)

Axelrad, Penina; Speed, Eden; Leitner, Jesse A. (Technical Monitor)

2002-01-01

This report summarizes the efforts to date in processing GPS measurements in High Earth Orbit (HEO) applications by the Colorado Center for Astrodynamics Research (CCAR). Two specific projects were conducted; initialization of the orbit propagation software, GEODE, using nominal orbital elements for the IMEX orbit, and processing of actual and simulated GPS data from the AMSAT satellite using a Doppler-only batch filter. CCAR has investigated a number of approaches for initialization of the GEODE orbit estimator with little a priori information. This document describes a batch solution approach that uses pseudorange or Doppler measurements collected over an orbital arc to compute an epoch state estimate. The algorithm is based on limited orbital element knowledge from which a coarse estimate of satellite position and velocity can be determined and used to initialize GEODE. This algorithm assumes knowledge of nominal orbital elements, (a, e, i, omega, omega) and uses a search on time of perigee passage (tau(sub p)) to estimate the host satellite position within the orbit and the approximate receiver clock bias. Results of the method are shown for a simulation including large orbital uncertainties and measurement errors. In addition, CCAR has attempted to process GPS data from the AMSAT satellite to obtain an initial estimation of the orbit. Limited GPS data have been received to date, with few satellites tracked and no computed point solutions. Unknown variables in the received data have made computations of a precise orbit using the recovered pseudorange difficult. This document describes the Doppler-only batch approach used to compute the AMSAT orbit. Both actual flight data from AMSAT, and simulated data generated using the Satellite Tool Kit and Goddard Space Flight Center's Flight Simulator, were processed. Results for each case and conclusion are presented.

Computer-aided software development process design

NASA Technical Reports Server (NTRS)

Lin, Chi Y.; Levary, Reuven R.

1989-01-01

The authors describe an intelligent tool designed to aid managers of software development projects in planning, managing, and controlling the development process of medium- to large-scale software projects. Its purpose is to reduce uncertainties in the budget, personnel, and schedule planning of software development projects. It is based on dynamic model for the software development and maintenance life-cycle process. This dynamic process is composed of a number of time-varying, interacting developmental phases, each characterized by its intended functions and requirements. System dynamics is used as a modeling methodology. The resulting Software LIfe-Cycle Simulator (SLICS) and the hybrid expert simulation system of which it is a subsystem are described.

Development of optimization-based probabilistic earthquake scenarios for the city of Tehran

NASA Astrophysics Data System (ADS)

Zolfaghari, M. R.; Peyghaleh, E.

2016-01-01

This paper presents the methodology and practical example for the application of optimization process to select earthquake scenarios which best represent probabilistic earthquake hazard in a given region. The method is based on simulation of a large dataset of potential earthquakes, representing the long-term seismotectonic characteristics in a given region. The simulation process uses Monte-Carlo simulation and regional seismogenic source parameters to generate a synthetic earthquake catalogue consisting of a large number of earthquakes, each characterized with magnitude, location, focal depth and fault characteristics. Such catalogue provides full distributions of events in time, space and size; however, demands large computation power when is used for risk assessment, particularly when other sources of uncertainties are involved in the process. To reduce the number of selected earthquake scenarios, a mixed-integer linear program formulation is developed in this study. This approach results in reduced set of optimization-based probabilistic earthquake scenario, while maintaining shape of hazard curves and full probabilistic picture by minimizing the error between hazard curves driven by full and reduced sets of synthetic earthquake scenarios. To test the model, the regional seismotectonic and seismogenic characteristics of northern Iran are used to simulate a set of 10,000-year worth of events consisting of some 84,000 earthquakes. The optimization model is then performed multiple times with various input data, taking into account probabilistic seismic hazard for Tehran city as the main constrains. The sensitivity of the selected scenarios to the user-specified site/return period error-weight is also assessed. The methodology could enhance run time process for full probabilistic earthquake studies like seismic hazard and risk assessment. The reduced set is the representative of the contributions of all possible earthquakes; however, it requires far less computation power. The authors have used this approach for risk assessment towards identification of effectiveness-profitability of risk mitigation measures, using optimization model for resource allocation. Based on the error-computation trade-off, 62-earthquake scenarios are chosen to be used for this purpose.

Model-as-a-service (MaaS) using the cloud service innovation platform (CSIP)

USDA-ARS?s Scientific Manuscript database

Cloud infrastructures for modelling activities such as data processing, performing environmental simulations, or conducting model calibrations/optimizations provide a cost effective alternative to traditional high performance computing approaches. Cloud-based modelling examples emerged into the more...

1D-3D hybrid modeling—from multi-compartment models to full resolution models in space and time

PubMed Central

Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M.; Queisser, Gillian

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator—which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics. PMID:25120463

Combination of inquiry learning model and computer simulation to improve mastery concept and the correlation with critical thinking skills (CTS)

NASA Astrophysics Data System (ADS)

Nugraha, Muhamad Gina; Kaniawati, Ida; Rusdiana, Dadi; Kirana, Kartika Hajar

2016-02-01

Among the purposes of physics learning at high school is to master the physics concepts and cultivate scientific attitude (including critical attitude), develop inductive and deductive reasoning skills. According to Ennis et al., inductive and deductive reasoning skills are part of critical thinking. Based on preliminary studies, both of the competence are lack achieved, it is seen from student learning outcomes is low and learning processes that are not conducive to cultivate critical thinking (teacher-centered learning). One of learning model that predicted can increase mastery concepts and train CTS is inquiry learning model aided computer simulations. In this model, students were given the opportunity to be actively involved in the experiment and also get a good explanation with the computer simulations. From research with randomized control group pretest-posttest design, we found that the inquiry learning model aided computer simulations can significantly improve students' mastery concepts than the conventional (teacher-centered) method. With inquiry learning model aided computer simulations, 20% of students have high CTS, 63.3% were medium and 16.7% were low. CTS greatly contribute to the students' mastery concept with a correlation coefficient of 0.697 and quite contribute to the enhancement mastery concept with a correlation coefficient of 0.603.

Towards constructing multi-bit binary adder based on Belousov-Zhabotinsky reaction

NASA Astrophysics Data System (ADS)

Zhang, Guo-Mao; Wong, Ieong; Chou, Meng-Ta; Zhao, Xin

2012-04-01

It has been proposed that the spatial excitable media can perform a wide range of computational operations, from image processing, to path planning, to logical and arithmetic computations. The realizations in the field of chemical logical and arithmetic computations are mainly concerned with single simple logical functions in experiments. In this study, based on Belousov-Zhabotinsky reaction, we performed simulations toward the realization of a more complex operation, the binary adder. Combining with some of the existing functional structures that have been verified experimentally, we designed a planar geometrical binary adder chemical device. Through numerical simulations, we first demonstrated that the device can implement the function of a single-bit full binary adder. Then we show that the binary adder units can be further extended in plane, and coupled together to realize a two-bit, or even multi-bit binary adder. The realization of chemical adders can guide the constructions of other sophisticated arithmetic functions, ultimately leading to the implementation of chemical computer and other intelligent systems.

Discovery Learning, Representation, and Explanation within a Computer-Based Simulation: Finding the Right Mix

ERIC Educational Resources Information Center

Rieber, Lloyd P.; Tzeng, Shyh-Chii; Tribble, Kelly

2004-01-01

The purpose of this research was to explore how adult users interact and learn during an interactive computer-based simulation supplemented with brief multimedia explanations of the content. A total of 52 college students interacted with a computer-based simulation of Newton's laws of motion in which they had control over the motion of a simple…

Feedback and Elaboration within a Computer-Based Simulation: A Dual Coding Perspective.

ERIC Educational Resources Information Center

Rieber, Lloyd P.; And Others

The purpose of this study was to explore how adult users interact and learn during a computer-based simulation given visual and verbal forms of feedback coupled with embedded elaborations of the content. A total of 52 college students interacted with a computer-based simulation of Newton's laws of motion in which they had control over the motion…

MITT writer and MITT writer advanced development: Developing authoring and training systems for complex technical domains

NASA Technical Reports Server (NTRS)

Wiederholt, Bradley J.; Browning, Elica J.; Norton, Jeffrey E.; Johnson, William B.

1991-01-01

MITT Writer is a software system for developing computer based training for complex technical domains. A training system produced by MITT Writer allows a student to learn and practice troubleshooting and diagnostic skills. The MITT (Microcomputer Intelligence for Technical Training) architecture is a reasonable approach to simulation based diagnostic training. MITT delivers training on available computing equipment, delivers challenging training and simulation scenarios, and has economical development and maintenance costs. A 15 month effort was undertaken in which the MITT Writer system was developed. A workshop was also conducted to train instructors in how to use MITT Writer. Earlier versions were used to develop an Intelligent Tutoring System for troubleshooting the Minuteman Missile Message Processing System.

DEVELOPMENT OF A CHEMICAL PROCESS MODELING ENVIRONMENT BASED ON CAPE-OPEN INTERFACE STANDARDS AND THE MICROSOFT .NET FRAMEWORK

EPA Science Inventory

Chemical process simulation has long been used as a design tool in the development of chemical plants, and has long been considered a means to evaluate different design options. With the advent of large scale computer networks and interface models for program components, it is po...

The Effects of Different Computer-Supported Collaboration Scripts on Students' Learning Processes and Outcome in a Simulation-Based Collaborative Learning Environment

ERIC Educational Resources Information Center

Wieland, Kristina

2010-01-01

Students benefit from collaborative learning activities, but they do not automatically reach desired learning outcomes when working together (Fischer, Kollar, Mandl, & Haake, 2007; King, 2007). Learners need instructional support to increase the quality of collaborative processes and individual learning outcomes. The core challenge is to find…

Trace contaminant control simulation computer program, version 8.1

NASA Technical Reports Server (NTRS)

Perry, J. L.

1994-01-01

The Trace Contaminant Control Simulation computer program is a tool for assessing the performance of various process technologies for removing trace chemical contamination from a spacecraft cabin atmosphere. Included in the simulation are chemical and physical adsorption by activated charcoal, chemical adsorption by lithium hydroxide, absorption by humidity condensate, and low- and high-temperature catalytic oxidation. Means are provided for simulating regenerable as well as nonregenerable systems. The program provides an overall mass balance of chemical contaminants in a spacecraft cabin given specified generation rates. Removal rates are based on device flow rates specified by the user and calculated removal efficiencies based on cabin concentration and removal technology experimental data. Versions 1.0 through 8.0 are documented in NASA TM-108409. TM-108409 also contains a source file listing for version 8.0. Changes to version 8.0 are documented in this technical memorandum and a source file listing for the modified version, version 8.1, is provided. Detailed descriptions for the computer program subprograms are extracted from TM-108409 and modified as necessary to reflect version 8.1. Version 8.1 supersedes version 8.0. Information on a separate user's guide is available from the author.

Modeling the fusion of cylindrical bioink particles in post bioprinting structure formation

NASA Astrophysics Data System (ADS)

McCune, Matt; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

2015-03-01

Cellular Particle Dynamics (CPD) is an effective computational method to describe the shape evolution and biomechanical relaxation processes in multicellular systems. Thus, CPD is a useful tool to predict the outcome of post-printing structure formation in bioprinting. The predictive power of CPD has been demonstrated for multicellular systems composed of spherical bioink units. Experiments and computer simulations were related through an independently developed theoretical formalism based on continuum mechanics. Here we generalize the CPD formalism to (i) include cylindrical bioink particles often used in specific bioprinting applications, (ii) describe the more realistic experimental situation in which both the length and the volume of the cylindrical bioink units decrease during post-printing structure formation, and (iii) directly connect CPD simulations to the corresponding experiments without the need of the intermediate continuum theory inherently based on simplifying assumptions. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

Numerical simulation of transient temperature profiles for canned apple puree in semi-rigid aluminum based packaging during pasteurization.

PubMed

Shafiekhani, Soraya; Zamindar, Nafiseh; Hojatoleslami, Mohammad; Toghraie, Davood

2016-06-01

Pasteurization of canned apple puree was simulated for a 3-D geometry in a semi-rigid aluminum based container which was heated from all sides at 378 K. The computational fluid dynamics code Ansys Fluent 14.0 was used and the governing equations for energy, momentum, and continuity were computed using a finite volume method. The food model was assumed to have temperature-dependent properties. To validate the simulation, the apple puree was pasteurized in a water cascading retort. The effect of the mesh structures was studied for the temperature profiles during thermal processing. The experimental temperature in the slowest heating zone in the container was compared with the temperature predicted by the model and the difference was not significant. The study also investigated the impact of head space (water-vapor) on heat transfer.

Physically Based Virtual Surgery Planning and Simulation Tools for Personal Health Care Systems

NASA Astrophysics Data System (ADS)

Dogan, Firat; Atilgan, Yasemin

The virtual surgery planning and simulation tools have gained a great deal of importance in the last decade in a consequence of increasing capacities at the information technology level. The modern hardware architectures, large scale database systems, grid based computer networks, agile development processes, better 3D visualization and all the other strong aspects of the information technology brings necessary instruments into almost every desk. The last decade’s special software and sophisticated super computer environments are now serving to individual needs inside “tiny smart boxes” for reasonable prices. However, resistance to learning new computerized environments, insufficient training and all the other old habits prevents effective utilization of IT resources by the specialists of the health sector. In this paper, all the aspects of the former and current developments in surgery planning and simulation related tools are presented, future directions and expectations are investigated for better electronic health care systems.

A coarse-grid-projection acceleration method for finite-element incompressible flow computations

NASA Astrophysics Data System (ADS)

Kashefi, Ali; Staples, Anne; FiN Lab Team

2015-11-01

Coarse grid projection (CGP) methodology provides a framework for accelerating computations by performing some part of the computation on a coarsened grid. We apply the CGP to pressure projection methods for finite element-based incompressible flow simulations. Based on it, the predicted velocity field data is restricted to a coarsened grid, the pressure is determined by solving the Poisson equation on the coarse grid, and the resulting data are prolonged to the preset fine grid. The contributions of the CGP method to the pressure correction technique are twofold: first, it substantially lessens the computational cost devoted to the Poisson equation, which is the most time-consuming part of the simulation process. Second, it preserves the accuracy of the velocity field. The velocity and pressure spaces are approximated by Galerkin spectral element using piecewise linear basis functions. A restriction operator is designed so that fine data are directly injected into the coarse grid. The Laplacian and divergence matrices are driven by taking inner products of coarse grid shape functions. Linear interpolation is implemented to construct a prolongation operator. A study of the data accuracy and the CPU time for the CGP-based versus non-CGP computations is presented. Laboratory for Fluid Dynamics in Nature.

Computer simulation of the NASA water vapor electrolysis reactor

NASA Technical Reports Server (NTRS)

Bloom, A. M.

1974-01-01

The water vapor electrolysis (WVE) reactor is a spacecraft waste reclamation system for extended-mission manned spacecraft. The WVE reactor's raw material is water, its product oxygen. A computer simulation of the WVE operational processes provided the data required for an optimal design of the WVE unit. The simulation process was implemented with the aid of a FORTRAN IV routine.

A Component-Based FPGA Design Framework for Neuronal Ion Channel Dynamics Simulations

PubMed Central

Mak, Terrence S. T.; Rachmuth, Guy; Lam, Kai-Pui; Poon, Chi-Sang

2008-01-01

Neuron-machine interfaces such as dynamic clamp and brain-implantable neuroprosthetic devices require real-time simulations of neuronal ion channel dynamics. Field Programmable Gate Array (FPGA) has emerged as a high-speed digital platform ideal for such application-specific computations. We propose an efficient and flexible component-based FPGA design framework for neuronal ion channel dynamics simulations, which overcomes certain limitations of the recently proposed memory-based approach. A parallel processing strategy is used to minimize computational delay, and a hardware-efficient factoring approach for calculating exponential and division functions in neuronal ion channel models is used to conserve resource consumption. Performances of the various FPGA design approaches are compared theoretically and experimentally in corresponding implementations of the AMPA and NMDA synaptic ion channel models. Our results suggest that the component-based design framework provides a more memory economic solution as well as more efficient logic utilization for large word lengths, whereas the memory-based approach may be suitable for time-critical applications where a higher throughput rate is desired. PMID:17190033

Analyst-to-Analyst Variability in Simulation-Based Prediction

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

Glickman, Matthew R.; Romero, Vicente J.

This report describes findings from the culminating experiment of the LDRD project entitled, "Analyst-to-Analyst Variability in Simulation-Based Prediction". For this experiment, volunteer participants solving a given test problem in engineering and statistics were interviewed at different points in their solution process. These interviews are used to trace differing solutions to differing solution processes, and differing processes to differences in reasoning, assumptions, and judgments. The issue that the experiment was designed to illuminate -- our paucity of understanding of the ways in which humans themselves have an impact on predictions derived from complex computational simulations -- is a challenging and openmore » one. Although solution of the test problem by analyst participants in this experiment has taken much more time than originally anticipated, and is continuing past the end of this LDRD, this project has provided a rare opportunity to explore analyst-to-analyst variability in significant depth, from which we derive evidence-based insights to guide further explorations in this important area.« less

Development of process control capability through the Browns Ferry Integrated Computer System using Reactor Water Clanup System as an example. Final report

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

Smith, J.; Mowrey, J.

1995-12-01

This report describes the design, development and testing of process controls for selected system operations in the Browns Ferry Nuclear Plant (BFNP) Reactor Water Cleanup System (RWCU) using a Computer Simulation Platform which simulates the RWCU System and the BFNP Integrated Computer System (ICS). This system was designed to demonstrate the feasibility of the soft control (video touch screen) of nuclear plant systems through an operator console. The BFNP Integrated Computer System, which has recently. been installed at BFNP Unit 2, was simulated to allow for operator control functions of the modeled RWCU system. The BFNP Unit 2 RWCU systemmore » was simulated using the RELAP5 Thermal/Hydraulic Simulation Model, which provided the steady-state and transient RWCU process variables and simulated the response of the system to control system inputs. Descriptions of the hardware and software developed are also included in this report. The testing and acceptance program and results are also detailed in this report. A discussion of potential installation of an actual RWCU process control system in BFNP Unit 2 is included. Finally, this report contains a section on industry issues associated with installation of process control systems in nuclear power plants.« less

Kinetic Monte Carlo Simulation of Cation Diffusion in Low-K Ceramics

NASA Technical Reports Server (NTRS)

Good, Brian

2013-01-01

Low thermal conductivity (low-K) ceramic materials are of interest to the aerospace community for use as the thermal barrier component of coating systems for turbine engine components. In particular, zirconia-based materials exhibit both low thermal conductivity and structural stability at high temperature, making them suitable for such applications. Because creep is one of the potential failure modes, and because diffusion is a mechanism by which creep takes place, we have performed computer simulations of cation diffusion in a variety of zirconia-based low-K materials. The kinetic Monte Carlo simulation method is an alternative to the more widely known molecular dynamics (MD) method. It is designed to study "infrequent-event" processes, such as diffusion, for which MD simulation can be highly inefficient. We describe the results of kinetic Monte Carlo computer simulations of cation diffusion in several zirconia-based materials, specifically, zirconia doped with Y, Gd, Nb and Yb. Diffusion paths are identified, and migration energy barriers are obtained from density functional calculations and from the literature. We present results on the temperature dependence of the diffusivity, and on the effects of the presence of oxygen vacancies in cation diffusion barrier complexes as well.

Queueing Network Models for Parallel Processing of Task Systems: an Operational Approach

NASA Technical Reports Server (NTRS)

Mak, Victor W. K.

1986-01-01

Computer performance modeling of possibly complex computations running on highly concurrent systems is considered. Earlier works in this area either dealt with a very simple program structure or resulted in methods with exponential complexity. An efficient procedure is developed to compute the performance measures for series-parallel-reducible task systems using queueing network models. The procedure is based on the concept of hierarchical decomposition and a new operational approach. Numerical results for three test cases are presented and compared to those of simulations.

SAGRAD: A Program for Neural Network Training with Simulated Annealing and the Conjugate Gradient Method

PubMed Central

Bernal, Javier; Torres-Jimenez, Jose

2015-01-01

SAGRAD (Simulated Annealing GRADient), a Fortran 77 program for computing neural networks for classification using batch learning, is discussed. Neural network training in SAGRAD is based on a combination of simulated annealing and Møller’s scaled conjugate gradient algorithm, the latter a variation of the traditional conjugate gradient method, better suited for the nonquadratic nature of neural networks. Different aspects of the implementation of the training process in SAGRAD are discussed, such as the efficient computation of gradients and multiplication of vectors by Hessian matrices that are required by Møller’s algorithm; the (re)initialization of weights with simulated annealing required to (re)start Møller’s algorithm the first time and each time thereafter that it shows insufficient progress in reaching a possibly local minimum; and the use of simulated annealing when Møller’s algorithm, after possibly making considerable progress, becomes stuck at a local minimum or flat area of weight space. Outlines of the scaled conjugate gradient algorithm, the simulated annealing procedure and the training process used in SAGRAD are presented together with results from running SAGRAD on two examples of training data. PMID:26958442

Research on monocentric model of urbanization by agent-based simulation

NASA Astrophysics Data System (ADS)

Xue, Ling; Yang, Kaizhong

2008-10-01

Over the past years, GIS have been widely used for modeling urbanization from a variety of perspectives such as digital terrain representation and overlay analysis using cell-based data platform. Similarly, simulation of urban dynamics has been achieved with the use of Cellular Automata. In contrast to these approaches, agent-based simulation provides a much more powerful set of tools. This allows researchers to set up a counterpart for real environmental and urban systems in computer for experimentation and scenario analysis. This Paper basically reviews the research on the economic mechanism of urbanization and an agent-based monocentric model is setup for further understanding the urbanization process and mechanism in China. We build an endogenous growth model with dynamic interactions between spatial agglomeration and urban development by using agent-based simulation. It simulates the migration decisions of two main types of agents, namely rural and urban households between rural and urban area. The model contains multiple economic interactions that are crucial in understanding urbanization and industrial process in China. These adaptive agents can adjust their supply and demand according to the market situation by a learning algorithm. The simulation result shows this agent-based urban model is able to perform the regeneration and to produce likely-to-occur projections of reality.

An Investigation of Computer-based Simulations for School Crises Management.

ERIC Educational Resources Information Center

Degnan, Edward; Bozeman, William

2001-01-01

Describes development of a computer-based simulation program for training school personnel in crisis management. Addresses the data collection and analysis involved in developing a simulated event, the systems requirements for simulation, and a case study of application and use of the completed simulation. (Contains 21 references.) (Authors/PKP)

Web-based system for surgical planning and simulation

NASA Astrophysics Data System (ADS)

Eldeib, Ayman M.; Ahmed, Mohamed N.; Farag, Aly A.; Sites, C. B.

1998-10-01

The growing scientific knowledge and rapid progress in medical imaging techniques has led to an increasing demand for better and more efficient methods of remote access to high-performance computer facilities. This paper introduces a web-based telemedicine project that provides interactive tools for surgical simulation and planning. The presented approach makes use of client-server architecture based on new internet technology where clients use an ordinary web browser to view, send, receive and manipulate patients' medical records while the server uses the supercomputer facility to generate online semi-automatic segmentation, 3D visualization, surgical simulation/planning and neuroendoscopic procedures navigation. The supercomputer (SGI ONYX 1000) is located at the Computer Vision and Image Processing Lab, University of Louisville, Kentucky. This system is under development in cooperation with the Department of Neurological Surgery, Alliant Health Systems, Louisville, Kentucky. The server is connected via a network to the Picture Archiving and Communication System at Alliant Health Systems through a DICOM standard interface that enables authorized clients to access patients' images from different medical modalities.

Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I

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

Schmalz, Mark S

2011-07-24

Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G}more » for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient parallel computation of particle and fluid dynamics simulations. These problems occur throughout DOE, military and commercial sectors: the potential payoff is high. We plan to license or sell the solution to contractors for military and domestic applications such as disaster simulation (aerodynamic and hydrodynamic), Government agencies (hydrological and environmental simulations), and medical applications (e.g., in tomographic image reconstruction). Keywords - High-performance Computing, Graphic Processing Unit, Fluid/Particle Simulation. Summary for Members of Congress - Department of Energy has many simulation codes that must compute faster, to be effective. The Phase I research parallelized particle/fluid simulations for rocket combustion, for high-performance computing systems.« less

Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience

PubMed Central

Mulugeta, Lealem; Drach, Andrew; Erdemir, Ahmet; Hunt, C. A.; Horner, Marc; Ku, Joy P.; Myers Jr., Jerry G.; Vadigepalli, Rajanikanth; Lytton, William W.

2018-01-01

Modeling and simulation in computational neuroscience is currently a research enterprise to better understand neural systems. It is not yet directly applicable to the problems of patients with brain disease. To be used for clinical applications, there must not only be considerable progress in the field but also a concerted effort to use best practices in order to demonstrate model credibility to regulatory bodies, to clinics and hospitals, to doctors, and to patients. In doing this for neuroscience, we can learn lessons from long-standing practices in other areas of simulation (aircraft, computer chips), from software engineering, and from other biomedical disciplines. In this manuscript, we introduce some basic concepts that will be important in the development of credible clinical neuroscience models: reproducibility and replicability; verification and validation; model configuration; and procedures and processes for credible mechanistic multiscale modeling. We also discuss how garnering strong community involvement can promote model credibility. Finally, in addition to direct usage with patients, we note the potential for simulation usage in the area of Simulation-Based Medical Education, an area which to date has been primarily reliant on physical models (mannequins) and scenario-based simulations rather than on numerical simulations. PMID:29713272

Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience.

PubMed

Mulugeta, Lealem; Drach, Andrew; Erdemir, Ahmet; Hunt, C A; Horner, Marc; Ku, Joy P; Myers, Jerry G; Vadigepalli, Rajanikanth; Lytton, William W

2018-01-01

Modeling and simulation in computational neuroscience is currently a research enterprise to better understand neural systems. It is not yet directly applicable to the problems of patients with brain disease. To be used for clinical applications, there must not only be considerable progress in the field but also a concerted effort to use best practices in order to demonstrate model credibility to regulatory bodies, to clinics and hospitals, to doctors, and to patients. In doing this for neuroscience, we can learn lessons from long-standing practices in other areas of simulation (aircraft, computer chips), from software engineering, and from other biomedical disciplines. In this manuscript, we introduce some basic concepts that will be important in the development of credible clinical neuroscience models: reproducibility and replicability; verification and validation; model configuration; and procedures and processes for credible mechanistic multiscale modeling. We also discuss how garnering strong community involvement can promote model credibility. Finally, in addition to direct usage with patients, we note the potential for simulation usage in the area of Simulation-Based Medical Education, an area which to date has been primarily reliant on physical models (mannequins) and scenario-based simulations rather than on numerical simulations.

Digital system for structural dynamics simulation

NASA Technical Reports Server (NTRS)

Krauter, A. I.; Lagace, L. J.; Wojnar, M. K.; Glor, C.

1982-01-01

State-of-the-art digital hardware and software for the simulation of complex structural dynamic interactions, such as those which occur in rotating structures (engine systems). System were incorporated in a designed to use an array of processors in which the computation for each physical subelement or functional subsystem would be assigned to a single specific processor in the simulator. These node processors are microprogrammed bit-slice microcomputers which function autonomously and can communicate with each other and a central control minicomputer over parallel digital lines. Inter-processor nearest neighbor communications busses pass the constants which represent physical constraints and boundary conditions. The node processors are connected to the six nearest neighbor node processors to simulate the actual physical interface of real substructures. Computer generated finite element mesh and force models can be developed with the aid of the central control minicomputer. The control computer also oversees the animation of a graphics display system, disk-based mass storage along with the individual processing elements.

Ultracold-atom quantum simulator for attosecond science

NASA Astrophysics Data System (ADS)

Sala, Simon; Förster, Johann; Saenz, Alejandro

2017-01-01

A quantum simulator based on ultracold optically trapped atoms for simulating the physics of atoms and molecules in ultrashort intense laser fields is introduced. The slowing down by about 13 orders of magnitude allows one to watch in slow motion the tunneling and recollision processes that form the heart of attosecond science. The extreme flexibility of the simulator promises a deeper understanding of strong-field physics, especially for many-body systems beyond the reach of classical computers. The quantum simulator can experimentally straightforwardly be realized and is shown to recover the ionization characteristics of atoms in the different regimes of laser-matter interaction.

Virtual fragment preparation for computational fragment-based drug design.

PubMed

Ludington, Jennifer L

2015-01-01

Fragment-based drug design (FBDD) has become an important component of the drug discovery process. The use of fragments can accelerate both the search for a hit molecule and the development of that hit into a lead molecule for clinical testing. In addition to experimental methodologies for FBDD such as NMR and X-ray Crystallography screens, computational techniques are playing an increasingly important role. The success of the computational simulations is due in large part to how the database of virtual fragments is prepared. In order to prepare the fragments appropriately it is necessary to understand how FBDD differs from other approaches and the issues inherent in building up molecules from smaller fragment pieces. The ultimate goal of these calculations is to link two or more simulated fragments into a molecule that has an experimental binding affinity consistent with the additive predicted binding affinities of the virtual fragments. Computationally predicting binding affinities is a complex process, with many opportunities for introducing error. Therefore, care should be taken with the fragment preparation procedure to avoid introducing additional inaccuracies.This chapter is focused on the preparation process used to create a virtual fragment database. Several key issues of fragment preparation which affect the accuracy of binding affinity predictions are discussed. The first issue is the selection of the two-dimensional atomic structure of the virtual fragment. Although the particular usage of the fragment can affect this choice (i.e., whether the fragment will be used for calibration, binding site characterization, hit identification, or lead optimization), general factors such as synthetic accessibility, size, and flexibility are major considerations in selecting the 2D structure. Other aspects of preparing the virtual fragments for simulation are the generation of three-dimensional conformations and the assignment of the associated atomic point charges.

Simulations in Cyber-Security: A Review of Cognitive Modeling of Network Attackers, Defenders, and Users.

PubMed

Veksler, Vladislav D; Buchler, Norbou; Hoffman, Blaine E; Cassenti, Daniel N; Sample, Char; Sugrim, Shridat

2018-01-01

Computational models of cognitive processes may be employed in cyber-security tools, experiments, and simulations to address human agency and effective decision-making in keeping computational networks secure. Cognitive modeling can addresses multi-disciplinary cyber-security challenges requiring cross-cutting approaches over the human and computational sciences such as the following: (a) adversarial reasoning and behavioral game theory to predict attacker subjective utilities and decision likelihood distributions, (b) human factors of cyber tools to address human system integration challenges, estimation of defender cognitive states, and opportunities for automation, (c) dynamic simulations involving attacker, defender, and user models to enhance studies of cyber epidemiology and cyber hygiene, and (d) training effectiveness research and training scenarios to address human cyber-security performance, maturation of cyber-security skill sets, and effective decision-making. Models may be initially constructed at the group-level based on mean tendencies of each subject's subgroup, based on known statistics such as specific skill proficiencies, demographic characteristics, and cultural factors. For more precise and accurate predictions, cognitive models may be fine-tuned to each individual attacker, defender, or user profile, and updated over time (based on recorded behavior) via techniques such as model tracing and dynamic parameter fitting.

2D modeling of direct laser metal deposition process using a finite particle method

NASA Astrophysics Data System (ADS)

Anedaf, T.; Abbès, B.; Abbès, F.; Li, Y. M.

2018-05-01

Direct laser metal deposition is one of the material additive manufacturing processes used to produce complex metallic parts. A thorough understanding of the underlying physical phenomena is required to obtain a high-quality parts. In this work, a mathematical model is presented to simulate the coaxial laser direct deposition process tacking into account of mass addition, heat transfer, and fluid flow with free surface and melting. The fluid flow in the melt pool together with mass and energy balances are solved using the Computational Fluid Dynamics (CFD) software NOGRID-points, based on the meshless Finite Pointset Method (FPM). The basis of the computations is a point cloud, which represents the continuum fluid domain. Each finite point carries all fluid information (density, velocity, pressure and temperature). The dynamic shape of the molten zone is explicitly described by the point cloud. The proposed model is used to simulate a single layer cladding.

Exploring the physical layer frontiers of cellular uplink: The Vienna LTE-A Uplink Simulator.

PubMed

Zöchmann, Erich; Schwarz, Stefan; Pratschner, Stefan; Nagel, Lukas; Lerch, Martin; Rupp, Markus

Communication systems in practice are subject to many technical/technological constraints and restrictions. Multiple input, multiple output (MIMO) processing in current wireless communications, as an example, mostly employs codebook-based pre-coding to save computational complexity at the transmitters and receivers. In such cases, closed form expressions for capacity or bit-error probability are often unattainable; effects of realistic signal processing algorithms on the performance of practical communication systems rather have to be studied in simulation environments. The Vienna LTE-A Uplink Simulator is a 3GPP LTE-A standard compliant MATLAB-based link level simulator that is publicly available under an academic use license, facilitating reproducible evaluations of signal processing algorithms and transceiver designs in wireless communications. This paper reviews research results that have been obtained by means of the Vienna LTE-A Uplink Simulator, highlights the effects of single-carrier frequency-division multiplexing (as the distinguishing feature to LTE-A downlink), extends known link adaptation concepts to uplink transmission, shows the implications of the uplink pilot pattern for gathering channel state information at the receiver and completes with possible future research directions.

Teaching Simulation and Modelling at Royal Military College.

ERIC Educational Resources Information Center

Bonin, Hugues W.; Weir, Ronald D.

1984-01-01

Describes a course designed to assist students in writing differential equations to represent chemical processes and to solve these problems on digital computers. Course outline and discussion of computer projects and the simulation and optimization of a continuously stirred tank reactor process are included. (JN)

Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains

NASA Technical Reports Server (NTRS)

Glaessgen, E. H.; Saether, E.; Yamakov, V.

2008-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, current analysis is limited to small domains and increasing the size of the MD domain quickly presents intractable computational demands. A preferred approach to surmount this computational limitation has been to combine continuum mechanics-based modeling procedures, such as the finite element method (FEM), with MD analyses thereby reducing the region of atomic scale refinement. Such multiscale modeling strategies can be divided into two broad classifications: concurrent multiscale methods that directly incorporate an atomistic domain within a continuum domain and sequential multiscale methods that extract an averaged response from the atomistic simulation for later use as a constitutive model in a continuum analysis.

Failure Analysis of a Sheet Metal Blanking Process Based on Damage Coupling Model

NASA Astrophysics Data System (ADS)

Wen, Y.; Chen, Z. H.; Zang, Y.

2013-11-01

In this paper, a blanking process of sheet metal is studied by the methods of numerical simulation and experimental observation. The effects of varying technological parameters related to the quality of products are investigated. An elastoplastic constitutive equation accounting for isotropic ductile damage is implemented into the finite element code ABAQUS with a user-defined material subroutine UMAT. The simulations of the damage evolution and ductile fracture in a sheet metal blanking process have been carried out by the FEM. In order to guarantee computation accuracy and avoid numerical divergence during large plastic deformation, a specified remeshing technique is successively applied when severe element distortion occurs. In the simulation, the evolutions of damage at different stage of the blanking process have been evaluated and the distributions of damage obtained from simulation are in proper agreement with the experimental results.

Scalable Cloning on Large-Scale GPU Platforms with Application to Time-Stepped Simulations on Grids

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

Yoginath, Srikanth B.; Perumalla, Kalyan S.

Cloning is a technique to efficiently simulate a tree of multiple what-if scenarios that are unraveled during the course of a base simulation. However, cloned execution is highly challenging to realize on large, distributed memory computing platforms, due to the dynamic nature of the computational load across clones, and due to the complex dependencies spanning the clone tree. In this paper, we present the conceptual simulation framework, algorithmic foundations, and runtime interface of CloneX, a new system we designed for scalable simulation cloning. It efficiently and dynamically creates whole logical copies of a dynamic tree of simulations across a largemore » parallel system without full physical duplication of computation and memory. The performance of a prototype implementation executed on up to 1,024 graphical processing units of a supercomputing system has been evaluated with three benchmarks—heat diffusion, forest fire, and disease propagation models—delivering a speed up of over two orders of magnitude compared to replicated runs. Finally, the results demonstrate a significantly faster and scalable way to execute many what-if scenario ensembles of large simulations via cloning using the CloneX interface.« less

Scalable Cloning on Large-Scale GPU Platforms with Application to Time-Stepped Simulations on Grids

DOE PAGES

Yoginath, Srikanth B.; Perumalla, Kalyan S.

2018-01-31

Cloning is a technique to efficiently simulate a tree of multiple what-if scenarios that are unraveled during the course of a base simulation. However, cloned execution is highly challenging to realize on large, distributed memory computing platforms, due to the dynamic nature of the computational load across clones, and due to the complex dependencies spanning the clone tree. In this paper, we present the conceptual simulation framework, algorithmic foundations, and runtime interface of CloneX, a new system we designed for scalable simulation cloning. It efficiently and dynamically creates whole logical copies of a dynamic tree of simulations across a largemore » parallel system without full physical duplication of computation and memory. The performance of a prototype implementation executed on up to 1,024 graphical processing units of a supercomputing system has been evaluated with three benchmarks—heat diffusion, forest fire, and disease propagation models—delivering a speed up of over two orders of magnitude compared to replicated runs. Finally, the results demonstrate a significantly faster and scalable way to execute many what-if scenario ensembles of large simulations via cloning using the CloneX interface.« less

Data and Workflow Management Challenges in Global Adjoint Tomography

NASA Astrophysics Data System (ADS)

Lei, W.; Ruan, Y.; Smith, J. A.; Modrak, R. T.; Orsvuran, R.; Krischer, L.; Chen, Y.; Balasubramanian, V.; Hill, J.; Turilli, M.; Bozdag, E.; Lefebvre, M. P.; Jha, S.; Tromp, J.

2017-12-01

It is crucial to take the complete physics of wave propagation into account in seismic tomography to further improve the resolution of tomographic images. The adjoint method is an efficient way of incorporating 3D wave simulations in seismic tomography. However, global adjoint tomography is computationally expensive, requiring thousands of wavefield simulations and massive data processing. Through our collaboration with the Oak Ridge National Laboratory (ORNL) computing group and an allocation on Titan, ORNL's GPU-accelerated supercomputer, we are now performing our global inversions by assimilating waveform data from over 1,000 earthquakes. The first challenge we encountered is dealing with the sheer amount of seismic data. Data processing based on conventional data formats and processing tools (such as SAC), which are not designed for parallel systems, becomes our major bottleneck. To facilitate the data processing procedures, we designed the Adaptive Seismic Data Format (ASDF) and developed a set of Python-based processing tools to replace legacy FORTRAN-based software. These tools greatly enhance reproducibility and accountability while taking full advantage of highly parallel system and showing superior scaling on modern computational platforms. The second challenge is that the data processing workflow contains more than 10 sub-procedures, making it delicate to handle and prone to human mistakes. To reduce human intervention as much as possible, we are developing a framework specifically designed for seismic inversion based on the state-of-the art workflow management research, specifically the Ensemble Toolkit (EnTK), in collaboration with the RADICAL team from Rutgers University. Using the initial developments of the EnTK, we are able to utilize the full computing power of the data processing cluster RHEA at ORNL while keeping human interaction to a minimum and greatly reducing the data processing time. Thanks to all the improvements, we are now able to perform iterations fast enough on more than a 1,000 earthquakes dataset. Starting from model GLAD-M15 (Bozdag et al., 2016), an elastic 3D model with a transversely isotropic upper mantle, we have successfully performed 5 iterations. Our goal is to finish 10 iterations, i.e., generating GLAD M25* by the end of this year.

Radar target classification studies: Software development and documentation

NASA Astrophysics Data System (ADS)

Kamis, A.; Garber, F.; Walton, E.

1985-09-01

Three computer programs were developed to process and analyze calibrated radar returns. The first program, called DATABASE, was developed to create and manage a random accessed data base. The second program, called FTRAN DB, was developed to process horizontal and vertical polarizations radar returns into different formats (i.e., time domain, circular polarizations and polarization parameters). The third program, called RSSE, was developed to simulate a variety of radar systems and to evaluate their ability to identify radar returns. Complete computer listings are included in the appendix volumes.

A novel track-before-detect algorithm based on optimal nonlinear filtering for detecting and tracking infrared dim target

NASA Astrophysics Data System (ADS)

Tian, Yuexin; Gao, Kun; Liu, Ying; Han, Lu

2015-08-01

Aiming at the nonlinear and non-Gaussian features of the real infrared scenes, an optimal nonlinear filtering based algorithm for the infrared dim target tracking-before-detecting application is proposed. It uses the nonlinear theory to construct the state and observation models and uses the spectral separation scheme based Wiener chaos expansion method to resolve the stochastic differential equation of the constructed models. In order to improve computation efficiency, the most time-consuming operations independent of observation data are processed on the fore observation stage. The other observation data related rapid computations are implemented subsequently. Simulation results show that the algorithm possesses excellent detection performance and is more suitable for real-time processing.

Using PC Software To Enhance the Student's Ability To Learn the Exporting Process.

ERIC Educational Resources Information Center

Buckles, Tom A.; Lange, Irene

This paper describes the advantages of using computer simulations in the classroom or managerial environment and the major premise and principal components of Export to Win!, a computer simulation used in international marketing seminars. A rationale for using computer simulations argues that they improve the quality of teaching by building…

Fluid Structure Interaction Techniques For Extrusion And Mixing Processes

NASA Astrophysics Data System (ADS)

Valette, Rudy; Vergnes, Bruno; Coupez, Thierry

2007-05-01

This work focuses on the development of numerical techniques devoted to the simulation of mixing processes of complex fluids such as twin-screw extrusion or batch mixing. In mixing process simulation, the absence of symmetry of the moving boundaries (the screws or the rotors) implies that their rigid body motion has to be taken into account by using a special treatment We therefore use a mesh immersion technique (MIT), which consists in using a P1+/P1-based (MINI-element) mixed finite element method for solving the velocity-pressure problem and then solving the problem in the whole barrel cavity by imposing a rigid motion (rotation) to nodes found located inside the so called immersed domain, each sub-domain (screw, rotor) being represented by a surface CAD mesh (or its mathematical equation in simple cases). The independent meshes are immersed into a unique background computational mesh by computing the distance function to their boundaries. Intersections of meshes are accounted for, allowing to compute a fill factor usable as for the VOF methodology. This technique, combined with the use of parallel computing, allows to compute the time-dependent flow of generalized Newtonian fluids including yield stress fluids in a complex system such as a twin screw extruder, including moving free surfaces, which are treated by a "level set" and Hamilton-Jacobi method.

Computational analysis of fluid dynamics in pharmaceutical freeze-drying.

PubMed

Alexeenko, Alina A; Ganguly, Arnab; Nail, Steven L

2009-09-01

Analysis of water vapor flows encountered in pharmaceutical freeze-drying systems, laboratory-scale and industrial, is presented based on the computational fluid dynamics (CFD) techniques. The flows under continuum gas conditions are analyzed using the solution of the Navier-Stokes equations whereas the rarefied flow solutions are obtained by the direct simulation Monte Carlo (DSMC) method for the Boltzmann equation. Examples of application of CFD techniques to laboratory-scale and industrial scale freeze-drying processes are discussed with an emphasis on the utility of CFD for improvement of design and experimental characterization of pharmaceutical freeze-drying hardware and processes. The current article presents a two-dimensional simulation of a laboratory scale dryer with an emphasis on the importance of drying conditions and hardware design on process control and a three-dimensional simulation of an industrial dryer containing a comparison of the obtained results with analytical viscous flow solutions. It was found that the presence of clean in place (CIP)/sterilize in place (SIP) piping in the duct lead to significant changes in the flow field characteristics. The simulation results for vapor flow rates in an industrial freeze-dryer have been compared to tunable diode laser absorption spectroscopy (TDLAS) and gravimetric measurements.

On the Validity of Continuum Computational Fluid Dynamics Approach Under Very Low-Pressure Plasma Spray Conditions

NASA Astrophysics Data System (ADS)

Ivchenko, Dmitrii; Zhang, Tao; Mariaux, Gilles; Vardelle, Armelle; Goutier, Simon; Itina, Tatiana E.

2018-01-01

Plasma spray physical vapor deposition aims to substantially evaporate powders in order to produce coatings with various microstructures. This is achieved by powder vapor condensation onto the substrate and/or by deposition of fine melted powder particles and nanoclusters. The deposition process typically operates at pressures ranging between 10 and 200 Pa. In addition to the experimental works, numerical simulations are performed to better understand the process and optimize the experimental conditions. However, the combination of high temperatures and low pressure with shock waves initiated by supersonic expansion of the hot gas in the low-pressure medium makes doubtful the applicability of the continuum approach for the simulation of such a process. This work investigates (1) effects of the pressure dependence of thermodynamic and transport properties on computational fluid dynamics (CFD) predictions and (2) the validity of the continuum approach for thermal plasma flow simulation under very low-pressure conditions. The study compares the flow fields predicted with a continuum approach using CFD software with those obtained by a kinetic-based approach using a direct simulation Monte Carlo method (DSMC). It also shows how the presence of high gradients can contribute to prediction errors for typical PS-PVD conditions.

A static data flow simulation study at Ames Research Center

NASA Technical Reports Server (NTRS)

Barszcz, Eric; Howard, Lauri S.

1987-01-01

Demands in computational power, particularly in the area of computational fluid dynamics (CFD), led NASA Ames Research Center to study advanced computer architectures. One architecture being studied is the static data flow architecture based on research done by Jack B. Dennis at MIT. To improve understanding of this architecture, a static data flow simulator, written in Pascal, has been implemented for use on a Cray X-MP/48. A matrix multiply and a two-dimensional fast Fourier transform (FFT), two algorithms used in CFD work at Ames, have been run on the simulator. Execution times can vary by a factor of more than 2 depending on the partitioning method used to assign instructions to processing elements. Service time for matching tokens has proved to be a major bottleneck. Loop control and array address calculation overhead can double the execution time. The best sustained MFLOPS rates were less than 50% of the maximum capability of the machine.

Seismic waveform modeling over cloud

NASA Astrophysics Data System (ADS)

Luo, Cong; Friederich, Wolfgang

2016-04-01

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

Development of computational small animal models and their applications in preclinical imaging and therapy research.

PubMed

Xie, Tianwu; Zaidi, Habib

2016-01-01

The development of multimodality preclinical imaging techniques and the rapid growth of realistic computer simulation tools have promoted the construction and application of computational laboratory animal models in preclinical research. Since the early 1990s, over 120 realistic computational animal models have been reported in the literature and used as surrogates to characterize the anatomy of actual animals for the simulation of preclinical studies involving the use of bioluminescence tomography, fluorescence molecular tomography, positron emission tomography, single-photon emission computed tomography, microcomputed tomography, magnetic resonance imaging, and optical imaging. Other applications include electromagnetic field simulation, ionizing and nonionizing radiation dosimetry, and the development and evaluation of new methodologies for multimodality image coregistration, segmentation, and reconstruction of small animal images. This paper provides a comprehensive review of the history and fundamental technologies used for the development of computational small animal models with a particular focus on their application in preclinical imaging as well as nonionizing and ionizing radiation dosimetry calculations. An overview of the overall process involved in the design of these models, including the fundamental elements used for the construction of different types of computational models, the identification of original anatomical data, the simulation tools used for solving various computational problems, and the applications of computational animal models in preclinical research. The authors also analyze the characteristics of categories of computational models (stylized, voxel-based, and boundary representation) and discuss the technical challenges faced at the present time as well as research needs in the future.

A PC-based simulation of the National Transonic Facitity's safety microprocessor

NASA Technical Reports Server (NTRS)

Thibodeaux, J. J.; Kilgore, W. A.; Balakrishna, S.

1993-01-01

A brief study was undertaken to demonstrate the feasibility of using a state-of-the-art off-the-shelf high speed personal computer for simulating a microprocessor presently used for wind tunnel safety purposes at Langley Research Center's National Transonic Facility (NTF). Currently, there is no active display of tunnel alarm/alert safety information provided to the tunnel operators, but rather such information is periodically recorded on a process monitoring computer printout. This does not provide on-line situational information nor permit rapid identification of safety operational violations which are able to halt tunnel operations. It was therefore decided to simulate the existing algorithms and briefly evaluate a real-time display which could provide both position and trouble shooting information.

Fiber pushout test: A three-dimensional finite element computational simulation

NASA Technical Reports Server (NTRS)

Mital, Subodh K.; Chamis, Christos C.

1990-01-01

A fiber pushthrough process was computationally simulated using three-dimensional finite element method. The interface material is replaced by an anisotropic material with greatly reduced shear modulus in order to simulate the fiber pushthrough process using a linear analysis. Such a procedure is easily implemented and is computationally very effective. It can be used to predict fiber pushthrough load for a composite system at any temperature. The average interface shear strength obtained from pushthrough load can easily be separated into its two components: one that comes from frictional stresses and the other that comes from chemical adhesion between fiber and the matrix and mechanical interlocking that develops due to shrinkage of the composite because of phase change during the processing. Step-by-step procedures are described to perform the computational simulation, to establish bounds on interfacial bond strength and to interpret interfacial bond quality.

Computer Science Techniques Applied to Parallel Atomistic Simulation

NASA Astrophysics Data System (ADS)

Nakano, Aiichiro

1998-03-01

Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

Petascale Kinetic Simulations in Space Sciences: New Simulations and Data Discovery Techniques and Physics Results

NASA Astrophysics Data System (ADS)

Karimabadi, Homa

2012-03-01

Recent advances in simulation technology and hardware are enabling breakthrough science where many longstanding problems can now be addressed for the first time. In this talk, we focus on kinetic simulations of the Earth's magnetosphere and magnetic reconnection process which is the key mechanism that breaks the protective shield of the Earth's dipole field, allowing the solar wind to enter the Earth's magnetosphere. This leads to the so-called space weather where storms on the Sun can affect space-borne and ground-based technological systems on Earth. The talk will consist of three parts: (a) overview of a new multi-scale simulation technique where each computational grid is updated based on its own unique timestep, (b) Presentation of a new approach to data analysis that we refer to as Physics Mining which entails combining data mining and computer vision algorithms with scientific visualization to extract physics from the resulting massive data sets. (c) Presentation of several recent discoveries in studies of space plasmas including the role of vortex formation and resulting turbulence in magnetized plasmas.

Simulating patient-specific heart shape and motion using SPECT perfusion images with the MCAT phantom

NASA Astrophysics Data System (ADS)

Faber, Tracy L.; Garcia, Ernest V.; Lalush, David S.; Segars, W. Paul; Tsui, Benjamin M.

2001-05-01

The spline-based Mathematical Cardiac Torso (MCAT) phantom is a realistic software simulation designed to simulate single photon emission computed tomographic (SPECT) data. It incorporates a heart model of known size and shape; thus, it is invaluable for measuring accuracy of acquisition, reconstruction, and post-processing routines. New functionality has been added by replacing the standard heart model with left ventricular (LV) epicaridal and endocardial surface points detected from actual patient SPECT perfusion studies. LV surfaces detected from standard post-processing quantitation programs are converted through interpolation in space and time into new B-spline models. Perfusion abnormalities are added to the model based on results of standard perfusion quantification. The new LV is translated and rotated to fit within existing atria and right ventricular models, which are scaled based on the size of the LV. Simulations were created for five different patients with myocardial infractions who had undergone SPECT perfusion imaging. Shape, size, and motion of the resulting activity map were compared visually to the original SPECT images. In all cases, size, shape and motion of simulated LVs matched well with the original images. Thus, realistic simulations with known physiologic and functional parameters can be created for evaluating efficacy of processing algorithms.

TH-E-18A-01: Developments in Monte Carlo Methods for Medical Imaging

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

Badal, A; Zbijewski, W; Bolch, W

Monte Carlo simulation methods are widely used in medical physics research and are starting to be implemented in clinical applications such as radiation therapy planning systems. Monte Carlo simulations offer the capability to accurately estimate quantities of interest that are challenging to measure experimentally while taking into account the realistic anatomy of an individual patient. Traditionally, practical application of Monte Carlo simulation codes in diagnostic imaging was limited by the need for large computational resources or long execution times. However, recent advancements in high-performance computing hardware, combined with a new generation of Monte Carlo simulation algorithms and novel postprocessing methods,more » are allowing for the computation of relevant imaging parameters of interest such as patient organ doses and scatter-to-primaryratios in radiographic projections in just a few seconds using affordable computational resources. Programmable Graphics Processing Units (GPUs), for example, provide a convenient, affordable platform for parallelized Monte Carlo executions that yield simulation times on the order of 10{sup 7} xray/ s. Even with GPU acceleration, however, Monte Carlo simulation times can be prohibitive for routine clinical practice. To reduce simulation times further, variance reduction techniques can be used to alter the probabilistic models underlying the x-ray tracking process, resulting in lower variance in the results without biasing the estimates. Other complementary strategies for further reductions in computation time are denoising of the Monte Carlo estimates and estimating (scoring) the quantity of interest at a sparse set of sampling locations (e.g. at a small number of detector pixels in a scatter simulation) followed by interpolation. Beyond reduction of the computational resources required for performing Monte Carlo simulations in medical imaging, the use of accurate representations of patient anatomy is crucial to the virtual generation of medical images and accurate estimation of radiation dose and other imaging parameters. For this, detailed computational phantoms of the patient anatomy must be utilized and implemented within the radiation transport code. Computational phantoms presently come in one of three format types, and in one of four morphometric categories. Format types include stylized (mathematical equation-based), voxel (segmented CT/MR images), and hybrid (NURBS and polygon mesh surfaces). Morphometric categories include reference (small library of phantoms by age at 50th height/weight percentile), patient-dependent (larger library of phantoms at various combinations of height/weight percentiles), patient-sculpted (phantoms altered to match the patient's unique outer body contour), and finally, patient-specific (an exact representation of the patient with respect to both body contour and internal anatomy). The existence and availability of these phantoms represents a very important advance for the simulation of realistic medical imaging applications using Monte Carlo methods. New Monte Carlo simulation codes need to be thoroughly validated before they can be used to perform novel research. Ideally, the validation process would involve comparison of results with those of an experimental measurement, but accurate replication of experimental conditions can be very challenging. It is very common to validate new Monte Carlo simulations by replicating previously published simulation results of similar experiments. This process, however, is commonly problematic due to the lack of sufficient information in the published reports of previous work so as to be able to replicate the simulation in detail. To aid in this process, the AAPM Task Group 195 prepared a report in which six different imaging research experiments commonly performed using Monte Carlo simulations are described and their results provided. The simulation conditions of all six cases are provided in full detail, with all necessary data on material composition, source, geometry, scoring and other parameters provided. The results of these simulations when performed with the four most common publicly available Monte Carlo packages are also provided in tabular form. The Task Group 195 Report will be useful for researchers needing to validate their Monte Carlo work, and for trainees needing to learn Monte Carlo simulation methods. In this symposium we will review the recent advancements in highperformance computing hardware enabling the reduction in computational resources needed for Monte Carlo simulations in medical imaging. We will review variance reduction techniques commonly applied in Monte Carlo simulations of medical imaging systems and present implementation strategies for efficient combination of these techniques with GPU acceleration. Trade-offs involved in Monte Carlo acceleration by means of denoising and “sparse sampling” will be discussed. A method for rapid scatter correction in cone-beam CT (<5 min/scan) will be presented as an illustration of the simulation speeds achievable with optimized Monte Carlo simulations. We will also discuss the development, availability, and capability of the various combinations of computational phantoms for Monte Carlo simulation of medical imaging systems. Finally, we will review some examples of experimental validation of Monte Carlo simulations and will present the AAPM Task Group 195 Report. Learning Objectives: Describe the advances in hardware available for performing Monte Carlo simulations in high performance computing environments. Explain variance reduction, denoising and sparse sampling techniques available for reduction of computational time needed for Monte Carlo simulations of medical imaging. List and compare the computational anthropomorphic phantoms currently available for more accurate assessment of medical imaging parameters in Monte Carlo simulations. Describe experimental methods used for validation of Monte Carlo simulations in medical imaging. Describe the AAPM Task Group 195 Report and its use for validation and teaching of Monte Carlo simulations in medical imaging.« less

Adiabatic topological quantum computing

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

Cesare, Chris; Landahl, Andrew J.; Bacon, Dave

Topological quantum computing promises error-resistant quantum computation without active error correction. However, there is a worry that during the process of executing quantum gates by braiding anyons around each other, extra anyonic excitations will be created that will disorder the encoded quantum information. Here, we explore this question in detail by studying adiabatic code deformations on Hamiltonians based on topological codes, notably Kitaev’s surface codes and the more recently discovered color codes. We develop protocols that enable universal quantum computing by adiabatic evolution in a way that keeps the energy gap of the system constant with respect to the computationmore » size and introduces only simple local Hamiltonian interactions. This allows one to perform holonomic quantum computing with these topological quantum computing systems. The tools we develop allow one to go beyond numerical simulations and understand these processes analytically.« less

Adiabatic topological quantum computing

DOE PAGES

Cesare, Chris; Landahl, Andrew J.; Bacon, Dave; ...

2015-07-31

Topological quantum computing promises error-resistant quantum computation without active error correction. However, there is a worry that during the process of executing quantum gates by braiding anyons around each other, extra anyonic excitations will be created that will disorder the encoded quantum information. Here, we explore this question in detail by studying adiabatic code deformations on Hamiltonians based on topological codes, notably Kitaev’s surface codes and the more recently discovered color codes. We develop protocols that enable universal quantum computing by adiabatic evolution in a way that keeps the energy gap of the system constant with respect to the computationmore » size and introduces only simple local Hamiltonian interactions. This allows one to perform holonomic quantum computing with these topological quantum computing systems. The tools we develop allow one to go beyond numerical simulations and understand these processes analytically.« less

Service-based analysis of biological pathways

PubMed Central

Zheng, George; Bouguettaya, Athman

2009-01-01

Background Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach. Results Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses. Conclusion Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper. PMID:19796403

Genetic demographic networks: Mathematical model and applications.

PubMed

Kimmel, Marek; Wojdyła, Tomasz

2016-10-01

Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans. Copyright © 2016 Elsevier Inc. All rights reserved.

Modelling and simulating decision processes of linked lives: An approach based on concurrent processes and stochastic race.

PubMed

Warnke, Tom; Reinhardt, Oliver; Klabunde, Anna; Willekens, Frans; Uhrmacher, Adelinde M

2017-10-01

Individuals' decision processes play a central role in understanding modern migration phenomena and other demographic processes. Their integration into agent-based computational demography depends largely on suitable support by a modelling language. We are developing the Modelling Language for Linked Lives (ML3) to describe the diverse decision processes of linked lives succinctly in continuous time. The context of individuals is modelled by networks the individual is part of, such as family ties and other social networks. Central concepts, such as behaviour conditional on agent attributes, age-dependent behaviour, and stochastic waiting times, are tightly integrated in the language. Thereby, alternative decisions are modelled by concurrent processes that compete by stochastic race. Using a migration model, we demonstrate how this allows for compact description of complex decisions, here based on the Theory of Planned Behaviour. We describe the challenges for the simulation algorithm posed by stochastic race between multiple concurrent complex decisions.

Planning intensive care unit design using computer simulation modeling: optimizing integration of clinical, operational, and architectural requirements.

PubMed

OʼHara, Susan

2014-01-01

Nurses have increasingly been regarded as critical members of the planning team as architects recognize their knowledge and value. But the nurses' role as knowledge experts can be expanded to leading efforts to integrate the clinical, operational, and architectural expertise through simulation modeling. Simulation modeling allows for the optimal merge of multifactorial data to understand the current state of the intensive care unit and predict future states. Nurses can champion the simulation modeling process and reap the benefits of a cost-effective way to test new designs, processes, staffing models, and future programming trends prior to implementation. Simulation modeling is an evidence-based planning approach, a standard, for integrating the sciences with real client data, to offer solutions for improving patient care.

Simulation of an Asynchronous Machine by using a Pseudo Bond Graph

NASA Astrophysics Data System (ADS)

Romero, Gregorio; Felez, Jesus; Maroto, Joaquin; Martinez, M. Luisa

2008-11-01

For engineers, computer simulation, is a basic tool since it enables them to understand how systems work without actually needing to see them. They can learn how they work in different circumstances and optimize their design with considerably less cost in terms of time and money than if they had to carry out tests on a physical system. However, if computer simulation is to be reliable it is essential for the simulation model to be validated. There is a wide range of commercial brands on the market offering products for electrical domain simulation (SPICE, LabVIEW PSCAD,Dymola, Simulink, Simplorer,...). These are powerful tools, but require the engineer to have a perfect knowledge of the electrical field. This paper shows an alternative methodology to can simulate an asynchronous machine using the multidomain Bond Graph technique and apply it in any program that permit the simulation of models based in this technique; no extraordinary knowledge of this technique and electric field are required to understand the process .

The Australian Computational Earth Systems Simulator

NASA Astrophysics Data System (ADS)

Mora, P.; Muhlhaus, H.; Lister, G.; Dyskin, A.; Place, D.; Appelbe, B.; Nimmervoll, N.; Abramson, D.

2001-12-01

Numerical simulation of the physics and dynamics of the entire earth system offers an outstanding opportunity for advancing earth system science and technology but represents a major challenge due to the range of scales and physical processes involved, as well as the magnitude of the software engineering effort required. However, new simulation and computer technologies are bringing this objective within reach. Under a special competitive national funding scheme to establish new Major National Research Facilities (MNRF), the Australian government together with a consortium of Universities and research institutions have funded construction of the Australian Computational Earth Systems Simulator (ACcESS). The Simulator or computational virtual earth will provide the research infrastructure to the Australian earth systems science community required for simulations of dynamical earth processes at scales ranging from microscopic to global. It will consist of thematic supercomputer infrastructure and an earth systems simulation software system. The Simulator models and software will be constructed over a five year period by a multi-disciplinary team of computational scientists, mathematicians, earth scientists, civil engineers and software engineers. The construction team will integrate numerical simulation models (3D discrete elements/lattice solid model, particle-in-cell large deformation finite-element method, stress reconstruction models, multi-scale continuum models etc) with geophysical, geological and tectonic models, through advanced software engineering and visualization technologies. When fully constructed, the Simulator aims to provide the software and hardware infrastructure needed to model solid earth phenomena including global scale dynamics and mineralisation processes, crustal scale processes including plate tectonics, mountain building, interacting fault system dynamics, and micro-scale processes that control the geological, physical and dynamic behaviour of earth systems. ACcESS represents a part of Australia's contribution to the APEC Cooperation for Earthquake Simulation (ACES) international initiative. Together with other national earth systems science initiatives including the Japanese Earth Simulator and US General Earthquake Model projects, ACcESS aims to provide a driver for scientific advancement and technological breakthroughs including: quantum leaps in understanding of earth evolution at global, crustal, regional and microscopic scales; new knowledge of the physics of crustal fault systems required to underpin the grand challenge of earthquake prediction; new understanding and predictive capabilities of geological processes such as tectonics and mineralisation.

NASA's Integrated Instrument Simulator Suite for Atmospheric Remote Sensing from Spaceborne Platforms (ISSARS) and Its Role for the ACE and GPM Missions

NASA Technical Reports Server (NTRS)

Tanelli, Simone; Tao, Wei-Kuo; Hostetler, Chris; Kuo, Kwo-Sen; Matsui, Toshihisa; Jacob, Joseph C.; Niamsuwam, Noppasin; Johnson, Michael P.; Hair, John; Butler, Carolyn;

Uranus: a rapid prototyping tool for FPGA embedded computer vision

NASA Astrophysics Data System (ADS)

Rosales-Hernández, Victor; Castillo-Jimenez, Liz; Viveros-Velez, Gilberto; Zuñiga-Grajeda, Virgilio; Treviño Torres, Abel; Arias-Estrada, M.

2007-01-01

The starting point for all successful system development is the simulation. Performing high level simulation of a system can help to identify, insolate and fix design problems. This work presents Uranus, a software tool for simulation and evaluation of image processing algorithms with support to migrate them to an FPGA environment for algorithm acceleration and embedded processes purposes. The tool includes an integrated library of previous coded operators in software and provides the necessary support to read and display image sequences as well as video files. The user can use the previous compiled soft-operators in a high level process chain, and code his own operators. Additional to the prototyping tool, Uranus offers FPGA-based hardware architecture with the same organization as the software prototyping part. The hardware architecture contains a library of FPGA IP cores for image processing that are connected with a PowerPC based system. The Uranus environment is intended for rapid prototyping of machine vision and the migration to FPGA accelerator platform, and it is distributed for academic purposes.

Accelerated GPU based SPECT Monte Carlo simulations.

PubMed

Garcia, Marie-Paule; Bert, Julien; Benoit, Didier; Bardiès, Manuel; Visvikis, Dimitris

2016-06-07

Monte Carlo (MC) modelling is widely used in the field of single photon emission computed tomography (SPECT) as it is a reliable technique to simulate very high quality scans. This technique provides very accurate modelling of the radiation transport and particle interactions in a heterogeneous medium. Various MC codes exist for nuclear medicine imaging simulations. Recently, new strategies exploiting the computing capabilities of graphical processing units (GPU) have been proposed. This work aims at evaluating the accuracy of such GPU implementation strategies in comparison to standard MC codes in the context of SPECT imaging. GATE was considered the reference MC toolkit and used to evaluate the performance of newly developed GPU Geant4-based Monte Carlo simulation (GGEMS) modules for SPECT imaging. Radioisotopes with different photon energies were used with these various CPU and GPU Geant4-based MC codes in order to assess the best strategy for each configuration. Three different isotopes were considered: (99m) Tc, (111)In and (131)I, using a low energy high resolution (LEHR) collimator, a medium energy general purpose (MEGP) collimator and a high energy general purpose (HEGP) collimator respectively. Point source, uniform source, cylindrical phantom and anthropomorphic phantom acquisitions were simulated using a model of the GE infinia II 3/8" gamma camera. Both simulation platforms yielded a similar system sensitivity and image statistical quality for the various combinations. The overall acceleration factor between GATE and GGEMS platform derived from the same cylindrical phantom acquisition was between 18 and 27 for the different radioisotopes. Besides, a full MC simulation using an anthropomorphic phantom showed the full potential of the GGEMS platform, with a resulting acceleration factor up to 71. The good agreement with reference codes and the acceleration factors obtained support the use of GPU implementation strategies for improving computational efficiency of SPECT imaging simulations.

GPU-Based Simulation of Ultrasound Imaging Artifacts for Cryosurgery Training.

PubMed

Keelan, Robert; Shimada, Kenji; Rabin, Yoed

2017-02-01

This study presents an efficient computational technique for the simulation of ultrasound imaging artifacts associated with cryosurgery based on nonlinear ray tracing. This study is part of an ongoing effort to develop computerized training tools for cryosurgery, with prostate cryosurgery as a development model. The capability of performing virtual cryosurgical procedures on a variety of test cases is essential for effective surgical training. Simulated ultrasound imaging artifacts include reverberation and reflection of the cryoprobes in the unfrozen tissue, reflections caused by the freezing front, shadowing caused by the frozen region, and tissue property changes in repeated freeze-thaw cycles procedures. The simulated artifacts appear to preserve the key features observed in a clinical setting. This study displays an example of how training may benefit from toggling between the undisturbed ultrasound image, the simulated temperature field, the simulated imaging artifacts, and an augmented hybrid presentation of the temperature field superimposed on the ultrasound image. The proposed method is demonstrated on a graphic processing unit at 100 frames per second, on a mid-range personal workstation, at two orders of magnitude faster than a typical cryoprocedure. This performance is based on computation with C++ accelerated massive parallelism and its interoperability with the DirectX-rendering application programming interface.

GPU-Based Simulation of Ultrasound Imaging Artifacts for Cryosurgery Training

PubMed Central

Keelan, Robert; Shimada, Kenji

2016-01-01

This study presents an efficient computational technique for the simulation of ultrasound imaging artifacts associated with cryosurgery based on nonlinear ray tracing. This study is part of an ongoing effort to develop computerized training tools for cryosurgery, with prostate cryosurgery as a development model. The capability of performing virtual cryosurgical procedures on a variety of test cases is essential for effective surgical training. Simulated ultrasound imaging artifacts include reverberation and reflection of the cryoprobes in the unfrozen tissue, reflections caused by the freezing front, shadowing caused by the frozen region, and tissue property changes in repeated freeze–thaw cycles procedures. The simulated artifacts appear to preserve the key features observed in a clinical setting. This study displays an example of how training may benefit from toggling between the undisturbed ultrasound image, the simulated temperature field, the simulated imaging artifacts, and an augmented hybrid presentation of the temperature field superimposed on the ultrasound image. The proposed method is demonstrated on a graphic processing unit at 100 frames per second, on a mid-range personal workstation, at two orders of magnitude faster than a typical cryoprocedure. This performance is based on computation with C++ accelerated massive parallelism and its interoperability with the DirectX-rendering application programming interface. PMID:26818026

Multi-GPU hybrid programming accelerated three-dimensional phase-field model in binary alloy

NASA Astrophysics Data System (ADS)

Zhu, Changsheng; Liu, Jieqiong; Zhu, Mingfang; Feng, Li

2018-03-01

In the process of dendritic growth simulation, the computational efficiency and the problem scales have extremely important influence on simulation efficiency of three-dimensional phase-field model. Thus, seeking for high performance calculation method to improve the computational efficiency and to expand the problem scales has a great significance to the research of microstructure of the material. A high performance calculation method based on MPI+CUDA hybrid programming model is introduced. Multi-GPU is used to implement quantitative numerical simulations of three-dimensional phase-field model in binary alloy under the condition of multi-physical processes coupling. The acceleration effect of different GPU nodes on different calculation scales is explored. On the foundation of multi-GPU calculation model that has been introduced, two optimization schemes, Non-blocking communication optimization and overlap of MPI and GPU computing optimization, are proposed. The results of two optimization schemes and basic multi-GPU model are compared. The calculation results show that the use of multi-GPU calculation model can improve the computational efficiency of three-dimensional phase-field obviously, which is 13 times to single GPU, and the problem scales have been expanded to 8193. The feasibility of two optimization schemes is shown, and the overlap of MPI and GPU computing optimization has better performance, which is 1.7 times to basic multi-GPU model, when 21 GPUs are used.

Domain Immersion Technique And Free Surface Computations Applied To Extrusion And Mixing Processes

NASA Astrophysics Data System (ADS)

Valette, Rudy; Vergnes, Bruno; Basset, Olivier; Coupez, Thierry

2007-04-01

This work focuses on the development of numerical techniques devoted to the simulation of mixing processes of complex fluids such as twin-screw extrusion or batch mixing. In mixing process simulation, the absence of symmetry of the moving boundaries (the screws or the rotors) implies that their rigid body motion has to be taken into account by using a special treatment. We therefore use a mesh immersion technique (MIT), which consists in using a P1+/P1-based (MINI-element) mixed finite element method for solving the velocity-pressure problem and then solving the problem in the whole barrel cavity by imposing a rigid motion (rotation) to nodes found located inside the so called immersed domain, each subdomain (screw, rotor) being represented by a surface CAD mesh (or its mathematical equation in simple cases). The independent meshes are immersed into a unique backgound computational mesh by computing the distance function to their boundaries. Intersections of meshes are accounted for, allowing to compute a fill factor usable as for the VOF methodology. This technique, combined with the use of parallel computing, allows to compute the time-dependent flow of generalized Newtonian fluids including yield stress fluids in a complex system such as a twin screw extruder, including moving free surfaces, which are treated by a "level set" and Hamilton-Jacobi method.

Digital data processing system dynamic loading analysis

NASA Technical Reports Server (NTRS)

Lagas, J. J.; Peterka, J. J.; Tucker, A. E.

1976-01-01

Simulation and analysis of the Space Shuttle Orbiter Digital Data Processing System (DDPS) are reported. The mated flight and postseparation flight phases of the space shuttle's approach and landing test configuration were modeled utilizing the Information Management System Interpretative Model (IMSIM) in a computerized simulation modeling of the ALT hardware, software, and workload. System requirements simulated for the ALT configuration were defined. Sensitivity analyses determined areas of potential data flow problems in DDPS operation. Based on the defined system requirements and the sensitivity analyses, a test design is described for adapting, parameterizing, and executing the IMSIM. Varying load and stress conditions for the model execution are given. The analyses of the computer simulation runs were documented as results, conclusions, and recommendations for DDPS improvements.

Space shuttle orbiter digital data processing system timing sensitivity analysis OFT ascent phase

NASA Technical Reports Server (NTRS)

Lagas, J. J.; Peterka, J. J.; Becker, D. A.

1977-01-01

Dynamic loads were investigated to provide simulation and analysis of the space shuttle orbiter digital data processing system (DDPS). Segments of the ascent test (OFT) configuration were modeled utilizing the information management system interpretive model (IMSIM) in a computerized simulation modeling of the OFT hardware and software workload. System requirements for simulation of the OFT configuration were defined, and sensitivity analyses determined areas of potential data flow problems in DDPS operation. Based on the defined system requirements and these sensitivity analyses, a test design was developed for adapting, parameterizing, and executing IMSIM, using varying load and stress conditions for model execution. Analyses of the computer simulation runs are documented, including results, conclusions, and recommendations for DDPS improvements.

Dynamic Voltage Frequency Scaling Simulator for Real Workflows Energy-Aware Management in Green Cloud Computing

PubMed Central

Cotes-Ruiz, Iván Tomás; Prado, Rocío P.; García-Galán, Sebastián; Muñoz-Expósito, José Enrique; Ruiz-Reyes, Nicolás

2017-01-01

Nowadays, the growing computational capabilities of Cloud systems rely on the reduction of the consumed power of their data centers to make them sustainable and economically profitable. The efficient management of computing resources is at the heart of any energy-aware data center and of special relevance is the adaptation of its performance to workload. Intensive computing applications in diverse areas of science generate complex workload called workflows, whose successful management in terms of energy saving is still at its beginning. WorkflowSim is currently one of the most advanced simulators for research on workflows processing, offering advanced features such as task clustering and failure policies. In this work, an expected power-aware extension of WorkflowSim is presented. This new tool integrates a power model based on a computing-plus-communication design to allow the optimization of new management strategies in energy saving considering computing, reconfiguration and networks costs as well as quality of service, and it incorporates the preeminent strategy for on host energy saving: Dynamic Voltage Frequency Scaling (DVFS). The simulator is designed to be consistent in different real scenarios and to include a wide repertory of DVFS governors. Results showing the validity of the simulator in terms of resources utilization, frequency and voltage scaling, power, energy and time saving are presented. Also, results achieved by the intra-host DVFS strategy with different governors are compared to those of the data center using a recent and successful DVFS-based inter-host scheduling strategy as overlapped mechanism to the DVFS intra-host technique. PMID:28085932

Dynamic Voltage Frequency Scaling Simulator for Real Workflows Energy-Aware Management in Green Cloud Computing.

PubMed

Cotes-Ruiz, Iván Tomás; Prado, Rocío P; García-Galán, Sebastián; Muñoz-Expósito, José Enrique; Ruiz-Reyes, Nicolás

2017-01-01

Nowadays, the growing computational capabilities of Cloud systems rely on the reduction of the consumed power of their data centers to make them sustainable and economically profitable. The efficient management of computing resources is at the heart of any energy-aware data center and of special relevance is the adaptation of its performance to workload. Intensive computing applications in diverse areas of science generate complex workload called workflows, whose successful management in terms of energy saving is still at its beginning. WorkflowSim is currently one of the most advanced simulators for research on workflows processing, offering advanced features such as task clustering and failure policies. In this work, an expected power-aware extension of WorkflowSim is presented. This new tool integrates a power model based on a computing-plus-communication design to allow the optimization of new management strategies in energy saving considering computing, reconfiguration and networks costs as well as quality of service, and it incorporates the preeminent strategy for on host energy saving: Dynamic Voltage Frequency Scaling (DVFS). The simulator is designed to be consistent in different real scenarios and to include a wide repertory of DVFS governors. Results showing the validity of the simulator in terms of resources utilization, frequency and voltage scaling, power, energy and time saving are presented. Also, results achieved by the intra-host DVFS strategy with different governors are compared to those of the data center using a recent and successful DVFS-based inter-host scheduling strategy as overlapped mechanism to the DVFS intra-host technique.

Computational Phenotyping in Psychiatry: A Worked Example

PubMed Central

2016-01-01

Abstract Computational psychiatry is a rapidly emerging field that uses model-based quantities to infer the behavioral and neuronal abnormalities that underlie psychopathology. If successful, this approach promises key insights into (pathological) brain function as well as a more mechanistic and quantitative approach to psychiatric nosology—structuring therapeutic interventions and predicting response and relapse. The basic procedure in computational psychiatry is to build a computational model that formalizes a behavioral or neuronal process. Measured behavioral (or neuronal) responses are then used to infer the model parameters of a single subject or a group of subjects. Here, we provide an illustrative overview over this process, starting from the modeling of choice behavior in a specific task, simulating data, and then inverting that model to estimate group effects. Finally, we illustrate cross-validation to assess whether between-subject variables (e.g., diagnosis) can be recovered successfully. Our worked example uses a simple two-step maze task and a model of choice behavior based on (active) inference and Markov decision processes. The procedural steps and routines we illustrate are not restricted to a specific field of research or particular computational model but can, in principle, be applied in many domains of computational psychiatry. PMID:27517087

Computational Phenotyping in Psychiatry: A Worked Example.

PubMed

Schwartenbeck, Philipp; Friston, Karl

2016-01-01

Computational psychiatry is a rapidly emerging field that uses model-based quantities to infer the behavioral and neuronal abnormalities that underlie psychopathology. If successful, this approach promises key insights into (pathological) brain function as well as a more mechanistic and quantitative approach to psychiatric nosology-structuring therapeutic interventions and predicting response and relapse. The basic procedure in computational psychiatry is to build a computational model that formalizes a behavioral or neuronal process. Measured behavioral (or neuronal) responses are then used to infer the model parameters of a single subject or a group of subjects. Here, we provide an illustrative overview over this process, starting from the modeling of choice behavior in a specific task, simulating data, and then inverting that model to estimate group effects. Finally, we illustrate cross-validation to assess whether between-subject variables (e.g., diagnosis) can be recovered successfully. Our worked example uses a simple two-step maze task and a model of choice behavior based on (active) inference and Markov decision processes. The procedural steps and routines we illustrate are not restricted to a specific field of research or particular computational model but can, in principle, be applied in many domains of computational psychiatry.

Full Monte Carlo-Based Biologic Treatment Plan Optimization System for Intensity Modulated Carbon Ion Therapy on Graphics Processing Unit.

PubMed

Qin, Nan; Shen, Chenyang; Tsai, Min-Yu; Pinto, Marco; Tian, Zhen; Dedes, Georgios; Pompos, Arnold; Jiang, Steve B; Parodi, Katia; Jia, Xun

2018-01-01

One of the major benefits of carbon ion therapy is enhanced biological effectiveness at the Bragg peak region. For intensity modulated carbon ion therapy (IMCT), it is desirable to use Monte Carlo (MC) methods to compute the properties of each pencil beam spot for treatment planning, because of their accuracy in modeling physics processes and estimating biological effects. We previously developed goCMC, a graphics processing unit (GPU)-oriented MC engine for carbon ion therapy. The purpose of the present study was to build a biological treatment plan optimization system using goCMC. The repair-misrepair-fixation model was implemented to compute the spatial distribution of linear-quadratic model parameters for each spot. A treatment plan optimization module was developed to minimize the difference between the prescribed and actual biological effect. We used a gradient-based algorithm to solve the optimization problem. The system was embedded in the Varian Eclipse treatment planning system under a client-server architecture to achieve a user-friendly planning environment. We tested the system with a 1-dimensional homogeneous water case and 3 3-dimensional patient cases. Our system generated treatment plans with biological spread-out Bragg peaks covering the targeted regions and sparing critical structures. Using 4 NVidia GTX 1080 GPUs, the total computation time, including spot simulation, optimization, and final dose calculation, was 0.6 hour for the prostate case (8282 spots), 0.2 hour for the pancreas case (3795 spots), and 0.3 hour for the brain case (6724 spots). The computation time was dominated by MC spot simulation. We built a biological treatment plan optimization system for IMCT that performs simulations using a fast MC engine, goCMC. To the best of our knowledge, this is the first time that full MC-based IMCT inverse planning has been achieved in a clinically viable time frame. Copyright © 2017 Elsevier Inc. All rights reserved.

A Framework for Modeling and Simulation of the Artificial

DTIC Science & Technology

2012-01-01

y or n) >> y Name: petra Simple Aspects: face_shape/thin, nose/small, skintone/light, hair_color/black, hair_type/curly Integrated Aspects...Multiconference. Orlando, FL (2012) 23. Mittal, S., Risco- Martin , J.: Netcentric System of Systems Engineering with DEVS Unified Process. CRC Press (2012) 24...Mittal, S., Risco- Martin , J., Zeigler, B.: DEVS-based simulation web services for net-centric T&E. In: Proceedings of the 2007 summer computer

PROCESS SIMULATION OF COLD PRESSING OF ARMSTRONG CP-Ti POWDERS

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

Sabau, Adrian S; Gorti, Sarma B; Peter, William H

A computational methodology is presented for the process simulation of cold pressing of Armstrong CP-Ti Powders. The computational model was implemented in the commercial finite element program ABAQUSTM. Since the powder deformation and consolidation is governed by specific pressure-dependent constitutive equations, several solution algorithms were developed for the ABAQUS user material subroutine, UMAT. The solution algorithms were developed for computing the plastic strain increments based on an implicit integration of the nonlinear yield function, flow rule, and hardening equations that describe the evolution of the state variables. Since ABAQUS requires the use of a full Newton-Raphson algorithm for the stress-strainmore » equations, an algorithm for obtaining the tangent/linearization moduli, which is consistent with the return-mapping algorithm, also was developed. Numerical simulation results are presented for the cold compaction of the Ti powders. Several simulations were conducted for cylindrical samples with different aspect ratios. The numerical simulation results showed that for the disk samples, the minimum von Mises stress was approximately half than its maximum value. The hydrostatic stress distribution exhibits a variation smaller than that of the von Mises stress. It was found that for the disk and cylinder samples the minimum hydrostatic stresses were approximately 23 and 50% less than its maximum value, respectively. It was also found that the minimum density was noticeably affected by the sample height.« less

The Simultaneous Production Model; A Model for the Construction, Testing, Implementation and Revision of Educational Computer Simulation Environments.

ERIC Educational Resources Information Center

Zillesen, Pieter G. van Schaick

This paper introduces a hardware and software independent model for producing educational computer simulation environments. The model, which is based on the results of 32 studies of educational computer simulations program production, implies that educational computer simulation environments are specified, constructed, tested, implemented, and…

Auditorium acoustics evaluation based on simulated impulse response

NASA Astrophysics Data System (ADS)

Wu, Shuoxian; Wang, Hongwei; Zhao, Yuezhe

2004-05-01

The impulse responses and other acoustical parameters of Huangpu Teenager Palace in Guangzhou were measured. Meanwhile, the acoustical simulation and auralization based on software ODEON were also made. The comparison between the parameters based on computer simulation and measuring is given. This case study shows that auralization technique based on computer simulation can be used for predicting the acoustical quality of a hall at its design stage.

Simulating Single Word Processing in the Classic Aphasia Syndromes Based on the Wernicke-Lichtheim-Geschwind Theory

ERIC Educational Resources Information Center

Weems, Scott A.; Reggia, James A.

2006-01-01

The Wernicke-Lichtheim-Geschwind (WLG) theory of the neurobiological basis of language is of great historical importance, and it continues to exert a substantial influence on most contemporary theories of language in spite of its widely recognized limitations. Here, we suggest that neurobiologically grounded computational models based on the WLG…

Experimental evaluation of the effect of a modified port-location mode on the performance of a three-zone simulated moving-bed process for the separation of valine and isoleucine.

PubMed

Park, Chanhun; Nam, Hee-Geun; Kim, Pung-Ho; Mun, Sungyong

2014-06-01

The removal of isoleucine from valine has been a key issue in the stage of valine crystallization, which is the final step in the valine production process in industry. To address this issue, a three-zone simulated moving-bed (SMB) process for the separation of valine and isoleucine has been developed previously. However, the previous process, which was based on a classical port-location mode, had some limitations in throughput and valine product concentration. In this study, a three-zone SMB process based on a modified port-location mode was applied to the separation of valine and isoleucine for the purpose of making a marked improvement in throughput and valine product concentration. Computer simulations and a lab-scale process experiment showed that the modified three-zone SMB for valine separation led to >65% higher throughput and >160% higher valine concentration compared to the previous three-zone SMB for the same separation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulation of a master-slave event set processor

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

Comfort, J.C.

1984-03-01

Event set manipulation may consume a considerable amount of the computation time spent in performing a discrete-event simulation. One way of minimizing this time is to allow event set processing to proceed in parallel with the remainder of the simulation computation. The paper describes a multiprocessor simulation computer, in which all non-event set processing is performed by the principal processor (called the host). Event set processing is coordinated by a front end processor (the master) and actually performed by several other functionally identical processors (the slaves). A trace-driven simulation program modeling this system was constructed, and was run with tracemore » output taken from two different simulation programs. Output from this simulation suggests that a significant reduction in run time may be realized by this approach. Sensitivity analysis was performed on the significant parameters to the system (number of slave processors, relative processor speeds, and interprocessor communication times). A comparison between actual and simulation run times for a one-processor system was used to assist in the validation of the simulation. 7 references.« less

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

PubMed Central

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic. PMID:26177039

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.

PubMed

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.

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

Zitney, S.E.

This presentation will examine process systems engineering R&D needs for application to advanced fossil energy (FE) systems and highlight ongoing research activities at the National Energy Technology Laboratory (NETL) under the auspices of a recently launched Collaboratory for Process & Dynamic Systems Research. The three current technology focus areas include: 1) High-fidelity systems with NETL's award-winning Advanced Process Engineering Co-Simulator (APECS) technology for integrating process simulation with computational fluid dynamics (CFD) and virtual engineering concepts, 2) Dynamic systems with R&D on plant-wide IGCC dynamic simulation, control, and real-time training applications, and 3) Systems optimization including large-scale process optimization, stochastic simulationmore » for risk/uncertainty analysis, and cost estimation. Continued R&D aimed at these and other key process systems engineering models, methods, and tools will accelerate the development of advanced gasification-based FE systems and produce increasingly valuable outcomes for DOE and the Nation.« less

Computational simulation of weld microstructure and distortion by considering process mechanics

NASA Astrophysics Data System (ADS)

Mochizuki, M.; Mikami, Y.; Okano, S.; Itoh, S.

2009-05-01

Highly precise fabrication of welded materials is in great demand, and so microstructure and distortion controls are essential. Furthermore, consideration of process mechanics is important for intelligent fabrication. In this study, the microstructure and hardness distribution in multi-pass weld metal are evaluated by computational simulations under the conditions of multiple heat cycles and phase transformation. Because conventional CCT diagrams of weld metal are not available even for single-pass weld metal, new diagrams for multi-pass weld metals are created. The weld microstructure and hardness distribution are precisely predicted when using the created CCT diagram for multi-pass weld metal and calculating the weld thermal cycle. Weld distortion is also investigated by using numerical simulation with a thermal elastic-plastic analysis. In conventional evaluations of weld distortion, the average heat input has been used as the dominant parameter; however, it is difficult to consider the effect of molten pool configurations on weld distortion based only on the heat input. Thus, the effect of welding process conditions on weld distortion is studied by considering molten pool configurations, determined by temperature distribution and history.

Brian Hears: Online Auditory Processing Using Vectorization Over Channels

PubMed Central

Fontaine, Bertrand; Goodman, Dan F. M.; Benichoux, Victor; Brette, Romain

2011-01-01

The human cochlea includes about 3000 inner hair cells which filter sounds at frequencies between 20 Hz and 20 kHz. This massively parallel frequency analysis is reflected in models of auditory processing, which are often based on banks of filters. However, existing implementations do not exploit this parallelism. Here we propose algorithms to simulate these models by vectorizing computation over frequency channels, which are implemented in “Brian Hears,” a library for the spiking neural network simulator package “Brian.” This approach allows us to use high-level programming languages such as Python, because with vectorized operations, the computational cost of interpretation represents a small fraction of the total cost. This makes it possible to define and simulate complex models in a simple way, while all previous implementations were model-specific. In addition, we show that these algorithms can be naturally parallelized using graphics processing units, yielding substantial speed improvements. We demonstrate these algorithms with several state-of-the-art cochlear models, and show that they compare favorably with existing, less flexible, implementations. PMID:21811453

Approaches to Classroom-Based Computational Science.

ERIC Educational Resources Information Center

Guzdial, Mark

Computational science includes the use of computer-based modeling and simulation to define and test theories about scientific phenomena. The challenge for educators is to develop techniques for implementing computational science in the classroom. This paper reviews some previous work on the use of simulation alone (without modeling), modeling…

Automatic Data Processing Equipment (ADPE) acquisition plan for the medical sciences

NASA Technical Reports Server (NTRS)

1979-01-01

An effective mechanism for meeting the SLSD/MSD data handling/processing requirements for Shuttle is discussed. The ability to meet these requirements depends upon the availability of a general purpose high speed digital computer system. This system is expected to implement those data base management and processing functions required across all SLSD/MSD programs during training, laboratory operations/analysis, simulations, mission operations, and post mission analysis/reporting.

A Computational Approach to Increase Time Scales in Brownian Dynamics–Based Reaction-Diffusion Modeling

PubMed Central

Frazier, Zachary

2012-01-01

Abstract Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling. PMID:22697237

Computer-Based Simulations for Maintenance Training: Current ARI Research. Technical Report 544.

ERIC Educational Resources Information Center

Knerr, Bruce W.; And Others

Three research efforts that used computer-based simulations for maintenance training were in progress when this report was written: Game-Based Learning, which investigated the use of computer-based games to train electronics diagnostic skills; Human Performance in Fault Diagnosis Tasks, which evaluated the use of context-free tasks to train…

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

PubMed

Chi, Yujie; Tian, Zhen; Jia, Xun

2016-08-07

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

Development of the ARISTOTLE webware for cloud-based rarefied gas flow modeling

NASA Astrophysics Data System (ADS)

Deschenes, Timothy R.; Grot, Jonathan; Cline, Jason A.

2016-11-01

Rarefied gas dynamics are important for a wide variety of applications. An improvement in the ability of general users to predict these gas flows will enable optimization of current, and discovery of future processes. Despite this potential, most rarefied simulation software is designed by and for experts in the community. This has resulted in low adoption of the methods outside of the immediate RGD community. This paper outlines an ongoing effort to create a rarefied gas dynamics simulation tool that can be used by a general audience. The tool leverages a direct simulation Monte Carlo (DSMC) library that is available to the entire community and a web-based simulation process that will enable all users to take advantage of high performance computing capabilities. First, the DSMC library and simulation architecture are described. Then the DSMC library is used to predict a number of representative transient gas flows that are applicable to the rarefied gas dynamics community. The paper closes with a summary and future direction.

Using Python to generate AHPS-based precipitation simulations over CONUS using Amazon distributed computing

NASA Astrophysics Data System (ADS)

Machalek, P.; Kim, S. M.; Berry, R. D.; Liang, A.; Small, T.; Brevdo, E.; Kuznetsova, A.

2012-12-01

We describe how the Climate Corporation uses Python and Clojure, a language impleneted on top of Java, to generate climatological forecasts for precipitation based on the Advanced Hydrologic Prediction Service (AHPS) radar based daily precipitation measurements. A 2-year-long forecasts is generated on each of the ~650,000 CONUS land based 4-km AHPS grids by constructing 10,000 ensembles sampled from a 30-year reconstructed AHPS history for each grid. The spatial and temporal correlations between neighboring AHPS grids and the sampling of the analogues are handled by Python. The parallelization for all the 650,000 CONUS stations is further achieved by utilizing the MAP-REDUCE framework (http://code.google.com/edu/parallel/mapreduce-tutorial.html). Each full scale computational run requires hundreds of nodes with up to 8 processors each on the Amazon Elastic MapReduce (http://aws.amazon.com/elasticmapreduce/) distributed computing service resulting in 3 terabyte datasets. We further describe how we have productionalized a monthly run of the simulations process at full scale of the 4km AHPS grids and how the resultant terabyte sized datasets are handled.

Introducing Molecular Life Science Students to Model Building Using Computer Simulations

ERIC Educational Resources Information Center

Aegerter-Wilmsen, Tinri; Kettenis, Dik; Sessink, Olivier; Hartog, Rob; Bisseling, Ton; Janssen, Fred

2006-01-01

Computer simulations can facilitate the building of models of natural phenomena in research, such as in the molecular life sciences. In order to introduce molecular life science students to the use of computer simulations for model building, a digital case was developed in which students build a model of a pattern formation process in…

An Investigation of the Effectiveness of Computer Simulation Programs as Tutorial Tools for Teaching Population Ecology at University.

ERIC Educational Resources Information Center

Korfiatis, K.; Papatheodorou, E.; Paraskevopoulous, S.; Stamou, G. P.

1999-01-01

Describes a study of the effectiveness of computer-simulation programs in enhancing biology students' familiarity with ecological modeling and concepts. Finds that computer simulations improved student comprehension of ecological processes expressed in mathematical form, but did not allow a full understanding of ecological concepts. Contains 28…

Using a Computer Simulation To Teach Science Process Skills to College Biology and Elementary Education Majors.

ERIC Educational Resources Information Center

Lee, Aimee T.; Hairston, Rosalina V.; Thames, Rachel; Lawrence, Tonya; Herron, Sherry S.

2002-01-01

Describes the Lateblight computer simulation implemented in the general biology laboratory and science methods course for elementary teachers to reinforce the processes of science and allow students to engage, explore, explain, elaborate, and evaluate the methods of building concepts in science. (Author/KHR)

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

ERIC Educational Resources Information Center

Waugh, Michael L.

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

Exploring the Perceptions of College Instructors towards Computer Simulation Software Programs: A Quantitative Study

ERIC Educational Resources Information Center

Punch, Raymond J.

2012-01-01

The purpose of the quantitative regression study was to explore and to identify relationships between attitudes toward use and perceptions of value of computer-based simulation programs, of college instructors, toward computer based simulation programs. A relationship has been reported between attitudes toward use and perceptions of the value of…

Theory, Modeling, Software and Hardware Development for Analytical and Computational Materials Science

NASA Technical Reports Server (NTRS)

Young, Gerald W.; Clemons, Curtis B.

2004-01-01

The focus of this Cooperative Agreement between the Computational Materials Laboratory (CML) of the Processing Science and Technology Branch of the NASA Glenn Research Center (GRC) and the Department of Theoretical and Applied Mathematics at The University of Akron was in the areas of system development of the CML workstation environment, modeling of microgravity and earth-based material processing systems, and joint activities in laboratory projects. These efforts complement each other as the majority of the modeling work involves numerical computations to support laboratory investigations. Coordination and interaction between the modelers, system analysts, and laboratory personnel are essential toward providing the most effective simulations and communication of the simulation results. Toward these means, The University of Akron personnel involved in the agreement worked at the Applied Mathematics Research Laboratory (AMRL) in the Department of Theoretical and Applied Mathematics while maintaining a close relationship with the personnel of the Computational Materials Laboratory at GRC. Network communication between both sites has been established. A summary of the projects we undertook during the time period 9/1/03 - 6/30/04 is included.

Multisensor surveillance data augmentation and prediction with optical multipath signal processing

NASA Astrophysics Data System (ADS)

Bush, G. T., III

1980-12-01

The spatial characteristics of an oil spill on the high seas are examined in the interest of determining whether linear-shift-invariant data processing implemented on an optical computer would be a useful tool in analyzing spill behavior. Simulations were performed on a digital computer using data obtained from a 25,000 gallon spill of soy bean oil in the open ocean. Marked changes occurred in the observed spatial frequencies when the oil spill was encountered. An optical detector may readily be developed to sound an alarm automatically when this happens. The average extent of oil spread between sequential observations was quantified by a simulation of non-holographic optical computation. Because a zero crossover was available in this computation, it may be possible to construct a system to measure automatically the amount of spread. Oil images were subjected to deconvolutional filtering to reveal the force field which acted upon the oil to cause spreading. Some features of spill-size prediction were observed. Calculations based on two sequential photos produced an image which exhibited characteristics of the third photo in that sequence.

Probabilistic risk assessment for CO2 storage in geological formations: robust design and support for decision making under uncertainty

NASA Astrophysics Data System (ADS)

Oladyshkin, Sergey; Class, Holger; Helmig, Rainer; Nowak, Wolfgang

2010-05-01

CO2 storage in geological formations is currently being discussed intensively as a technology for mitigating CO2 emissions. However, any large-scale application requires a thorough analysis of the potential risks. Current numerical simulation models are too expensive for probabilistic risk analysis and for stochastic approaches based on brute-force repeated simulation. Even single deterministic simulations may require parallel high-performance computing. The multiphase flow processes involved are too non-linear for quasi-linear error propagation and other simplified stochastic tools. As an alternative approach, we propose a massive stochastic model reduction based on the probabilistic collocation method. The model response is projected onto a orthogonal basis of higher-order polynomials to approximate dependence on uncertain parameters (porosity, permeability etc.) and design parameters (injection rate, depth etc.). This allows for a non-linear propagation of model uncertainty affecting the predicted risk, ensures fast computation and provides a powerful tool for combining design variables and uncertain variables into one approach based on an integrative response surface. Thus, the design task of finding optimal injection regimes explicitly includes uncertainty, which leads to robust designs of the non-linear system that minimize failure probability and provide valuable support for risk-informed management decisions. We validate our proposed stochastic approach by Monte Carlo simulation using a common 3D benchmark problem (Class et al. Computational Geosciences 13, 2009). A reasonable compromise between computational efforts and precision was reached already with second-order polynomials. In our case study, the proposed approach yields a significant computational speedup by a factor of 100 compared to Monte Carlo simulation. We demonstrate that, due to the non-linearity of the flow and transport processes during CO2 injection, including uncertainty in the analysis leads to a systematic and significant shift of predicted leakage rates towards higher values compared with deterministic simulations, affecting both risk estimates and the design of injection scenarios. This implies that, neglecting uncertainty can be a strong simplification for modeling CO2 injection, and the consequences can be stronger than when neglecting several physical phenomena (e.g. phase transition, convective mixing, capillary forces etc.). The authors would like to thank the German Research Foundation (DFG) for financial support of the project within the Cluster of Excellence in Simulation Technology (EXC 310/1) at the University of Stuttgart. Keywords: polynomial chaos; CO2 storage; multiphase flow; porous media; risk assessment; uncertainty; integrative response surfaces

Architectural Improvements and New Processing Tools for the Open XAL Online Model

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

Allen, Christopher K; Pelaia II, Tom; Freed, Jonathan M

The online model is the component of Open XAL providing accelerator modeling, simulation, and dynamic synchronization to live hardware. Significant architectural changes and feature additions have been recently made in two separate areas: 1) the managing and processing of simulation data, and 2) the modeling of RF cavities. Simulation data and data processing have been completely decoupled. A single class manages all simulation data while standard tools were developed for processing the simulation results. RF accelerating cavities are now modeled as composite structures where parameter and dynamics computations are distributed. The beam and hardware models both maintain their relative phasemore » information, which allows for dynamic phase slip and elapsed time computation.« less

Accelerating cardiac bidomain simulations using graphics processing units.

PubMed

Neic, A; Liebmann, M; Hoetzl, E; Mitchell, L; Vigmond, E J; Haase, G; Plank, G

2012-08-01

Anatomically realistic and biophysically detailed multiscale computer models of the heart are playing an increasingly important role in advancing our understanding of integrated cardiac function in health and disease. Such detailed simulations, however, are computationally vastly demanding, which is a limiting factor for a wider adoption of in-silico modeling. While current trends in high-performance computing (HPC) hardware promise to alleviate this problem, exploiting the potential of such architectures remains challenging since strongly scalable algorithms are necessitated to reduce execution times. Alternatively, acceleration technologies such as graphics processing units (GPUs) are being considered. While the potential of GPUs has been demonstrated in various applications, benefits in the context of bidomain simulations where large sparse linear systems have to be solved in parallel with advanced numerical techniques are less clear. In this study, the feasibility of multi-GPU bidomain simulations is demonstrated by running strong scalability benchmarks using a state-of-the-art model of rabbit ventricles. The model is spatially discretized using the finite element methods (FEM) on fully unstructured grids. The GPU code is directly derived from a large pre-existing code, the Cardiac Arrhythmia Research Package (CARP), with very minor perturbation of the code base. Overall, bidomain simulations were sped up by a factor of 11.8 to 16.3 in benchmarks running on 6-20 GPUs compared to the same number of CPU cores. To match the fastest GPU simulation which engaged 20 GPUs, 476 CPU cores were required on a national supercomputing facility.

Accelerating Cardiac Bidomain Simulations Using Graphics Processing Units

PubMed Central

Neic, Aurel; Liebmann, Manfred; Hoetzl, Elena; Mitchell, Lawrence; Vigmond, Edward J.; Haase, Gundolf

2013-01-01

Anatomically realistic and biophysically detailed multiscale computer models of the heart are playing an increasingly important role in advancing our understanding of integrated cardiac function in health and disease. Such detailed simulations, however, are computationally vastly demanding, which is a limiting factor for a wider adoption of in-silico modeling. While current trends in high-performance computing (HPC) hardware promise to alleviate this problem, exploiting the potential of such architectures remains challenging since strongly scalable algorithms are necessitated to reduce execution times. Alternatively, acceleration technologies such as graphics processing units (GPUs) are being considered. While the potential of GPUs has been demonstrated in various applications, benefits in the context of bidomain simulations where large sparse linear systems have to be solved in parallel with advanced numerical techniques are less clear. In this study, the feasibility of multi-GPU bidomain simulations is demonstrated by running strong scalability benchmarks using a state-of-the-art model of rabbit ventricles. The model is spatially discretized using the finite element methods (FEM) on fully unstructured grids. The GPU code is directly derived from a large pre-existing code, the Cardiac Arrhythmia Research Package (CARP), with very minor perturbation of the code base. Overall, bidomain simulations were sped up by a factor of 11.8 to 16.3 in benchmarks running on 6–20 GPUs compared to the same number of CPU cores. To match the fastest GPU simulation which engaged 20GPUs, 476 CPU cores were required on a national supercomputing facility. PMID:22692867