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Sample records for algorithms simulation results

  1. Simulation results for the Viterbi decoding algorithm

    NASA Technical Reports Server (NTRS)

    Batson, B. H.; Moorehead, R. W.; Taqvi, S. Z. H.

    1972-01-01

    Concepts involved in determining the performance of coded digital communications systems are introduced. The basic concepts of convolutional encoding and decoding are summarized, and hardware implementations of sequential and maximum likelihood decoders are described briefly. Results of parametric studies of the Viterbi decoding algorithm are summarized. Bit error probability is chosen as the measure of performance and is calculated, by using digital computer simulations, for various encoder and decoder parameters. Results are presented for code rates of one-half and one-third, for constraint lengths of 4 to 8, for both hard-decision and soft-decision bit detectors, and for several important systematic and nonsystematic codes. The effect of decoder block length on bit error rate also is considered, so that a more complete estimate of the relationship between performance and decoder complexity can be made.

  2. Numerical simulation of dynamical gluinos: experience with a multi-bosonic algorithm and first results

    NASA Astrophysics Data System (ADS)

    Kirchner, R.; Luckmann, S.; Montvay, I.; Spanderen, K.; Westphalen, J.; DESY-Münster Collaboration

    1999-03-01

    We report on our experience with the two-step multi-bosonic algorithm in a large scale Monte Carlo simulation of the SU(2) Yang-Mills theory with dynamical gluinos. First results are described on the low lying spectrum of bound states, the string tension and the gluino condensate.

  3. A comparison of two position estimate algorithms that use ILS localizer and DME information. Simulation and flight test results

    NASA Technical Reports Server (NTRS)

    Knox, C. E.; Vicroy, D. D.; Scanlon, C.

    1984-01-01

    Simulation and flight tests were conducted to compare the accuracy of two algorithms designed to compute a position estimate with an airborne navigation computer. Both algorithms used ILS localizer and DME radio signals to compute a position difference vector to be used as an input to the navigation computer position estimate filter. The results of these tests show that the position estimate accuracy and response to artificially induced errors are improved when the position estimate is computed by an algorithm that geometrically combines DME and ILS localizer information to form a single component of error rather than by an algorithm that produces two independent components of error, one from a DMD input and the other from the ILS localizer input.

  4. Simulation Results of the Huygens Probe Entry and Descent Trajectory Reconstruction Algorithm

    NASA Technical Reports Server (NTRS)

    Kazeminejad, B.; Atkinson, D. H.; Perez-Ayucar, M.

    2005-01-01

    Cassini/Huygens is a joint NASA/ESA mission to explore the Saturnian system. The ESA Huygens probe is scheduled to be released from the Cassini spacecraft on December 25, 2004, enter the atmosphere of Titan in January, 2005, and descend to Titan s surface using a sequence of different parachutes. To correctly interpret and correlate results from the probe science experiments and to provide a reference set of data for "ground-truthing" Orbiter remote sensing measurements, it is essential that the probe entry and descent trajectory reconstruction be performed as early as possible in the postflight data analysis phase. The Huygens Descent Trajectory Working Group (DTWG), a subgroup of the Huygens Science Working Team (HSWT), is responsible for developing a methodology and performing the entry and descent trajectory reconstruction. This paper provides an outline of the trajectory reconstruction methodology, preliminary probe trajectory retrieval test results using a simulated synthetic Huygens dataset developed by the Huygens Project Scientist Team at ESA/ESTEC, and a discussion of strategies for recovery from possible instrument failure.

  5. Simulation and experimental results for a phase retrieval-based algorithm for far-field beam steering and shaping

    NASA Astrophysics Data System (ADS)

    Roggemann, Michael C.; Welsh, Byron M.; Stone, Bradley R.; Su, Ting Ei

    2002-02-01

    Active laser-based electro-optical (EO) sensors on future aircraft and spacecraft will be used for a variety of missions and will be required to have a number of demanding technical characteristics. A key challenge to achieving these characteristics is the development of inexpensive, high degree of freedom optical wave front control devices, and the development of effective algorithms for controlling these devices. In this paper we present our research in the development of phase retrieval-based wave front control algorithms that can be used implemented with segmented liquid crystal-based wave front control devices. We have developed a wave front control algorithm that allows dynamic small-angle beam steering and shaping in the presence of an aberrating output window. Our approach is based on a phase retrieval algorithm to determine the optimal figure of a segmented wave front control device. Simulation and experimental results presented here show that this approach allows shaped far field patterns to be created and steered over small angles.

  6. Profiling Wind and Greenhouse Gases by Infrared-laser Occultation: Algorithm and Results from Simulations in Windy Air

    NASA Astrophysics Data System (ADS)

    Plach, Andreas; Proschek, Veronika; Kirchengast, Gottfried

    2014-05-01

    We employ the Low Earth Orbit (LEO-LEO) microwave and infrared-laser occultation (LMIO) method to derive a full set of thermodynamic state variables from microwave signals and climate benchmark profiling of greenhouse gases (GHGs) and line-of-sight (l.o.s.) wind using infrared-laser signals. The focus lies on the upper troposphere/lower stratosphere region (UTLS - 5 km to 35 km). The GHG retrieval errors are generally smaller than 1% to 3% r.m.s., at a vertical resolution of about 1 km. In this study we focus on the infrared-laser part of LMIO, where we introduce a new, advanced wind retrieval algorithm to derive accurate l.o.s. wind profiles. The wind retrieval uses the reasonable assumption of the wind blowing along spherical shells (horizontal winds) and therefore the l.o.s. wind speed can be retrieved by using an Abel integral transform. A 'delta-differential transmission' principle is applied to two thoroughly selected infrared-laser signals placed at the wings of the highly symmetric C18OO absorption line (nominally ±0.004 cm-1 from the line center near 4767 cm-1) plus a related 'off-line' reference signal. The delta-differential transmission obtained by differencing these signals is clear from atmospheric broadband effects and is proportional to the wind-induced Doppler shift; it serves as the integrand of the Abel transform. The Doppler frequency shift calculated along with the wind retrieval is in turn also used in the GHG retrieval to correct the frequency of GHG-sensitive infrared-laser signals for the wind-induced Doppler shift, which enables improved GHG estimation. This step therefore provides the capability to correct potential wind-induced residual errors of the GHG retrieval in case of strong winds. We performed end-to-end simulations to test the performance of the new retrieval in windy air. The simulations used realistic atmospheric conditions (thermodynamic state variables and wind profiles) from an analysis field of the European Centre for

  7. A retrodictive stochastic simulation algorithm

    SciTech Connect

    Vaughan, T.G. Drummond, P.D.; Drummond, A.J.

    2010-05-20

    In this paper we describe a simple method for inferring the initial states of systems evolving stochastically according to master equations, given knowledge of the final states. This is achieved through the use of a retrodictive stochastic simulation algorithm which complements the usual predictive stochastic simulation approach. We demonstrate the utility of this new algorithm by applying it to example problems, including the derivation of likely ancestral states of a gene sequence given a Markovian model of genetic mutation.

  8. Fractal Landscape Algorithms for Environmental Simulations

    NASA Astrophysics Data System (ADS)

    Mao, H.; Moran, S.

    2014-12-01

    Natural science and geographical research are now able to take advantage of environmental simulations that more accurately test experimental hypotheses, resulting in deeper understanding. Experiments affected by the natural environment can benefit from 3D landscape simulations capable of simulating a variety of terrains and environmental phenomena. Such simulations can employ random terrain generation algorithms that dynamically simulate environments to test specific models against a variety of factors. Through the use of noise functions such as Perlin noise, Simplex noise, and diamond square algorithms, computers can generate simulations that model a variety of landscapes and ecosystems. This study shows how these algorithms work together to create realistic landscapes. By seeding values into the diamond square algorithm, one can control the shape of landscape. Perlin noise and Simplex noise are also used to simulate moisture and temperature. The smooth gradient created by coherent noise allows more realistic landscapes to be simulated. Terrain generation algorithms can be used in environmental studies and physics simulations. Potential studies that would benefit from simulations include the geophysical impact of flash floods or drought on a particular region and regional impacts on low lying area due to global warming and rising sea levels. Furthermore, terrain generation algorithms also serve as aesthetic tools to display landscapes (Google Earth), and simulate planetary landscapes. Hence, it can be used as a tool to assist science education. Algorithms used to generate these natural phenomena provide scientists a different approach in analyzing our world. The random algorithms used in terrain generation not only contribute to the generating the terrains themselves, but are also capable of simulating weather patterns.

  9. Simulation of orographic effects with a Quasi-3-D Multiscale Modeling Framework: Basic algorithm and preliminary results

    NASA Astrophysics Data System (ADS)

    Jung, J.

    2016-12-01

    The global atmospheric models based on the Multi-scale Modeling Framework (MMF) are able to explicitly resolve subgrid-scale processes by using embedded 2-D Cloud-Resolving Models (CRMs). Up to now, however, those models do not include the orographic effects on the CRM grid scale. This study shows that the effects of CRM grid-scale orography can be simulated reasonably well by the Quasi-3-D MMF (Q3D MMF), which has been developed as a second-generation MMF. In the Q3D framework, the surface topography can be included in the CRM component by using a block representation of the mountains, so that no smoothing of the topographic height is necessary. To demonstrate the performance of such a model, the orographic effects over a steep mountain are simulated in an idealized experimental setup with each of the Q3D MMF and the full 3-D CRM. The latter is used as a benchmark. Comparison of the results shows that the Q3D MMF is able to reproduce the horizontal distribution of orographic precipitation and the flow changes around mountains as simulated by the 3-D CRM, even though the embedded CRMs of the Q3D MMF recognize only some aspects of the complex 3-D topography. It is also shown that the use of 3-D CRMs in the Q3D framework, rather than 2-D CRMs, has positive impacts on the simulation of wind fields but does not substantially change the simulated precipitation.

  10. Simulation of orographic effects with a Quasi-3-D Multiscale Modeling Framework: Basic algorithm and preliminary results

    SciTech Connect

    Jung, Joon -Hee

    2016-10-11

    Here, the global atmospheric models based on the Multi-scale Modeling Framework (MMF) are able to explicitly resolve subgrid-scale processes by using embedded 2-D Cloud-Resolving Models (CRMs). Up to now, however, those models do not include the orographic effects on the CRM grid scale. This study shows that the effects of CRM grid-scale orography can be simulated reasonably well by the Quasi-3-D MMF (Q3D MMF), which has been developed as a second-generation MMF. In the Q3D framework, the surface topography can be included in the CRM component by using a block representation of the mountains, so that no smoothing of the topographic height is necessary. To demonstrate the performance of such a model, the orographic effects over a steep mountain are simulated in an idealized experimental setup with each of the Q3D MMF and the full 3-D CRM. The latter is used as a benchmark. Comparison of the results shows that the Q3D MMF is able to reproduce the horizontal distribution of orographic precipitation and the flow changes around mountains as simulated by the 3-D CRM, even though the embedded CRMs of the Q3D MMF recognize only some aspects of the complex 3-D topography. It is also shown that the use of 3-D CRMs in the Q3D framework, rather than 2-D CRMs, has positive impacts on the simulation of wind fields but does not substantially change the simulated precipitation.

  11. Simulation of orographic effects with a Quasi-3-D Multiscale Modeling Framework: Basic algorithm and preliminary results

    DOE PAGES

    Jung, Joon -Hee

    2016-10-11

    Here, the global atmospheric models based on the Multi-scale Modeling Framework (MMF) are able to explicitly resolve subgrid-scale processes by using embedded 2-D Cloud-Resolving Models (CRMs). Up to now, however, those models do not include the orographic effects on the CRM grid scale. This study shows that the effects of CRM grid-scale orography can be simulated reasonably well by the Quasi-3-D MMF (Q3D MMF), which has been developed as a second-generation MMF. In the Q3D framework, the surface topography can be included in the CRM component by using a block representation of the mountains, so that no smoothing of themore » topographic height is necessary. To demonstrate the performance of such a model, the orographic effects over a steep mountain are simulated in an idealized experimental setup with each of the Q3D MMF and the full 3-D CRM. The latter is used as a benchmark. Comparison of the results shows that the Q3D MMF is able to reproduce the horizontal distribution of orographic precipitation and the flow changes around mountains as simulated by the 3-D CRM, even though the embedded CRMs of the Q3D MMF recognize only some aspects of the complex 3-D topography. It is also shown that the use of 3-D CRMs in the Q3D framework, rather than 2-D CRMs, has positive impacts on the simulation of wind fields but does not substantially change the simulated precipitation.« less

  12. The Results of a Simulator Study to Determine the Effects on Pilot Performance of Two Different Motion Cueing Algorithms and Various Delays, Compensated and Uncompensated

    NASA Technical Reports Server (NTRS)

    Guo, Li-Wen; Cardullo, Frank M.; Telban, Robert J.; Houck, Jacob A.; Kelly, Lon C.

    2003-01-01

    A study was conducted employing the Visual Motion Simulator (VMS) at the NASA Langley Research Center, Hampton, Virginia. This study compared two motion cueing algorithms, the NASA adaptive algorithm and a new optimal control based algorithm. Also, the study included the effects of transport delays and the compensation thereof. The delay compensation algorithm employed is one developed by Richard McFarland at NASA Ames Research Center. This paper reports on the analyses of the results of analyzing the experimental data collected from preliminary simulation tests. This series of tests was conducted to evaluate the protocols and the methodology of data analysis in preparation for more comprehensive tests which will be conducted during the spring of 2003. Therefore only three pilots were used. Nevertheless some useful results were obtained. The experimental conditions involved three maneuvers; a straight-in approach with a rotating wind vector, an offset approach with turbulence and gust, and a takeoff with and without an engine failure shortly after liftoff. For each of the maneuvers the two motion conditions were combined with four delay conditions (0, 50, 100 & 200ms), with and without compensation.

  13. Formation Algorithms and Simulation Testbed

    NASA Technical Reports Server (NTRS)

    Wette, Matthew; Sohl, Garett; Scharf, Daniel; Benowitz, Edward

    2004-01-01

    Formation flying for spacecraft is a rapidly developing field that will enable a new era of space science. For one of its missions, the Terrestrial Planet Finder (TPF) project has selected a formation flying interferometer design to detect earth-like planets orbiting distant stars. In order to advance technology needed for the TPF formation flying interferometer, the TPF project has been developing a distributed real-time testbed to demonstrate end-to-end operation of formation flying with TPF-like functionality and precision. This is the Formation Algorithms and Simulation Testbed (FAST) . This FAST was conceived to bring out issues in timing, data fusion, inter-spacecraft communication, inter-spacecraft sensing and system-wide formation robustness. In this paper we describe the FAST and show results from a two-spacecraft formation scenario. The two-spacecraft simulation is the first time that precision end-to-end formation flying operation has been demonstrated in a distributed real-time simulation environment.

  14. Recursive Branching Simulated Annealing Algorithm

    NASA Technical Reports Server (NTRS)

    Bolcar, Matthew; Smith, J. Scott; Aronstein, David

    2012-01-01

    This innovation is a variation of a simulated-annealing optimization algorithm that uses a recursive-branching structure to parallelize the search of a parameter space for the globally optimal solution to an objective. The algorithm has been demonstrated to be more effective at searching a parameter space than traditional simulated-annealing methods for a particular problem of interest, and it can readily be applied to a wide variety of optimization problems, including those with a parameter space having both discrete-value parameters (combinatorial) and continuous-variable parameters. It can take the place of a conventional simulated- annealing, Monte-Carlo, or random- walk algorithm. In a conventional simulated-annealing (SA) algorithm, a starting configuration is randomly selected within the parameter space. The algorithm randomly selects another configuration from the parameter space and evaluates the objective function for that configuration. If the objective function value is better than the previous value, the new configuration is adopted as the new point of interest in the parameter space. If the objective function value is worse than the previous value, the new configuration may be adopted, with a probability determined by a temperature parameter, used in analogy to annealing in metals. As the optimization continues, the region of the parameter space from which new configurations can be selected shrinks, and in conjunction with lowering the annealing temperature (and thus lowering the probability for adopting configurations in parameter space with worse objective functions), the algorithm can converge on the globally optimal configuration. The Recursive Branching Simulated Annealing (RBSA) algorithm shares some features with the SA algorithm, notably including the basic principles that a starting configuration is randomly selected from within the parameter space, the algorithm tests other configurations with the goal of finding the globally optimal

  15. APL simulation of Grover's algorithm

    NASA Astrophysics Data System (ADS)

    Lipovaca, Samir

    2012-02-01

    Grover's algorithm is a fast quantum search algorithm. Classically, to solve the search problem for a search space of size N we need approximately N operations. Grover's algorithm offers a quadratic speedup. Since present quantum computers are not robust enough for code writing and execution, to experiment with Grover's algorithm, we will simulate it using the APL programming language. The APL programming language is especially suited for this task. For example, to compute Walsh-Hadamard transformation matrix for N quantum states via a tensor product of N Hadamard matrices we need to iterate N-1 times only one line of the code. Initial study indicates the quantum mechanical amplitude of the solution is almost independent of the search space size and rapidly reaches 0.999 values with slight variations at higher decimal places.

  16. Simulated annealing algorithm for optimal capital growth

    NASA Astrophysics Data System (ADS)

    Luo, Yong; Zhu, Bo; Tang, Yong

    2014-08-01

    We investigate the problem of dynamic optimal capital growth of a portfolio. A general framework that one strives to maximize the expected logarithm utility of long term growth rate was developed. Exact optimization algorithms run into difficulties in this framework and this motivates the investigation of applying simulated annealing optimized algorithm to optimize the capital growth of a given portfolio. Empirical results with real financial data indicate that the approach is inspiring for capital growth portfolio.

  17. Phase unwrapping algorithms in laser propagation simulation

    NASA Astrophysics Data System (ADS)

    Du, Rui; Yang, Lijia

    2013-08-01

    Currently simulating on laser propagation in atmosphere usually need to deal with beam in strong turbulence, which may lose a part of information via Fourier Transform to simulate the transmission, makes the phase of beam as a 2-D array wrap by 2π . An effective unwrapping algorithm is needed for continuing result and faster calculation. The unwrapping algorithms in atmospheric propagation are similar to the unwrapping algorithm in radar or 3-D surface rebuilding, but not the same. In this article, three classic unwrapping algorithms: the block least squares (BLS), mask-cut (MCUT), and the Flynn's minimal discontinuity algorithm (FMD) are tried in wave-front reconstruction simulation. Each of those algorithms are tested 100 times in 6 same conditions, including low(64x64), medium(128x128), and high(256x256) resolution phase array, with and without noises. Compared the results, the conclusions are delivered as follows. The BLS-based algorithm is the fastest, and the result is acceptable in low resolution environment without noise. The MCUT are higher in accuracy, though they are slower with the array resolution increased, and it is sensitive to noise, resulted in large area errors. Flynn's algorithm has the better accuracy, and it occupies large memory in calculation. After all, the article delivered a new algorithm that based on Active on Vertex (AOV) Network, to build a logical graph to cut the search space then find minimal discontinuity solution. The AOV is faster than MCUT in dealing with high resolution phase arrays, and better accuracy as FMD that has been tested.

  18. Quantum Algorithms for Fermionic Simulations

    NASA Astrophysics Data System (ADS)

    Ortiz, Gerardo

    2001-06-01

    The probabilistic simulation of quantum systems in classical computers is known to be limited by the so-called sign or phase problem, a problem believed to be of exponential complexity. This ``disease" manifests itself by the exponentially hard task of estimating the expectation value of an observable with a given error. Therefore, probabilistic simulations on a classical computer do not seem to qualify as a practical computational scheme for general quantum many-body problems. The limiting factors, for whatever reasons, are negative or complex-valued probabilities whether the simulations are done in real or imaginary time. In 1981 Richard Feynman raised some provocative questions in connection to the ``exact imitation'' of such systems using a special device named a ``quantum computer.'' Feynman hesitated about the possibility of imitating fermion systems using such a device. Here we address some of his concerns and, in particular, investigate the simulation of fermionic systems. We show how quantum algorithms avoid the sign problem by reducing the complexity from exponential to polynomial. Our demonstration is based upon the use of isomorphisms of *-algebras (spin-particle transformations) which connect different models of quantum computation. In particular, we present fermionic models (the fabled ``Grassmann Chip''); but, of course, these models are not the only ones since our spin-particle connections allow us to introduce more ``esoteric'' models of computation. We present specific quantum algorithms that illustrate the main points of our algebraic approach.

  19. Feedback algorithm for simulation of multi-segmented cracks

    SciTech Connect

    Chady, T.; Napierala, L.

    2011-06-23

    In this paper, a method for obtaining a three dimensional crack model from a radiographic image is discussed. A genetic algorithm aiming at close simulation of crack's shape is presented. Results obtained with genetic algorithm are compared to those achieved in authors' previous work. The described algorithm has been tested on both simulated and real-life cracks.

  20. Preliminary results from MERIS Land Algorithm

    NASA Astrophysics Data System (ADS)

    Gobron, N.; Pinty, B.; Taberner, M.; Melin, F.; Verstraete, M. M.; Widlowski, J.-L.

    2003-04-01

    This paper presents a first and preliminary evaluation of the performance of the algorithm implemented in the Medium Resolution Imaging Spectrometer (MERIS) ground segment for assessing the status of land surfaces. First, we propose an updated version of the MERIS algorithm itself, which improves the accuracy of the product. Second, we analyze the first results by inter-comparing the MERIS Global Vegetation Index (MGVI) to similar products derived from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) that are generated at the European Commission Joint Research Center (EC-JRC). The first evaluation between MERIS and SeaWiFS derived products is made using data acquired on the same day by both instruments. The results show acceptable agreement and the differences are well understood by radiation transfer model simulations.

  1. The systems biology simulation core algorithm

    PubMed Central

    2013-01-01

    Background With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases. Results This article describes an efficient algorithm to solve SBML models that are interpreted in terms of ordinary differential equations. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven project providing a large collection of numerical solvers and a sophisticated interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and all models of BioModels Database. Conclusions The formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. The reference implementation can be used as a simulation backend for Java™-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from http://simulation-core.sourceforge.net. Feature requests, bug reports, contributions, or any further discussion can be directed to the mailing list simulation-core-development@lists.sourceforge.net. PMID:23826941

  2. Clutter discrimination algorithm simulation in pulse laser radar imaging

    NASA Astrophysics Data System (ADS)

    Zhang, Yan-mei; Li, Huan; Guo, Hai-chao; Su, Xuan; Zhu, Fule

    2015-10-01

    Pulse laser radar imaging performance is greatly influenced by different kinds of clutter. Various algorithms are developed to mitigate clutter. However, estimating performance of a new algorithm is difficult. Here, a simulation model for estimating clutter discrimination algorithms is presented. This model consists of laser pulse emission, clutter jamming, laser pulse reception and target image producing. Additionally, a hardware platform is set up gathering clutter data reflected by ground and trees. The data logging is as clutter jamming input in the simulation model. The hardware platform includes a laser diode, a laser detector and a high sample rate data logging circuit. The laser diode transmits short laser pulses (40ns FWHM) at 12.5 kilohertz pulse rate and at 905nm wavelength. An analog-to-digital converter chip integrated in the sample circuit works at 250 mega samples per second. The simulation model and the hardware platform contribute to a clutter discrimination algorithm simulation system. Using this system, after analyzing clutter data logging, a new compound pulse detection algorithm is developed. This new algorithm combines matched filter algorithm and constant fraction discrimination (CFD) algorithm. Firstly, laser echo pulse signal is processed by matched filter algorithm. After the first step, CFD algorithm comes next. Finally, clutter jamming from ground and trees is discriminated and target image is produced. Laser radar images are simulated using CFD algorithm, matched filter algorithm and the new algorithm respectively. Simulation result demonstrates that the new algorithm achieves the best target imaging effect of mitigating clutter reflected by ground and trees.

  3. General simulation algorithm for autocorrelated binary processes

    NASA Astrophysics Data System (ADS)

    Serinaldi, Francesco; Lombardo, Federico

    2017-02-01

    The apparent ubiquity of binary random processes in physics and many other fields has attracted considerable attention from the modeling community. However, generation of binary sequences with prescribed autocorrelation is a challenging task owing to the discrete nature of the marginal distributions, which makes the application of classical spectral techniques problematic. We show that such methods can effectively be used if we focus on the parent continuous process of beta distributed transition probabilities rather than on the target binary process. This change of paradigm results in a simulation procedure effectively embedding a spectrum-based iterative amplitude-adjusted Fourier transform method devised for continuous processes. The proposed algorithm is fully general, requires minimal assumptions, and can easily simulate binary signals with power-law and exponentially decaying autocorrelation functions corresponding, for instance, to Hurst-Kolmogorov and Markov processes. An application to rainfall intermittency shows that the proposed algorithm can also simulate surrogate data preserving the empirical autocorrelation.

  4. A theoretical comparison of evolutionary algorithms and simulated annealing

    SciTech Connect

    Hart, W.E.

    1995-08-28

    This paper theoretically compares the performance of simulated annealing and evolutionary algorithms. Our main result is that under mild conditions a wide variety of evolutionary algorithms can be shown to have greater performance than simulated annealing after a sufficiently large number of function evaluations. This class of EAs includes variants of evolutionary strategie and evolutionary programming, the canonical genetic algorithm, as well as a variety of genetic algorithms that have been applied to combinatorial optimization problems. The proof of this result is based on a performance analysis of a very general class of stochastic optimization algorithms, which has implications for the performance of a variety of other optimization algorithm.

  5. ICAAS piloted simulation results

    NASA Astrophysics Data System (ADS)

    Landy, R. J.; Halski, P. J.; Meyer, R. P.

    1994-05-01

    This paper reports piloted simulation results from the Integrated Control and Avionics for Air Superiority (ICAAS) piloted simulation evaluations. The program was to develop, integrate, and demonstrate critical technologies which will enable United States Air Force tactical fighter 'blue' aircraft to achieve superiority and survive when outnumbered by as much as four to one by enemy aircraft during air combat engagements. Primary emphasis was placed on beyond visual range (BVR) combat with provisions for effective transition to close-in combat. The ICAAS system was developed and tested in two stages. The first stage, called low risk ICAAS, was defined as employing aircraft and avionics technology with an initial operational date no later than 1995. The second stage, called medium risk ICAAS, was defined as employing aircraft and avionics technology with an initial operational date no later than 1998. Descriptions of the low risk and medium risk simulation configurations are given. Normalized (unclassified) results from both the low risk and medium risk ICAAS simulations are discussed. The results show the ICAAS system provided a significant improvement in air combat performance when compared to a current weapon system. Data are presented for both current generation and advanced fighter aircraft. The ICAAS technologies which are ready for flight testing in order to transition to the fighter fleet are described along with technologies needing additional development.

  6. New Results in Astrodynamics Using Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Coverstone-Carroll, V.; Hartmann, J. W.; Williams, S. N.; Mason, W. J.

    1998-01-01

    Generic algorithms have gained popularity as an effective procedure for obtaining solutions to traditionally difficult space mission optimization problems. In this paper, a brief survey of the use of genetic algorithms to solve astrodynamics problems is presented and is followed by new results obtained from applying a Pareto genetic algorithm to the optimization of low-thrust interplanetary spacecraft missions.

  7. New Results in Astrodynamics Using Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Coverstone-Carroll, V.; Hartmann, J. W.; Williams, S. N.; Mason, W. J.

    1998-01-01

    Generic algorithms have gained popularity as an effective procedure for obtaining solutions to traditionally difficult space mission optimization problems. In this paper, a brief survey of the use of genetic algorithms to solve astrodynamics problems is presented and is followed by new results obtained from applying a Pareto genetic algorithm to the optimization of low-thrust interplanetary spacecraft missions.

  8. Comparing simulation results of SBML capable simulators

    PubMed Central

    Bergmann, Frank T.; Sauro, Herbert M.

    2008-01-01

    Motivation: Simulations are an essential tool when analyzing biochemical networks. Researchers and developers seeking to refine simulation tools or develop new ones would benefit greatly from being able to compare their simulation results. Summary: We present an approach to compare simulation results between several SBML capable simulators and provide a website for the community to share simulation results. Availability: The website with simulation results and additional material can be found under: http://sys-bio.org/sbwWiki/compare. The software used to generate the simulation results is available on the website for download. Contact: fbergman@u.washington.edu PMID:18579569

  9. Efficient algorithm for simulation of isoelectric focusing.

    PubMed

    Yoo, Kisoo; Shim, Jaesool; Liu, Jin; Dutta, Prashanta

    2014-03-01

    IEF simulation is an effective tool to investigate the transport phenomena and separation performance as well as to design IEF microchip. However, multidimensional IEF simulations are computationally intensive as one has to solve a large number of mass conservation equations for ampholytes to simulate a realistic case. In this study, a parallel scheme for a 2D IEF simulation is developed to reduce the computational time. The calculation time for each equation is analyzed to identify which procedure is suitable for parallelization. As expected, simultaneous solution of mass conservation equations of ampholytes is identified as the computational hot spot, and the computational time can be significantly reduced by parallelizing the solution procedure for that. Moreover, to optimize the computing time, electric potential behavior during transient state is investigated. It is found that for a straight channel the transient variation of electric potential along the channel is negligible in a narrow pH range (5∼8) IEF. Thus the charge conservation equation is solved for the first time step only, and the electric potential obtain from that is used for subsequent calculations. IEF simulations are carried out using this algorithm for separation of cardiac troponin I from serum albumin in a pH range of 5-8 using 192 biprotic ampholytes. Significant reduction in simulation time is achieved using the parallel algorithm. We also study the effect of number of ampholytes to form the pH gradient and its effect in the focusing and separation behavior of cardiac troponin I and albumin. Our results show that, at the completion of separation phase, the pH profile is stepwise for lower number of ampholytes, but becomes smooth as the number of ampholytes increases. Numerical results also show that higher protein concentration can be obtained using higher number of ampholytes.

  10. An exact accelerated stochastic simulation algorithm.

    PubMed

    Mjolsness, Eric; Orendorff, David; Chatelain, Philippe; Koumoutsakos, Petros

    2009-04-14

    An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present "ER-leap" algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 23 power of the number of reaction events in a Galton-Watson process.

  11. A simulation algorithm for ultrasound liver backscattered signals.

    PubMed

    Zatari, D; Botros, N; Dunn, F

    1995-11-01

    In this study, we present a simulation algorithm for the backscattered ultrasound signal from liver tissue. The algorithm simulates backscattered signals from normal liver and three different liver abnormalities. The performance of the algorithm has been tested by statistically comparing the simulated signals with corresponding signals obtained from a previous in vivo study. To verify that the simulated signals can be classified correctly we have applied a classification technique based on an artificial neural network. The acoustic features extracted from the spectrum over a 2.5 MHz bandwidth are the attenuation coefficient and the change of speed of sound with frequency (dispersion). Our results show that the algorithm performs satisfactorily. Further testing of the algorithm is conducted by the use of a data acquisition and analysis system designed by the authors, where several simulated signals are stored in memory chips and classified according to their abnormalities.

  12. Wake Vortex Algorithm Scoring Results

    NASA Technical Reports Server (NTRS)

    Robins, R. E.; Delisi, D. P.; Hinton, David (Technical Monitor)

    2002-01-01

    This report compares the performance of two models of trailing vortex evolution for which interaction with the ground is not a significant factor. One model uses eddy dissipation rate (EDR) and the other uses the kinetic energy of turbulence fluctuations (TKE) to represent the effect of turbulence. In other respects, the models are nearly identical. The models are evaluated by comparing their predictions of circulation decay, vertical descent, and lateral transport to observations for over four hundred cases from Memphis and Dallas/Fort Worth International Airports. These observations were obtained during deployments in support of NASA's Aircraft Vortex Spacing System (AVOSS). The results of the comparisons show that the EDR model usually performs slightly better than the TKE model.

  13. Efficient hybrid algorithms for collisional plasma simulation

    NASA Astrophysics Data System (ADS)

    Dimits, A. M.; Cohen, B. I.; Caflisch, R. E.; Wang, C. M.; Huang, Y.

    2009-11-01

    We report on the development of efficient hybrid simulation algorithms for plasma systems that span a wide range of collisionality. Investigations of their performance, using ion-sheath and electron-transport test problems, are presented. In these schemes the distribution function is decomposed of into kinetic and fluid components. The fluid component is treated via Eulerian fluid simulation methods. In one class of algorithms, the kinetic component is treated using a combination of fixed-weight particle-in-cell (PIC) and binary Monte-Carlo collision methods. Particles are created by sampling from the fluid component, and paired for collisions with the kinetic particles. In the other class of algorithms, the kinetic component is treated using evolving-weight delta-f-PIC schemes and collision-field algorithms. The performance these algorithms depends strongly on the particular sets of criteria for (a) exchange between the particle and fluid components and (b) creation, destruction, and retention of the simulation particles.

  14. Algorithmic quantum simulation of memory effects

    NASA Astrophysics Data System (ADS)

    Alvarez-Rodriguez, U.; Di Candia, R.; Casanova, J.; Sanz, M.; Solano, E.

    2017-02-01

    We propose a method for the algorithmic quantum simulation of memory effects described by integrodifferential evolution equations. It consists in the systematic use of perturbation theory techniques and a Markovian quantum simulator. Our method aims to efficiently simulate both completely positive and nonpositive dynamics without the requirement of engineering non-Markovian environments. Finally, we find that small error bounds can be reached with polynomially scaling resources, evaluated as the time required for the simulation.

  15. Selection of views to materialize using simulated annealing algorithms

    NASA Astrophysics Data System (ADS)

    Zhou, Lijuan; Liu, Chi; Wang, Hongfeng; Liu, Daixin

    2002-03-01

    A data warehouse contains lots of materialized views over the data provided by the distributed heterogeneous databases for the purpose of efficiently implementing decision-support or OLAP queries. It is important to select the right view to materialize that answer a given set of queries. The goal is the minimization of the combination of the query evaluation and view maintenance costs. In this paper, we have addressed and designed algorithms for selecting a set of views to be materialized so that the sum of processing a set of queries and maintaining the materialized views is minimized. We develop an approach using simulated annealing algorithms to solve it. First, we explore simulated annealing algorithms to optimize the selection of materialized views. Then we use experiments to demonstrate our approach. The results show that our algorithm works better. We implemented our algorithms and a performance study of the algorithms shows that the proposed algorithm gives an optimal solution.

  16. Empirical study of parallel LRU simulation algorithms

    NASA Technical Reports Server (NTRS)

    Carr, Eric; Nicol, David M.

    1994-01-01

    This paper reports on the performance of five parallel algorithms for simulating a fully associative cache operating under the LRU (Least-Recently-Used) replacement policy. Three of the algorithms are SIMD, and are implemented on the MasPar MP-2 architecture. Two other algorithms are parallelizations of an efficient serial algorithm on the Intel Paragon. One SIMD algorithm is quite simple, but its cost is linear in the cache size. The two other SIMD algorithm are more complex, but have costs that are independent on the cache size. Both the second and third SIMD algorithms compute all stack distances; the second SIMD algorithm is completely general, whereas the third SIMD algorithm presumes and takes advantage of bounds on the range of reference tags. Both MIMD algorithm implemented on the Paragon are general and compute all stack distances; they differ in one step that may affect their respective scalability. We assess the strengths and weaknesses of these algorithms as a function of problem size and characteristics, and compare their performance on traces derived from execution of three SPEC benchmark programs.

  17. A splitting algorithm for Vlasov simulation with filamentation filtration

    NASA Technical Reports Server (NTRS)

    Klimas, A. J.; Farrell, W. M.

    1994-01-01

    A Fourier-Fourier transformed version of the splitting algorithm for simulating solutions of the Vlasov-Poisson system of equations is introduced. It is shown that with the inclusion of filamentation filtration in this transformed algorithm it is both faster and more stable than the standard splitting algorithm. It is further shown that in a scalar computer environment this new algorithm is approximately equal in speed and far less noisy than its particle-in-cell counterpart. It is conjectured that in a multiprocessor environment the filtered splitting algorithm would be faster while producing more precise results.

  18. Improved ant colony algorithm and its simulation study

    NASA Astrophysics Data System (ADS)

    Wang, Zongjiang

    2013-03-01

    Ant colony algorithm is development a new heuristic algorithm through simulation ant foraging. For its convergence rate slow, easy to fall into local optimal solution proposed for the adjustment of key parameters, pheromone update to improve the way and through the issue of TSP experiments, results showed that the improved algorithm has better overall search capabilities and demonstrated the feasibility and effectiveness of this method.

  19. Quantitative tomography simulations and reconstruction algorithms

    SciTech Connect

    Martz, H E; Aufderheide, M B; Goodman, D; Schach von Wittenau, A; Logan, C; Hall, J; Jackson, J; Slone, D

    2000-11-01

    X-ray, neutron and proton transmission radiography and computed tomography (CT) are important diagnostic tools that are at the heart of LLNLs effort to meet the goals of the DOE's Advanced Radiography Campaign. This campaign seeks to improve radiographic simulation and analysis so that radiography can be a useful quantitative diagnostic tool for stockpile stewardship. Current radiographic accuracy does not allow satisfactory separation of experimental effects from the true features of an object's tomographically reconstructed image. This can lead to difficult and sometimes incorrect interpretation of the results. By improving our ability to simulate the whole radiographic and CT system, it will be possible to examine the contribution of system components to various experimental effects, with the goal of removing or reducing them. In this project, we are merging this simulation capability with a maximum-likelihood (constrained-conjugate-gradient-CCG) reconstruction technique yielding a physics-based, forward-model image-reconstruction code. In addition, we seek to improve the accuracy of computed tomography from transmission radiographs by studying what physics is needed in the forward model. During FY 2000, an improved version of the LLNL ray-tracing code called HADES has been coupled with a recently developed LLNL CT algorithm known as CCG. The problem of image reconstruction is expressed as a large matrix equation relating a model for the object being reconstructed to its projections (radiographs). Using a constrained-conjugate-gradient search algorithm, a maximum likelihood solution is sought. This search continues until the difference between the input measured radiographs or projections and the simulated or calculated projections is satisfactorily small. We developed a 2D HADES-CCG CT code that uses full ray-tracing simulations from HADES as the projector. Often an object has axial symmetry and it is desirable to reconstruct into a 2D r-z mesh with a limited

  20. An exact accelerated stochastic simulation algorithm

    NASA Astrophysics Data System (ADS)

    Mjolsness, Eric; Orendorff, David; Chatelain, Philippe; Koumoutsakos, Petros

    2009-04-01

    An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present "ER-leap" algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 2/3 power of the number of reaction events in a Galton-Watson process.

  1. An exact accelerated stochastic simulation algorithm

    PubMed Central

    Mjolsness, Eric; Orendorff, David; Chatelain, Philippe; Koumoutsakos, Petros

    2009-01-01

    An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present “ER-leap” algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 2∕3 power of the number of reaction events in a Galton–Watson process. PMID:19368432

  2. The Soil Moisture Active Passive Mission (SMAP) Science Data Products: Results of Testing with Field Experiment and Algorithm Testbed Simulation Environment Data

    NASA Technical Reports Server (NTRS)

    Entekhabi, Dara; Njoku, Eni E.; O'Neill, Peggy E.; Kellogg, Kent H.; Entin, Jared K.

    2010-01-01

    Talk outline 1. Derivation of SMAP basic and applied science requirements from the NRC Earth Science Decadal Survey applications 2. Data products and latencies 3. Algorithm highlights 4. SMAP Algorithm Testbed 5. SMAP Working Groups and community engagement

  3. Genetic Algorithms for Digital Quantum Simulations.

    PubMed

    Las Heras, U; Alvarez-Rodriguez, U; Solano, E; Sanz, M

    2016-06-10

    We propose genetic algorithms, which are robust optimization techniques inspired by natural selection, to enhance the versatility of digital quantum simulations. In this sense, we show that genetic algorithms can be employed to increase the fidelity and optimize the resource requirements of digital quantum simulation protocols while adapting naturally to the experimental constraints. Furthermore, this method allows us to reduce not only digital errors but also experimental errors in quantum gates. Indeed, by adding ancillary qubits, we design a modular gate made out of imperfect gates, whose fidelity is larger than the fidelity of any of the constituent gates. Finally, we prove that the proposed modular gates are resilient against different gate errors.

  4. A hierarchical exact accelerated stochastic simulation algorithm

    NASA Astrophysics Data System (ADS)

    Orendorff, David; Mjolsness, Eric

    2012-12-01

    A new algorithm, "HiER-leap" (hierarchical exact reaction-leaping), is derived which improves on the computational properties of the ER-leap algorithm for exact accelerated simulation of stochastic chemical kinetics. Unlike ER-leap, HiER-leap utilizes a hierarchical or divide-and-conquer organization of reaction channels into tightly coupled "blocks" and is thereby able to speed up systems with many reaction channels. Like ER-leap, HiER-leap is based on the use of upper and lower bounds on the reaction propensities to define a rejection sampling algorithm with inexpensive early rejection and acceptance steps. But in HiER-leap, large portions of intra-block sampling may be done in parallel. An accept/reject step is used to synchronize across blocks. This method scales well when many reaction channels are present and has desirable asymptotic properties. The algorithm is exact, parallelizable and achieves a significant speedup over the stochastic simulation algorithm and ER-leap on certain problems. This algorithm offers a potentially important step towards efficient in silico modeling of entire organisms.

  5. The systems biology simulation core algorithm.

    PubMed

    Keller, Roland; Dörr, Alexander; Tabira, Akito; Funahashi, Akira; Ziller, Michael J; Adams, Richard; Rodriguez, Nicolas; Le Novère, Nicolas; Hiroi, Noriko; Planatscher, Hannes; Zell, Andreas; Dräger, Andreas

    2013-07-05

    With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases. This article describes an efficient algorithm to solve SBML models that are interpreted in terms of ordinary differential equations. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven project providing a large collection of numerical solvers and a sophisticated interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and all models of BioModels Database. The formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. The reference implementation can be used as a simulation backend for Java™-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from http://simulation-core.sourceforge.net. Feature requests, bug reports, contributions, or any further discussion can be directed to the mailing list simulation-core-development@lists.sourceforge.net.

  6. Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.

    PubMed

    Omelyan, I P

    2006-09-01

    A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations.

  7. The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Lampoudi, Sotiria; Gillespie, Dan T.; Petzold, Linda R.

    2009-03-01

    The Inhomogeneous Stochastic Simulation Algorithm (ISSA) is a variant of the stochastic simulation algorithm in which the spatially inhomogeneous volume of the system is divided into homogeneous subvolumes, and the chemical reactions in those subvolumes are augmented by diffusive transfers of molecules between adjacent subvolumes. The ISSA can be prohibitively slow when the system is such that diffusive transfers occur much more frequently than chemical reactions. In this paper we present the Multinomial Simulation Algorithm (MSA), which is designed to, on the one hand, outperform the ISSA when diffusive transfer events outnumber reaction events, and on the other, to handle small reactant populations with greater accuracy than deterministic-stochastic hybrid algorithms. The MSA treats reactions in the usual ISSA fashion, but uses appropriately conditioned binomial random variables for representing the net numbers of molecules diffusing from any given subvolume to a neighbor within a prescribed distance. Simulation results illustrate the benefits of the algorithm.

  8. Open cherry picker simulation results

    NASA Technical Reports Server (NTRS)

    Nathan, C. A.

    1982-01-01

    The simulation program associated with a key piece of support equipment to be used to service satellites directly from the Shuttle is assessed. The Open Cherry Picker (OCP) is a manned platform mounted at the end of the remote manipulator system (RMS) and is used to enhance extra vehicular activities (EVA). The results of simulations performed on the Grumman Large Amplitude Space Simulator (LASS) and at the JSC Water Immersion Facility are summarized.

  9. Open cherry picker simulation results

    NASA Technical Reports Server (NTRS)

    Nathan, C. A.

    1982-01-01

    The simulation program associated with a key piece of support equipment to be used to service satellites directly from the Shuttle is assessed. The Open Cherry Picker (OCP) is a manned platform mounted at the end of the remote manipulator system (RMS) and is used to enhance extra vehicular activities (EVA). The results of simulations performed on the Grumman Large Amplitude Space Simulator (LASS) and at the JSC Water Immersion Facility are summarized.

  10. Computational plasticity algorithm for particle dynamics simulations

    NASA Astrophysics Data System (ADS)

    Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.

    2017-03-01

    The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.

  11. Computational algorithms for simulations in atmospheric optics.

    PubMed

    Konyaev, P A; Lukin, V P

    2016-04-20

    A computer simulation technique for atmospheric and adaptive optics based on parallel programing is discussed. A parallel propagation algorithm is designed and a modified spectral-phase method for computer generation of 2D time-variant random fields is developed. Temporal power spectra of Laguerre-Gaussian beam fluctuations are considered as an example to illustrate the applications discussed. Implementation of the proposed algorithms using Intel MKL and IPP libraries and NVIDIA CUDA technology is shown to be very fast and accurate. The hardware system for the computer simulation is an off-the-shelf desktop with an Intel Core i7-4790K CPU operating at a turbo-speed frequency up to 5 GHz and an NVIDIA GeForce GTX-960 graphics accelerator with 1024 1.5 GHz processors.

  12. Simulation of the Galileo spacecraft axial - Delta-V algorithm

    NASA Technical Reports Server (NTRS)

    Longuski, J. M.

    1983-01-01

    Preliminary results are presented from the analysis of the Galileo spacecraft axial delta-V algorithm. The Galileo spacecraft is a dual spin interplanetary spacecraft which will study the four Galilean moons of Jupiter as well as the Jovian environment and atmosphere. In order to achieve orbit about Jupiter and accurately deliver the probe to the planet's upper atmosphere, the Galileo spacecraft must be capable of performing many trajectory corrections or delta-V maneuvers. Twelve 10 Newton thrusters and one 400 Newton engine are utilized for this purpose. There are many maneuver modes and control algorithms available to the spacecraft. In this paper only the analysis of the axial delta-V algorithm will be discussed. The analysis consists of two parts: an analytic study and a simulation study. The analytic results are based on rigid body dynamics, while the simulation includes the first order effect of the flexible magnetometer boom and nutation damper. The simulation utilizes a program developed at JPL which allows flexible body effects to be simulated by modeling a collection of rigid bodies attached together by hinges, springs and dampers. In this preliminary study of the Galileo only two rigid bodies were used in the simulation, but many more can and will be used in the final tests. In this analysis, the algorithm appears to be working correctly and the analytic and simulation results agree very well.

  13. Comparative testing of DNA segmentation algorithms using benchmark simulations.

    PubMed

    Elhaik, Eran; Graur, Dan; Josic, Kresimir

    2010-05-01

    Numerous segmentation methods for the detection of compositionally homogeneous domains within genomic sequences have been proposed. Unfortunately, these methods yield inconsistent results. Here, we present a benchmark consisting of two sets of simulated genomic sequences for testing the performances of segmentation algorithms. Sequences in the first set are composed of fixed-sized homogeneous domains, distinct in their between-domain guanine and cytosine (GC) content variability. The sequences in the second set are composed of a mosaic of many short domains and a few long ones, distinguished by sharp GC content boundaries between neighboring domains. We use these sets to test the performance of seven segmentation algorithms in the literature. Our results show that recursive segmentation algorithms based on the Jensen-Shannon divergence outperform all other algorithms. However, even these algorithms perform poorly in certain instances because of the arbitrary choice of a segmentation-stopping criterion.

  14. Simulations of optical autofocus algorithms based on PGA in SAIL

    NASA Astrophysics Data System (ADS)

    Xu, Nan; Liu, Liren; Xu, Qian; Zhou, Yu; Sun, Jianfeng

    2011-09-01

    The phase perturbations due to propagation effects can destroy the high resolution imagery of Synthetic Aperture Imaging Ladar (SAIL). Some autofocus algorithms for Synthetic Aperture Radar (SAR) were developed and implemented. Phase Gradient Algorithm (PGA) is a well-known one for its robustness and wide application, and Phase Curvature Algorithm (PCA) as a similar algorithm expands its applied field to strip map mode. In this paper the autofocus algorithms utilized in optical frequency domain are proposed, including optical PGA and PCA respectively implemented in spotlight and strip map mode. Firstly, the mathematical flows of optical PGA and PCA in SAIL are derived. The simulations model of the airborne SAIL is established, and the compensation simulations of the synthetic aperture laser images corrupted by the random errors, linear phase errors and quadratic phase errors are executed. The compensation effect and the cycle index of the simulation are discussed. The simulation results show that both the two optical autofocus algorithms are effective while the optical PGA outperforms the optical PCA, which keeps consistency with the theory.

  15. Combined simulated annealing algorithm for the discrete facility location problem.

    PubMed

    Qin, Jin; Ni, Ling-Lin; Shi, Feng

    2012-01-01

    The combined simulated annealing (CSA) algorithm was developed for the discrete facility location problem (DFLP) in the paper. The method is a two-layer algorithm, in which the external subalgorithm optimizes the decision of the facility location decision while the internal subalgorithm optimizes the decision of the allocation of customer's demand under the determined location decision. The performance of the CSA is tested by 30 instances with different sizes. The computational results show that CSA works much better than the previous algorithm on DFLP and offers a new reasonable alternative solution method to it.

  16. Concluding Report: Quantitative Tomography Simulations and Reconstruction Algorithms

    SciTech Connect

    Aufderheide, M B; Martz, H E; Slone, D M; Jackson, J A; Schach von Wittenau, A E; Goodman, D M; Logan, C M; Hall, J M

    2002-02-01

    In this report we describe the original goals and final achievements of this Laboratory Directed Research and Development project. The Quantitative was Tomography Simulations and Reconstruction Algorithms project (99-ERD-015) funded as a multi-directorate, three-year effort to advance the state of the art in radiographic simulation and tomographic reconstruction by improving simulation and including this simulation in the tomographic reconstruction process. Goals were to improve the accuracy of radiographic simulation, and to couple advanced radiographic simulation tools with a robust, many-variable optimization algorithm. In this project, we were able to demonstrate accuracy in X-Ray simulation at the 2% level, which is an improvement of roughly a factor of 5 in accuracy, and we have successfully coupled our simulation tools with the CCG (Constrained Conjugate Gradient) optimization algorithm, allowing reconstructions that include spectral effects and blurring in the reconstructions. Another result of the project was the assembly of a low-scatter X-Ray imaging facility for use in nondestructive evaluation applications. We conclude with a discussion of future work.

  17. Thermodynamics of supersaturated steam: Molecular simulation results

    NASA Astrophysics Data System (ADS)

    Moučka, Filip; Nezbeda, Ivo

    2016-12-01

    Supersaturated steam modeled by the Gaussian charge polarizable model [P. Paricaud, M. Předota, and A. A. Chialvo, J. Chem. Phys. 122, 244511 (2005)] and BK3 model [P. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)] has been simulated at conditions occurring in steam turbines using the multiple-particle-move Monte Carlo for both the homogeneous phase and also implemented for the Gibbs ensemble Monte Carlo molecular simulation methods. Because of these thermodynamic conditions, a specific simulation algorithm has been developed to bypass common simulation problems resulting from very low densities of steam and cluster formation therein. In addition to pressure-temperature-density and orthobaric data, the distribution of clusters has also been evaluated. The obtained extensive data of high precision should serve as a basis for development of reliable molecular-based equations for properties of metastable steam.

  18. Fast computation algorithms for speckle pattern simulation

    SciTech Connect

    Nascov, Victor; Samoilă, Cornel; Ursuţiu, Doru

    2013-11-13

    We present our development of a series of efficient computation algorithms, generally usable to calculate light diffraction and particularly for speckle pattern simulation. We use mainly the scalar diffraction theory in the form of Rayleigh-Sommerfeld diffraction formula and its Fresnel approximation. Our algorithms are based on a special form of the convolution theorem and the Fast Fourier Transform. They are able to evaluate the diffraction formula much faster than by direct computation and we have circumvented the restrictions regarding the relative sizes of the input and output domains, met on commonly used procedures. Moreover, the input and output planes can be tilted each to other and the output domain can be off-axis shifted.

  19. Cluster hybrid Monte Carlo simulation algorithms.

    PubMed

    Plascak, J A; Ferrenberg, Alan M; Landau, D P

    2002-06-01

    We show that addition of Metropolis single spin flips to the Wolff cluster-flipping Monte Carlo procedure leads to a dramatic increase in performance for the spin-1/2 Ising model. We also show that adding Wolff cluster flipping to the Metropolis or heat bath algorithms in systems where just cluster flipping is not immediately obvious (such as the spin-3/2 Ising model) can substantially reduce the statistical errors of the simulations. A further advantage of these methods is that systematic errors introduced by the use of imperfect random-number generation may be largely healed by hybridizing single spin flips with cluster flipping.

  20. Cluster hybrid Monte Carlo simulation algorithms

    NASA Astrophysics Data System (ADS)

    Plascak, J. A.; Ferrenberg, Alan M.; Landau, D. P.

    2002-06-01

    We show that addition of Metropolis single spin flips to the Wolff cluster-flipping Monte Carlo procedure leads to a dramatic increase in performance for the spin-1/2 Ising model. We also show that adding Wolff cluster flipping to the Metropolis or heat bath algorithms in systems where just cluster flipping is not immediately obvious (such as the spin-3/2 Ising model) can substantially reduce the statistical errors of the simulations. A further advantage of these methods is that systematic errors introduced by the use of imperfect random-number generation may be largely healed by hybridizing single spin flips with cluster flipping.

  1. Parallel algorithm strategies for circuit simulation.

    SciTech Connect

    Thornquist, Heidi K.; Schiek, Richard Louis; Keiter, Eric Richard

    2010-01-01

    Circuit simulation tools (e.g., SPICE) have become invaluable in the development and design of electronic circuits. However, they have been pushed to their performance limits in addressing circuit design challenges that come from the technology drivers of smaller feature scales and higher integration. Improving the performance of circuit simulation tools through exploiting new opportunities in widely-available multi-processor architectures is a logical next step. Unfortunately, not all traditional simulation applications are inherently parallel, and quickly adapting mature application codes (even codes designed to parallel applications) to new parallel paradigms can be prohibitively difficult. In general, performance is influenced by many choices: hardware platform, runtime environment, languages and compilers used, algorithm choice and implementation, and more. In this complicated environment, the use of mini-applications small self-contained proxies for real applications is an excellent approach for rapidly exploring the parameter space of all these choices. In this report we present a multi-core performance study of Xyce, a transistor-level circuit simulation tool, and describe the future development of a mini-application for circuit simulation.

  2. Central line simulation: a new training algorithm.

    PubMed

    Britt, Rebecca C; Reed, Scott F; Britt, L D

    2007-07-01

    Recent development of a partial task simulator for central line placement has altered the training algorithm from one of supervised learning on patients to mannequin-based practice to proficiency before patient interaction. There are little data published on the efficacy of this type of simulator. We reviewed our initial resident experience with central line simulation. Education to proficiency using the CentralLine Man simulator is completed by all interns during orientation. At the completion of training, te residents were asked to complete a voluntary, anonymous questionnaire with a 5-point Likert scale as well as open-ended questions. Additionally, the residents were asked to maintain a log of the initial 10 central lines placed. Retrospective review of the questionnaire and logs were done with analysis of simulator experience as well as initial line experience. Seventeen trainees completed the central line simulation course and returned the initial survey. Before the course, the trainees had placed an average of 0.4 internal jugular (IJ) and 1 subclavian (SC) line. On the simulator, an average of 3 SC attempts and 2.5 IJ attempts led to resident comfort with the procedure. On the first attempt, the vessel was accessed after an average of 1.5 SC and 1.9 IJ needlesticks, which improved to 1 SC and 1.3 IJ by the fifth simulated attempt. A total of 4 pneumothorax and 5 carotid sticks were done. Overall, the residents were highly satisfied with the course with an average score of 4.8 for didactics, 4.8 for equipment, 4.5 for the mannequin, and 4.8 for practice opportunity. Nine of the 11 residents who completed logs felt the simulation improved performance on the patient. On the first patient attempt, an average of 1.8 needlesticks was done with an average of 1.3 by the tenth line. For the first patient line documented in the logs, comfort with the anatomy was rated 3.8 with comfort with the procedure rated 2.8. Central line simulation before actual performance on

  3. Efficient algorithms for wildland fire simulation

    NASA Astrophysics Data System (ADS)

    Kondratenko, Volodymyr Y.

    In this dissertation, we develop the multiple-source shortest path algorithms and examine their application importance in real world problems, such as wildfire modeling. The theoretical basis and its implementation in the Weather Research Forecasting (WRF) model coupled with the fire spread code SFIRE (WRF-SFIRE model) are described. We present a data assimilation method that gives the fire spread model the ability to start the fire simulation from an observed fire perimeter instead of an ignition point. While the model is running, the fire state in the model changes in accordance with the new arriving data by data assimilation. As the fire state changes, the atmospheric state (which is strongly effected by heat flux) does not stay consistent with the fire state. The main difficulty of this methodology occurs in coupled fire-atmosphere models, because once the fire state is modified to match a given starting perimeter, the atmospheric circulation is no longer in sync with it. One of the possible solutions to this problem is a formation of the artificial time of ignition history from an earlier fire state, which is later used to replay the fire progression to the new perimeter with the proper heat fluxes fed into the atmosphere, so that the fire induced circulation is established. In this work, we develop efficient algorithms that start from the fire arrival times given at the set of points (called a perimeter) and create the artificial fire time of ignition and fire spread rate history. Different algorithms were developed in order to suit possible demands of the user, such as implementation in parallel programming, minimization of the required amount of iterations and memory use, and use of the rate of spread as a time dependent variable. For the algorithms that deal with the homogeneous rate of spread, it was proven that the values of fire arrival times they produce are optimal. It was also shown that starting from arbitrary initial state the algorithms have

  4. Rayleigh wave inversion using heat-bath simulated annealing algorithm

    NASA Astrophysics Data System (ADS)

    Lu, Yongxu; Peng, Suping; Du, Wenfeng; Zhang, Xiaoyang; Ma, Zhenyuan; Lin, Peng

    2016-11-01

    The dispersion of Rayleigh waves can be used to obtain near-surface shear (S)-wave velocity profiles. This is performed mainly by inversion of the phase velocity dispersion curves, which has been proven to be a highly nonlinear and multimodal problem, and it is unsuitable to use local search methods (LSMs) as the inversion algorithm. In this study, a new strategy is proposed based on a variant of simulated annealing (SA) algorithm. SA, which simulates the annealing procedure of crystalline solids in nature, is one of the global search methods (GSMs). There are many variants of SA, most of which contain two steps: the perturbation of model and the Metropolis-criterion-based acceptance of the new model. In this paper we propose a one-step SA variant known as heat-bath SA. To test the performance of the heat-bath SA, two models are created. Both noise-free and noisy synthetic data are generated. Levenberg-Marquardt (LM) algorithm and a variant of SA, known as the fast simulated annealing (FSA) algorithm, are also adopted for comparison. The inverted results of the synthetic data show that the heat-bath SA algorithm is a reasonable choice for Rayleigh wave dispersion curve inversion. Finally, a real-world inversion example from a coal mine in northwestern China is shown, which proves that the scheme we propose is applicable.

  5. Final Technical Report "Multiscale Simulation Algorithms for Biochemical Systems"

    SciTech Connect

    Petzold, Linda R.

    2012-10-25

    Biochemical systems are inherently multiscale and stochastic. In microscopic systems formed by living cells, the small numbers of reactant molecules can result in dynamical behavior that is discrete and stochastic rather than continuous and deterministic. An analysis tool that respects these dynamical characteristics is the stochastic simulation algorithm (SSA, Gillespie, 1976), a numerical simulation procedure that is essentially exact for chemical systems that are spatially homogeneous or well stirred. Despite recent improvements, as a procedure that simulates every reaction event, the SSA is necessarily inefficient for most realistic problems. There are two main reasons for this, both arising from the multiscale nature of the underlying problem: (1) stiffness, i.e. the presence of multiple timescales, the fastest of which are stable; and (2) the need to include in the simulation both species that are present in relatively small quantities and should be modeled by a discrete stochastic process, and species that are present in larger quantities and are more efficiently modeled by a deterministic differential equation (or at some scale in between). This project has focused on the development of fast and adaptive algorithms, and the fun- damental theory upon which they must be based, for the multiscale simulation of biochemical systems. Areas addressed by this project include: (1) Theoretical and practical foundations for ac- celerated discrete stochastic simulation (tau-leaping); (2) Dealing with stiffness (fast reactions) in an efficient and well-justified manner in discrete stochastic simulation; (3) Development of adaptive multiscale algorithms for spatially homogeneous discrete stochastic simulation; (4) Development of high-performance SSA algorithms.

  6. Simulating and Synthesizing Substructures Using Neural Network and Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Liu, Youhua; Kapania, Rakesh K.; VanLandingham, Hugh F.

    1997-01-01

    The feasibility of simulating and synthesizing substructures by computational neural network models is illustrated by investigating a statically indeterminate beam, using both a 1-D and a 2-D plane stress modelling. The beam can be decomposed into two cantilevers with free-end loads. By training neural networks to simulate the cantilever responses to different loads, the original beam problem can be solved as a match-up between two subsystems under compatible interface conditions. The genetic algorithms are successfully used to solve the match-up problem. Simulated results are found in good agreement with the analytical or FEM solutions.

  7. A fast MPP algorithm for Ising spin exchange simulations

    NASA Technical Reports Server (NTRS)

    Sullivan, Francis; Mountain, Raymond D.

    1987-01-01

    A very efficient massively parallel processor (MPP) algorithm is described for performing one important class of Ising spin simulations. Results and physical significance of MPP calculations using the method described is discussed elsewhere. A few comments, however, are made on the problem under study and results so far are reported. Ted Einstein provided guidance in interpreting the initial results and in suggesting calculations to perform.

  8. Parameter estimation for chaotic systems using a hybrid adaptive cuckoo search with simulated annealing algorithm

    NASA Astrophysics Data System (ADS)

    Sheng, Zheng; Wang, Jun; Zhou, Shudao; Zhou, Bihua

    2014-03-01

    This paper introduces a novel hybrid optimization algorithm to establish the parameters of chaotic systems. In order to deal with the weaknesses of the traditional cuckoo search algorithm, the proposed adaptive cuckoo search with simulated annealing algorithm is presented, which incorporates the adaptive parameters adjusting operation and the simulated annealing operation in the cuckoo search algorithm. Normally, the parameters of the cuckoo search algorithm are kept constant that may result in decreasing the efficiency of the algorithm. For the purpose of balancing and enhancing the accuracy and convergence rate of the cuckoo search algorithm, the adaptive operation is presented to tune the parameters properly. Besides, the local search capability of cuckoo search algorithm is relatively weak that may decrease the quality of optimization. So the simulated annealing operation is merged into the cuckoo search algorithm to enhance the local search ability and improve the accuracy and reliability of the results. The functionality of the proposed hybrid algorithm is investigated through the Lorenz chaotic system under the noiseless and noise condition, respectively. The numerical results demonstrate that the method can estimate parameters efficiently and accurately in the noiseless and noise condition. Finally, the results are compared with the traditional cuckoo search algorithm, genetic algorithm, and particle swarm optimization algorithm. Simulation results demonstrate the effectiveness and superior performance of the proposed algorithm.

  9. Parameter estimation for chaotic systems using a hybrid adaptive cuckoo search with simulated annealing algorithm

    SciTech Connect

    Sheng, Zheng; Wang, Jun; Zhou, Bihua; Zhou, Shudao

    2014-03-15

    This paper introduces a novel hybrid optimization algorithm to establish the parameters of chaotic systems. In order to deal with the weaknesses of the traditional cuckoo search algorithm, the proposed adaptive cuckoo search with simulated annealing algorithm is presented, which incorporates the adaptive parameters adjusting operation and the simulated annealing operation in the cuckoo search algorithm. Normally, the parameters of the cuckoo search algorithm are kept constant that may result in decreasing the efficiency of the algorithm. For the purpose of balancing and enhancing the accuracy and convergence rate of the cuckoo search algorithm, the adaptive operation is presented to tune the parameters properly. Besides, the local search capability of cuckoo search algorithm is relatively weak that may decrease the quality of optimization. So the simulated annealing operation is merged into the cuckoo search algorithm to enhance the local search ability and improve the accuracy and reliability of the results. The functionality of the proposed hybrid algorithm is investigated through the Lorenz chaotic system under the noiseless and noise condition, respectively. The numerical results demonstrate that the method can estimate parameters efficiently and accurately in the noiseless and noise condition. Finally, the results are compared with the traditional cuckoo search algorithm, genetic algorithm, and particle swarm optimization algorithm. Simulation results demonstrate the effectiveness and superior performance of the proposed algorithm.

  10. Parameter estimation for chaotic systems using a hybrid adaptive cuckoo search with simulated annealing algorithm.

    PubMed

    Sheng, Zheng; Wang, Jun; Zhou, Shudao; Zhou, Bihua

    2014-03-01

    This paper introduces a novel hybrid optimization algorithm to establish the parameters of chaotic systems. In order to deal with the weaknesses of the traditional cuckoo search algorithm, the proposed adaptive cuckoo search with simulated annealing algorithm is presented, which incorporates the adaptive parameters adjusting operation and the simulated annealing operation in the cuckoo search algorithm. Normally, the parameters of the cuckoo search algorithm are kept constant that may result in decreasing the efficiency of the algorithm. For the purpose of balancing and enhancing the accuracy and convergence rate of the cuckoo search algorithm, the adaptive operation is presented to tune the parameters properly. Besides, the local search capability of cuckoo search algorithm is relatively weak that may decrease the quality of optimization. So the simulated annealing operation is merged into the cuckoo search algorithm to enhance the local search ability and improve the accuracy and reliability of the results. The functionality of the proposed hybrid algorithm is investigated through the Lorenz chaotic system under the noiseless and noise condition, respectively. The numerical results demonstrate that the method can estimate parameters efficiently and accurately in the noiseless and noise condition. Finally, the results are compared with the traditional cuckoo search algorithm, genetic algorithm, and particle swarm optimization algorithm. Simulation results demonstrate the effectiveness and superior performance of the proposed algorithm.

  11. Algorithm for Simulating Atmospheric Turbulence and Aeroelastic Effects on Simulator Motion Systems

    NASA Technical Reports Server (NTRS)

    Ercole, Anthony V.; Cardullo, Frank M.; Kelly, Lon C.; Houck, Jacob A.

    2012-01-01

    Atmospheric turbulence produces high frequency accelerations in aircraft, typically greater than the response to pilot input. Motion system equipped flight simulators must present cues representative of the aircraft response to turbulence in order to maintain the integrity of the simulation. Currently, turbulence motion cueing produced by flight simulator motion systems has been less than satisfactory because the turbulence profiles have been attenuated by the motion cueing algorithms. This report presents a new turbulence motion cueing algorithm, referred to as the augmented turbulence channel. Like the previous turbulence algorithms, the output of the channel only augments the vertical degree of freedom of motion. This algorithm employs a parallel aircraft model and an optional high bandwidth cueing filter. Simulation of aeroelastic effects is also an area where frequency content must be preserved by the cueing algorithm. The current aeroelastic implementation uses a similar secondary channel that supplements the primary motion cue. Two studies were conducted using the NASA Langley Visual Motion Simulator and Cockpit Motion Facility to evaluate the effect of the turbulence channel and aeroelastic model on pilot control input. Results indicate that the pilot is better correlated with the aircraft response, when the augmented channel is in place.

  12. Adaptively resizing populations: Algorithm, analysis, and first results

    NASA Technical Reports Server (NTRS)

    Smith, Robert E.; Smuda, Ellen

    1993-01-01

    Deciding on an appropriate population size for a given Genetic Algorithm (GA) application can often be critical to the algorithm's success. Too small, and the GA can fall victim to sampling error, affecting the efficacy of its search. Too large, and the GA wastes computational resources. Although advice exists for sizing GA populations, much of this advice involves theoretical aspects that are not accessible to the novice user. An algorithm for adaptively resizing GA populations is suggested. This algorithm is based on recent theoretical developments that relate population size to schema fitness variance. The suggested algorithm is developed theoretically, and simulated with expected value equations. The algorithm is then tested on a problem where population sizing can mislead the GA. The work presented suggests that the population sizing algorithm may be a viable way to eliminate the population sizing decision from the application of GA's.

  13. Simulated annealing algorithm applied in adaptive near field beam shaping

    NASA Astrophysics Data System (ADS)

    Yu, Zhan; Ma, Hao-tong; Du, Shao-jun

    2010-11-01

    Laser beam shaping is required in many applications for improving the efficiency of the laser systems. In this paper, the near field beam shaping based on the combination of simulated annealing algorithm and Zernike polynomials is demonstrated. Considering phase distribution can be represented by the expansion of Zernike polynomials, the problem of searching appropriate phase distribution can be changed into a problem of optimizing a vector made up of Zernike coefficients. The feasibility of this method is validated theoretically by translating the Gaussian beam into square quasi-flattop beam in the near field. Finally, the closed control loop system constituted by phase only liquid crystal spatial light modulator and simulated annealing algorithm is used to prove the validity of the technique. The experiment results show that the system can generate laser beam with desired intensity distributions.

  14. Potts-model grain growth simulations: Parallel algorithms and applications

    SciTech Connect

    Wright, S.A.; Plimpton, S.J.; Swiler, T.P.

    1997-08-01

    Microstructural morphology and grain boundary properties often control the service properties of engineered materials. This report uses the Potts-model to simulate the development of microstructures in realistic materials. Three areas of microstructural morphology simulations were studied. They include the development of massively parallel algorithms for Potts-model grain grow simulations, modeling of mass transport via diffusion in these simulated microstructures, and the development of a gradient-dependent Hamiltonian to simulate columnar grain growth. Potts grain growth models for massively parallel supercomputers were developed for the conventional Potts-model in both two and three dimensions. Simulations using these parallel codes showed self similar grain growth and no finite size effects for previously unapproachable large scale problems. In addition, new enhancements to the conventional Metropolis algorithm used in the Potts-model were developed to accelerate the calculations. These techniques enable both the sequential and parallel algorithms to run faster and use essentially an infinite number of grain orientation values to avoid non-physical grain coalescence events. Mass transport phenomena in polycrystalline materials were studied in two dimensions using numerical diffusion techniques on microstructures generated using the Potts-model. The results of the mass transport modeling showed excellent quantitative agreement with one dimensional diffusion problems, however the results also suggest that transient multi-dimension diffusion effects cannot be parameterized as the product of the grain boundary diffusion coefficient and the grain boundary width. Instead, both properties are required. Gradient-dependent grain growth mechanisms were included in the Potts-model by adding an extra term to the Hamiltonian. Under normal grain growth, the primary driving term is the curvature of the grain boundary, which is included in the standard Potts-model Hamiltonian.

  15. Bio-inspired algorithms applied to molecular docking simulations.

    PubMed

    Heberlé, G; de Azevedo, W F

    2011-01-01

    Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs). These algorithms mimic biological systems to create new paradigms for computation, such as neural networks, evolutionary computing, and swarm intelligence. This review provides a description of the main concepts behind BIAs applied to molecular docking simulations. Special attention is devoted to evolutionary algorithms, guided-directed evolutionary algorithms, and Lamarckian genetic algorithms. Recent applications of these methodologies to protein targets identified in the Mycobacterium tuberculosis genome are described.

  16. Kriging-approximation simulated annealing algorithm for groundwater modeling

    NASA Astrophysics Data System (ADS)

    Shen, C. H.

    2015-12-01

    Optimization algorithms are often applied to search best parameters for complex groundwater models. Running the complex groundwater models to evaluate objective function might be time-consuming. This research proposes a Kriging-approximation simulated annealing algorithm. Kriging is a spatial statistics method used to interpolate unknown variables based on surrounding given data. In the algorithm, Kriging method is used to estimate complicate objective function and is incorporated with simulated annealing. The contribution of the Kriging-approximation simulated annealing algorithm is to reduce calculation time and increase efficiency.

  17. Summarizing Simulation Results using Causally-relevant States

    PubMed Central

    Parikh, Nidhi; Marathe, Madhav; Swarup, Samarth

    2016-01-01

    As increasingly large-scale multiagent simulations are being implemented, new methods are becoming necessary to make sense of the results of these simulations. Even concisely summarizing the results of a given simulation run is a challenge. Here we pose this as the problem of simulation summarization: how to extract the causally-relevant descriptions of the trajectories of the agents in the simulation. We present a simple algorithm to compress agent trajectories through state space by identifying the state transitions which are relevant to determining the distribution of outcomes at the end of the simulation. We present a toy-example to illustrate the working of the algorithm, and then apply it to a complex simulation of a major disaster in an urban area. PMID:28042620

  18. An improved simulated annealing algorithm for standard cell placement

    NASA Technical Reports Server (NTRS)

    Jones, Mark; Banerjee, Prithviraj

    1988-01-01

    Simulated annealing is a general purpose Monte Carlo optimization technique that was applied to the problem of placing standard logic cells in a VLSI ship so that the total interconnection wire length is minimized. An improved standard cell placement algorithm that takes advantage of the performance enhancements that appear to come from parallelizing the uniprocessor simulated annealing algorithm is presented. An outline of this algorithm is given.

  19. The Aquarius Salinity Retrieval Algorithm: Early Results

    NASA Technical Reports Server (NTRS)

    Meissner, Thomas; Wentz, Frank J.; Lagerloef, Gary; LeVine, David

    2012-01-01

    The Aquarius L-band radiometer/scatterometer system is designed to provide monthly salinity maps at 150 km spatial scale to a 0.2 psu accuracy. The sensor was launched on June 10, 2011, aboard the Argentine CONAE SAC-D spacecraft. The L-band radiometers and the scatterometer have been taking science data observations since August 25, 2011. The first part of this presentation gives an overview over the Aquarius salinity retrieval algorithm. The instrument calibration converts Aquarius radiometer counts into antenna temperatures (TA). The salinity retrieval algorithm converts those TA into brightness temperatures (TB) at a flat ocean surface. As a first step, contributions arising from the intrusion of solar, lunar and galactic radiation are subtracted. The antenna pattern correction (APC) removes the effects of cross-polarization contamination and spillover. The Aquarius radiometer measures the 3rd Stokes parameter in addition to vertical (v) and horizontal (h) polarizations, which allows for an easy removal of ionospheric Faraday rotation. The atmospheric absorption at L-band is almost entirely due to O2, which can be calculated based on auxiliary input fields from numerical weather prediction models and then successively removed from the TB. The final step in the TA to TB conversion is the correction for the roughness of the sea surface due to wind. This is based on the radar backscatter measurements by the scatterometer. The TB of the flat ocean surface can now be matched to a salinity value using a surface emission model that is based on a model for the dielectric constant of sea water and an auxiliary field for the sea surface temperature. In the current processing (as of writing this abstract) only v-pol TB are used for this last process and NCEP winds are used for the roughness correction. Before the salinity algorithm can be operationally implemented and its accuracy assessed by comparing versus in situ measurements, an extensive calibration and validation

  20. Daylighting simulation: methods, algorithms, and resources

    SciTech Connect

    Carroll, William L.

    1999-12-01

    This document presents work conducted as part of Subtask C, ''Daylighting Design Tools'', Subgroup C2, ''New Daylight Algorithms'', of the IEA SHC Task 21 and the ECBCS Program Annex 29 ''Daylight in Buildings''. The search for and collection of daylighting analysis methods and algorithms led to two important observations. First, there is a wide range of needs for different types of methods to produce a complete analysis tool. These include: Geometry; Light modeling; Characterization of the natural illumination resource; Materials and components properties, representations; and Usability issues (interfaces, interoperability, representation of analysis results, etc). Second, very advantageously, there have been rapid advances in many basic methods in these areas, due to other forces. They are in part driven by: The commercial computer graphics community (commerce, entertainment); The lighting industry; Architectural rendering and visualization for projects; and Academia: Course materials, research. This has led to a very rich set of information resources that have direct applicability to the small daylighting analysis community. Furthermore, much of this information is in fact available online. Because much of the information about methods and algorithms is now online, an innovative reporting strategy was used: the core formats are electronic, and used to produce a printed form only secondarily. The electronic forms include both online WWW pages and a downloadable .PDF file with the same appearance and content. Both electronic forms include live primary and indirect links to actual information sources on the WWW. In most cases, little additional commentary is provided regarding the information links or citations that are provided. This in turn allows the report to be very concise. The links are expected speak for themselves. The report consists of only about 10+ pages, with about 100+ primary links, but with potentially thousands of indirect links. For purposes of

  1. Motion Cueing Algorithm Modification for Improved Turbulence Simulation

    NASA Technical Reports Server (NTRS)

    Ercole, Anthony V.; Cardullo, Frank M.; Zaychik, Kirill; Kelly, Lon C.; Houck, Jacob

    2009-01-01

    Atmospheric turbulence cueing produced by flight simulator motion systems has been less than satisfactory because the turbulence profiles have been attenuated by the motion cueing algorithms. Cardullo and Ellor initially addressed this problem by directly porting the turbulence model output to the motion system. Reid and Robinson addressed the problem by employing a parallel aircraft model, which is only stimulated by the turbulence inputs and adding a filter specially designed to pass the higher turbulence frequencies. There have been advances in motion cueing algorithm development at the Man-Machine Systems Laboratory, at SUNY Binghamton. In particular, the system used to generate turbulence cues has been studied. The Reid approach, implemented by Telban and Cardullo, was employed to augment the optimal motion cueing algorithm installed at the NASA LaRC Simulation Laboratory, driving the Visual Motion Simulator. In this implementation, the output of the primary flight channel was added to the output of the turbulence channel and then sent through a non-linear cueing filter. The cueing filter is an adaptive filter; therefore, it is not desirable for the output of the turbulence channel to be augmented by this type of filter. The likelihood of the signal becoming divergent was also an issue in this design. After testing on-site it became apparent that the architecture of the turbulence algorithm was generating unacceptable cues. As mentioned above, this cueing algorithm comprised a filter that was designed to operate at low bandwidth. Therefore, the turbulence was also filtered, augmenting the cues generated by the model. If any filtering is to be done to the turbulence, it will utilize a filter with a much higher bandwidth, above the frequencies produced by the aircraft response to turbulence. The authors have developed an implementation wherein only the signal from the primary flight channel passes through the nonlinear cueing filter. This paper discusses three

  2. MOPSA: A microfluidics-optimized particle simulation algorithm.

    PubMed

    Wang, Junchao; Rodgers, Victor G J; Brisk, Philip; Grover, William H

    2017-05-01

    Computer simulation plays a growing role in the design of microfluidic chips. However, the particle tracers in some existing commercial computational fluid dynamics software are not well suited for accurately simulating the trajectories of particles such as cells, microbeads, and droplets in microfluidic systems. To address this issue, we present a microfluidics-optimized particle simulation algorithm (MOPSA) that simulates the trajectories of cells, droplets, and other particles in microfluidic chips with more lifelike results than particle tracers in existing commercial software. When calculating the velocity of a particle, MOPSA treats the particle as a two-dimensional rigid circular object instead of a single point. MOPSA also checks for unrealistic interactions between particles and channel walls and applies an empirical correcting function to eliminate these errors. To validate the performance of MOPSA, we used it to simulate a variety of important features of microfluidic devices like channel intersections and deterministic lateral displacement (DLD) particle sorter chips. MOPSA successfully predicted that different particle sizes will have different trajectories in six published DLD experiments from three research groups; these DLD chips were used to sort a variety of different cells, particles, and droplets. While some of these particles are not actually rigid or spherical, MOPSA's approximation of these particles as rigid spheres nonetheless resulted in lifelike simulations of the behaviors of these particles (at least for the particle sizes and types shown here). In contrast, existing commercial software failed to replicate these experiments. Finally, to demonstrate that MOPSA can be extended to simulate other properties of particles, we added support for simulating particle density to MOPSA and then used MOPSA to simulate the operation of a microfluidic chip capable of sorting cells by their density. By enabling researchers to accurately simulate the

  3. A hybrid algorithm for parallel molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mangiardi, Chris M.; Meyer, R.

    2017-10-01

    This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

  4. Developments in Human Centered Cueing Algorithms for Control of Flight Simulator Motion Systems

    NASA Technical Reports Server (NTRS)

    Houck, Jacob A.; Telban, Robert J.; Cardullo, Frank M.

    1997-01-01

    The authors conducted further research with cueing algorithms for control of flight simulator motion systems. A variation of the so-called optimal algorithm was formulated using simulated aircraft angular velocity input as a basis. Models of the human vestibular sensation system, i.e. the semicircular canals and otoliths, are incorporated within the algorithm. Comparisons of angular velocity cueing responses showed a significant improvement over a formulation using angular acceleration input. Results also compared favorably with the coordinated adaptive washout algorithm, yielding similar results for angular velocity cues while eliminating false cues and reducing the tilt rate for longitudinal cues. These results were confirmed in piloted tests on the current motion system at NASA-Langley, the Visual Motion Simulator (VMS). Proposed future developments by the authors in cueing algorithms are revealed. The new motion system, the Cockpit Motion Facility (CMF), where the final evaluation of the cueing algorithms will be conducted, is also described.

  5. Parametric Quantum Search Algorithm as Quantum Walk: A Quantum Simulation

    NASA Astrophysics Data System (ADS)

    Ellinas, Demosthenes; Konstandakis, Christos

    2016-02-01

    Parametric quantum search algorithm (PQSA) is a form of quantum search that results by relaxing the unitarity of the original algorithm. PQSA can naturally be cast in the form of quantum walk, by means of the formalism of oracle algebra. This is due to the fact that the completely positive trace preserving search map used by PQSA, admits a unitarization (unitary dilation) a la quantum walk, at the expense of introducing auxiliary quantum coin-qubit space. The ensuing QW describes a process of spiral motion, chosen to be driven by two unitary Kraus generators, generating planar rotations of Bloch vector around an axis. The quadratic acceleration of quantum search translates into an equivalent quadratic saving of the number of coin qubits in the QW analogue. The associated to QW model Hamiltonian operator is obtained and is shown to represent a multi-particle long-range interacting quantum system that simulates parametric search. Finally, the relation of PQSA-QW simulator to the QW search algorithm is elucidated.

  6. Control algorithm for multiscale flow simulations of water

    NASA Astrophysics Data System (ADS)

    Kotsalis, Evangelos M.; Walther, Jens H.; Kaxiras, Efthimios; Koumoutsakos, Petros

    2009-04-01

    We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions. The use of a mass conserving specular wall results in turn to spurious oscillations in the density profile of the atomistic description of water. These oscillations can be eliminated by using an external boundary force that effectively accounts for the virial component of the pressure. In this Rapid Communication, we extend a control algorithm, previously introduced for monatomic molecules, to the case of atomistic water and demonstrate the effectiveness of this approach. The proposed computational method is validated for the cases of equilibrium and Couette flow of water.

  7. Control algorithm for multiscale flow simulations of water.

    PubMed

    Kotsalis, Evangelos M; Walther, Jens H; Kaxiras, Efthimios; Koumoutsakos, Petros

    2009-04-01

    We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions. The use of a mass conserving specular wall results in turn to spurious oscillations in the density profile of the atomistic description of water. These oscillations can be eliminated by using an external boundary force that effectively accounts for the virial component of the pressure. In this Rapid Communication, we extend a control algorithm, previously introduced for monatomic molecules, to the case of atomistic water and demonstrate the effectiveness of this approach. The proposed computational method is validated for the cases of equilibrium and Couette flow of water.

  8. D-leaping: Accelerating stochastic simulation algorithms for reactions with delays

    SciTech Connect

    Bayati, Basil; Chatelain, Philippe; Koumoutsakos, Petros

    2009-09-01

    We propose a novel, accelerated algorithm for the approximate stochastic simulation of biochemical systems with delays. The present work extends existing accelerated algorithms by distributing, in a time adaptive fashion, the delayed reactions so as to minimize the computational effort while preserving their accuracy. The accuracy of the present algorithm is assessed by comparing its results to those of the corresponding delay differential equations for a representative biochemical system. In addition, the fluctuations produced from the present algorithm are comparable to those from an exact stochastic simulation with delays. The algorithm is used to simulate biochemical systems that model oscillatory gene expression. The results indicate that the present algorithm is competitive with existing works for several benchmark problems while it is orders of magnitude faster for certain systems of biochemical reactions.

  9. Adaptive Mesh and Algorithm Refinement Using Direct Simulation Monte Carlo

    NASA Astrophysics Data System (ADS)

    Garcia, Alejandro L.; Bell, John B.; Crutchfield, William Y.; Alder, Berni J.

    1999-09-01

    Adaptive mesh and algorithm refinement (AMAR) embeds a particle method within a continuum method at the finest level of an adaptive mesh refinement (AMR) hierarchy. The coupling between the particle region and the overlaying continuum grid is algorithmically equivalent to that between the fine and coarse levels of AMR. Direct simulation Monte Carlo (DSMC) is used as the particle algorithm embedded within a Godunov-type compressible Navier-Stokes solver. Several examples are presented and compared with purely continuum calculations.

  10. Duality quantum algorithm efficiently simulates open quantum systems

    PubMed Central

    Wei, Shi-Jie; Ruan, Dong; Long, Gui-Lu

    2016-01-01

    Because of inevitable coupling with the environment, nearly all practical quantum systems are open system, where the evolution is not necessarily unitary. In this paper, we propose a duality quantum algorithm for simulating Hamiltonian evolution of an open quantum system. In contrast to unitary evolution in a usual quantum computer, the evolution operator in a duality quantum computer is a linear combination of unitary operators. In this duality quantum algorithm, the time evolution of the open quantum system is realized by using Kraus operators which is naturally implemented in duality quantum computer. This duality quantum algorithm has two distinct advantages compared to existing quantum simulation algorithms with unitary evolution operations. Firstly, the query complexity of the algorithm is O(d3) in contrast to O(d4) in existing unitary simulation algorithm, where d is the dimension of the open quantum system. Secondly, By using a truncated Taylor series of the evolution operators, this duality quantum algorithm provides an exponential improvement in precision compared with previous unitary simulation algorithm. PMID:27464855

  11. Duality quantum algorithm efficiently simulates open quantum systems

    NASA Astrophysics Data System (ADS)

    Wei, Shi-Jie; Ruan, Dong; Long, Gui-Lu

    2016-07-01

    Because of inevitable coupling with the environment, nearly all practical quantum systems are open system, where the evolution is not necessarily unitary. In this paper, we propose a duality quantum algorithm for simulating Hamiltonian evolution of an open quantum system. In contrast to unitary evolution in a usual quantum computer, the evolution operator in a duality quantum computer is a linear combination of unitary operators. In this duality quantum algorithm, the time evolution of the open quantum system is realized by using Kraus operators which is naturally implemented in duality quantum computer. This duality quantum algorithm has two distinct advantages compared to existing quantum simulation algorithms with unitary evolution operations. Firstly, the query complexity of the algorithm is O(d3) in contrast to O(d4) in existing unitary simulation algorithm, where d is the dimension of the open quantum system. Secondly, By using a truncated Taylor series of the evolution operators, this duality quantum algorithm provides an exponential improvement in precision compared with previous unitary simulation algorithm.

  12. Duality quantum algorithm efficiently simulates open quantum systems.

    PubMed

    Wei, Shi-Jie; Ruan, Dong; Long, Gui-Lu

    2016-07-28

    Because of inevitable coupling with the environment, nearly all practical quantum systems are open system, where the evolution is not necessarily unitary. In this paper, we propose a duality quantum algorithm for simulating Hamiltonian evolution of an open quantum system. In contrast to unitary evolution in a usual quantum computer, the evolution operator in a duality quantum computer is a linear combination of unitary operators. In this duality quantum algorithm, the time evolution of the open quantum system is realized by using Kraus operators which is naturally implemented in duality quantum computer. This duality quantum algorithm has two distinct advantages compared to existing quantum simulation algorithms with unitary evolution operations. Firstly, the query complexity of the algorithm is O(d(3)) in contrast to O(d(4)) in existing unitary simulation algorithm, where d is the dimension of the open quantum system. Secondly, By using a truncated Taylor series of the evolution operators, this duality quantum algorithm provides an exponential improvement in precision compared with previous unitary simulation algorithm.

  13. LAWS simulation: Sampling strategies and wind computation algorithms

    NASA Technical Reports Server (NTRS)

    Emmitt, G. D. A.; Wood, S. A.; Houston, S. H.

    1989-01-01

    In general, work has continued on developing and evaluating algorithms designed to manage the Laser Atmospheric Wind Sounder (LAWS) lidar pulses and to compute the horizontal wind vectors from the line-of-sight (LOS) measurements. These efforts fall into three categories: Improvements to the shot management and multi-pair algorithms (SMA/MPA); observing system simulation experiments; and ground-based simulations of LAWS.

  14. A fast recursive algorithm for molecular dynamics simulation

    NASA Technical Reports Server (NTRS)

    Jain, A.; Vaidehi, N.; Rodriguez, G.

    1993-01-01

    The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

  15. Maximizing influence in a social network: Improved results using a genetic algorithm

    NASA Astrophysics Data System (ADS)

    Zhang, Kaiqi; Du, Haifeng; Feldman, Marcus W.

    2017-07-01

    The influence maximization problem focuses on finding a small subset of nodes in a social network that maximizes the spread of influence. While the greedy algorithm and some improvements to it have been applied to solve this problem, the long solution time remains a problem. Stochastic optimization algorithms, such as simulated annealing, are other choices for solving this problem, but they often become trapped in local optima. We propose a genetic algorithm to solve the influence maximization problem. Through multi-population competition, using this algorithm we achieve an optimal result while maintaining diversity of the solution. We tested our method with actual networks, and our genetic algorithm performed slightly worse than the greedy algorithm but better than other algorithms.

  16. Matrix Product Operator Simulations of Quantum Algorithms

    DTIC Science & Technology

    2015-02-01

    Communications, pages 174–188. Springer, 1999. Bibliography 145 [21] Michelangelo Grigni, Leonard Schulman, Monica Vazirani, and Umesh Vazirani...2007. [27] Andrew M Childs, Leonard J Schulman, and Umesh V Vazirani. Quan- tum algorithms for hidden nonlinear structures. In Foundations of...and quantum in- formation. Cambridge University Press, Cambridge, 2000. [86] Charles H Bennett, Ethan Bernstein, Gilles Brassard, and Umesh Vazirani

  17. A fast image simulation algorithm for scanning transmission electron microscopy.

    PubMed

    Ophus, Colin

    2017-01-01

    Image simulation for scanning transmission electron microscopy at atomic resolution for samples with realistic dimensions can require very large computation times using existing simulation algorithms. We present a new algorithm named PRISM that combines features of the two most commonly used algorithms, namely the Bloch wave and multislice methods. PRISM uses a Fourier interpolation factor f that has typical values of 4-20 for atomic resolution simulations. We show that in many cases PRISM can provide a speedup that scales with f(4) compared to multislice simulations, with a negligible loss of accuracy. We demonstrate the usefulness of this method with large-scale scanning transmission electron microscopy image simulations of a crystalline nanoparticle on an amorphous carbon substrate.

  18. Application of integration algorithms in a parallel processing environment for the simulation of jet engines

    SciTech Connect

    Krosel, S.M.; Milner, E.J.

    1982-01-01

    Illustrates the application of predictor-corrector integration algorithms developed for the digital parallel processing environment. The algorithms are implemented and evaluated through the use of a software simulator which provides an approximate representation of the parallel processing hardware. Test cases which focus on the use of the algorithms are presented and a specific application using a linear model of a turbofan engine is considered. Results are presented showing the effects of integration step size and the number of processors on simulation accuracy. Real-time performance, inter-processor communication and algorithm startup are also discussed. 10 references.

  19. Application of integration algorithms in a parallel processing environment for the simulation of jet engines

    NASA Technical Reports Server (NTRS)

    Krosel, S. M.; Milner, E. J.

    1982-01-01

    The application of Predictor corrector integration algorithms developed for the digital parallel processing environment are investigated. The algorithms are implemented and evaluated through the use of a software simulator which provides an approximate representation of the parallel processing hardware. Test cases which focus on the use of the algorithms are presented and a specific application using a linear model of a turbofan engine is considered. Results are presented showing the effects of integration step size and the number of processors on simulation accuracy. Real time performance, interprocessor communication, and algorithm startup are also discussed.

  20. Efficient Parallel Algorithm For Direct Numerical Simulation of Turbulent Flows

    NASA Technical Reports Server (NTRS)

    Moitra, Stuti; Gatski, Thomas B.

    1997-01-01

    A distributed algorithm for a high-order-accurate finite-difference approach to the direct numerical simulation (DNS) of transition and turbulence in compressible flows is described. This work has two major objectives. The first objective is to demonstrate that parallel and distributed-memory machines can be successfully and efficiently used to solve computationally intensive and input/output intensive algorithms of the DNS class. The second objective is to show that the computational complexity involved in solving the tridiagonal systems inherent in the DNS algorithm can be reduced by algorithm innovations that obviate the need to use a parallelized tridiagonal solver.

  1. Multidiscontinuity algorithm for world-line Monte Carlo simulations.

    PubMed

    Kato, Yasuyuki

    2013-01-01

    We introduce a multidiscontinuity algorithm for the efficient global update of world-line configurations in Monte Carlo simulations of interacting quantum systems. This algorithm is a generalization of the two-discontinuity algorithms introduced in Refs. [N. Prokof'ev, B. Svistunov, and I. Tupitsyn, Phys. Lett. A 238, 253 (1998)] and [O. F. Syljuåsen and A. W. Sandvik, Phys. Rev. E 66, 046701 (2002)]. This generalization is particularly effective for studying Bose-Einstein condensates (BECs) of composite particles. In particular, we demonstrate the utility of the generalized algorithm by simulating a Hamiltonian for an S=1 antiferromagnet with strong uniaxial single-ion anisotropy. The multidiscontinuity algorithm not only solves the freezing problem that arises in this limit, but also allows the efficient computing of the off-diagonal correlator that characterizes a BEC of composite particles.

  2. Fully explicit algorithms for fluid simulation

    NASA Astrophysics Data System (ADS)

    Clausen, Jonathan

    2011-11-01

    Computing hardware is trending towards distributed, massively parallel architectures in order to achieve high computational throughput. For example, Intrepid at Argonne uses 163,840 cores, and next generation machines, such as Sequoia at Lawrence Livermore, will use over one million cores. Harnessing the increasingly parallel nature of computational resources will require algorithms that scale efficiently on these architectures. The advent of GPU-based computation will serve to accelerate this behavior, as a single GPU contains hundreds of processor ``cores.'' Explicit algorithms avoid the communication associated with a linear solve, thus parallel scalability of these algorithms is typically high. This work will explore the efficiency and accuracy of three explicit solution methodologies for the Navier-Stokes equations: traditional artificial compressibility schemes, the lattice-Boltzmann method, and the recently proposed kinetically reduced local Navier-Stokes equations [Borok, Ansumali, and Karlin (2007)]. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  3. Noise properties of the EM algorithm: II. Monte Carlo simulations.

    PubMed

    Wilson, D W; Tsui, B M; Barrett, H H

    1994-05-01

    In an earlier paper we derived a theoretical formulation for estimating the statistical properties of images reconstructed using the iterative ML-EM algorithm. To gain insight into this complex problem, two levels of approximation were considered in the theory. These techniques revealed the dependence of the variance and covariance of the reconstructed image noise on the source distribution, imaging system transfer function, and iteration number. In this paper a Monte Carlo approach was taken to study the noise properties of the ML-EM algorithm and to test the predictions of the theory. The study also served to evaluate the approximations used in the theory. Simulated data from phantoms were used in the Monte Carlo experiments. The ML-EM statistical properties were calculated from sample averages of a large number of images with different noise realizations. The agreement between the more exact form of the theoretical formulation and the Monte Carlo formulation was better than 10% in most cases examined, and for many situations the agreement was within the expected error of the Monte Carlo experiments. Results from the studies provide valuable information about the noise characteristics of ML-EM reconstructed images. Furthermore, the studies demonstrate the power of the theoretical and Monte Carlo approaches for investigating noise properties of statistical reconstruction algorithms.

  4. Evaluation of alternative algorithms used to simulate pasture intake in grazing dairy cows.

    PubMed

    Vazquez, O P; Smith, T R

    2001-04-01

    Four algorithms used to simulate pasture intake in grazing dairy cows in a dairy decision support system were proposed and evaluated with data from the literature. The algorithms proposed were: 1) an algorithm combining the approach used in a published model to determine dry matter intake based on neutral detergent fiber intake as a percentage of the BW, energy requirements, pasture availability and a standard supplementation (PIest), 2) the previous algorithm modified to consider the type and amount of supplementation (PIsup), 3) an algorithm which considers the effect of selection of pasture (PIsel), and 4) the combination of algorithms 2 and 3 (PIsupsel). Pasture intake data of 27 grazing experiments from the literature were used to evaluate those algorithms. Two methods of evaluation were used: 1) simple linear regression between reported and simulated values, and 2) analysis of variance for the difference between reported and simulated values considering pasture availability and type of supplementation. The R2 of the linear regression and average proportional bias between reported values and simulated values were 0.24 and 19% for PIest, 0.42, and 23% for PIsup, 0.45 and 2% for PIsel and 0.41 and 10% for PIsupsel. Those results showed that PIsel had the lower variability and the values closer to pasture intake. The algorithm PIsup had low variability but tended to underpredict pasture intake. The algorithm PIest values were closer to reported values for low pasture availability. The modeling results show the influence of pasture selection in grazing systems.

  5. Domain splitting algorithms for the Li-ion battery simulation

    NASA Astrophysics Data System (ADS)

    Iliev, O.; Zakharov, P. E.

    2016-11-01

    Numerical simulation of electrochemical processes in rechargeable batteries has important applications in an energy technology. In this paper we have developed and compared three domain splitting algorithms for the Li-ion battery simulation. Li-ion battery simulation is based on microscopic model, which contains nonlinear equations for Li-ion concentration and potential. On the interface of electrodes and electrolyte the Lithium ions intercalation are described by nonlinear equation. This nonlinear interface condition affects the Newton's method iterations and computation time. To simplify numerical simulations we use domain splitting algorithms, which split the original problem into three independent subproblems in two electrodes and electrolyte. We investigate the numerical convergence and efficiency of the algorithms on a 2D model problem.

  6. An Improved SoC Test Scheduling Method Based on Simulated Annealing Algorithm

    NASA Astrophysics Data System (ADS)

    Zheng, Jingjing; Shen, Zhihang; Gao, Huaien; Chen, Bianna; Zheng, Weida; Xiong, Xiaoming

    2017-02-01

    In this paper, we propose an improved SoC test scheduling method based on simulated annealing algorithm (SA). It is our first to disorganize IP core assignment for each TAM to produce a new solution for SA, allocate TAM width for each TAM using greedy algorithm and calculate corresponding testing time. And accepting the core assignment according to the principle of simulated annealing algorithm and finally attain the optimum solution. Simultaneously, we run the test scheduling experiment with the international reference circuits provided by International Test Conference 2002(ITC’02) and the result shows that our algorithm is superior to the conventional integer linear programming algorithm (ILP), simulated annealing algorithm (SA) and genetic algorithm(GA). When TAM width reaches to 48,56 and 64, the testing time based on our algorithm is lesser than the classic methods and the optimization rates are 30.74%, 3.32%, 16.13% respectively. Moreover, the testing time based on our algorithm is very close to that of improved genetic algorithm (IGA), which is state-of-the-art at present.

  7. Research on coal-mine gas monitoring system controlled by annealing simulating algorithm

    NASA Astrophysics Data System (ADS)

    Zhou, Mengran; Li, Zhenbi

    2007-12-01

    This paper introduces the principle and schematic diagram of gas monitoring system by means of infrared method. Annealing simulating algorithm is adopted to find the whole optimum solution and the Metroplis criterion is used to make iterative algorithm combination optimization by control parameter decreasing aiming at solving large-scale combination optimization problem. Experiment result obtained by the performing scheme of realizing algorithm training and flow of realizing algorithm training indicates that annealing simulating algorithm applied to identify gas is better than traditional linear local search method. It makes the algorithm iterate to the optimum value rapidly so that the quality of the solution is improved efficiently. The CPU time is shortened and the identifying rate of gas is increased. For the mines with much-gas gushing fatalness the regional danger and disaster advanced forecast can be realized. The reliability of coal-mine safety is improved.

  8. An algorithm to build mock galaxy catalogues using MICE simulations

    NASA Astrophysics Data System (ADS)

    Carretero, J.; Castander, F. J.; Gaztañaga, E.; Crocce, M.; Fosalba, P.

    2015-02-01

    We present a method to build mock galaxy catalogues starting from a halo catalogue that uses halo occupation distribution (HOD) recipes as well as the subhalo abundance matching (SHAM) technique. Combining both prescriptions we are able to push the absolute magnitude of the resulting catalogue to fainter luminosities than using just the SHAM technique and can interpret our results in terms of the HOD modelling. We optimize the method by populating with galaxies friends-of-friends dark matter haloes extracted from the Marenostrum Institut de Ciències de l'Espai dark matter simulations and comparing them to observational constraints. Our resulting mock galaxy catalogues manage to reproduce the observed local galaxy luminosity function and the colour-magnitude distribution as observed by the Sloan Digital Sky Survey. They also reproduce the observed galaxy clustering properties as a function of luminosity and colour. In order to achieve that, the algorithm also includes scatter in the halo mass-galaxy luminosity relation derived from direct SHAM and a modified Navarro-Frenk-White mass density profile to place satellite galaxies in their host dark matter haloes. Improving on general usage of the HOD that fits the clustering for given magnitude limited samples, our catalogues are constructed to fit observations at all luminosities considered and therefore for any luminosity subsample. Overall, our algorithm is an economic procedure of obtaining galaxy mock catalogues down to faint magnitudes that are necessary to understand and interpret galaxy surveys.

  9. X-ray simulation algorithms used in ISP

    SciTech Connect

    Sullivan, John P.

    2016-07-29

    ISP is a simulation code which is sometimes used in the USNDS program. ISP is maintained by Sandia National Lab. However, the X-ray simulation algorithm used by ISP was written by scientists at LANL – mainly by Ed Fenimore with some contributions from John Sullivan and George Neuschaefer and probably others. In email to John Sullivan on July 25, 2016, Jill Rivera, ISP project lead, said “ISP uses the function xdosemeters_sim from the xgen library.” The is a fortran subroutine which is also used to simulate the X-ray response in consim (a descendant of xgen). Therefore, no separate documentation of the X-ray simulation algorithms in ISP have been written – the documentation for the consim simulation can be used.

  10. Improved delay-leaping simulation algorithm for biochemical reaction systems with delays

    NASA Astrophysics Data System (ADS)

    Yi, Na; Zhuang, Gang; Da, Liang; Wang, Yifei

    2012-04-01

    In biochemical reaction systems dominated by delays, the simulation speed of the stochastic simulation algorithm depends on the size of the wait queue. As a result, it is important to control the size of the wait queue to improve the efficiency of the simulation. An improved accelerated delay stochastic simulation algorithm for biochemical reaction systems with delays, termed the improved delay-leaping algorithm, is proposed in this paper. The update method for the wait queue is effective in reducing the size of the queue as well as shortening the storage and access time, thereby accelerating the simulation speed. Numerical simulation on two examples indicates that this method not only obtains a more significant efficiency compared with the existing methods, but also can be widely applied in biochemical reaction systems with delays.

  11. Dynamic damping control: Implementation issues and simulation results

    SciTech Connect

    Anderson, R.J.

    1989-01-01

    Computed torque algorithms are used to compensate for the changing dynamics of robot manipulators in order to ensure that a constant level of damping is maintained for all configurations. Unfortunately, there are three significant problems with existing computed torque algorithms. First, they are nonpassive and can lead to unstable behavior; second, they make inefficient use of actuator capability; and third, they cannot be used to maintain a constant end-effector stiffness for force control tasks. Recently, we introduced a new control algorithm for robots which, like computed torque, uses a model of the manipulator's dynamics to maintain a constant level of damping in the system, but does so passively. This new class of passive control algorithms has guaranteed stability properties, utilizes actuators more effectively, and can also be used to maintain constant end-effector stiffness. In this paper, this approach is described in detail, implementation issues are discussed, and simulation results are given. 15 refs., 6 figs., 2 tabs.

  12. An Optimization Algorithm for Multipath Parallel Allocation for Service Resource in the Simulation Task Workflow

    PubMed Central

    Zhang, Hongjun; Zhang, Rui; Li, Yong; Zhang, Xuliang

    2014-01-01

    Service oriented modeling and simulation are hot issues in the field of modeling and simulation, and there is need to call service resources when simulation task workflow is running. How to optimize the service resource allocation to ensure that the task is complete effectively is an important issue in this area. In military modeling and simulation field, it is important to improve the probability of success and timeliness in simulation task workflow. Therefore, this paper proposes an optimization algorithm for multipath service resource parallel allocation, in which multipath service resource parallel allocation model is built and multiple chains coding scheme quantum optimization algorithm is used for optimization and solution. The multiple chains coding scheme quantum optimization algorithm is to extend parallel search space to improve search efficiency. Through the simulation experiment, this paper investigates the effect for the probability of success in simulation task workflow from different optimization algorithm, service allocation strategy, and path number, and the simulation result shows that the optimization algorithm for multipath service resource parallel allocation is an effective method to improve the probability of success and timeliness in simulation task workflow. PMID:24963506

  13. An optimization algorithm for multipath parallel allocation for service resource in the simulation task workflow.

    PubMed

    Wang, Zhiteng; Zhang, Hongjun; Zhang, Rui; Li, Yong; Zhang, Xuliang

    2014-01-01

    Service oriented modeling and simulation are hot issues in the field of modeling and simulation, and there is need to call service resources when simulation task workflow is running. How to optimize the service resource allocation to ensure that the task is complete effectively is an important issue in this area. In military modeling and simulation field, it is important to improve the probability of success and timeliness in simulation task workflow. Therefore, this paper proposes an optimization algorithm for multipath service resource parallel allocation, in which multipath service resource parallel allocation model is built and multiple chains coding scheme quantum optimization algorithm is used for optimization and solution. The multiple chains coding scheme quantum optimization algorithm is to extend parallel search space to improve search efficiency. Through the simulation experiment, this paper investigates the effect for the probability of success in simulation task workflow from different optimization algorithm, service allocation strategy, and path number, and the simulation result shows that the optimization algorithm for multipath service resource parallel allocation is an effective method to improve the probability of success and timeliness in simulation task workflow.

  14. Algorithm design for a gun simulator based on image processing

    NASA Astrophysics Data System (ADS)

    Liu, Yu; Wei, Ping; Ke, Jun

    2015-08-01

    In this paper, an algorithm is designed for shooting games under strong background light. Six LEDs are uniformly distributed on the edge of a game machine screen. They are located at the four corners and in the middle of the top and the bottom edges. Three LEDs are enlightened in the odd frames, and the other three are enlightened in the even frames. A simulator is furnished with one camera, which is used to obtain the image of the LEDs by applying inter-frame difference between the even and odd frames. In the resulting images, six LED are six bright spots. To obtain the LEDs' coordinates rapidly, we proposed a method based on the area of the bright spots. After calibrating the camera based on a pinhole model, four equations can be found using the relationship between the image coordinate system and the world coordinate system with perspective transformation. The center point of the image of LEDs is supposed to be at the virtual shooting point. The perspective transformation matrix is applied to the coordinate of the center point. Then we can obtain the virtual shooting point's coordinate in the world coordinate system. When a game player shoots a target about two meters away, using the method discussed in this paper, the calculated coordinate error is less than ten mm. We can obtain 65 coordinate results per second, which meets the requirement of a real-time system. It proves the algorithm is reliable and effective.

  15. Reliable results from stochastic simulation models

    Treesearch

    Donald L., Jr. Gochenour; Leonard R. Johnson

    1973-01-01

    Development of a computer simulation model is usually done without fully considering how long the model should run (e.g. computer time) before the results are reliable. However construction of confidence intervals (CI) about critical output parameters from the simulation model makes it possible to determine the point where model results are reliable. If the results are...

  16. Analogue Simulation and Orbital Solving Algorithm of Astrometric Exoplanet Detection

    NASA Astrophysics Data System (ADS)

    Huang, P. H.; Ji, J. H.

    2016-09-01

    Astrometry is an effective method to detect exoplanets. It has many advantages that other detection methods do not bear, such as providing three dimensional planetary orbit and determining the planetary mass. Astrometry will enrich the sample of exoplanets. As the high-precision astrometric satellite Gaia (Global Astrometry interferometer for Astrophysics) was launched in 2013, there will be abundant long-period Jupiter-size planets to be discovered by Gaia. In this paper, we specify the α Centauri A, HD 62509, and GJ 876 systems, and generate the synthetic astrometric data with the single astrometric precision of Gaia. Then we use the Lomb-Scargle periodogram to analyse the signature of planets and the Markov Chain Monte Carlo (MCMC) algorithm to fit the orbit of planets. The simulation results are well coincide with the initial solutions.

  17. Thermal Performance Simulation of MWNT/NR composites Based on Levenberg-Marquard Algorithm

    NASA Astrophysics Data System (ADS)

    Yu, Z. Z.; Liu, J. S.

    2017-02-01

    In this paper, Levenberg-Marquard algorithm was used to simulate thermal performance of aligned carbon nanotubes-filled rubber composite, and the effect of temperature, filling amount, MWNTs orientation and other factors on thermal performance were studied. The research results showed: MWNTs orientation can greatly improve the thermal conductivity of composite materials, the thermal performance improvement of overall orientation was higher than the local orientation. Volume fraction can affect thermal performance, thermal conductivity increased with the increase of volume fraction. Temperature had no significant effect on the thermal conductivity. The simulation results correlated well with experimental results, which showed that the simulation algorithm is effective and feasible.

  18. Stochastic simulation for imaging spatial uncertainty: Comparison and evaluation of available algorithms

    SciTech Connect

    Gotway, C.A.; Rutherford, B.M.

    1993-09-01

    Stochastic simulation has been suggested as a viable method for characterizing the uncertainty associated with the prediction of a nonlinear function of a spatially-varying parameter. Geostatistical simulation algorithms generate realizations of a random field with specified statistical and geostatistical properties. A nonlinear function is evaluated over each realization to obtain an uncertainty distribution of a system response that reflects the spatial variability and uncertainty in the parameter. Crucial management decisions, such as potential regulatory compliance of proposed nuclear waste facilities and optimal allocation of resources in environmental remediation, are based on the resulting system response uncertainty distribution. Many geostatistical simulation algorithms have been developed to generate the random fields, and each algorithm will produce fields with different statistical properties. These different properties will result in different distributions for system response, and potentially, different managerial decisions. The statistical properties of the resulting system response distributions are not completely understood, nor is the ability of the various algorithms to generate response distributions that adequately reflect the associated uncertainty. This paper reviews several of the algorithms available for generating random fields. Algorithms are compared in a designed experiment using seven exhaustive data sets with different statistical and geostatistical properties. For each exhaustive data set, a number of realizations are generated using each simulation algorithm. The realizations are used with each of several deterministic transfer functions to produce a cumulative uncertainty distribution function of a system response. The uncertainty distributions are then compared to the single value obtained from the corresponding exhaustive data set.

  19. Forced detection Monte Carlo algorithms for accelerated blood vessel image simulations.

    PubMed

    Fredriksson, Ingemar; Larsson, Marcus; Strömberg, Tomas

    2009-03-01

    Two forced detection (FD) variance reduction Monte Carlo algorithms for image simulations of tissue-embedded objects with matched refractive index are presented. The principle of the algorithms is to force a fraction of the photon weight to the detector at each and every scattering event. The fractional weight is given by the probability for the photon to reach the detector without further interactions. Two imaging setups are applied to a tissue model including blood vessels, where the FD algorithms produce identical results as traditional brute force simulations, while being accelerated with two orders of magnitude. Extending the methods to include refraction mismatches is discussed.

  20. List-Based Simulated Annealing Algorithm for Traveling Salesman Problem

    PubMed Central

    Zhan, Shi-hua; Lin, Juan; Zhang, Ze-jun

    2016-01-01

    Simulated annealing (SA) algorithm is a popular intelligent optimization algorithm which has been successfully applied in many fields. Parameters' setting is a key factor for its performance, but it is also a tedious work. To simplify parameters setting, we present a list-based simulated annealing (LBSA) algorithm to solve traveling salesman problem (TSP). LBSA algorithm uses a novel list-based cooling schedule to control the decrease of temperature. Specifically, a list of temperatures is created first, and then the maximum temperature in list is used by Metropolis acceptance criterion to decide whether to accept a candidate solution. The temperature list is adapted iteratively according to the topology of the solution space of the problem. The effectiveness and the parameter sensitivity of the list-based cooling schedule are illustrated through benchmark TSP problems. The LBSA algorithm, whose performance is robust on a wide range of parameter values, shows competitive performance compared with some other state-of-the-art algorithms. PMID:27034650

  1. A kinetic chain growth algorithm in coarse-grained simulations.

    PubMed

    Liu, Hong; Zhu, You-Liang; Lu, Zhong-Yuan; Müller-Plathe, Florian

    2016-11-15

    We propose a kinetic chain growth algorithm for coarse-grained (CG) simulations in this work. By defining the reaction probability, it delivers a description of consecutive polymerization process. This algorithm is validated by modeling the process of individual styrene monomers polymerizing into polystyrene chains, which is proved to correctly reproduce the properties of polymers in experiments. By bridging the relationship between the generic chain growth process in CG simulations and the chemical details, the impediment to reaction can be reflected. Regarding to the kinetics, it models a polymerization process with an Arrhenius-type reaction rate coefficient. Moreover, this algorithm can model both the gradual and jump processes of the bond formation, thus it readily encompasses several kinds of previous CG models of chain growth. With conducting smooth simulations, this algorithm can be potentially applied to describe the variable macroscopic features of polymers with the process of polymerization. The algorithm details and techniques are introduced in this article. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  2. Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.

    NASA Astrophysics Data System (ADS)

    Elliott, William Dewey

    1995-01-01

    A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over

  3. Convergence Results on Iteration Algorithms to Linear Systems

    PubMed Central

    Wang, Zhuande; Yang, Chuansheng; Yuan, Yubo

    2014-01-01

    In order to solve the large scale linear systems, backward and Jacobi iteration algorithms are employed. The convergence is the most important issue. In this paper, a unified backward iterative matrix is proposed. It shows that some well-known iterative algorithms can be deduced with it. The most important result is that the convergence results have been proved. Firstly, the spectral radius of the Jacobi iterative matrix is positive and the one of backward iterative matrix is strongly positive (lager than a positive constant). Secondly, the mentioned two iterations have the same convergence results (convergence or divergence simultaneously). Finally, some numerical experiments show that the proposed algorithms are correct and have the merit of backward methods. PMID:24991640

  4. Fast stochastic algorithm for simulating evolutionary population dynamics

    NASA Astrophysics Data System (ADS)

    Tsimring, Lev; Hasty, Jeff; Mather, William

    2012-02-01

    Evolution and co-evolution of ecological communities are stochastic processes often characterized by vastly different rates of reproduction and mutation and a coexistence of very large and very small sub-populations of co-evolving species. This creates serious difficulties for accurate statistical modeling of evolutionary dynamics. In this talk, we introduce a new exact algorithm for fast fully stochastic simulations of birth/death/mutation processes. It produces a significant speedup compared to the direct stochastic simulation algorithm in a typical case when the total population size is large and the mutation rates are much smaller than birth/death rates. We illustrate the performance of the algorithm on several representative examples: evolution on a smooth fitness landscape, NK model, and stochastic predator-prey system.

  5. The VIIRS Ocean Data Simulator Enhancements and Results

    NASA Technical Reports Server (NTRS)

    Robinson, Wayne D.; Patt, Fredrick S.; Franz, Bryan A.; Turpie, Kevin R.; McClain, Charles R.

    2011-01-01

    The VIIRS Ocean Science Team (VOST) has been developing an Ocean Data Simulator to create realistic VIIRS SDR datasets based on MODIS water-leaving radiances. The simulator is helping to assess instrument performance and scientific processing algorithms. Several changes were made in the last two years to complete the simulator and broaden its usefulness. The simulator is now fully functional and includes all sensor characteristics measured during prelaunch testing, including electronic and optical crosstalk influences, polarization sensitivity, and relative spectral response. Also included is the simulation of cloud and land radiances to make more realistic data sets and to understand their important influence on nearby ocean color data. The atmospheric tables used in the processing, including aerosol and Rayleigh reflectance coefficients, have been modeled using VIIRS relative spectral responses. The capabilities of the simulator were expanded to work in an unaggregated sample mode and to produce scans with additional samples beyond the standard scan. These features improve the capability to realistically add artifacts which act upon individual instrument samples prior to aggregation and which may originate from beyond the actual scan boundaries. The simulator was expanded to simulate all 16 M-bands and the EDR processing was improved to use these bands to make an SST product. The simulator is being used to generate global VIIRS data from and in parallel with the MODIS Aqua data stream. Studies have been conducted using the simulator to investigate the impact of instrument artifacts. This paper discusses the simulator improvements and results from the artifact impact studies.

  6. Milestone M4900: Simulant Mixing Analytical Results

    SciTech Connect

    Kaplan, D.I.

    2001-07-26

    This report addresses Milestone M4900, ''Simulant Mixing Sample Analysis Results,'' and contains the data generated during the ''Mixing of Process Heels, Process Solutions, and Recycle Streams: Small-Scale Simulant'' task. The Task Technical and Quality Assurance Plan for this task is BNF-003-98-0079A. A report with a narrative description and discussion of the data will be issued separately.

  7. Computational algorithms to simulate the steel continuous casting

    NASA Astrophysics Data System (ADS)

    Ramírez-López, A.; Soto-Cortés, G.; Palomar-Pardavé, M.; Romero-Romo, M. A.; Aguilar-López, R.

    2010-10-01

    Computational simulation is a very powerful tool to analyze industrial processes to reduce operating risks and improve profits from equipment. The present work describes the development of some computational algorithms based on the numerical method to create a simulator for the continuous casting process, which is the most popular method to produce steel products for metallurgical industries. The kinematics of industrial processing was computationally reproduced using subroutines logically programmed. The cast steel by each strand was calculated using an iterative method nested in the main loop. The process was repeated at each time step (Δ t) to calculate the casting time, simultaneously, the steel billets produced were counted and stored. The subroutines were used for creating a computational representation of a continuous casting plant (CCP) and displaying the simulation of the steel displacement through the CCP. These algorithms have been developed to create a simulator using the programming language C++. Algorithms for computer animation of the continuous casting process were created using a graphical user interface (GUI). Finally, the simulator functionality was shown and validated by comparing with the industrial information of the steel production of three casters.

  8. A global optimization algorithm for simulation-based problems via the extended DIRECT scheme

    NASA Astrophysics Data System (ADS)

    Liu, Haitao; Xu, Shengli; Wang, Xiaofang; Wu, Junnan; Song, Yang

    2015-11-01

    This article presents a global optimization algorithm via the extension of the DIviding RECTangles (DIRECT) scheme to handle problems with computationally expensive simulations efficiently. The new optimization strategy improves the regular partition scheme of DIRECT to a flexible irregular partition scheme in order to utilize information from irregular points. The metamodelling technique is introduced to work with the flexible partition scheme to speed up the convergence, which is meaningful for simulation-based problems. Comparative results on eight representative benchmark problems and an engineering application with some existing global optimization algorithms indicate that the proposed global optimization strategy is promising for simulation-based problems in terms of efficiency and accuracy.

  9. Preliminary results from the ASF/GPS ice classification algorithm

    NASA Technical Reports Server (NTRS)

    Cunningham, G.; Kwok, R.; Holt, B.

    1992-01-01

    The European Space Agency Remote Sensing Satellite (ERS-1) satellite carried a C-band synthetic aperture radar (SAR) to study the earth's polar regions. The radar returns from sea ice can be used to infer properties of ice, including ice type. An algorithm has been developed for the Alaska SAR facility (ASF)/Geophysical Processor System (GPS) to infer ice type from the SAR observations over sea ice and open water. The algorithm utilizes look-up tables containing expected backscatter values from various ice types. An analysis has been made of two overlapping strips with 14 SAR images. The backscatter values of specific ice regions were sampled to study the backscatter characteristics of the ice in time and space. Results show both stability of the backscatter values in time and a good separation of multiyear and first-year ice signals, verifying the approach used in the classification algorithm.

  10. Preliminary results from the ASF/GPS ice classification algorithm

    NASA Technical Reports Server (NTRS)

    Cunningham, G.; Kwok, R.; Holt, B.

    1992-01-01

    The European Space Agency Remote Sensing Satellite (ERS-1) satellite carried a C-band synthetic aperture radar (SAR) to study the earth's polar regions. The radar returns from sea ice can be used to infer properties of ice, including ice type. An algorithm has been developed for the Alaska SAR facility (ASF)/Geophysical Processor System (GPS) to infer ice type from the SAR observations over sea ice and open water. The algorithm utilizes look-up tables containing expected backscatter values from various ice types. An analysis has been made of two overlapping strips with 14 SAR images. The backscatter values of specific ice regions were sampled to study the backscatter characteristics of the ice in time and space. Results show both stability of the backscatter values in time and a good separation of multiyear and first-year ice signals, verifying the approach used in the classification algorithm.

  11. Evaluation of registration, compression and classification algorithms. Volume 1: Results

    NASA Technical Reports Server (NTRS)

    Jayroe, R.; Atkinson, R.; Callas, L.; Hodges, J.; Gaggini, B.; Peterson, J.

    1979-01-01

    The registration, compression, and classification algorithms were selected on the basis that such a group would include most of the different and commonly used approaches. The results of the investigation indicate clearcut, cost effective choices for registering, compressing, and classifying multispectral imagery.

  12. A novel wavefront-based algorithm for numerical simulation of quasi-optical systems

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoling; Lou, Zheng; Hu, Jie; Zhou, Kangmin; Zuo, Yingxi; Shi, Shengcai

    2016-11-01

    A novel wavefront-based algorithm for the beam simulation of both reflective and refractive optics in a complicated quasi-optical system is proposed. The algorithm can be regarded as the extension to the conventional Physical Optics algorithm to handle dielectrics. Internal reflections are modeled in an accurate fashion, and coating and flossy materials can be treated in a straightforward manner. A parallel implementation of the algorithm has been developed and numerical examples show that the algorithm yields sufficient accuracy by comparing with experimental results, while the computational complexity is much less than the full-wave methods. The algorithm offers an alternative approach to the modeling of quasi-optical systems in addition to the Geometrical Optics modeling and full-wave methods.

  13. Understanding disordered systems through numerical simulation and algorithm development

    NASA Astrophysics Data System (ADS)

    Sweeney, Sean Michael

    Disordered systems arise in many physical contexts. Not all matter is uniform, and impurities or heterogeneities can be modeled by fixed random disorder. Numerous complex networks also possess fixed disorder, leading to applications in transportation systems, telecommunications, social networks, and epidemic modeling, to name a few. Due to their random nature and power law critical behavior, disordered systems are difficult to study analytically. Numerical simulation can help overcome this hurdle by allowing for the rapid computation of system states. In order to get precise statistics and extrapolate to the thermodynamic limit, large systems must be studied over many realizations. Thus, innovative algorithm development is essential in order reduce memory or running time requirements of simulations. This thesis presents a review of disordered systems, as well as a thorough study of two particular systems through numerical simulation, algorithm development and optimization, and careful statistical analysis of scaling properties. Chapter 1 provides a thorough overview of disordered systems, the history of their study in the physics community, and the development of techniques used to study them. Topics of quenched disorder, phase transitions, the renormalization group, criticality, and scale invariance are discussed. Several prominent models of disordered systems are also explained. Lastly, analysis techniques used in studying disordered systems are covered. In Chapter 2, minimal spanning trees on critical percolation clusters are studied, motivated in part by an analytic perturbation expansion by Jackson and Read that I check against numerical calculations. This system has a direct mapping to the ground state of the strongly disordered spin glass. We compute the path length fractal dimension of these trees in dimensions d = {2, 3, 4, 5} and find our results to be compatible with the analytic results suggested by Jackson and Read. In Chapter 3, the random bond Ising

  14. A fast and high accuracy numerical simulation algorithm of the polymer spherulite at the mesoscale Level

    NASA Astrophysics Data System (ADS)

    Liu, Yongzhi; Geng, Tie; (Tom Turng, Lih-Sheng; Liu, Chuntai; Cao, Wei; Shen, Changyu

    2017-09-01

    In the multiscale numerical simulation of polymer crystallization during the processing period, flow and temperature of the polymer melt are simulated on the macroscale level, while nucleation and growth of the spherulite are simulated at the mesoscale level. As a part of the multiscale simulation, the meso-simulation requires a fast solving speed because the meso-simulation software must be run several times in every macro-element at each macro-step. Meanwhile, the accuracy of the calculation results is also very important. It is known that the simulation geometry of crystallization includes planar (2D) and three-dimensional space (3D). The 3D calculations are more accurate but more expensive because of the long CPU time consumed. On the contrary, 2D calculations are always much faster but lower in accuracy. To reach the desirable speed and high accuracy at the same time, an algorithm is presented, in which the Delesse law coupled with the Monte Carlo method and pixel method are employed to simulate the nucleation, growth, and impingement of the polymer spherulite at the mesoscale level. Based on this algorithm, a software is developed with the Visual C++ language, and its numerical examples’ results prove that the solving speed of this algorithm is as fast as the 2D classical simulation and the calculation accuracy is at the same level as the 3D simulation.

  15. New human-centered linear and nonlinear motion cueing algorithms for control of simulator motion systems

    NASA Astrophysics Data System (ADS)

    Telban, Robert J.

    While the performance of flight simulator motion system hardware has advanced substantially, the development of the motion cueing algorithm, the software that transforms simulated aircraft dynamics into realizable motion commands, has not kept pace. To address this, new human-centered motion cueing algorithms were developed. A revised "optimal algorithm" uses time-invariant filters developed by optimal control, incorporating human vestibular system models. The "nonlinear algorithm" is a novel approach that is also formulated by optimal control, but can also be updated in real time. It incorporates a new integrated visual-vestibular perception model that includes both visual and vestibular sensation and the interaction between the stimuli. A time-varying control law requires the matrix Riccati equation to be solved in real time by a neurocomputing approach. Preliminary pilot testing resulted in the optimal algorithm incorporating a new otolith model, producing improved motion cues. The nonlinear algorithm vertical mode produced a motion cue with a time-varying washout, sustaining small cues for longer durations and washing out large cues more quickly compared to the optimal algorithm. The inclusion of the integrated perception model improved the responses to longitudinal and lateral cues. False cues observed with the NASA adaptive algorithm were absent. As a result of unsatisfactory sensation, an augmented turbulence cue was added to the vertical mode for both the optimal and nonlinear algorithms. The relative effectiveness of the algorithms, in simulating aircraft maneuvers, was assessed with an eleven-subject piloted performance test conducted on the NASA Langley Visual Motion Simulator (VMS). Two methods, the quasi-objective NASA Task Load Index (TLX), and power spectral density analysis of pilot control, were used to assess pilot workload. TLX analysis reveals, in most cases, less workload and variation among pilots with the nonlinear algorithm. Control input

  16. Comparison of Automated Flare Location Algorithm Results to Solar Truth

    NASA Astrophysics Data System (ADS)

    Plunkett, S. P.; Newmark, J. S.; Kunkel, V.; Patsourakos, S.; McMullin, D. R.; Hill, S. M.

    2008-12-01

    Accurate and timely detection of solar flares and determination of their heliocentric coordinates are key requirements for space weather forecasting. We report the results of a study to compare the results of multiple algorithms for automated determination of flare locations to "solar truth". The XFL algorithm determines flare locations in near real-time using GOES-12 SXI image data, and is triggered by GOES-12 XRS flare detections. We also consider H-alpha flare locations reported in the FLA data set, and the Latest Events (LEV) locations produced by LMSAL, based on GOES-12 SXI or SOHO EIT observations. We compare the results of each of these algorithms to solar truth heliocentric flare locations determined from analysis of GOES-12 SXI images of several hundred flares of C class and higher, during periods of high, moderate, and low solar activity between 2003 and 2006. We also compare the relative effectiveness of each of these algorithms for determining flare locations in near real-time, considering both timeliness and accuracy of the reported flare locations.

  17. Time parallelization of plasma simulations using the parareal algorithm

    SciTech Connect

    Samaddar, D.; Houlberg, Wayne A; Berry, Lee A; Elwasif, Wael R; Huysmans, G; Batchelor, Donald B

    2011-01-01

    Simulation of fusion plasmas involve a broad range of timescales. In magnetically confined plasmas, such as in ITER, the timescale associated with the microturbulence responsible for transport and confinement timescales vary by an order of 10^6 10^9. Simulating this entire range of timescales is currently impossible, even on the most powerful supercomputers available. Space parallelization has so far been the most common approach to solve partial differential equations. Space parallelization alone has led to computational saturation for fluid codes, which means that the walltime for computaion does not linearly decrease with the increasing number of processors used. The application of the parareal algorithm to simulations of fusion plasmas ushers in a new avenue of parallelization, namely temporal parallelization. The algorithm has been successfully applied to plasma turbulence simulations, prior to which it has been applied to other relatively simpler problems. This work explores the extension of the applicability of the parareal algorithm to ITER relevant problems, starting with a diffusion-convection model.

  18. A performance comparison of integration algorithms in simulating flexible structures

    NASA Technical Reports Server (NTRS)

    Howe, R. M.

    1989-01-01

    Asymptotic formulas for the characteristic root errors as well as transfer function gain and phase errors are presented for a number of traditional and new integration methods. Normalized stability regions in the lambda h plane are compared for the various methods. In particular, it is shown that a modified form of Euler integration with root matching is an especially efficient method for simulating lightly-damped structural modes. The method has been used successfully for structural bending modes in the real-time simulation of missiles. Performance of this algorithm is compared with other special algorithms, including the state-transition method. A predictor-corrector version of the modified Euler algorithm permits it to be extended to the simulation of nonlinear models of the type likely to be obtained when using the discretized structure approach. Performance of the different integration methods is also compared for integration step sizes larger than those for which the asymptotic formulas are valid. It is concluded that many traditional integration methods, such as RD-4, are not competitive in the simulation of lightly damped structures.

  19. A generic algorithm for Monte Carlo simulation of proton transport

    NASA Astrophysics Data System (ADS)

    Salvat, Francesc

    2013-12-01

    A mixed (class II) algorithm for Monte Carlo simulation of the transport of protons, and other heavy charged particles, in matter is presented. The emphasis is on the electromagnetic interactions (elastic and inelastic collisions) which are simulated using strategies similar to those employed in the electron-photon code PENELOPE. Elastic collisions are described in terms of numerical differential cross sections (DCSs) in the center-of-mass frame, calculated from the eikonal approximation with the Dirac-Hartree-Fock-Slater atomic potential. The polar scattering angle is sampled by employing an adaptive numerical algorithm which allows control of interpolation errors. The energy transferred to the recoiling target atoms (nuclear stopping) is consistently described by transformation to the laboratory frame. Inelastic collisions are simulated from DCSs based on the plane-wave Born approximation (PWBA), making use of the Sternheimer-Liljequist model of the generalized oscillator strength, with parameters adjusted to reproduce (1) the electronic stopping power read from the input file, and (2) the total cross sections for impact ionization of inner subshells. The latter were calculated from the PWBA including screening and Coulomb corrections. This approach provides quite a realistic description of the energy-loss distribution in single collisions, and of the emission of X-rays induced by proton impact. The simulation algorithm can be readily modified to include nuclear reactions, when the corresponding cross sections and emission probabilities are available, and bremsstrahlung emission.

  20. Two-Dimensional Inlet Simulation Using a Diagonal Implicit Algorithm

    NASA Technical Reports Server (NTRS)

    Chaussee, D.S.; Pulliam, T. H.

    1981-01-01

    A modification of an implicit approximate-factorization finite-difference algorithm applied to the two-dimensional Euler and Navier-Stokes equations in general curvilinear coordinates is presented for supersonic freestream flow about and through inlets. The modification transforms the coupled system of equations Into an uncoupled diagonal form which requires less computation work. For steady-state applications the resulting diagonal algorithm retains the stability and accuracy characteristics of the original algorithm. Solutions are given for inviscid and laminar flow about a two-dimensional wedge inlet configuration. Comparisons are made between computed results and exact theory.

  1. A Contextual Fire Detection Algorithm for Simulated HJ-1B Imagery.

    PubMed

    Qian, Yonggang; Yan, Guangjian; Duan, Sibo; Kong, Xiangsheng

    2009-01-01

    The HJ-1B satellite, which was launched on September 6, 2008, is one of the small ones placed in the constellation for disaster prediction and monitoring. HJ-1B imagery was simulated in this paper, which contains fires of various sizes and temperatures in a wide range of terrestrial biomes and climates, including RED, NIR, MIR and TIR channels. Based on the MODIS version 4 contextual algorithm and the characteristics of HJ-1B sensor, a contextual fire detection algorithm was proposed and tested using simulated HJ-1B data. It was evaluated by the probability of fire detection and false alarm as functions of fire temperature and fire area. Results indicate that when the simulated fire area is larger than 45 m(2) and the simulated fire temperature is larger than 800 K, the algorithm has a higher probability of detection. But if the simulated fire area is smaller than 10 m(2), only when the simulated fire temperature is larger than 900 K, may the fire be detected. For fire areas about 100 m(2), the proposed algorithm has a higher detection probability than that of the MODIS product. Finally, the omission and commission error were evaluated which are important factors to affect the performance of this algorithm. It has been demonstrated that HJ-1B satellite data are much sensitive to smaller and cooler fires than MODIS or AVHRR data and the improved capabilities of HJ-1B data will offer a fine opportunity for the fire detection.

  2. A Contextual Fire Detection Algorithm for Simulated HJ-1B Imagery

    PubMed Central

    Qian, Yonggang; Yan, Guangjian; Duan, Sibo; Kong, Xiangsheng

    2009-01-01

    The HJ-1B satellite, which was launched on September 6, 2008, is one of the small ones placed in the constellation for disaster prediction and monitoring. HJ-1B imagery was simulated in this paper, which contains fires of various sizes and temperatures in a wide range of terrestrial biomes and climates, including RED, NIR, MIR and TIR channels. Based on the MODIS version 4 contextual algorithm and the characteristics of HJ-1B sensor, a contextual fire detection algorithm was proposed and tested using simulated HJ-1B data. It was evaluated by the probability of fire detection and false alarm as functions of fire temperature and fire area. Results indicate that when the simulated fire area is larger than 45 m2 and the simulated fire temperature is larger than 800 K, the algorithm has a higher probability of detection. But if the simulated fire area is smaller than 10 m2, only when the simulated fire temperature is larger than 900 K, may the fire be detected. For fire areas about 100 m2, the proposed algorithm has a higher detection probability than that of the MODIS product. Finally, the omission and commission error were evaluated which are important factors to affect the performance of this algorithm. It has been demonstrated that HJ-1B satellite data are much sensitive to smaller and cooler fires than MODIS or AVHRR data and the improved capabilities of HJ-1B data will offer a fine opportunity for the fire detection. PMID:22399950

  3. A fast 3D image simulation algorithm of moving target for scanning laser radar

    NASA Astrophysics Data System (ADS)

    Li, Jicheng; Shi, Zhiguang; Chen, Xiao; Chen, Dong

    2014-10-01

    Scanning Laser Radar has been widely used in many military and civil areas. Usually there are relative movements between the target and the radar, so the moving target image modeling and simulation is an important research content in the field of signal processing and system design of scan-imaging laser radar. In order to improve the simulation speed and hold the accuracy of the image simulation simultaneously, a novel fast simulation algorithm is proposed in this paper. Firstly, for moving target or varying scene, an inequation that can judge the intersection relations between the pixel and target bins is obtained by deriving the projection of target motion trajectories on the image plane. Then, by utilizing the time subdivision and approximate treatments, the potential intersection relations of pixel and target bins are determined. Finally, the goal of reducing the number of intersection operations could be achieved by testing all the potential relations and finding which of them is real intersection. To test the method's performance, we perform computer simulations of both the new proposed algorithm and a literature's algorithm for six targets. The simulation results show that the two algorithm yield the same imaging result, whereas the number of intersection operations of former is equivalent to only 1% of the latter, and the calculation efficiency increases a hundredfold. The novel simulation acceleration idea can be applied extensively in other more complex application environments and provide equally acceleration effect. It is very suitable for the case to produce a great large number of laser radar images.

  4. Molecular dynamics algorithm enforcing energy conservation for microcanonical simulations.

    PubMed

    Salueña, Clara; Avalos, Josep Bonet

    2014-05-01

    A reversible algorithm [enforced energy conservation (EEC)] that enforces total energy conservation for microcanonical simulations is presented. The key point is the introduction of the discrete-gradient method to define the forces from the conservative potentials, instead of the direct use of the force field at the actual position of the particle. We have studied the performance and accuracy of the EEC in two cases, namely Lennard-Jones fluid and a simple electrolyte model. Truncated potentials that usually induce inaccuracies in energy conservation are used. In particular, the reaction field approach is used in the latter. The EEC is able to preserve energy conservation for a long time, and, in addition, it performs better than the Verlet algorithm for these kinds of simulations.

  5. Improved Contact Algorithms for Implicit FE Simulation of Sheet Forming

    NASA Astrophysics Data System (ADS)

    Zhuang, S.; Lee, M. G.; Keum, Y. T.; Wagoner, R. H.

    2007-05-01

    Implicit finite element simulations of sheet forming processes do not always converge, particularly for complex tool geometries and rapidly changing contact. The SHEET-3 program exhibits remarkable stability and strong convergence by use of its special N-CFS algorithm and a sheet normal defined by the mesh, but these features alone do not always guarantee convergence and accuracy. An improved contact capability within the N-CFS algorithm is formulated taking into account sheet thickness within the framework of shell elements. Two imaginary surfaces offset from the mid-plane of shell elements are implemented along the mesh normal direction. An efficient contact searching algorithm based on the mesh-patch tool description is formulated along the mesh normal direction. The contact search includes a general global searching procedure and a new local searching procedure enforcing the contact condition along the mesh normal direction. The processes of unconstrained cylindrical bending and drawing through a drawbead are simulated to verify the accuracy and convergence of the improved contact algorithm.

  6. Predicting patchy particle crystals: Variable box shape simulations and evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    Bianchi, Emanuela; Doppelbauer, Günther; Filion, Laura; Dijkstra, Marjolein; Kahl, Gerhard

    2012-06-01

    We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an approach based on Monte Carlo simulations in the isobaric-isothermal ensemble and (ii) an optimization technique based on ideas of evolutionary algorithms. We show that the two methods are equally successful and provide consistent results on crystalline phases of patchy particle systems.

  7. Advanced Dynamically Adaptive Algorithms for Stochastic Simulations on Extreme Scales

    SciTech Connect

    Xiu, Dongbin

    2016-06-21

    The focus of the project is the development of mathematical methods and high-performance com- putational tools for stochastic simulations, with a particular emphasis on computations on extreme scales. The core of the project revolves around the design of highly e cient and scalable numer- ical algorithms that can adaptively and accurately, in high dimensional spaces, resolve stochastic problems with limited smoothness, even containing discontinuities.

  8. SMMR Simulator radiative transfer calibration model. 2: Algorithm development

    NASA Technical Reports Server (NTRS)

    Link, S.; Calhoon, C.; Krupp, B.

    1980-01-01

    Passive microwave measurements performed from Earth orbit can be used to provide global data on a wide range of geophysical and meteorological phenomena. A Scanning Multichannel Microwave Radiometer (SMMR) is being flown on the Nimbus-G satellite. The SMMR Simulator duplicates the frequency bands utilized in the spacecraft instruments through an amalgamate of radiometer systems. The algorithm developed utilizes data from the fall 1978 NASA CV-990 Nimbus-G underflight test series and subsequent laboratory testing.

  9. Sampling of general correlators in worm-algorithm based simulations

    NASA Astrophysics Data System (ADS)

    Rindlisbacher, Tobias; Åkerlund, Oscar; de Forcrand, Philippe

    2016-08-01

    Using the complex ϕ4-model as a prototype for a system which is simulated by a worm algorithm, we show that not only the charged correlator <ϕ* (x) ϕ (y) >, but also more general correlators such as < | ϕ (x) | | ϕ (y) | > or < arg ⁡ (ϕ (x)) arg ⁡ (ϕ (y)) >, as well as condensates like < | ϕ | >, can be measured at every step of the Monte Carlo evolution of the worm instead of on closed-worm configurations only. The method generalizes straightforwardly to other systems simulated by worms, such as spin or sigma models.

  10. Reliable prediction of adsorption isotherms via genetic algorithm molecular simulation.

    PubMed

    LoftiKatooli, L; Shahsavand, A

    2017-01-01

    Conventional molecular simulation techniques such as grand canonical Monte Carlo (GCMC) strictly rely on purely random search inside the simulation box for predicting the adsorption isotherms. This blind search is usually extremely time demanding for providing a faithful approximation of the real isotherm and in some cases may lead to non-optimal solutions. A novel approach is presented in this article which does not use any of the classical steps of the standard GCMC method, such as displacement, insertation, and removal. The new approach is based on the well-known genetic algorithm to find the optimal configuration for adsorption of any adsorbate on a structured adsorbent under prevailing pressure and temperature. The proposed approach considers the molecular simulation problem as a global optimization challenge. A detailed flow chart of our so-called genetic algorithm molecular simulation (GAMS) method is presented, which is entirely different from traditions molecular simulation approaches. Three real case studies (for adsorption of CO2 and H2 over various zeolites) are borrowed from literature to clearly illustrate the superior performances of the proposed method over the standard GCMC technique. For the present method, the average absolute values of percentage errors are around 11% (RHO-H2), 5% (CHA-CO2), and 16% (BEA-CO2), while they were about 70%, 15%, and 40% for the standard GCMC technique, respectively.

  11. A Parallel, Finite-Volume Algorithm for Large-Eddy Simulation of Turbulent Flows

    NASA Technical Reports Server (NTRS)

    Bui, Trong T.

    1999-01-01

    A parallel, finite-volume algorithm has been developed for large-eddy simulation (LES) of compressible turbulent flows. This algorithm includes piecewise linear least-square reconstruction, trilinear finite-element interpolation, Roe flux-difference splitting, and second-order MacCormack time marching. Parallel implementation is done using the message-passing programming model. In this paper, the numerical algorithm is described. To validate the numerical method for turbulence simulation, LES of fully developed turbulent flow in a square duct is performed for a Reynolds number of 320 based on the average friction velocity and the hydraulic diameter of the duct. Direct numerical simulation (DNS) results are available for this test case, and the accuracy of this algorithm for turbulence simulations can be ascertained by comparing the LES solutions with the DNS results. The effects of grid resolution, upwind numerical dissipation, and subgrid-scale dissipation on the accuracy of the LES are examined. Comparison with DNS results shows that the standard Roe flux-difference splitting dissipation adversely affects the accuracy of the turbulence simulation. For accurate turbulence simulations, only 3-5 percent of the standard Roe flux-difference splitting dissipation is needed.

  12. An improved sink particle algorithm for SPH simulations

    NASA Astrophysics Data System (ADS)

    Hubber, D. A.; Walch, S.; Whitworth, A. P.

    2013-04-01

    Numerical simulations of star formation frequently rely on the implementation of sink particles: (a) to avoid expending computational resource on the detailed internal physics of individual collapsing protostars, (b) to derive mass functions, binary statistics and clustering kinematics (and hence to make comparisons with observation), and (c) to model radiative and mechanical feedback; sink particles are also used in other contexts, for example to represent accreting black holes in galactic nuclei. We present a new algorithm for creating and evolving sink particles in smoothed particle hydrodynamic (SPH) simulations, which appears to represent a significant improvement over existing algorithms - particularly in situations where sinks are introduced after the gas has become optically thick to its own cooling radiation and started to heat up by adiabatic compression. (i) It avoids spurious creation of sinks. (ii) It regulates the accretion of matter on to a sink so as to mitigate non-physical perturbations in the vicinity of the sink. (iii) Sinks accrete matter, but the associated angular momentum is transferred back to the surrounding medium. With the new algorithm - and modulo the need to invoke sufficient resolution to capture the physics preceding sink formation - the properties of sinks formed in simulations are essentially independent of the user-defined parameters of sink creation, or the number of SPH particles used.

  13. Massively parallel algorithms for trace-driven cache simulations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Greenberg, Albert G.; Lubachevsky, Boris D.

    1991-01-01

    Trace driven cache simulation is central to computer design. A trace is a very long sequence of reference lines from main memory. At the t(exp th) instant, reference x sub t is hashed into a set of cache locations, the contents of which are then compared with x sub t. If at the t sup th instant x sub t is not present in the cache, then it is said to be a miss, and is loaded into the cache set, possibly forcing the replacement of some other memory line, and making x sub t present for the (t+1) sup st instant. The problem of parallel simulation of a subtrace of N references directed to a C line cache set is considered, with the aim of determining which references are misses and related statistics. A simulation method is presented for the Least Recently Used (LRU) policy, which regradless of the set size C runs in time O(log N) using N processors on the exclusive read, exclusive write (EREW) parallel model. A simpler LRU simulation algorithm is given that runs in O(C log N) time using N/log N processors. Timings are presented of the second algorithm's implementation on the MasPar MP-1, a machine with 16384 processors. A broad class of reference based line replacement policies are considered, which includes LRU as well as the Least Frequently Used and Random replacement policies. A simulation method is presented for any such policy that on any trace of length N directed to a C line set runs in the O(C log N) time with high probability using N processors on the EREW model. The algorithms are simple, have very little space overhead, and are well suited for SIMD implementation.

  14. Advanced time integration algorithms for dislocation dynamics simulations of work hardening

    DOE PAGES

    Sills, Ryan B.; Aghaei, Amin; Cai, Wei

    2016-04-25

    Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relativemore » to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.« less

  15. Advanced time integration algorithms for dislocation dynamics simulations of work hardening

    SciTech Connect

    Sills, Ryan B.; Aghaei, Amin; Cai, Wei

    2016-04-25

    Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relative to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.

  16. Advanced time integration algorithms for dislocation dynamics simulations of work hardening

    SciTech Connect

    Sills, Ryan B.; Aghaei, Amin; Cai, Wei

    2016-04-25

    Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relative to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.

  17. An Event-Driven Hybrid Molecular Dynamics and Direct Simulation Monte Carlo Algorithm

    SciTech Connect

    Donev, A; Garcia, A L; Alder, B J

    2007-07-30

    A novel algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with the solvent particles with hard core potentials. The algorithm uses event-driven molecular dynamics (MD) for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in event-driven algorithms, rather, the momentum and energy exchange in the solvent is determined stochastically using the Direct Simulation Monte Carlo (DSMC) method. The coupling between the solvent and the solute is consistently represented at the particle level, however, unlike full MD simulations of both the solvent and the solute, the spatial structure of the solvent is ignored. The algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard wall subjected to uniform shear. The algorithm closely reproduces full MD simulations with two orders of magnitude greater efficiency. Results do not confirm the existence of periodic (cycling) motion of the polymer chain.

  18. Results of AO simulations for ELTs

    NASA Astrophysics Data System (ADS)

    Conan, Rodolphe; Le Louarn, Miska; Braud, J.; Fedrigo, Enrico; Hubin, Norbert N.

    2003-01-01

    The design and elaboration of Extremely Large Telescopes (ELT) with primary mirror from 20m to 100m face with many challenges: mechanical, optical, computational, etc. To benefit completely of the full potentiality of such facilities, an Adaptive Optics System (AOS) have also to be designed for these telescopes. For whole field--of--view compensation and full sky coverage, the new but promising Multi--Conjugated Adaptive Optics (MCAO) technique has to be envisaged. The first step towards the design of an MCAO system is the numerical simulation. This is the first challenge we have to face. The scale of AO simulations being imposed by the ratio (D/r0), the simulation requirements of a MCAOS for an ELT, in terms of computing power and memory available to store the data, reach and sometimes overcome the capacity of actual computers. In ESO, we have evaluated different hardware and software strategies to achieve MCAO simulations goals. Two codes have been developed to simulate MCAOS using an analytical and an end-to-end model. The goals and advantages/limitations of both approaches is shown. The hardware requirements for both methods is also given through the size of their largest matrices. And finally, results of hardware and software tests for MCAO simulations with PC--cluster and paralleled code are presented.

  19. Simulating chemical energies to high precision with fully-scalable quantum algorithms on superconducting qubits

    NASA Astrophysics Data System (ADS)

    O'Malley, Peter; Babbush, Ryan; Kivlichan, Ian; Romero, Jhonathan; McClean, Jarrod; Tranter, Andrew; Barends, Rami; Kelly, Julian; Chen, Yu; Chen, Zijun; Jeffrey, Evan; Fowler, Austin; Megrant, Anthony; Mutus, Josh; Neill, Charles; Quintana, Christopher; Roushan, Pedram; Sank, Daniel; Vainsencher, Amit; Wenner, James; White, Theodore; Love, Peter; Aspuru-Guzik, Alan; Neven, Hartmut; Martinis, John

    Quantum simulations of molecules have the potential to calculate industrially-important chemical parameters beyond the reach of classical methods with relatively modest quantum resources. Recent years have seen dramatic progress both superconducting qubits and quantum chemistry algorithms. Here, we present experimental demonstrations of two fully-scalable algorithms for finding the dissociation energy of hydrogen: the variational quantum eigensolver and iterative phase estimation. This represents the first calculation of a dissociation energy to chemical accuracy with a non-precompiled algorithm. These results show the promise of chemistry as the ``killer app'' for quantum computers, even before the advent of full error-correction.

  20. Frist preliminary results of carbon dioxide retrieval algorithm

    NASA Astrophysics Data System (ADS)

    Jung, Y.; Kim, W. V.; Lee, H.; Kim, J.; Boesch, H.

    2013-12-01

    The significant increase in atmospheric carbon dioxide (CO2) over the last two hundred years represents critical variations both to the atmosphere and the global carbon cycle. Satellite measurement is one of the most effective approaches to monitor the global distributions of CO2 with high spatio-temporal resolutions and is expected to improve the accuracy of carbon source and sink estimates (Rayner and O'Brien, 2001; Houweling et al., 2004). The Greenhouse Gases Observing SATellite (GOSAT), which was launched on January 2009, is the world's first satellite dedicated to measure the atmospheric concentrations of CO2 from space. Even though many studies to develop the CO2 retrieval algorithms are performed, there have been serious limitations in spatial coverage and uncertainties due to aerosols and thin cirrus clouds. In this study, we demonstrate our retrieval algorithms of CO2 concentrations from GOSAT and show its preliminary results showing the variations CO2 concentration in global. The quality of the preliminary results in this study will be evaluated through comparison with collocated ground-based observations at several TCCON sites. In the future, we plan to investigate interferences by aerosols using our independent aerosol retrieval algorithms and improve its retrieval quality. This study would be informative to study the estimate the carbon sources and sinks in more detail.

  1. A simple algorithm for analyzing uncertainty of accident reconstruction results.

    PubMed

    Zou, Tiefang; Hu, Lin; Li, Pingfan; Wu, Hequan

    2015-12-01

    In order to analyzing the uncertainty in accident reconstruction, based on the theory of extreme value and the convex model theory, the uncertainty analysis problem is turn to an extreme value problem. In order to calculate the range of the dependent variable, the extreme value in the definition domain and on the boundary of the definition domain are calculated independently, and then the upper and lower bound of the dependent variable can be given by these obtained extreme values. Based on such idea and through analyzing five numerical cases, a simple algorithm for calculating the range of an accident reconstruction result was given; appropriate results can be obtained through the proposed algorithm in these cases. Finally, a real world vehicle-motorcycle accident was given, the range of the reconstructed velocity of the vehicle was calculated by employing the Pc-Crash, the response surface methodology and the new proposed algorithm, the range was [66.1-67.3] km/h. This research will provide another choice for uncertainty analysis in accident reconstruction. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  2. A parallel simulated annealing algorithm for standard cell placement on a hypercube computer

    NASA Technical Reports Server (NTRS)

    Jones, Mark Howard

    1987-01-01

    A parallel version of a simulated annealing algorithm is presented which is targeted to run on a hypercube computer. A strategy for mapping the cells in a two dimensional area of a chip onto processors in an n-dimensional hypercube is proposed such that both small and large distance moves can be applied. Two types of moves are allowed: cell exchanges and cell displacements. The computation of the cost function in parallel among all the processors in the hypercube is described along with a distributed data structure that needs to be stored in the hypercube to support parallel cost evaluation. A novel tree broadcasting strategy is used extensively in the algorithm for updating cell locations in the parallel environment. Studies on the performance of the algorithm on example industrial circuits show that it is faster and gives better final placement results than the uniprocessor simulated annealing algorithms. An improved uniprocessor algorithm is proposed which is based on the improved results obtained from parallelization of the simulated annealing algorithm.

  3. An Initial Examination for Verifying Separation Algorithms by Simulation

    NASA Technical Reports Server (NTRS)

    White, Allan L.; Neogi, Natasha; Herencia-Zapana, Heber

    2012-01-01

    An open question in algorithms for aircraft is what can be validated by simulation where the simulation shows that the probability of undesirable events is below some given level at some confidence level. The problem is including enough realism to be convincing while retaining enough efficiency to run the large number of trials needed for high confidence. The paper first proposes a goal based on the number of flights per year in several regions. The paper examines the probabilistic interpretation of this goal and computes the number of trials needed to establish it at an equivalent confidence level. Since any simulation is likely to consider the algorithms for only one type of event and there are several types of events, the paper examines under what conditions this separate consideration is valid. This paper is an initial effort, and as such, it considers separation maneuvers, which are elementary but include numerous aspects of aircraft behavior. The scenario includes decisions under uncertainty since the position of each aircraft is only known to the other by broadcasting where GPS believes each aircraft to be (ADS-B). Each aircraft operates under feedback control with perturbations. It is shown that a scenario three or four orders of magnitude more complex is feasible. The question of what can be validated by simulation remains open, but there is reason to be optimistic.

  4. Ventricular Fibrillation in Mammalian Hearts: Simulation Results

    NASA Astrophysics Data System (ADS)

    Fenton, Flavio H.

    2002-03-01

    The computational approach to understanding the initiation and evolution of cardiac arrhythmias forms a necessary link between experiment and theory. Numerical simulations combine useful mathematical models and complex geometry while offering clean and comprehensive data acquisition, reproducible results that can be compared to experiments, and the flexibility of exploring parameter space systematically. However, because cardiac dynamics occurs on many scales (on the order of 10^9 cells of size 10-100 microns with more than 40 ionic currents and time scales as fast as 0.01ms), roughly 10^17 operations are required to simulate just one second of real time. These intense computational requirements lead to significant implementation challenges even on existing supercomputers. Nevertheless, progress over the last decade in understanding the effects of some spatial scales and spatio-temporal dynamics on cardiac cell and tissue behavior justifies the use of certain simplifications which, along with improved models for cellular dynamics and detailed digital models of cardiac anatomy, are allowing simulation studies of full-size ventricles and atria. We describe this simulation problem from a combined numerical, physical and biological point of view, with an emphasis on the dynamics and stability of scroll waves of electrical activity in mammalian hearts and their relation to tachycardia, fibrillation and sudden death. Detailed simulations of electrical activity in ventricles including complex anatomy, anisotropic fiber structure, and electrophysiological effects of two drugs (DAM and CytoD) are presented and compared with experimental results.

  5. An improved differential evolution algorithm for enhancing biochemical pathways simulation and production.

    PubMed

    Chong, Chuii Khim; Mohamad, Mohd Saberi; Deris, Safaai; Shamsir, Mohd Shahir; Abdullah, Afnizanfaizal

    2014-01-01

    This paper presents an Improved Differential Evolution (IDE) algorithm to improve the kinetic parameter estimation in simulating the glycolysis pathway and the threonine biosynthesis pathway. Experimentally derived time series kinetic data are noisy and possess many unknown parameters. These characteristics of kinetic data cause lengthy computational time to compute the optimum value of the kinetic parameters. To solve this problem, this study had been conducted to develop a hybrid method that combined the Differential Evolution algorithm (DE) and the Kalman Filter (KF) to produce IDE. Results have shown that lesser computation time (6% and 18.5% faster) and more robust to noisy data with significant reduced error rates (93% and 79% reduced error rates) compared with the Genetic Algorithm (GA) and DE, respectively, in glycolysis and threonine biosynthesis pathway simulations. IDE is reliable as it demonstrated consistent standard deviation values which were close to mean values. We foresee the applicability of IDE into other metabolic pathway simulations.

  6. Confidence range estimate of extended source imagery acquisition algorithms via computer simulations. [in optical communication systems

    NASA Technical Reports Server (NTRS)

    Chen, CHIEN-C.; Hui, Elliot; Okamoto, Garret

    1992-01-01

    Spatial acquisition using the sun-lit Earth as a beacon source provides several advantages over active beacon-based systems for deep-space optical communication systems. However, since the angular extend of the Earth image is large compared to the laser beam divergence, the acquisition subsystem must be capable of resolving the image to derive the proper pointing orientation. The algorithms used must be capable of deducing the receiver location given the blurring introduced by the imaging optics and the large Earth albedo fluctuation. Furthermore, because of the complexity of modelling the Earth and the tracking algorithms, an accurate estimate of the algorithm accuracy can only be made via simulation using realistic Earth images. An image simulator was constructed for this purpose, and the results of the simulation runs are reported.

  7. Confidence range estimate of extended source imagery acquisition algorithms via computer simulations

    NASA Astrophysics Data System (ADS)

    Chen, Chien-C.; Hui, Elliot; Okamoto, Garret

    1992-06-01

    Spatial acquisition using the sun-lit Earth as a beacon source provides several advantages over active beacon-based systems for deep-space optical communication systems. However, since the angular extend of the Earth image is large compared to the laser beam divergence, the acquisition subsystem must be capable of resolving the image to derive the proper pointing orientation. The algorithms used must be capable of deducing the receiver location given the blurring introduced by the imaging optics and the large Earth albedo fluctuation. Furthermore, because of the complexity of modelling the Earth and the tracking algorithms, an accurate estimate of the algorithm accuracy can only be made via simulation using realistic Earth images. An image simulator was constructed for this purpose, and the results of the simulation runs are reported.

  8. Confidence range estimate of extended source imagery acquisition algorithms via computer simulations. [in optical communication systems

    NASA Technical Reports Server (NTRS)

    Chen, CHIEN-C.; Hui, Elliot; Okamoto, Garret

    1992-01-01

    Spatial acquisition using the sun-lit Earth as a beacon source provides several advantages over active beacon-based systems for deep-space optical communication systems. However, since the angular extend of the Earth image is large compared to the laser beam divergence, the acquisition subsystem must be capable of resolving the image to derive the proper pointing orientation. The algorithms used must be capable of deducing the receiver location given the blurring introduced by the imaging optics and the large Earth albedo fluctuation. Furthermore, because of the complexity of modelling the Earth and the tracking algorithms, an accurate estimate of the algorithm accuracy can only be made via simulation using realistic Earth images. An image simulator was constructed for this purpose, and the results of the simulation runs are reported.

  9. The Effect of Pansharpening Algorithms on the Resulting Orthoimagery

    NASA Astrophysics Data System (ADS)

    Agrafiotis, P.; Georgopoulos, A.; Karantzalos, K.

    2016-06-01

    This paper evaluates the geometric effects of pansharpening algorithms on automatically generated DSMs and thus on the resulting orthoimagery through a quantitative assessment of the accuracy on the end products. The main motivation was based on the fact that for automatically generated Digital Surface Models, an image correlation step is employed for extracting correspondences between the overlapping images. Thus their accuracy and reliability is strictly related to image quality, while pansharpening may result into lower image quality which may affect the DSM generation and the resulting orthoimage accuracy. To this direction, an iterative methodology was applied in order to combine the process described by Agrafiotis and Georgopoulos (2015) with different pansharpening algorithms and check the accuracy of orthoimagery resulting from pansharpened data. Results are thoroughly examined and statistically analysed. The overall evaluation indicated that the pansharpening process didn't affect the geometric accuracy of the resulting DSM with a 10m interval, as well as the resulting orthoimagery. Although some residuals in the orthoimages were observed, their magnitude cannot adversely affect the accuracy of the final orthoimagery.

  10. Early Results from the MODIS Atmosphere Cloud Algorithms

    NASA Technical Reports Server (NTRS)

    Platnick, S.; Ackerman, S. A.; King, M. D.; Menzel, W. P.; Gao, B.-C.; Einaudi, Franco (Technical Monitor)

    2000-01-01

    The Moderate Resolution Imaging Spectroradiometer (MODIS) is one of five instruments aboard the Terra Earth Observing System platform launched in December 1999. With 36 spectral bands from the visible through the infrared, and spatial resolution from 250m to 1km, the instrument provides an unprecedented opportunity for global cloud studies. A comprehensive set of remote sensing algorithms for cloud masking and retrieval of cloud physical and optical properties have been developed by members of the MODIS atmosphere team. The archived products from these algorithms have applications in climate change studies, climate modeling, numerical weather prediction, as well as fundamental atmospheric research. In addition to an extensive cloud mask, products include cloud top physical parameters (temperature, pressure, emissivity), cloud phase, cloud optical parameters (optical depth, effective particle radius, water path), visible cirrus reflectance, a contrail flag, and other derived parameters. All products are archived into two categories: pixel-level retrievals at a 1 km or 5 km spatial resolution at nadir (referred to as Level-2 products) and 1 degree global gridded statistics (Level-3 products). An overview of the MODIS atmosphere algorithms and products, their status, validation activities, and early level-2 and -3 results will be presented.

  11. Titan's organic chemistry: Results of simulation experiments

    NASA Technical Reports Server (NTRS)

    Sagan, Carl; Thompson, W. Reid; Khare, Bishun N.

    1992-01-01

    Recent low pressure continuous low plasma discharge simulations of the auroral electron driven organic chemistry in Titan's mesosphere are reviewed. These simulations yielded results in good accord with Voyager observations of gas phase organic species. Optical constants of the brownish solid tholins produced in similar experiments are in good accord with Voyager observations of the Titan haze. Titan tholins are rich in prebiotic organic constituents; the Huygens entry probe may shed light on some of the processes that led to the origin of life on Earth.

  12. Titan's organic chemistry: Results of simulation experiments

    NASA Technical Reports Server (NTRS)

    Sagan, Carl; Thompson, W. Reid; Khare, Bishun N.

    1992-01-01

    Recent low pressure continuous low plasma discharge simulations of the auroral electron driven organic chemistry in Titan's mesosphere are reviewed. These simulations yielded results in good accord with Voyager observations of gas phase organic species. Optical constants of the brownish solid tholins produced in similar experiments are in good accord with Voyager observations of the Titan haze. Titan tholins are rich in prebiotic organic constituents; the Huygens entry probe may shed light on some of the processes that led to the origin of life on Earth.

  13. A conflict-free, path-level parallelization approach for sequential simulation algorithms

    NASA Astrophysics Data System (ADS)

    Rasera, Luiz Gustavo; Machado, Péricles Lopes; Costa, João Felipe C. L.

    2015-07-01

    Pixel-based simulation algorithms are the most widely used geostatistical technique for characterizing the spatial distribution of natural resources. However, sequential simulation does not scale well for stochastic simulation on very large grids, which are now commonly found in many petroleum, mining, and environmental studies. With the availability of multiple-processor computers, there is an opportunity to develop parallelization schemes for these algorithms to increase their performance and efficiency. Here we present a conflict-free, path-level parallelization strategy for sequential simulation. The method consists of partitioning the simulation grid into a set of groups of nodes and delegating all available processors for simulation of multiple groups of nodes concurrently. An automated classification procedure determines which groups are simulated in parallel according to their spatial arrangement in the simulation grid. The major advantage of this approach is that it does not require conflict resolution operations, and thus allows exact reproduction of results. Besides offering a large performance gain when compared to the traditional serial implementation, the method provides efficient use of computational resources and is generic enough to be adapted to several sequential algorithms.

  14. 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

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

    PubMed

    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

  16. Parallel simulated annealing algorithms for cell placement on hypercube multiprocessors

    NASA Technical Reports Server (NTRS)

    Banerjee, Prithviraj; Jones, Mark Howard; Sargent, Jeff S.

    1990-01-01

    Two parallel algorithms for standard cell placement using simulated annealing are developed to run on distributed-memory message-passing hypercube multiprocessors. The cells can be mapped in a two-dimensional area of a chip onto processors in an n-dimensional hypercube in two ways, such that both small and large cell exchange and displacement moves can be applied. The computation of the cost function in parallel among all the processors in the hypercube is described, along with a distributed data structure that needs to be stored in the hypercube to support the parallel cost evaluation. A novel tree broadcasting strategy is used extensively for updating cell locations in the parallel environment. A dynamic parallel annealing schedule estimates the errors due to interacting parallel moves and adapts the rate of synchronization automatically. Two novel approaches in controlling error in parallel algorithms are described: heuristic cell coloring and adaptive sequence control.

  17. Parallel simulated annealing algorithms for cell placement on hypercube multiprocessors

    NASA Technical Reports Server (NTRS)

    Banerjee, Prithviraj; Jones, Mark Howard; Sargent, Jeff S.

    1990-01-01

    Two parallel algorithms for standard cell placement using simulated annealing are developed to run on distributed-memory message-passing hypercube multiprocessors. The cells can be mapped in a two-dimensional area of a chip onto processors in an n-dimensional hypercube in two ways, such that both small and large cell exchange and displacement moves can be applied. The computation of the cost function in parallel among all the processors in the hypercube is described, along with a distributed data structure that needs to be stored in the hypercube to support the parallel cost evaluation. A novel tree broadcasting strategy is used extensively for updating cell locations in the parallel environment. A dynamic parallel annealing schedule estimates the errors due to interacting parallel moves and adapts the rate of synchronization automatically. Two novel approaches in controlling error in parallel algorithms are described: heuristic cell coloring and adaptive sequence control.

  18. Concurrent Algorithm For Particle-In-Cell Simulations

    NASA Technical Reports Server (NTRS)

    Liewer, Paulett C.; Decyk, Viktor K.

    1990-01-01

    Separate decompositions used for particle-motion and field calculations. General Concurrent Particle-in-Cell (GCPIC) algorithm used to implement motions of individual plasma particles (ions and electrons) under influence of particle-in-cell (PIC) computer codes on concurrent processors. Simulates motions of individual plasma particles under influence of electromagnetic fields generated by particles themselves. Performed to study variety of nonlinear problems in plasma physics, including magnetic and inertial fusion, plasmas in outer space, propagation of electron and ion beams, free-electron lasers, and particle accelerators.

  19. A gene network simulator to assess reverse engineering algorithms.

    PubMed

    Di Camillo, Barbara; Toffolo, Gianna; Cobelli, Claudio

    2009-03-01

    In the context of reverse engineering of biological networks, simulators are helpful to test and compare the accuracy of different reverse-engineering approaches in a variety of experimental conditions. A novel gene-network simulator is presented that resembles some of the main features of transcriptional regulatory networks related to topology, interaction among regulators of transcription, and expression dynamics. The simulator generates network topology according to the current knowledge of biological network organization, including scale-free distribution of the connectivity and clustering coefficient independent of the number of nodes in the network. It uses fuzzy logic to represent interactions among the regulators of each gene, integrated with differential equations to generate continuous data, comparable to real data for variety and dynamic complexity. Finally, the simulator accounts for saturation in the response to regulation and transcription activation thresholds and shows robustness to perturbations. It therefore provides a reliable and versatile test bed for reverse engineering algorithms applied to microarray data. Since the simulator describes regulatory interactions and expression dynamics as two distinct, although interconnected aspects of regulation, it can also be used to test reverse engineering approaches that use both microarray and protein-protein interaction data in the process of learning. A first software release is available at http://www.dei.unipd.it/~dicamill/software/netsim as an R programming language package.

  20. Ground return signal simulation and retrieval algorithm of spaceborne integrated path DIAL for CO2 measurements

    NASA Astrophysics Data System (ADS)

    Liu, Bing-Yi; Wang, Jun-Yang; Liu, Zhi-Shen

    2014-11-01

    Spaceborne integrated path differential absorption (IPDA) lidar is an active-detection system which is able to perform global CO2 measurement with high accuracy of 1ppmv at day and night over ground and clouds. To evaluate the detection performance of the system, simulation of the ground return signal and retrieval algorithm for CO2 concentration are presented in this paper. Ground return signals of spaceborne IPDA lidar under various ground surface reflectivity and atmospheric aerosol optical depths are simulated using given system parameters, standard atmosphere profiles and HITRAN database, which can be used as reference for determining system parameters. The simulated signals are further applied to the research on retrieval algorithm for CO2 concentration. The column-weighted dry air mixing ratio of CO2 denoted by XCO2 is obtained. As the deviations of XCO2 between the initial values for simulation and the results from retrieval algorithm are within the expected error ranges, it is proved that the simulation and retrieval algorithm are reliable.

  1. An Adaptive Mesh Algorithm for Evolving Surfaces: Simulations of Drop Breakup and Coalescence

    NASA Astrophysics Data System (ADS)

    Cristini, Vittorio; Bławzdziewicz, Jerzy; Loewenberg, Michael

    2001-04-01

    An algorithm is presented for the adaptive restructuring of meshes on evolving surfaces. The resolution of the relevant local length scale is maintained everywhere with prescribed accuracy through the minimization of an appropriate mesh energy function by a sequence of local restructuring operations. The resulting discretization depends on the instantaneous configuration of the surface but is insensitive to the deformation history. Application of the adaptive discretization algorithm is illustrated with three-dimensional boundary-integral simulations of deformable drops in Stokes flow. The results show that the algorithm can accurately resolve detailed features of deformed fluid interfaces, including slender filaments associated with drop breakup and dimpled regions associated with drop coalescence. Our algorithm should be useful in a variety of fields, including computational fluid dynamics, image processing, geographical information systems, and biomedical engineering problems.

  2. An optimization algorithm for individualized biomechanical analysis and simulation of tibia fractures.

    PubMed

    Roland, M; Tjardes, T; Otchwemah, R; Bouillon, B; Diebels, S

    2015-04-13

    An algorithmic strategy to determine the minimal fusion area of a tibia pseudarthrosis to achieve mechanical stability is presented. For this purpose, a workflow capable for implementation into clinical routine workup of tibia pseudarthrosis was developed using visual computing algorithms for image segmentation, that is a coarsening protocol to reduce computational effort resulting in an individualized volume-mesh based on computed tomography data. An algorithm detecting the minimal amount of fracture union necessary to allow physiological loading without subjecting the implant to stresses and strains that might result in implant failure is developed. The feasibility of the algorithm in terms of computational effort is demonstrated. Numerical finite element simulations show that the minimal fusion area of a tibia pseudarthrosis can be less than 90% of the full circumferential area given a defined maximal von Mises stress in the implant of 80% of the total stress arising in a complete pseudarthrosis of the tibia.

  3. An optimization method of relativistic backward wave oscillator using particle simulation and genetic algorithms

    SciTech Connect

    Chen, Zaigao; Wang, Jianguo; Wang, Yue; Qiao, Hailiang; Zhang, Dianhui; Guo, Weijie

    2013-11-15

    Optimal design method of high-power microwave source using particle simulation and parallel genetic algorithms is presented in this paper. The output power, simulated by the fully electromagnetic particle simulation code UNIPIC, of the high-power microwave device is given as the fitness function, and the float-encoding genetic algorithms are used to optimize the high-power microwave devices. Using this method, we encode the heights of non-uniform slow wave structure in the relativistic backward wave oscillators (RBWO), and optimize the parameters on massively parallel processors. Simulation results demonstrate that we can obtain the optimal parameters of non-uniform slow wave structure in the RBWO, and the output microwave power enhances 52.6% after the device is optimized.

  4. An optimization method of relativistic backward wave oscillator using particle simulation and genetic algorithms

    NASA Astrophysics Data System (ADS)

    Chen, Zaigao; Wang, Jianguo; Wang, Yue; Qiao, Hailiang; Zhang, Dianhui; Guo, Weijie

    2013-11-01

    Optimal design method of high-power microwave source using particle simulation and parallel genetic algorithms is presented in this paper. The output power, simulated by the fully electromagnetic particle simulation code UNIPIC, of the high-power microwave device is given as the fitness function, and the float-encoding genetic algorithms are used to optimize the high-power microwave devices. Using this method, we encode the heights of non-uniform slow wave structure in the relativistic backward wave oscillators (RBWO), and optimize the parameters on massively parallel processors. Simulation results demonstrate that we can obtain the optimal parameters of non-uniform slow wave structure in the RBWO, and the output microwave power enhances 52.6% after the device is optimized.

  5. Simulations of Shor's algorithm using matrix product states

    NASA Astrophysics Data System (ADS)

    Wang, D. S.; Hill, Charles D.; Hollenberg, L. C. L.

    2017-07-01

    We show that under the matrix product state formalism the states produced in Shor's algorithm can be represented using O(\\max (4lr^2, 2^{2l})) space, where l is the number of bits in the number to factorise and r is the order and the solution to the related order-finding problem. The reduction in space compared to an amplitude formalism approach is significant, allowing simulations as large as 42 qubits to be run on a single processor with 32 GB RAM. This approach is readily adapted to a distributed memory environment, and we have simulated a 45-qubit case using 8 cores with 16 GB RAM in approximately 1 h.

  6. Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits

    PubMed Central

    Watanabe, Leandro H.; Myers, Chris J.

    2014-01-01

    This paper describes a hierarchical stochastic simulation algorithm, which has been implemented within iBioSim, a tool used to model, analyze, and visualize genetic circuits. Many biological analysis tools flatten out hierarchy before simulation, but there are many disadvantages associated with this approach. First, the memory required to represent the model can quickly expand in the process. Second, the flattening process is computationally expensive. Finally, when modeling a dynamic cellular population within iBioSim, inlining the hierarchy of the model is inefficient since models must grow dynamically over time. This paper discusses a new approach to handle hierarchy on the fly to make the tool faster and more memory-efficient. This approach yields significant performance improvements as compared to the former flat analysis method. PMID:25506588

  7. A PISO-like algorithm to simulate superfluid helium flow with the two-fluid model

    NASA Astrophysics Data System (ADS)

    Soulaine, Cyprien; Quintard, Michel; Allain, Hervé; Baudouy, Bertrand; Van Weelderen, Rob

    2015-02-01

    This paper presents a segregated algorithm to solve numerically the superfluid helium (He II) equations using the two-fluid model. In order to validate the resulting code and illustrate its potential, different simulations have been performed. First, the flow through a capillary filled with He II with a heated area on one side is simulated and results are compared to analytical solutions in both Landau and Gorter-Mellink flow regimes. Then, transient heat transfer of a forced flow of He II is investigated. Finally, some two-dimensional simulations in a porous medium model are carried out.

  8. Sensitivity of CO2 Simulation in a GCM to the Convective Transport Algorithms

    NASA Technical Reports Server (NTRS)

    Zhu, Z.; Pawson, S.; Collatz, G. J.; Gregg, W. W.; Kawa, S. R.; Baker, D.; Ott, L.

    2014-01-01

    Convection plays an important role in the transport of heat, moisture and trace gases. In this study, we simulated CO2 concentrations with an atmospheric general circulation model (GCM). Three different convective transport algorithms were used. One is a modified Arakawa-Shubert scheme that was native to the GCM; two others used in two off-line chemical transport models (CTMs) were added to the GCM here for comparison purposes. Advanced CO2 surfaced fluxes were used for the simulations. The results were compared to a large quantity of CO2 observation data. We find that the simulation results are sensitive to the convective transport algorithms. Overall, the three simulations are quite realistic and similar to each other in the remote marine regions, but are significantly different in some land regions with strong fluxes such as Amazon and Siberia during the convection seasons. Large biases against CO2 measurements are found in these regions in the control run, which uses the original GCM. The simulation with the simple diffusive algorithm is better. The difference of the two simulations is related to the very different convective transport speed.

  9. Constant-complexity stochastic simulation algorithm with optimal binning.

    PubMed

    Sanft, Kevin R; Othmer, Hans G

    2015-08-21

    At the molecular level, biochemical processes are governed by random interactions between reactant molecules, and the dynamics of such systems are inherently stochastic. When the copy numbers of reactants are large, a deterministic description is adequate, but when they are small, such systems are often modeled as continuous-time Markov jump processes that can be described by the chemical master equation. Gillespie's Stochastic Simulation Algorithm (SSA) generates exact trajectories of these systems, but the amount of computational work required for each step of the original SSA is proportional to the number of reaction channels, leading to computational complexity that scales linearly with the problem size. The original SSA is therefore inefficient for large problems, which has prompted the development of several alternative formulations with improved scaling properties. We describe an exact SSA that uses a table data structure with event time binning to achieve constant computational complexity with respect to the number of reaction channels for weakly coupled reaction networks. We present a novel adaptive binning strategy and discuss optimal algorithm parameters. We compare the computational efficiency of the algorithm to existing methods and demonstrate excellent scaling for large problems. This method is well suited for generating exact trajectories of large weakly coupled models, including those that can be described by the reaction-diffusion master equation that arises from spatially discretized reaction-diffusion processes.

  10. Constant-complexity stochastic simulation algorithm with optimal binning

    SciTech Connect

    Sanft, Kevin R.; Othmer, Hans G.

    2015-08-21

    At the molecular level, biochemical processes are governed by random interactions between reactant molecules, and the dynamics of such systems are inherently stochastic. When the copy numbers of reactants are large, a deterministic description is adequate, but when they are small, such systems are often modeled as continuous-time Markov jump processes that can be described by the chemical master equation. Gillespie’s Stochastic Simulation Algorithm (SSA) generates exact trajectories of these systems, but the amount of computational work required for each step of the original SSA is proportional to the number of reaction channels, leading to computational complexity that scales linearly with the problem size. The original SSA is therefore inefficient for large problems, which has prompted the development of several alternative formulations with improved scaling properties. We describe an exact SSA that uses a table data structure with event time binning to achieve constant computational complexity with respect to the number of reaction channels for weakly coupled reaction networks. We present a novel adaptive binning strategy and discuss optimal algorithm parameters. We compare the computational efficiency of the algorithm to existing methods and demonstrate excellent scaling for large problems. This method is well suited for generating exact trajectories of large weakly coupled models, including those that can be described by the reaction-diffusion master equation that arises from spatially discretized reaction-diffusion processes.

  11. Numerical simulations of catastrophic disruption: Recent results

    NASA Technical Reports Server (NTRS)

    Benz, W.; Asphaug, E.; Ryan, E. V.

    1994-01-01

    Numerical simulations have been used to study high velocity two-body impacts. In this paper, a two-dimensional Largrangian finite difference hydro-code and a three-dimensional smooth particle hydro-code (SPH) are described and initial results reported. These codes can be, and have been, used to make specific predictions about particular objects in our solar system. But more significantly, they allow us to explore a broad range of collisional events. Certain parameters (size, time) can be studied only over a very restricted range within the laboratory; other parameters (initial spin, low gravity, exotic structure or composition) are difficult to study at all experimentally. The outcomes of numerical simulations lead to a more general and accurate understanding of impacts in their many forms.

  12. Modifications to Axially Symmetric Simulations Using New DSMC (2007) Algorithms

    NASA Technical Reports Server (NTRS)

    Liechty, Derek S.

    2008-01-01

    Several modifications aimed at improving physical accuracy are proposed for solving axially symmetric problems building on the DSMC (2007) algorithms introduced by Bird. Originally developed to solve nonequilibrium, rarefied flows, the DSMC method is now regularly used to solve complex problems over a wide range of Knudsen numbers. These new algorithms include features such as nearest neighbor collisions excluding the previous collision partners, separate collision and sampling cells, automatically adaptive variable time steps, a modified no-time counter procedure for collisions, and discontinuous and event-driven physical processes. Axially symmetric solutions require radial weighting for the simulated molecules since the molecules near the axis represent fewer real molecules than those farther away from the axis due to the difference in volume of the cells. In the present methodology, these radial weighting factors are continuous, linear functions that vary with the radial position of each simulated molecule. It is shown that how one defines the number of tentative collisions greatly influences the mean collision time near the axis. The method by which the grid is treated for axially symmetric problems also plays an important role near the axis, especially for scalar pressure. A new method to treat how the molecules are traced through the grid is proposed to alleviate the decrease in scalar pressure at the axis near the surface. Also, a modification to the duplication buffer is proposed to vary the duplicated molecular velocities while retaining the molecular kinetic energy and axially symmetric nature of the problem.

  13. An adaptive multi-level simulation algorithm for stochastic biological systems.

    PubMed

    Lester, C; Yates, C A; Giles, M B; Baker, R E

    2015-01-14

    Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, "Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics," SIAM Multiscale Model. Simul. 10(1), 146-179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the

  14. An adaptive multi-level simulation algorithm for stochastic biological systems

    SciTech Connect

    Lester, C. Giles, M. B.; Baker, R. E.; Yates, C. A.

    2015-01-14

    Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10(1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the

  15. Verifying Algorithms for Autonomous Aircraft by Simulation Generalities and Example

    NASA Technical Reports Server (NTRS)

    White, Allan L.

    2010-01-01

    An open question in Air Traffic Management is what procedures can be validated by simulation where the simulation shows that the probability of undesirable events is below the required level at some confidence level. The problem is including enough realism to be convincing while retaining enough efficiency to run the large number of trials needed for high confidence. The paper first examines the probabilistic interpretation of a typical requirement by a regulatory agency and computes the number of trials needed to establish the requirement at an equivalent confidence level. Since any simulation is likely to consider only one type of event and there are several types of events, the paper examines under what conditions this separate consideration is valid. The paper establishes a separation algorithm at the required confidence level where the aircraft operates under feedback control as is subject to perturbations. There is a discussion where it is shown that a scenario three of four orders of magnitude more complex is feasible. The question of what can be validated by simulation remains open, but there is reason to be optimistic.

  16. An improved algorithm of three B-spline curve interpolation and simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Wanjun; Xu, Dongmei; Meng, Xinhong; Zhang, Feng

    2017-03-01

    As a key interpolation technique in CNC system machine tool, three B-spline curve interpolator has been proposed to change the drawbacks caused by linear and circular interpolator, Such as interpolation time bigger, three B-spline curves step error are not easy changed,and so on. This paper an improved algorithm of three B-spline curve interpolation and simulation is proposed. By Using MATALAB 7.0 computer soft in three B-spline curve interpolation is developed for verifying the proposed modification algorithm of three B-spline curve interpolation experimentally. The simulation results show that the algorithm is correct; it is consistent with a three B-spline curve interpolation requirements.

  17. R-leaping: accelerating the stochastic simulation algorithm by reaction leaps.

    PubMed

    Auger, Anne; Chatelain, Philippe; Koumoutsakos, Petros

    2006-08-28

    A novel algorithm is proposed for the acceleration of the exact stochastic simulation algorithm by a predefined number of reaction firings (R-leaping) that may occur across several reaction channels. In the present approach, the numbers of reaction firings are correlated binomial distributions and the sampling procedure is independent of any permutation of the reaction channels. This enables the algorithm to efficiently handle large systems with disparate rates, providing substantial computational savings in certain cases. Several mechanisms for controlling the accuracy and the appearance of negative species are described. The advantages and drawbacks of R-leaping are assessed by simulations on a number of benchmark problems and the results are discussed in comparison with established methods.

  18. R-leaping: Accelerating the stochastic simulation algorithm by reaction leaps

    NASA Astrophysics Data System (ADS)

    Auger, Anne; Chatelain, Philippe; Koumoutsakos, Petros

    2006-08-01

    A novel algorithm is proposed for the acceleration of the exact stochastic simulation algorithm by a predefined number of reaction firings (R-leaping) that may occur across several reaction channels. In the present approach, the numbers of reaction firings are correlated binomial distributions and the sampling procedure is independent of any permutation of the reaction channels. This enables the algorithm to efficiently handle large systems with disparate rates, providing substantial computational savings in certain cases. Several mechanisms for controlling the accuracy and the appearance of negative species are described. The advantages and drawbacks of R-leaping are assessed by simulations on a number of benchmark problems and the results are discussed in comparison with established methods.

  19. Photovoltaic-electrolyzer system transient simulation results

    SciTech Connect

    Leigh, R.W.; Metz, P.D.; Michalek, K.

    1986-05-01

    Brookhaven National Laboratory has developed a Hydrogen Technology Evaluation Center to illustrate advanced hydrogen technology. The first phase of this effort investigated the use of solar energy to produce hydrogen from water via photovoltaic-powered electrolysis. A coordinated program of system testing, computer simulation, and economic analysis has been adopted to characterize and optimize the photovoltaic-electrolyzer system. This paper presents the initial transient simulation results. Innovative features of the modeling include the use of real weather data, detailed hourly modeling of thermal characteristics of the PV array and of system control strategies, and examination of systems over a wide range of power and voltage ratings. The transient simulation system TRNSYS was used, incorporating existing, modified or new component subroutines as required. For directly coupled systems, the authors found the PV array voltage which maximizes hydrogen production to be quite near the nominal electrolyzer voltage for a wide range of PV array powers. The array voltage which maximizes excess electricity production is slightly higher. The use of an ideal (100 percent efficient) maximum power tracking system provides only a six percent increase in annual hydrogen production. An examination of the effect of the PV array tilt indicates, as expected, that annual hydrogen production is insensitive to tilt angle within +-20 deg of latitude. Summer production greatly exceeds winter generation. Tilting the array, even to 90 deg, produces no significant increase in winter hydrogen production.

  20. Photovoltaic-electrolyzer system transient simulation results

    SciTech Connect

    Leigh, R.W.; Metz, P.D.; Michalek, K.

    1983-12-01

    Brookhaven National Laboratory is developing an integrated test bed to illustrate advanced hydrogen technology. The first phase of this effort will investigate the use of solar energy to produce hydrogen from water via photovoltaic-powered electrolysis. A coordinated program of system testing, computer simulation, and economic analysis has been adopted to characterize and optimize the photovoltaic-electrolyzer system. This paper presents the initial transient simulation results. Innovative features of the modeling include the use of real weather data, detailed hourly modeling of the thermal characteristics of the PV array and of system control strategies, and examination of systems over a wide range of power and voltage ratings. The transient simulation system TRNSYS was used, incorporating existing, modified or new component subroutines as required. For directly coupled systems, we found the PV array voltage which maximizes hydrogen production to be quite near the nominal electrolyzer voltage for a wide range of PV array powers. The array voltage which maximizes excess electricity production is slightly higher. The use of an ideal (100% efficient) maximum power tracking system provides only a six percent increase in annual hydrogen production. An examination of the effect of PV array tilt indicates, as expected, that annual hydrogen production is insensitive to tilt angle within +- 20/sup 0/ of latitude. Summer production greatly exceeds winter generation. Tilting the array, even to 90/sup 0/, produces no significant increase in winter hydrogen production.

  1. Study on the algorithm for Newton-Rapson iteration interpolation of NURBS curve and simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Wanjun; Gao, Shanping; Cheng, Xiyan; Zhang, Feng

    2017-04-01

    In order to solve the problems of Newton-Rapson iteration interpolation method of NURBS Curve, Such as interpolation time bigger, calculation more complicated, and NURBS curve step error are not easy changed and so on. This paper proposed a study on the algorithm for Newton-Rapson iteration interpolation method of NURBS curve and simulation. We can use Newton-Rapson iterative that calculate (xi, yi, zi). Simulation results show that the proposed NURBS curve interpolator meet the high-speed and high-accuracy interpolation requirements of CNC systems. The interpolation of NURBS curve should be finished. The simulation results show that the algorithm is correct; it is consistent with a NURBS curve interpolation requirements.

  2. On constructing optimistic simulation algorithms for the discrete event system specification

    SciTech Connect

    Nutaro, James J

    2008-01-01

    This article describes a Time Warp simulation algorithm for discrete event models that are described in terms of the Discrete Event System Specification (DEVS). The article shows how the total state transition and total output function of a DEVS atomic model can be transformed into an event processing procedure for a logical process. A specific Time Warp algorithm is constructed around this logical process, and it is shown that the algorithm correctly simulates a DEVS coupled model that consists entirely of interacting atomic models. The simulation algorithm is presented abstractly; it is intended to provide a basis for implementing efficient and scalable parallel algorithms that correctly simulate DEVS models.

  3. Simulation approach to charge sharing compensation algorithms with experimental cross-check

    NASA Astrophysics Data System (ADS)

    Krzyżanowska, A.; Deptuch, G.; Maj, P.; Gryboś, P.; Szczygieł, R.

    2017-03-01

    Hybrid pixel detectors for X-ray imaging, working in a single photon counting mode, find applications in a variety of fields, such as medical imaging, material science or industry. However, charge sharing, which occurs when a photon hits a detector in the area between two or four pixels, becomes more significant with decreasing pixel size. If the charge generated when a photon interacts with a detector is collected by more than one pixel, the photon energy and the event position may be improperly detected. Therefore, algorithms for minimization of the impact of charge sharing on a pixel detector for X-ray detection need to be implemented. Firstly, such algorithms must be assessed on a simulation level. The goal is to implement the simulations in such a way that the simulation accuracy and simulation time are optimized. A model should be flexible enough so that it can be quickly adapted for other uses. We propose behavioral models implemented in the Cadence® Virtuoso® environment. This is a solution that enables fast validation of the system at the higher level of abstraction allowing deep verification. A readout channel of a chip is represented using parameterized behavioral blocks of different functionality, such as, a charge sensitive amplifier, shapers, discriminators, comparators. The inter-pixel connections are taken into account. This approach enables top-down design and optimization of parameters. The model was implemented in particular to test the C8P1 algorithm used in the Chase Jr. chip, however, due to its modular implementation, it can be easily adjusted to further test of the algorithms. The simulation approach is described and the simulation results are presented together with the experimental data obtained during synchrotron measurements for the Chase Jr. chip with the C8P1 algorithm implemented.

  4. Fast Plasma Instrument for MMS: Simulation Results

    NASA Technical Reports Server (NTRS)

    Figueroa-Vinas, Adolfo; Adrian, Mark L.; Lobell, James V.; Simpson, David G.; Barrie, Alex; Winkert, George E.; Yeh, Pen-Shu; Moore, Thomas E.

    2008-01-01

    Magnetospheric Multiscale (MMS) mission will study small-scale reconnection structures and their rapid motions from closely spaced platforms using instruments capable of high angular, energy, and time resolution measurements. The Dual Electron Spectrometer (DES) of the Fast Plasma Instrument (FPI) for MMS meets these demanding requirements by acquiring the electron velocity distribution functions (VDFs) for the full sky with high-resolution angular measurements every 30 ms. This will provide unprecedented access to electron scale dynamics within the reconnection diffusion region. The DES consists of eight half-top-hat energy analyzers. Each analyzer has a 6 deg. x 11.25 deg. Full-sky coverage is achieved by electrostatically stepping the FOV of each of the eight sensors through four discrete deflection look directions. Data compression and burst memory management will provide approximately 30 minutes of high time resolution data during each orbit of the four MMS spacecraft. Each spacecraft will intelligently downlink the data sequences that contain the greatest amount of temporal structure. Here we present the results of a simulation of the DES analyzer measurements, data compression and decompression, as well as ground-based analysis using as a seed re-processed Cluster/PEACE electron measurements. The Cluster/PEACE electron measurements have been reprocessed through virtual DES analyzers with their proper geometrical, energy, and timing scale factors and re-mapped via interpolation to the DES angular and energy phase-space sampling measurements. The results of the simulated DES measurements are analyzed and the full moments of the simulated VDFs are compared with those obtained from the Cluster/PEACE spectrometer using a standard quadrature moment, a newly implemented spectral spherical harmonic method, and a singular value decomposition method. Our preliminary moment calculations show a remarkable agreement within the uncertainties of the measurements, with the

  5. Fast Plasma Instrument for MMS: Simulation Results

    NASA Technical Reports Server (NTRS)

    Figueroa-Vinas, Adolfo; Adrian, Mark L.; Lobell, James V.; Simpson, David G.; Barrie, Alex; Winkert, George E.; Yeh, Pen-Shu; Moore, Thomas E.

    2008-01-01

    Magnetospheric Multiscale (MMS) mission will study small-scale reconnection structures and their rapid motions from closely spaced platforms using instruments capable of high angular, energy, and time resolution measurements. The Dual Electron Spectrometer (DES) of the Fast Plasma Instrument (FPI) for MMS meets these demanding requirements by acquiring the electron velocity distribution functions (VDFs) for the full sky with high-resolution angular measurements every 30 ms. This will provide unprecedented access to electron scale dynamics within the reconnection diffusion region. The DES consists of eight half-top-hat energy analyzers. Each analyzer has a 6 deg. x 11.25 deg. Full-sky coverage is achieved by electrostatically stepping the FOV of each of the eight sensors through four discrete deflection look directions. Data compression and burst memory management will provide approximately 30 minutes of high time resolution data during each orbit of the four MMS spacecraft. Each spacecraft will intelligently downlink the data sequences that contain the greatest amount of temporal structure. Here we present the results of a simulation of the DES analyzer measurements, data compression and decompression, as well as ground-based analysis using as a seed re-processed Cluster/PEACE electron measurements. The Cluster/PEACE electron measurements have been reprocessed through virtual DES analyzers with their proper geometrical, energy, and timing scale factors and re-mapped via interpolation to the DES angular and energy phase-space sampling measurements. The results of the simulated DES measurements are analyzed and the full moments of the simulated VDFs are compared with those obtained from the Cluster/PEACE spectrometer using a standard quadrature moment, a newly implemented spectral spherical harmonic method, and a singular value decomposition method. Our preliminary moment calculations show a remarkable agreement within the uncertainties of the measurements, with the

  6. Humanoid robot gait optimization: Stretched simulated annealing and genetic algorithm a comparative study

    NASA Astrophysics Data System (ADS)

    Pereira, Ana I.; Lima, José; Costa, Paulo

    2013-10-01

    There are several approaches to create the Humanoid robot gait planning. This problem presents a large number of unknown parameters that should be found to make the humanoid robot to walk. Optimization in simulation models can be used to find the gait based on several criteria such as energy minimization, acceleration, step length among the others. The presented paper addresses a comparison between two optimization methods, the Stretched Simulated Annealing and the Genetic Algorithm, that runs in an accurate and stable simulation model. Final results show the comparative study and demonstrate that optimization is a valid gait planning technique.

  7. A real-time simulation evaluation of an advanced detection. Isolation and accommodation algorithm for sensor failures in turbine engines

    NASA Technical Reports Server (NTRS)

    Merrill, W. C.; Delaat, J. C.

    1986-01-01

    An advanced sensor failure detection, isolation, and accommodation (ADIA) algorithm has been developed for use with an aircraft turbofan engine control system. In a previous paper the authors described the ADIA algorithm and its real-time implementation. Subsequent improvements made to the algorithm and implementation are discussed, and the results of an evaluation presented. The evaluation used a real-time, hybrid computer simulation of an F100 turbofan engine.

  8. A real-time simulation evaluation of an advanced detection, isolation and accommodation algorithm for sensor failures in turbine engines

    NASA Technical Reports Server (NTRS)

    Merrill, W. C.; Delaat, J. C.

    1986-01-01

    An advanced sensor failure detection, isolation, and accommodation (ADIA) algorithm has been developed for use with an aircraft turbofan engine control system. In a previous paper the authors described the ADIA algorithm and its real-time implementation. Subsequent improvements made to the algorithm and implementation are discussed, and the results of an evaluation presented. The evaluation used a real-time, hybrid computer simulation of an F100 turbofan engine.

  9. Evaluation of effective-stress-function algorithm for nuclear fuel simulation

    SciTech Connect

    Kim, H. C.; Yang, Y. S.; Koo, Y. H.

    2013-07-01

    In a pressurized water reactor (PWR), the mechanical integrity of nuclear fuel is the most critical issue as it is an important barrier for fission products released into the environment. The integrity of zirconium cladding that surrounds uranium oxide can be threatened during off-normal operation owing to a pellet-cladding mechanical interaction (PCMI). To analyze the fuel and cladding behavior during off-operation, the fuel performance code should calculate an inelastic analysis in two - or three-dimensional calculations. In this paper, the effective stress function (ESF) algorithm based on a two-dimensional FE module has been implemented to simulate the inelastic behavior of the cladding with stability and accuracy. The ESF algorithm solves the governing equations of the inelastic constitutive behavior by calculating the zero of the appropriate effective-stress-function. To verify the accuracy of the ESF algorithm for an inelastic analysis, a code-to-code benchmark was performed using the commercial FE code, ANSYS 13.0. To demonstrate the stability and convergence of the implemented algorithm, the number of iterations in the ESF algorithm was compared with that in a sequential algorithm in the case of an inelastic problem. Consequently, the evaluation results demonstrate that the implemented ESF algorithm improves the efficiency of the computation without a loss of accuracy for an inelastic analysis. (authors)

  10. An Algorithm for Interactive Modeling of Space-Transportation Engine Simulations: A Constraint Satisfaction Approach

    NASA Technical Reports Server (NTRS)

    Mitra, Debasis; Thomas, Ajai; Hemminger, Joseph; Sakowski, Barbara

    2001-01-01

    In this research we have developed an algorithm for the purpose of constraint processing by utilizing relational algebraic operators. Van Beek and others have investigated in the past this type of constraint processing from within a relational algebraic framework, producing some unique results. Apart from providing new theoretical angles, this approach also gives the opportunity to use the existing efficient implementations of relational database management systems as the underlying data structures for any relevant algorithm. Our algorithm here enhances that framework. The algorithm is quite general in its current form. Weak heuristics (like forward checking) developed within the Constraint-satisfaction problem (CSP) area could be also plugged easily within this algorithm for further enhancements of efficiency. The algorithm as developed here is targeted toward a component-oriented modeling problem that we are currently working on, namely, the problem of interactive modeling for batch-simulation of engineering systems (IMBSES). However, it could be adopted for many other CSP problems as well. The research addresses the algorithm and many aspects of the problem IMBSES that we are currently handling.

  11. Optimal design of minimum mean-square error noise reduction algorithms using the simulated annealing technique.

    PubMed

    Bai, Mingsian R; Hsieh, Ping-Ju; Hur, Kur-Nan

    2009-02-01

    The performance of the minimum mean-square error noise reduction (MMSE-NR) algorithm in conjunction with time-recursive averaging (TRA) for noise estimation is found to be very sensitive to the choice of two recursion parameters. To address this problem in a more systematic manner, this paper proposes an optimization method to efficiently search the optimal parameters of the MMSE-TRA-NR algorithms. The objective function is based on a regression model, whereas the optimization process is carried out with the simulated annealing algorithm that is well suited for problems with many local optima. Another NR algorithm proposed in the paper employs linear prediction coding as a preprocessor for extracting the correlated portion of human speech. Objective and subjective tests were undertaken to compare the optimized MMSE-TRA-NR algorithm with several conventional NR algorithms. The results of subjective tests were processed by using analysis of variance to justify the statistic significance. A post hoc test, Tukey's Honestly Significant Difference, was conducted to further assess the pairwise difference between the NR algorithms.

  12. Simulation Results Related to Stochastic Electrodynamics

    NASA Astrophysics Data System (ADS)

    Cole, Daniel C.

    2006-01-01

    Stochastic electrodynamics (SED) is a classical theory of nature advanced significantly in the 1960s by Trevor Marshall and Timothy Boyer. Since then, SED has continued to be investigated by a very small group of physicists. Early investigations seemed promising, as SED was shown to agree with quantum mechanics (QM) and quantum electrodynamics (QED) for a few linear systems. In particular, agreement was found for the simple harmonic electric dipole oscillator, physical systems composed of such oscillators and interacting electromagnetically, and free electromagnetic fields with boundary conditions imposed such as would enter into Casimir-type force calculations. These results were found to hold for both zero-point and non-zero temperature conditions. However, by the late 1970s and then into the early 1980s, researchers found that when investigating nonlinear systems, SED did not appear to provide agreement with the predictions of QM and QED. A proposed reason for this disagreement was advocated by Boyer and Cole that such nonlinear systems are not sufficiently realistic for describing atomic and molecular physical systems, which should be fundamentally based on the Coulombic binding potential. Analytic attempts on these systems have proven to be most difficult. Consequently, in recent years more attention has been placed on numerically simulating the interaction of a classical electron in a Coulombic binding potential, with classical electromagnetic radiation acting on the classical electron. Good agreement was found for this numerical simulation work as compared with predictions from QM. Here this worked is reviewed and possible directions are discussed. Recent simulation work involving subharmonic resonances for the classical hydrogen atom is also discussed; some of the properties of these subharmonic resonances seem quite interesting and unusual.

  13. The design and results of an algorithm for intelligent ground vehicles

    NASA Astrophysics Data System (ADS)

    Duncan, Matthew; Milam, Justin; Tote, Caleb; Riggins, Robert N.

    2010-01-01

    This paper addresses the design, design method, test platform, and test results of an algorithm used in autonomous navigation for intelligent vehicles. The Bluefield State College (BSC) team created this algorithm for its 2009 Intelligent Ground Vehicle Competition (IGVC) robot called Anassa V. The BSC robotics team is comprised of undergraduate computer science, engineering technology, marketing students, and one robotics faculty advisor. The team has participated in IGVC since the year 2000. A major part of the design process that the BSC team uses each year for IGVC is a fully documented "Post-IGVC Analysis." Over the nine years since 2000, the lessons the students learned from these analyses have resulted in an ever-improving, highly successful autonomous algorithm. The algorithm employed in Anassa V is a culmination of past successes and new ideas, resulting in Anassa V earning several excellent IGVC 2009 performance awards, including third place overall. The paper will discuss all aspects of the design of this autonomous robotic system, beginning with the design process and ending with test results for both simulation and real environments.

  14. Hybrid Simulated Annealing and Genetic Algorithms for Industrial Production Management Problems

    NASA Astrophysics Data System (ADS)

    Vasant, Pandian; Barsoum, Nader

    2009-08-01

    This paper describes the origin and significant contribution on the development of the Hybrid Simulated Annealing and Genetic Algorithms (HSAGA) approach for finding global optimization. HSAGA provide an insight approach to handle in solving complex optimization problems. The method is, the combination of meta-heuristic approaches of Simulated Annealing and novel Genetic Algorithms for solving a non-linear objective function with uncertain technical coefficients in an industrial production management problems. The proposed novel hybrid method is designed to search for global optimal for the non-linear objective function and search for the best feasible solutions of the decision variables. Simulated experiments were carried out rigorously to reflect the advantages of the proposed method. A description of the well developed method and the advanced computational experiment with MATLAB technical tool is presented. An industrial production management optimization problem is solved using HSAGA technique. The results are very much promising.

  15. Algorithmic approach to simulate Hamiltonian dynamics and an NMR simulation of quantum state transfer

    NASA Astrophysics Data System (ADS)

    Ajoy, Ashok; Rao, Rama Koteswara; Kumar, Anil; Rungta, Pranaw

    2012-03-01

    We propose an iterative algorithm to simulate the dynamics generated by any n-qubit Hamiltonian. The simulation entails decomposing the unitary time evolution operator U (unitary) into a product of different time-step unitaries. The algorithm product-decomposes U in a chosen operator basis by identifying a certain symmetry of U that is intimately related to the number of gates in the decomposition. We illustrate the algorithm by first obtaining a polynomial decomposition in the Pauli basis of the n-qubit quantum state transfer unitary by Di Franco [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.101.230502 101, 230502 (2008)] that transports quantum information from one end of a spin chain to the other, and then implement it in nuclear magnetic resonance to demonstrate that the decomposition is experimentally viable. We further experimentally test the resilience of the state transfer to static errors in the coupling parameters of the simulated Hamiltonian. This is done by decomposing and simulating the corresponding imperfect unitaries.

  16. An efficient algorithm for corona simulation with complex chemical models

    NASA Astrophysics Data System (ADS)

    Villa, Andrea; Barbieri, Luca; Gondola, Marco; Leon-Garzon, Andres R.; Malgesini, Roberto

    2017-05-01

    The simulation of cold plasma discharges is a leading field of applied sciences with many applications ranging from pollutant control to surface treatment. Many of these applications call for the development of novel numerical techniques to implement fully three-dimensional corona solvers that can utilize complex and physically detailed chemical databases. This is a challenging task since it multiplies the difficulties inherent to a three-dimensional approach by the complexity of databases comprising tens of chemical species and hundreds of reactions. In this paper a novel approach, capable of reducing significantly the computational burden, is developed. The proposed method is based on a proper time stepping algorithm capable of decomposing the original problem into simpler ones: each of them has then been tackled with either finite element, finite volume or ordinary differential equations solvers. This last solver deals with the chemical model and its efficient implementation is one of the main contributions of this work.

  17. Magnetic Storm Simulation With Multiple Ion Fluids: Algorithm

    NASA Astrophysics Data System (ADS)

    Toth, G.; Glocer, A.; Gombosi, T.

    2008-12-01

    We describe our progress in extending the capabilities of the BATS-R-US MHD code to model multiple ion fluids. We solve the full multiion equations with no assumptions about the relative motion of the ion fluids. We discuss the numerical difficulties and the algorithmic solutions: the use of a total ion fluid in combination with the individual ion fluids, the use of point-implicit source terms with analytic Jacobian, using a simple criterion to separate the single-ion and multiion regions in our magnetosphere applications, and an artificial friction term to limit the relative velocities of the ion fluids to reasonable values. This latter term is used to mimic the effect of two-stream instabilities in a crude manner. The new code is fully integrated into the Space Weather Modeling Framework and it has been coupled with the ionosphere, inner magnetosphere and polar wind models to simulate the May 4 1998 magnetic storm.

  18. Lattice Boltzmann algorithm to simulate isotropic-nematic emulsions.

    PubMed

    Sulaiman, N; Marenduzzo, D; Yeomans, J M

    2006-10-01

    We present lattice Boltzmann simulations of the dynamical equations of motion of a drop of isotropic fluid in a nematic liquid crystal solvent, both in the absence and in the presence of an electric field. The coupled equations we solve are the Beris-Edward equations for the dynamics of the tensor order parameter describing the nematic solvent, the Cahn-Hilliard equation for the concentration evolution, and the Navier-Stokes equations for the determination of the instantaneous velocity field. We implement the lattice Boltzmann algorithm to ensure that spurious velocities are close to zero in equilibrium. We first study the effects of the liquid crystal elastic constant, K, anchoring strength, W, and surface tension, sigma, on the shape of the droplet and on the director field texture in equilibrium. We then consider how the drop behaves as the director field is switched by an applied electric field. We also show that the algorithm allows us to follow the motion of a drop of isotropic fluid placed in a liquid crystal cell with a tilted director field at the boundaries.

  19. A parallel finite volume algorithm for large-eddy simulation of turbulent flows

    NASA Astrophysics Data System (ADS)

    Bui, Trong Tri

    1998-11-01

    A parallel unstructured finite volume algorithm is developed for large-eddy simulation of compressible turbulent flows. Major components of the algorithm include piecewise linear least-square reconstruction of the unknown variables, trilinear finite element interpolation for the spatial coordinates, Roe flux difference splitting, and second-order MacCormack explicit time marching. The computer code is designed from the start to take full advantage of the additional computational capability provided by the current parallel computer systems. Parallel implementation is done using the message passing programming model and message passing libraries such as the Parallel Virtual Machine (PVM) and Message Passing Interface (MPI). The development of the numerical algorithm is presented in detail. The parallel strategy and issues regarding the implementation of a flow simulation code on the current generation of parallel machines are discussed. The results from parallel performance studies show that the algorithm is well suited for parallel computer systems that use the message passing programming model. Nearly perfect parallel speedup is obtained on MPP systems such as the Cray T3D and IBM SP2. Performance comparison with the older supercomputer systems such as the Cray YMP show that the simulations done on the parallel systems are approximately 10 to 30 times faster. The results of the accuracy and performance studies for the current algorithm are reported. To validate the flow simulation code, a number of Euler and Navier-Stokes simulations are done for internal duct flows. Inviscid Euler simulation of a very small amplitude acoustic wave interacting with a shock wave in a quasi-1D convergent-divergent nozzle shows that the algorithm is capable of simultaneously tracking the very small disturbances of the acoustic wave and capturing the shock wave. Navier-Stokes simulations are made for fully developed laminar flow in a square duct, developing laminar flow in a

  20. Application of Simulated Annealing and Related Algorithms to TWTA Design

    NASA Technical Reports Server (NTRS)

    Radke, Eric M.

    2004-01-01

    Simulated Annealing (SA) is a stochastic optimization algorithm used to search for global minima in complex design surfaces where exhaustive searches are not computationally feasible. The algorithm is derived by simulating the annealing process, whereby a solid is heated to a liquid state and then cooled slowly to reach thermodynamic equilibrium at each temperature. The idea is that atoms in the solid continually bond and re-bond at various quantum energy levels, and with sufficient cooling time they will rearrange at the minimum energy state to form a perfect crystal. The distribution of energy levels is given by the Boltzmann distribution: as temperature drops, the probability of the presence of high-energy bonds decreases. In searching for an optimal design, local minima and discontinuities are often present in a design surface. SA presents a distinct advantage over other optimization algorithms in its ability to escape from these local minima. Just as high-energy atomic configurations are visited in the actual annealing process in order to eventually reach the minimum energy state, in SA highly non-optimal configurations are visited in order to find otherwise inaccessible global minima. The SA algorithm produces a Markov chain of points in the design space at each temperature, with a monotonically decreasing temperature. A random point is started upon, and the objective function is evaluated at that point. A stochastic perturbation is then made to the parameters of the point to arrive at a proposed new point in the design space, at which the objection function is evaluated as well. If the change in objective function values (Delta)E is negative, the proposed new point is accepted. If (Delta)E is positive, the proposed new point is accepted according to the Metropolis criterion: rho((Delta)f) = exp((-Delta)E/T), where T is the temperature for the current Markov chain. The process then repeats for the remainder of the Markov chain, after which the temperature is

  1. Application of Simulated Annealing and Related Algorithms to TWTA Design

    NASA Technical Reports Server (NTRS)

    Radke, Eric M.

    2004-01-01

    Simulated Annealing (SA) is a stochastic optimization algorithm used to search for global minima in complex design surfaces where exhaustive searches are not computationally feasible. The algorithm is derived by simulating the annealing process, whereby a solid is heated to a liquid state and then cooled slowly to reach thermodynamic equilibrium at each temperature. The idea is that atoms in the solid continually bond and re-bond at various quantum energy levels, and with sufficient cooling time they will rearrange at the minimum energy state to form a perfect crystal. The distribution of energy levels is given by the Boltzmann distribution: as temperature drops, the probability of the presence of high-energy bonds decreases. In searching for an optimal design, local minima and discontinuities are often present in a design surface. SA presents a distinct advantage over other optimization algorithms in its ability to escape from these local minima. Just as high-energy atomic configurations are visited in the actual annealing process in order to eventually reach the minimum energy state, in SA highly non-optimal configurations are visited in order to find otherwise inaccessible global minima. The SA algorithm produces a Markov chain of points in the design space at each temperature, with a monotonically decreasing temperature. A random point is started upon, and the objective function is evaluated at that point. A stochastic perturbation is then made to the parameters of the point to arrive at a proposed new point in the design space, at which the objection function is evaluated as well. If the change in objective function values (Delta)E is negative, the proposed new point is accepted. If (Delta)E is positive, the proposed new point is accepted according to the Metropolis criterion: rho((Delta)f) = exp((-Delta)E/T), where T is the temperature for the current Markov chain. The process then repeats for the remainder of the Markov chain, after which the temperature is

  2. A method for data handling numerical results in parallel OpenFOAM simulations

    SciTech Connect

    Anton, Alin; Muntean, Sebastian

    2015-12-31

    Parallel computational fluid dynamics simulations produce vast amount of numerical result data. This paper introduces a method for reducing the size of the data by replaying the interprocessor traffic. The results are recovered only in certain regions of interest configured by the user. A known test case is used for several mesh partitioning scenarios using the OpenFOAM toolkit{sup ®}[1]. The space savings obtained with classic algorithms remain constant for more than 60 Gb of floating point data. Our method is most efficient on large simulation meshes and is much better suited for compressing large scale simulation results than the regular algorithms.

  3. Simulating Future GPS Clock Scenarios with Two Composite Clock Algorithms

    NASA Technical Reports Server (NTRS)

    Suess, Matthias; Matsakis, Demetrios; Greenhall, Charles A.

    2010-01-01

    Using the GPS Toolkit, the GPS constellation is simulated using 31 satellites (SV) and a ground network of 17 monitor stations (MS). At every 15-minutes measurement epoch, the monitor stations measure the time signals of all satellites above a parameterized elevation angle. Once a day, the satellite clock estimates the station and satellite clocks. The first composite clock (B) is based on the Brown algorithm, and is now used by GPS. The second one (G) is based on the Greenhall algorithm. The composite clock of G and B performance are investigated using three ground-clock models. Model C simulates the current GPS configuration, in which all stations are equipped with cesium clocks, except for masers at USNO and Alternate Master Clock (AMC) sites. Model M is an improved situation in which every station is equipped with active hydrogen masers. Finally, Models F and O are future scenarios in which the USNO and AMC stations are equipped with fountain clocks instead of masers. Model F is a rubidium fountain, while Model O is more precise but futuristic Optical Fountain. Each model is evaluated using three performance metrics. The timing-related user range error having all satellites available is the first performance index (PI1). The second performance index (PI2) relates to the stability of the broadcast GPS system time itself. The third performance index (PI3) evaluates the stability of the time scales computed by the two composite clocks. A distinction is made between the "Signal-in-Space" accuracy and that available through a GNSS receiver.

  4. SimBA: simulation algorithm to fit extant-population distributions.

    PubMed

    Parida, Laxmi; Haiminen, Niina

    2015-03-14

    Simulation of populations with specified characteristics such as allele frequencies, linkage disequilibrium etc., is an integral component of many studies, including in-silico breeding optimization. Since the accuracy and sensitivity of population simulation is critical to the quality of the output of the applications that use them, accurate algorithms are required to provide a strong foundation to the methods in these studies. In this paper we present SimBA (Simulation using Best-fit Algorithm) a non-generative approach, based on a combination of stochastic techniques and discrete methods. We optimize a hill climbing algorithm and extend the framework to include multiple subpopulation structures. Additionally, we show that SimBA is very sensitive to the input specifications, i.e., very similar but distinct input characteristics result in distinct outputs with high fidelity to the specified distributions. This property of the simulation is not explicitly modeled or studied by previous methods. We show that SimBA outperforms the existing population simulation methods, both in terms of accuracy as well as time-efficiency. Not only does it construct populations that meet the input specifications more stringently than other published methods, SimBA is also easy to use. It does not require explicit parameter adaptations or calibrations. Also, it can work with input specified as distributions, without an exemplar matrix or population as required by some methods. SimBA is available at http://researcher.ibm.com/project/5669 .

  5. Algorithm for loading shot noise microbunching in multidimensional, free-electron laser simulation codes

    NASA Astrophysics Data System (ADS)

    Fawley, William M.

    2002-07-01

    We discuss the underlying reasoning behind and the details of the numerical algorithm used in the GINGER free-electron laser simulation code to load the initial shot noise microbunching on the electron beam. In particular, we point out that there are some additional subtleties which must be followed for multidimensional codes which are not necessary for one-dimensional formulations. Moreover, requiring that the higher harmonics of the microbunching also be properly initialized with the correct statistics leads to additional complexities. We present some numerical results including the predicted incoherent, spontaneous emission as tests of the shot noise algorithm's correctness.

  6. Algorithm for loading shot noise microbunching in multi-dimensional, free-electron laser simulation codes

    SciTech Connect

    Fawley, William M.

    2002-03-25

    We discuss the underlying reasoning behind and the details of the numerical algorithm used in the GINGER free-electron laser(FEL) simulation code to load the initial shot noise microbunching on the electron beam. In particular, we point out that there are some additional subtleties which must be followed for multi-dimensional codes which are not necessary for one-dimensional formulations. Moreover, requiring that the higher harmonics of the microbunching also be properly initialized with the correct statistics leads to additional complexities. We present some numerical results including the predicted incoherent, spontaneous emission as tests of the shot noise algorithm's correctness.

  7. Medical Simulation Practices 2010 Survey Results

    NASA Technical Reports Server (NTRS)

    McCrindle, Jeffrey J.

    2011-01-01

    Medical Simulation Centers are an essential component of our learning infrastructure to prepare doctors and nurses for their careers. Unlike the military and aerospace simulation industry, very little has been published regarding the best practices currently in use within medical simulation centers. This survey attempts to provide insight into the current simulation practices at medical schools, hospitals, university nursing programs and community college nursing programs. Students within the MBA program at Saint Joseph's University conducted a survey of medical simulation practices during the summer 2010 semester. A total of 115 institutions responded to the survey. The survey resus discuss overall effectiveness of current simulation centers as well as the tools and techniques used to conduct the simulation activity

  8. Centroid-Based Document Classification Algorithms: Analysis & Experimental Results

    DTIC Science & Technology

    2000-03-06

    in terms of zero-one loss (misclassification rate ). Linear Classifiers Linear classifiers [31] are a family of text categorization learning...training set and and a test set. The error rates of algorithms A and B on the test set are recorded. Let p (i)A be the error rate of algorithm A and p(i...B be the error rate of algorithm B during trial i . Then Student’s t test can be computed using the statistic: t = p̄ √ n √ ∑n i=1(p(i)− p̄)2 n−1

  9. Obtaining identical results on varying numbers of processors in domain decomposed particle Monte Carlo simulations.

    SciTech Connect

    Brunner, Thomas A.; Kalos, Malvin H.; Gentile, Nicholas A.

    2005-03-01

    Domain decomposed Monte Carlo codes, like other domain-decomposed codes, are difficult to debug. Domain decomposition is prone to error, and interactions between the domain decomposition code and the rest of the algorithm often produces subtle bugs. These bugs are particularly difficult to find in a Monte Carlo algorithm, in which the results have statistical noise. Variations in the results due to statistical noise can mask errors when comparing the results to other simulations or analytic results.

  10. Simulation System of Car Crash Test in C-NCAP Analysis Based on an Improved Apriori Algorithm*

    NASA Astrophysics Data System (ADS)

    Xiang, LI

    In order to analysis car crash test in C-NCAP, an improved algorithm is given based on Apriori algorithm in this paper. The new algorithm is implemented with vertical data layout, breadth first searching, and intersecting. It takes advantage of the efficiency of vertical data layout and intersecting, and prunes candidate frequent item sets like Apriori. Finally, the new algorithm is applied in simulation of car crash test analysis system. The result shows that the relations will affect the C-NCAP test results, and it can provide a reference for the automotive design.

  11. Planck 2015 results. XII. Full focal plane simulations

    NASA Astrophysics Data System (ADS)

    Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Arnaud, M.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartlett, J. G.; Bartolo, N.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Boulanger, F.; Bucher, M.; Burigana, C.; Butler, R. C.; Calabrese, E.; Cardoso, J.-F.; Castex, G.; Catalano, A.; Challinor, A.; Chamballu, A.; Chiang, H. C.; Christensen, P. R.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Combet, C.; Couchot, F.; Coulais, A.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Delouis, J.-M.; Désert, F.-X.; Dickinson, C.; Diego, J. M.; Dolag, K.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Fergusson, J.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Frejsel, A.; Galeotta, S.; Galli, S.; Ganga, K.; Ghosh, T.; Giard, M.; Giraud-Héraud, Y.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Gudmundsson, J. E.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Henrot-Versillé, S.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Hurier, G.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Karakci, A.; Keihänen, E.; Keskitalo, R.; Kiiveri, K.; Kisner, T. S.; Kneissl, R.; Knoche, J.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Leonardi, R.; Lesgourgues, J.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; Lindholm, V.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maggio, G.; Maino, D.; Mandolesi, N.; Mangilli, A.; Maris, M.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; McGehee, P.; Meinhold, P. R.; Melchiorri, A.; Melin, J.-B.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Noviello, F.; Novikov, D.; Novikov, I.; Oxborrow, C. A.; Paci, F.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Patanchon, G.; Pearson, T. J.; Perdereau, O.; Perotto, L.; Perrotta, F.; Pettorino, V.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Renzi, A.; Ristorcelli, I.; Rocha, G.; Roman, M.; Rosset, C.; Rossetti, M.; Roudier, G.; Rubiño-Martín, J. A.; Rusholme, B.; Sandri, M.; Santos, D.; Savelainen, M.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Wehus, I. K.; Welikala, N.; Yvon, D.; Zacchei, A.; Zonca, A.

    2016-09-01

    We present the 8th full focal plane simulation set (FFP8), deployed in support of the Planck 2015 results. FFP8 consists of 10 fiducial mission realizations reduced to 18 144 maps, together with the most massive suite of Monte Carlo realizations of instrument noise and CMB ever generated, comprising 104 mission realizations reduced to about 106 maps. The resulting maps incorporate the dominant instrumental, scanning, and data analysis effects, and the remaining subdominant effects will be included in future updates. Generated at a cost of some 25 million CPU-hours spread across multiple high-performance-computing (HPC) platforms, FFP8 is used to validate and verify analysis algorithms and their implementations, and to remove biases from and quantify uncertainties in the results of analyses of the real data.

  12. Planck 2015 results: XII. Full focal plane simulations

    DOE PAGES

    Ade, P. A. R.; Aghanim, N.; Arnaud, M.; ...

    2016-09-20

    In this paper, we present the 8th full focal plane simulation set (FFP8), deployed in support of the Planck 2015 results. FFP8 consists of 10 fiducial mission realizations reduced to 18 144 maps, together with the most massive suite of Monte Carlo realizations of instrument noise and CMB ever generated, comprising 104 mission realizations reduced to about 106 maps. The resulting maps incorporate the dominant instrumental, scanning, and data analysis effects, and the remaining subdominant effects will be included in future updates. Finally, generated at a cost of some 25 million CPU-hours spread across multiple high-performance-computing (HPC) platforms, FFP8 ismore » used to validate and verify analysis algorithms and their implementations, and to remove biases from and quantify uncertainties in the results of analyses of the real data.« less

  13. Robotic space simulation integration of vision algorithms into an orbital operations simulation

    NASA Technical Reports Server (NTRS)

    Bochsler, Daniel C.

    1987-01-01

    In order to successfully plan and analyze future space activities, computer-based simulations of activities in low earth orbit will be required to model and integrate vision and robotic operations with vehicle dynamics and proximity operations procedures. The orbital operations simulation (OOS) is configured and enhanced as a testbed for robotic space operations. Vision integration algorithms are being developed in three areas: preprocessing, recognition, and attitude/attitude rates. The vision program (Rice University) was modified for use in the OOS. Systems integration testing is now in progress.

  14. Implementation of low communication frequency 3D FFT algorithm for ultra-large-scale micromagnetics simulation

    NASA Astrophysics Data System (ADS)

    Tsukahara, Hiroshi; Iwano, Kaoru; Mitsumata, Chiharu; Ishikawa, Tadashi; Ono, Kanta

    2016-10-01

    We implement low communication frequency three-dimensional fast Fourier transform algorithms on micromagnetics simulator for calculations of a magnetostatic field which occupies a significant portion of large-scale micromagnetics simulation. This fast Fourier transform algorithm reduces the frequency of all-to-all communications from six to two times. Simulation times with our simulator show high scalability in parallelization, even if we perform the micromagnetics simulation using 32 768 physical computing cores. This low communication frequency fast Fourier transform algorithm enables world largest class micromagnetics simulations to be carried out with over one billion calculation cells.

  15. Adaptive Sampling Algorithms for Probabilistic Risk Assessment of Nuclear Simulations

    SciTech Connect

    Diego Mandelli; Dan Maljovec; Bei Wang; Valerio Pascucci; Peer-Timo Bremer

    2013-09-01

    Nuclear simulations are often computationally expensive, time-consuming, and high-dimensional with respect to the number of input parameters. Thus exploring the space of all possible simulation outcomes is infeasible using finite computing resources. During simulation-based probabilistic risk analysis, it is important to discover the relationship between a potentially large number of input parameters and the output of a simulation using as few simulation trials as possible. This is a typical context for performing adaptive sampling where a few observations are obtained from the simulation, a surrogate model is built to represent the simulation space, and new samples are selected based on the model constructed. The surrogate model is then updated based on the simulation results of the sampled points. In this way, we attempt to gain the most information possible with a small number of carefully selected sampled points, limiting the number of expensive trials needed to understand features of the simulation space. We analyze the specific use case of identifying the limit surface, i.e., the boundaries in the simulation space between system failure and system success. In this study, we explore several techniques for adaptively sampling the parameter space in order to reconstruct the limit surface. We focus on several adaptive sampling schemes. First, we seek to learn a global model of the entire simulation space using prediction models or neighborhood graphs and extract the limit surface as an iso-surface of the global model. Second, we estimate the limit surface by sampling in the neighborhood of the current estimate based on topological segmentations obtained locally. Our techniques draw inspirations from topological structure known as the Morse-Smale complex. We highlight the advantages and disadvantages of using a global prediction model versus local topological view of the simulation space, comparing several different strategies for adaptive sampling in both

  16. Implementation of a combined algorithm designed to increase the reliability of information systems: simulation modeling

    NASA Astrophysics Data System (ADS)

    Popov, A.; Zolotarev, V.; Bychkov, S.

    2016-11-01

    This paper examines the results of experimental studies of a previously submitted combined algorithm designed to increase the reliability of information systems. The data that illustrates the organization and conduct of the studies is provided. Within the framework of a comparison of As a part of the study conducted, the comparison of the experimental data of simulation modeling and the data of the functioning of the real information system was made. The hypothesis of the homogeneity of the logical structure of the information systems was formulated, thus enabling to reconfigure the algorithm presented, - more specifically, to transform it into the model for the analysis and prediction of arbitrary information systems. The results presented can be used for further research in this direction. The data of the opportunity to predict the functioning of the information systems can be used for strategic and economic planning. The algorithm can be used as a means for providing information security.

  17. Experiences with serial and parallel algorithms for channel routing using simulated annealing

    NASA Technical Reports Server (NTRS)

    Brouwer, Randall Jay

    1988-01-01

    Two algorithms for channel routing using simulated annealing are presented. Simulated annealing is an optimization methodology which allows the solution process to back up out of local minima that may be encountered by inappropriate selections. By properly controlling the annealing process, it is very likely that the optimal solution to an NP-complete problem such as channel routing may be found. The algorithm presented proposes very relaxed restrictions on the types of allowable transformations, including overlapping nets. By freeing that restriction and controlling overlap situations with an appropriate cost function, the algorithm becomes very flexible and can be applied to many extensions of channel routing. The selection of the transformation utilizes a number of heuristics, still retaining the pseudorandom nature of simulated annealing. The algorithm was implemented as a serial program for a workstation, and a parallel program designed for a hypercube computer. The details of the serial implementation are presented, including many of the heuristics used and some of the resulting solutions.

  18. An algorithm for Monte Carlo simulation of coupled electron-photon transport

    NASA Astrophysics Data System (ADS)

    Salvat, F.; Fernández-Varea, J. M.; Sempau, J.; Acosta, E.; Baró, J.

    1997-11-01

    An algorithm for Monte Carlo simulation of coupled electron-photon transport is described. Electron and positron tracks are generated by means of PENELOPE, a mixed procedure developed by Baró et al. [Nucl. Instr. and Meth. B 100 (1995) 31]. The simulation of photon transport follows the conventional, detailed method. Photons are assumed to interact via coherent and incoherent scattering, photoelectric absorption and electron-positron pair production. Photon interactions are simulated through analytical differential cross sections, derived from simple physical models and renormalized to reproduce accurate attenuation coefficients available from the literature. The combined algorithm has been implemented in a FORTRAN 77 computer code that generates electron-photon showers in arbitrary materials for the energy range from ˜1 GeV down to 1 keV or the binding energy of the L-shell of the heaviest element in the medium, whichever is the largest. The code is capable of following secondary particles that are generated within this energy range. The reliability of the algorithm and computer code is demonstrated by comparing simulation results with experimental data and with results from other Monte Carlo codes.

  19. Simulation and optimization of a pulsating heat pipe using artificial neural network and genetic algorithm

    NASA Astrophysics Data System (ADS)

    Jokar, Ali; Godarzi, Ali Abbasi; Saber, Mohammad; Shafii, Mohammad Behshad

    2016-11-01

    In this paper, a novel approach has been presented to simulate and optimize the pulsating heat pipes (PHPs). The used pulsating heat pipe setup was designed and constructed for this study. Due to the lack of a general mathematical model for exact analysis of the PHPs, a method has been applied for simulation and optimization using the natural algorithms. In this way, the simulator consists of a kind of multilayer perceptron neural network, which is trained by experimental results obtained from our PHP setup. The results show that the complex behavior of PHPs can be successfully described by the non-linear structure of this simulator. The input variables of the neural network are input heat flux to evaporator (q″), filling ratio (FR) and inclined angle (IA) and its output is thermal resistance of PHP. Finally, based upon the simulation results and considering the heat pipe's operating constraints, the optimum operating point of the system is obtained by using genetic algorithm (GA). The experimental results show that the optimum FR (38.25 %), input heat flux to evaporator (39.93 W) and IA (55°) that obtained from GA are acceptable.

  20. The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

    SciTech Connect

    Gillespie, Daniel T. Gillespie, Carol A.; Seitaridou, Effrosyni

    2014-12-21

    Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A. 107, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results.

  1. The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

    NASA Astrophysics Data System (ADS)

    Gillespie, Daniel T.; Seitaridou, Effrosyni; Gillespie, Carol A.

    2014-12-01

    Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A. 107, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results.

  2. The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

    PubMed Central

    Seitaridou, Effrosyni

    2014-01-01

    Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A.141, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results. PMID:25527927

  3. SALTSTONE MATRIX CHARACTERIZATION AND STADIUM SIMULATION RESULTS

    SciTech Connect

    Langton, C.

    2009-07-30

    SIMCO Technologies, Inc. was contracted to evaluate the durability of the saltstone matrix material and to measure saltstone transport properties. This information will be used to: (1) Parameterize the STADIUM{reg_sign} service life code, (2) Predict the leach rate (degradation rate) for the saltstone matrix over 10,000 years using the STADIUM{reg_sign} concrete service life code, and (3) Validate the modeled results by conducting leaching (water immersion) tests. Saltstone durability for this evaluation is limited to changes in the matrix itself and does not include changes in the chemical speciation of the contaminants in the saltstone. This report summarized results obtained to date which include: characterization data for saltstone cured up to 365 days and characterization of saltstone cured for 137 days and immersed in water for 31 days. Chemicals for preparing simulated non-radioactive salt solution were obtained from chemical suppliers. The saltstone slurry was mixed according to directions provided by SRNL. However SIMCO Technologies Inc. personnel made a mistake in the premix proportions. The formulation SIMCO personnel used to prepare saltstone premix was not the reference mix proportions: 45 wt% slag, 45 wt% fly ash, and 10 wt% cement. SIMCO Technologies Inc. personnel used the following proportions: 21 wt% slag, 65 wt% fly ash, and 14 wt% cement. The mistake was acknowledged and new mixes have been prepared and are curing. The results presented in this report are assumed to be conservative since the excessive fly ash was used in the SIMCO saltstone. The SIMCO mixes are low in slag which is very reactive in the caustic salt solution. The impact is that the results presented in this report are expected to be conservative since the samples prepared were deficient in slag and contained excess fly ash. The hydraulic reactivity of slag is about four times that of fly ash so the amount of hydrated binder formed per unit volume in the SIMCO saltstone samples is

  4. Exploring Space Physics Concepts Using Simulation Results

    NASA Astrophysics Data System (ADS)

    Gross, N. A.

    2008-05-01

    The Center for Integrated Space Weather Modeling (CISM), a Science and Technology Center (STC) funded by the National Science Foundation, has the goal of developing a suite of integrated physics based computer models of the space environment that can follow the evolution of a space weather event from the Sun to the Earth. In addition to the research goals, CISM is also committed to training the next generation of space weather professionals who are imbued with a system view of space weather. This view should include an understanding of both helio-spheric and geo-space phenomena. To this end, CISM offers a yearly Space Weather Summer School targeted to first year graduate students, although advanced undergraduates and space weather professionals have also attended. This summer school uses a number of innovative pedagogical techniques including devoting each afternoon to a computer lab exercise that use results from research quality simulations and visualization techniques, along with ground based and satellite data to explore concepts introduced during the morning lectures. These labs are suitable for use in wide variety educational settings from formal classroom instruction to outreach programs. The goal of this poster is to outline the goals and content of the lab materials so that instructors may evaluate their potential use in the classroom or other settings.

  5. GPU-based single-cluster algorithm for the simulation of the Ising model

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro; Okabe, Yutaka

    2012-02-01

    We present the GPU calculation with the common unified device architecture (CUDA) for the Wolff single-cluster algorithm of the Ising model. Proposing an algorithm for a quasi-block synchronization, we realize the Wolff single-cluster Monte Carlo simulation with CUDA. We perform parallel computations for the newly added spins in the growing cluster. As a result, the GPU calculation speed for the two-dimensional Ising model at the critical temperature with the linear size L = 4096 is 5.60 times as fast as the calculation speed on a current CPU core. For the three-dimensional Ising model with the linear size L = 256, the GPU calculation speed is 7.90 times as fast as the CPU calculation speed. The idea of quasi-block synchronization can be used not only in the cluster algorithm but also in many fields where the synchronization of all threads is required.

  6. The extrapolated reference values procedure: Theory, algorithm, and results in patients and control subjects.

    PubMed

    Nandedkar, Sanjeev D; Sanders, Donald B; Hobson-Webb, Lisa D; Billakota, Santoshi; Barkhaus, Paul E; Stålberg, Erik V

    2017-02-09

    Reference values (RVs) are required to separate normal from abnormal values obtained in electrodiagnostic (EDx) testing. However, it is frequently impractical to perform studies on control subjects to obtain RVs. The Extrapolated Reference Values (E-Ref) procedure extracts RVs from data obtained during clinically indicated EDx testing. We compared the E-Ref results with established RVs in several sets of EDx data. The mathematical basis for E-Ref was explored to develop an algorithm for the E-Ref procedure. To test the validity of this algorithm, it was applied to simulated and real jitter measurements from control subjects and patients with myasthenia gravis, and to nerve conduction studies from patients with various conditions referred for EDx studies. There was good concordance between E-Ref and RVs for all evaluated data sets. E-Ref is a promising method to develop RVs. Muscle Nerve, 2017. © 2017 Wiley Periodicals, Inc.

  7. The response of flexible manipulators to a new computed torque control strategy: Simulation results

    NASA Astrophysics Data System (ADS)

    Looke, T. D.; Bayoumi, M. M.; Farooq, M.

    The need for faster and lighter autonomous and teleoperated robots, especially in military land, undersea, and space applications, requires control algorithms which account for the elastic response of lightweight, flexible structures. The numerical analysis and testing of these control algorithms further requires accurate simulation techniques. The finite element simulation method generally yields very accurate predictions of the transient dynamic response of flexible structures to applied loads. It is shown that a standard finite element simulation package (ANSYS) may be used to test computed torque and adaptive feedback control algorithms for multi-link flexible manipulators. The response of one- and two-link, planar and non-planar flexible manipulators to computed torque algorithms is illustrated. The results demonstrate the usefulness of the new computed torque approach.

  8. A smooth particle-mesh Ewald algorithm for Stokes suspension simulations: The sedimentation of fibers

    NASA Astrophysics Data System (ADS)

    Saintillan, David; Darve, Eric; Shaqfeh, Eric S. G.

    2005-03-01

    Large-scale simulations of non-Brownian rigid fibers sedimenting under gravity at zero Reynolds number have been performed using a fast algorithm. The mathematical formulation follows the previous simulations by Butler and Shaqfeh ["Dynamic simulations of the inhomogeneous sedimentation of rigid fibres," J. Fluid Mech. 468, 205 (2002)]. The motion of the fibers is described using slender-body theory, and the line distribution of point forces along their lengths is approximated by a Legendre polynomial in which only the total force, torque, and particle stresslet are retained. Periodic boundary conditions are used to simulate an infinite suspension, and both far-field hydrodynamic interactions and short-range lubrication forces are considered in all simulations. The calculation of the hydrodynamic interactions, which is typically the bottleneck for large systems with periodic boundary conditions, is accelerated using a smooth particle-mesh Ewald (SPME) algorithm previously used in molecular dynamics simulations. In SPME the slowly decaying Green's function is split into two fast-converging sums: the first involves the distribution of point forces and accounts for the singular short-range part of the interactions, while the second is expressed in terms of the Fourier transform of the force distribution and accounts for the smooth and long-range part. Because of its smoothness, the second sum can be computed efficiently on an underlying grid using the fast Fourier transform algorithm, resulting in a significant speed-up of the calculations. Systems of up to 512 fibers were simulated on a single-processor workstation, providing a different insight into the formation, structure, and dynamics of the inhomogeneities that occur in sedimenting fiber suspensions.

  9. A fast variable step size integration algorithm suitable for computer simulations of physiological systems

    NASA Technical Reports Server (NTRS)

    Neal, L.

    1981-01-01

    A simple numerical algorithm was developed for use in computer simulations of systems which are both stiff and stable. The method is implemented in subroutine form and applied to the simulation of physiological systems.

  10. A fast variable step size integration algorithm suitable for computer simulations of physiological systems

    NASA Technical Reports Server (NTRS)

    Neal, L.

    1981-01-01

    A simple numerical algorithm was developed for use in computer simulations of systems which are both stiff and stable. The method is implemented in subroutine form and applied to the simulation of physiological systems.

  11. Full-scale engine demonstration of an advanced sensor failure detection, isolation and accommodation algorithm: Preliminary results

    NASA Astrophysics Data System (ADS)

    Merrill, Walter C.; Delaat, John C.; Kroszkewicz, Steven M.; Abdelwahab, Mahmood

    The objective of the advanced detection, isolation, and accommodation (ADIA) program is to improve the overall demonstrated reliability of digital electronic control systems for turbine engines. For this purpose, algorithms were developed which detect, isolate, and accommodate sensor failures using analytical redundancy. Preliminary results of a full scale engine demonstration of the ADIA algorithm are presented. Minimum detectable levels of sensor failures for an F100 turbofan engine control system are determined and compared to those obtained during a previous evaluation of this algorithm using a real-time hybrid computer simulation of the engine.

  12. Full-scale engine demonstration of an advanced sensor failure detection isolation, and accommodation algorithm - Preliminary results

    NASA Technical Reports Server (NTRS)

    Merrill, Walter C.; Delaat, John C.; Kroszkewicz, Steven M.; Abdelwahab, Mahmood

    1987-01-01

    The objective of the advanced detection, isolation, and accommodation (ADIA) program is to improve the overall demonstrated reliability of digital electronic control systems for turbine engines. For this purpose, algorithms were developed which detect, isolate, and accommodate sensor failures using analytical redundancy. Preliminary results of a full scale engine demonstration of the ADIA algorithm are presented. Minimum detectable levels of sensor failures for an F100 turbofan engine control system are determined and compared to those obtained during a previous evaluation of this algorithm using a real-time hybrid computer simulation of the engine.

  13. Full-scale engine demonstration of an advanced sensor failure detection, isolation and accommodation algorithm: Preliminary results

    NASA Technical Reports Server (NTRS)

    Merrill, Walter C.; Delaat, John C.; Kroszkewicz, Steven M.; Abdelwahab, Mahmood

    1987-01-01

    The objective of the advanced detection, isolation, and accommodation (ADIA) program is to improve the overall demonstrated reliability of digital electronic control systems for turbine engines. For this purpose, algorithms were developed which detect, isolate, and accommodate sensor failures using analytical redundancy. Preliminary results of a full scale engine demonstration of the ADIA algorithm are presented. Minimum detectable levels of sensor failures for an F100 turbofan engine control system are determined and compared to those obtained during a previous evaluation of this algorithm using a real-time hybrid computer simulation of the engine.

  14. Simulation of MR angiography imaging for validation of cerebral arteries segmentation algorithms.

    PubMed

    Klepaczko, Artur; Szczypiński, Piotr; Deistung, Andreas; Reichenbach, Jürgen R; Materka, Andrzej

    2016-12-01

    Accurate vessel segmentation of magnetic resonance angiography (MRA) images is essential for computer-aided diagnosis of cerebrovascular diseases such as stenosis or aneurysm. The ability of a segmentation algorithm to correctly reproduce the geometry of the arterial system should be expressed quantitatively and observer-independently to ensure objectivism of the evaluation. This paper introduces a methodology for validating vessel segmentation algorithms using a custom-designed MRA simulation framework. For this purpose, a realistic reference model of an intracranial arterial tree was developed based on a real Time-of-Flight (TOF) MRA data set. With this specific geometry blood flow was simulated and a series of TOF images was synthesized using various acquisition protocol parameters and signal-to-noise ratios. The synthesized arterial tree was then reconstructed using a level-set segmentation algorithm available in the Vascular Modeling Toolkit (VMTK). Moreover, to present versatile application of the proposed methodology, validation was also performed for two alternative techniques: a multi-scale vessel enhancement filter and the Chan-Vese variant of the level-set-based approach, as implemented in the Insight Segmentation and Registration Toolkit (ITK). The segmentation results were compared against the reference model. The accuracy in determining the vessels centerline courses was very high for each tested segmentation algorithm (mean error rate = 5.6% if using VMTK). However, the estimated radii exhibited deviations from ground truth values with mean error rates ranging from 7% up to 79%, depending on the vessel size, image acquisition and segmentation method. We demonstrated the practical application of the designed MRA simulator as a reliable tool for quantitative validation of MRA image processing algorithms that provides objective, reproducible results and is observer independent. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  15. The weirdest SDSS galaxies: results from an outlier detection algorithm

    NASA Astrophysics Data System (ADS)

    Baron, Dalya; Poznanski, Dovi

    2017-03-01

    How can we discover objects we did not know existed within the large data sets that now abound in astronomy? We present an outlier detection algorithm that we developed, based on an unsupervised Random Forest. We test the algorithm on more than two million galaxy spectra from the Sloan Digital Sky Survey and examine the 400 galaxies with the highest outlier score. We find objects which have extreme emission line ratios and abnormally strong absorption lines, objects with unusual continua, including extremely reddened galaxies. We find galaxy-galaxy gravitational lenses, double-peaked emission line galaxies and close galaxy pairs. We find galaxies with high ionization lines, galaxies that host supernovae and galaxies with unusual gas kinematics. Only a fraction of the outliers we find were reported by previous studies that used specific and tailored algorithms to find a single class of unusual objects. Our algorithm is general and detects all of these classes, and many more, regardless of what makes them peculiar. It can be executed on imaging, time series and other spectroscopic data, operates well with thousands of features, is not sensitive to missing values and is easily parallelizable.

  16. A new deadlock resolution protocol and message matching algorithm for the extreme-scale simulator

    DOE PAGES

    Engelmann, Christian; Naughton, III, Thomas J.

    2016-03-22

    Investigating the performance of parallel applications at scale on future high-performance computing (HPC) architectures and the performance impact of different HPC architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale Simulator (xSim) is a simulation toolkit for investigating the performance of parallel applications at scale. xSim scales to millions of simulated Message Passing Interface (MPI) processes. The overhead introduced by a simulation tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1)~a new deadlock resolution protocol to reduce the parallel discrete event simulation overhead and (2)~a new simulated MPI message matchingmore » algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement. The simulation overhead for running the NAS Parallel Benchmark suite was reduced from 102% to 0% for the embarrassingly parallel (EP) benchmark and from 1,020% to 238% for the conjugate gradient (CG) benchmark. xSim offers a highly accurate simulation mode for better tracking of injected MPI process failures. Furthermore, with highly accurate simulation, the overhead was reduced from 3,332% to 204% for EP and from 37,511% to 13,808% for CG.« less

  17. A new deadlock resolution protocol and message matching algorithm for the extreme-scale simulator

    SciTech Connect

    Engelmann, Christian; Naughton, III, Thomas J.

    2016-03-22

    Investigating the performance of parallel applications at scale on future high-performance computing (HPC) architectures and the performance impact of different HPC architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale Simulator (xSim) is a simulation toolkit for investigating the performance of parallel applications at scale. xSim scales to millions of simulated Message Passing Interface (MPI) processes. The overhead introduced by a simulation tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1)~a new deadlock resolution protocol to reduce the parallel discrete event simulation overhead and (2)~a new simulated MPI message matching algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement. The simulation overhead for running the NAS Parallel Benchmark suite was reduced from 102% to 0% for the embarrassingly parallel (EP) benchmark and from 1,020% to 238% for the conjugate gradient (CG) benchmark. xSim offers a highly accurate simulation mode for better tracking of injected MPI process failures. Furthermore, with highly accurate simulation, the overhead was reduced from 3,332% to 204% for EP and from 37,511% to 13,808% for CG.

  18. Forecasting nonlinear chaotic time series with function expression method based on an improved genetic-simulated annealing algorithm.

    PubMed

    Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

    2015-01-01

    The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior.

  19. Forecasting Nonlinear Chaotic Time Series with Function Expression Method Based on an Improved Genetic-Simulated Annealing Algorithm

    PubMed Central

    Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

    2015-01-01

    The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior. PMID:26000011

  20. The control algorithm improving performance of electric load simulator

    NASA Astrophysics Data System (ADS)

    Guo, Chenxia; Yang, Ruifeng; Zhang, Peng; Fu, Mengyao

    2017-01-01

    In order to improve dynamic performance and signal tracking accuracy of electric load simulator, the influence of the moment of inertia, stiffness, friction, gaps and other factors on the system performance were analyzed on the basis of researching the working principle of load simulator in this paper. The PID controller based on Wavelet Neural Network was used to achieve the friction nonlinear compensation, while the gap inverse model was used to compensate the gap nonlinear. The compensation results were simulated by MATLAB software. It was shown that the follow-up performance of sine response curve of the system became better after compensating, the track error was significantly reduced, the accuracy was improved greatly and the system dynamic performance was improved.

  1. Optimized simulations of Olami-Feder-Christensen systems using parallel algorithms

    NASA Astrophysics Data System (ADS)

    Dominguez, Rachele; Necaise, Rance; Montag, Eric

    The sequential nature of the Olami-Feder-Christensen (OFC) model for earthquake simulations limits the benefits of parallel computing approaches because of the frequent communication required between processors. We developed a parallel version of the OFC algorithm for multi-core processors. Our data, even for relatively small system sizes and low numbers of processors, indicates that increasing the number of processors provides significantly faster simulations; producing more efficient results than previous attempts that used network-based Beowulf clusters. Our algorithm optimizes performance by exploiting the multi-core processor architecture, minimizing communication time in contrast to the networked Beowulf-cluster approaches. Our multi-core algorithm is the basis for a new algorithm using GPUs that will drastically increase the number of processors available. Previous studies incorporating realistic structural features of faults into OFC models have revealed spatial and temporal patterns observed in real earthquake systems. The computational advances presented here will allow for studying interacting networks of faults, rather than individual faults, further enhancing our understanding of the relationship between the earth's structure and the triggering process. Support for this project comes from the Chenery Research Fund, the Rashkind Family Endowment, the Walter Williams Craigie Teaching Endowment, and the Schapiro Undergraduate Research Fellowship.

  2. The Separatrix Algorithm for synthesis and analysis of stochastic simulations with applications in disease modeling.

    PubMed

    Klein, Daniel J; Baym, Michael; Eckhoff, Philip

    2014-01-01

    Decision makers in epidemiology and other disciplines are faced with the daunting challenge of designing interventions that will be successful with high probability and robust against a multitude of uncertainties. To facilitate the decision making process in the context of a goal-oriented objective (e.g., eradicate polio by [Formula: see text]), stochastic models can be used to map the probability of achieving the goal as a function of parameters. Each run of a stochastic model can be viewed as a Bernoulli trial in which "success" is returned if and only if the goal is achieved in simulation. However, each run can take a significant amount of time to complete, and many replicates are required to characterize each point in parameter space, so specialized algorithms are required to locate desirable interventions. To address this need, we present the Separatrix Algorithm, which strategically locates parameter combinations that are expected to achieve the goal with a user-specified probability of success (e.g. 95%). Technically, the algorithm iteratively combines density-corrected binary kernel regression with a novel information-gathering experiment design to produce results that are asymptotically correct and work well in practice. The Separatrix Algorithm is demonstrated on several test problems, and on a detailed individual-based simulation of malaria.

  3. Image noise reduction algorithm for digital subtraction angiography: clinical results.

    PubMed

    Söderman, Michael; Holmin, Staffan; Andersson, Tommy; Palmgren, Charlotta; Babic, Draženko; Hoornaert, Bart

    2013-11-01

    To test the hypothesis that an image noise reduction algorithm designed for digital subtraction angiography (DSA) in interventional neuroradiology enables a reduction in the patient entrance dose by a factor of 4 while maintaining image quality. This clinical prospective study was approved by the local ethics committee, and all 20 adult patients provided informed consent. DSA was performed with the default reference DSA program, a quarter-dose DSA program with modified acquisition parameters (to reduce patient radiation dose exposure), and a real-time noise-reduction algorithm. Two consecutive biplane DSA data sets were acquired in each patient. The dose-area product (DAP) was calculated for each image and compared. A randomized, blinded, offline reading study was conducted to show noninferiority of the quarter-dose image sets. Overall, 40 samples per treatment group were necessary to acquire 80% power, which was calculated by using a one-sided α level of 2.5%. The mean DAP with the quarter-dose program was 25.3% ± 0.8 of that with the reference program. The median overall image quality scores with the reference program were 9, 13, and 12 for readers 1, 2, and 3, respectively. These scores increased slightly to 12, 15, and 12, respectively, with the quarter-dose program imaging chain. In DSA, a change in technique factors combined with a real-time noise-reduction algorithm will reduce the patient entrance dose by 75%, without a loss of image quality. RSNA, 2013

  4. A Non-Intrusive Algorithm for Sensitivity Analysis of Chaotic Flow Simulations

    NASA Technical Reports Server (NTRS)

    Blonigan, Patrick J.; Wang, Qiqi; Nielsen, Eric J.; Diskin, Boris

    2017-01-01

    We demonstrate a novel algorithm for computing the sensitivity of statistics in chaotic flow simulations to parameter perturbations. The algorithm is non-intrusive but requires exposing an interface. Based on the principle of shadowing in dynamical systems, this algorithm is designed to reduce the effect of the sampling error in computing sensitivity of statistics in chaotic simulations. We compare the effectiveness of this method to that of the conventional finite difference method.

  5. Optimizing isotope substitution in graphene for thermal conductivity minimization by genetic algorithm driven molecular simulations

    NASA Astrophysics Data System (ADS)

    Davies, Michael; Ganapathysubramanian, Baskar; Balasubramanian, Ganesh

    2017-03-01

    We present results from a computational framework integrating genetic algorithm and molecular dynamics simulations to systematically design isotope engineered graphene structures for reduced thermal conductivity. In addition to the effect of mass disorder, our results reveal the importance of atomic distribution on thermal conductivity for the same isotopic concentration. Distinct groups of isotope-substituted graphene sheets are identified based on the atomic composition and distribution. Our results show that in structures with equiatomic compositions, the enhanced scattering by lattice vibrations results in lower thermal conductivities due to the absence of isotopic clusters.

  6. Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.

    PubMed

    Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesén, Björn; Kasson, Peter M; Lindahl, Erik

    2015-06-09

    Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers-particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide more processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

  7. Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression.

    PubMed

    Roussel, Marc R; Zhu, Rui

    2006-12-08

    The quantitative modeling of gene transcription and translation requires a treatment of two key features: stochastic fluctuations due to the limited copy numbers of key molecules (genes, RNA polymerases, ribosomes), and delayed output due to the time required for biopolymer synthesis. Recently proposed algorithms allow for efficient simulations of such systems. However, it is critical to know whether the results of delay stochastic simulations agree with those from more detailed models of the transcription and translation processes. We present a generalization of previous delay stochastic simulation algorithms which allows both for multiple delays and for distributions of delay times. We show that delay stochastic simulations closely approximate simulations of a detailed transcription model except when two-body effects (e.g. collisions between polymerases on a template strand) are important. Finally, we study a delay stochastic model of prokaryotic transcription and translation which reproduces observations from a recent experimental study in which a single gene was expressed under the control of a repressed lac promoter in E. coli cells. This demonstrates our ability to quantitatively model gene expression using these new methods.

  8. Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression

    NASA Astrophysics Data System (ADS)

    Roussel, Marc R.; Zhu, Rui

    2006-12-01

    The quantitative modeling of gene transcription and translation requires a treatment of two key features: stochastic fluctuations due to the limited copy numbers of key molecules (genes, RNA polymerases, ribosomes), and delayed output due to the time required for biopolymer synthesis. Recently proposed algorithms allow for efficient simulations of such systems. However, it is critical to know whether the results of delay stochastic simulations agree with those from more detailed models of the transcription and translation processes. We present a generalization of previous delay stochastic simulation algorithms which allows both for multiple delays and for distributions of delay times. We show that delay stochastic simulations closely approximate simulations of a detailed transcription model except when two-body effects (e.g. collisions between polymerases on a template strand) are important. Finally, we study a delay stochastic model of prokaryotic transcription and translation which reproduces observations from a recent experimental study in which a single gene was expressed under the control of a repressed lac promoter in E. coli cells. This demonstrates our ability to quantitatively model gene expression using these new methods.

  9. Blocking Moving Window algorithm: Conditioning multiple-point simulations to hydrogeological data

    NASA Astrophysics Data System (ADS)

    Alcolea, Andres; Renard, Philippe

    2010-08-01

    Connectivity constraints and measurements of state variables contain valuable information on aquifer architecture. Multiple-point (MP) geostatistics allow one to simulate aquifer architectures, presenting a predefined degree of global connectivity. In this context, connectivity data are often disregarded. The conditioning to state variables is usually carried out by minimizing a suitable objective function (i.e., solving an inverse problem). However, the discontinuous nature of lithofacies distributions and of the corresponding objective function discourages the use of traditional sensitivity-based inversion techniques. This work presents the Blocking Moving Window algorithm (BMW), aimed at overcoming these limitations by conditioning MP simulations to hydrogeological data such as connectivity and heads. The BMW evolves iteratively until convergence: (1) MP simulation of lithofacies from geological/geophysical data and connectivity constraints, where only a random portion of the domain is simulated at every iteration (i.e., the blocking moving window, whose size is user-defined); (2) population of hydraulic properties at the intrafacies; (3) simulation of state variables; and (4) acceptance or rejection of the MP simulation depending on the quality of the fit of measured state variables. The outcome is a stack of MP simulations that (1) resemble a prior geological model depicted by a training image, (2) honor lithological data and connectivity constraints, (3) correlate with geophysical data, and (4) fit available measurements of state variables well. We analyze the performance of the algorithm on a 2-D synthetic example. Results show that (1) the size of the blocking moving window controls the behavior of the BMW, (2) conditioning to state variable data enhances dramatically the initial simulation (which accounts for geological/geophysical data only), and (3) connectivity constraints speed up the convergence but do not enhance the stack if the number of iterations

  10. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels.

    PubMed Central

    Im, W; Seefeld, S; Roux, B

    2000-01-01

    A computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) is described to simulate the movement of ions in membrane channels. The proposed algorithm, GCMC/BD, allows the simulation of ion channels with a realistic implementation of boundary conditions of concentration and transmembrane potential. The method is consistent with a statistical mechanical formulation of the equilibrium properties of ion channels (; Biophys. J. 77:139-153). The GCMC/BD algorithm is illustrated with simulations of simple test systems and of the OmpF porin of Escherichia coli. The approach provides a framework for simulating ion permeation in the context of detailed microscopic models. PMID:10920012

  11. Analogue Simulation and Orbit Solution Algorithm of Astrometric Exoplanet Detection

    NASA Astrophysics Data System (ADS)

    Huang, Ping-hui; Ji, Jiang-hui

    2017-07-01

    Astrometry is an effective measure to detect exoplanets. It has many advantages that other detection methods do not bear, such as providing three dimensional planetary orbit, and determining planetary mass, etc. Astrometry will enrich the sample of exoplanets. As the high-precision astrometric satellite Gaia (Global Astrometry Interferometer for Astrophysics) was launched in 2013, it is predictable that there will be abundant long-period Jupiter-size planets to be discovered by Gaia. In this paper, we specify the α Centauri A, HD 62509, and GJ 876 systems, and generate the synthetic astrometric data with the single-time astrometric precision of Gaia. Then we use the Lomb-Scargle periodogram to analyze the periodical signal of planetary orbit, and use the Markov Chain Monte Carlo (MCMC) algorithm to make the orbit inversion of the planetary system, the obtained result is well coincident with the initial parameters of the planet.

  12. A parallel algorithm for switch-level timing simulation on a hypercube multiprocessor

    NASA Technical Reports Server (NTRS)

    Rao, Hariprasad Nannapaneni

    1989-01-01

    The parallel approach to speeding up simulation is studied, specifically the simulation of digital LSI MOS circuitry on the Intel iPSC/2 hypercube. The simulation algorithm is based on RSIM, an event driven switch-level simulator that incorporates a linear transistor model for simulating digital MOS circuits. Parallel processing techniques based on the concepts of Virtual Time and rollback are utilized so that portions of the circuit may be simulated on separate processors, in parallel for as large an increase in speed as possible. A partitioning algorithm is also developed in order to subdivide the circuit for parallel processing.

  13. MODA: a new algorithm to compute optical depths in multidimensional hydrodynamic simulations

    NASA Astrophysics Data System (ADS)

    Perego, Albino; Gafton, Emanuel; Cabezón, Rubén; Rosswog, Stephan; Liebendörfer, Matthias

    2014-08-01

    Aims: We introduce the multidimensional optical depth algorithm (MODA) for the calculation of optical depths in approximate multidimensional radiative transport schemes, equally applicable to neutrinos and photons. Motivated by (but not limited to) neutrino transport in three-dimensional simulations of core-collapse supernovae and neutron star mergers, our method makes no assumptions about the geometry of the matter distribution, apart from expecting optically transparent boundaries. Methods: Based on local information about opacities, the algorithm figures out an escape route that tends to minimize the optical depth without assuming any predefined paths for radiation. Its adaptivity makes it suitable for a variety of astrophysical settings with complicated geometry (e.g., core-collapse supernovae, compact binary mergers, tidal disruptions, star formation, etc.). We implement the MODA algorithm into both a Eulerian hydrodynamics code with a fixed, uniform grid and into an SPH code where we use a tree structure that is otherwise used for searching neighbors and calculating gravity. Results: In a series of numerical experiments, we compare the MODA results with analytically known solutions. We also use snapshots from actual 3D simulations and compare the results of MODA with those obtained with other methods, such as the global and local ray-by-ray method. It turns out that MODA achieves excellent accuracy at a moderate computational cost. In appendix we also discuss implementation details and parallelization strategies.

  14. Material growth in thermoelastic continua: Theory, algorithmics, and simulation

    NASA Astrophysics Data System (ADS)

    Vignes, Chet Monroe

    Within the medical community, there has been increasing interest in understanding material growth in biomaterials. Material growth is the capability of a biomaterial to gain or lose mass. This research interest is driven by the host of health implications and medical problems related to this unique biomaterial property. Health providers are keen to understand the role of growth in healing and recovery so that surgical techniques, medical procedures, and physical therapy may be designed and implemented to stimulate healing and minimize recovery time. With this motivation, research seeks to identify and model mechanisms of material growth as well as growth-inducing factors in biomaterials. To this end, a theoretical formulation of stress-induced volumetric material growth in thermoelastic continua is developed. The theory derives, without the classical continuum mechanics assumption of mass conservation, the balance laws governing the mechanics of solids capable of growth. Also, a proposed extension of classical thermodynamic theory provides a foundation for developing general constitutive relations. The theory is consistent in the sense that classical thermoelastic continuum theory is embedded as a special case. Two growth mechanisms, a kinematic and a constitutive contribution, coupled in the most general case of growth, are identified. This identification allows for the commonly employed special cases of density-preserving growth and volume-preserving growth to be easily recovered. In the theory, material growth is regulated by a three-surface activation criterion and corresponding flow rules. A simple model for rate-independent finite growth is proposed based on this formulation. The associated algorithmic implementation, including a method for solving the underlying differential/algebraic equations for growth, is examined in the context of an implicit finite element method. Selected numerical simulations are presented that showcase the predictive capacity of the

  15. Simulation Results for Airborne Precision Spacing along Continuous Descent Arrivals

    NASA Technical Reports Server (NTRS)

    Barmore, Bryan E.; Abbott, Terence S.; Capron, William R.; Baxley, Brian T.

    2008-01-01

    This paper describes the results of a fast-time simulation experiment and a high-fidelity simulator validation with merging streams of aircraft flying Continuous Descent Arrivals through generic airspace to a runway at Dallas-Ft Worth. Aircraft made small speed adjustments based on an airborne-based spacing algorithm, so as to arrive at the threshold exactly at the assigned time interval behind their Traffic-To-Follow. The 40 aircraft were initialized at different altitudes and speeds on one of four different routes, and then merged at different points and altitudes while flying Continuous Descent Arrivals. This merging and spacing using flight deck equipment and procedures to augment or implement Air Traffic Management directives is called Flight Deck-based Merging and Spacing, an important subset of a larger Airborne Precision Spacing functionality. This research indicates that Flight Deck-based Merging and Spacing initiated while at cruise altitude and well prior to the Terminal Radar Approach Control entry can significantly contribute to the delivery of aircraft at a specified interval to the runway threshold with a high degree of accuracy and at a reduced pilot workload. Furthermore, previously documented work has shown that using a Continuous Descent Arrival instead of a traditional step-down descent can save fuel, reduce noise, and reduce emissions. Research into Flight Deck-based Merging and Spacing is a cooperative effort between government and industry partners.

  16. MUlti-Dimensional Spline-Based Estimator (MUSE) for Motion Estimation: Algorithm Development and Initial Results

    PubMed Central

    Viola, Francesco; Coe, Ryan L.; Owen, Kevin; Guenther, Drake A.; Walker, William F.

    2008-01-01

    Image registration and motion estimation play central roles in many fields, including RADAR, SONAR, light microscopy, and medical imaging. Because of its central significance, estimator accuracy, precision, and computational cost are of critical importance. We have previously presented a highly accurate, spline-based time delay estimator that directly determines sub-sample time delay estimates from sampled data. The algorithm uses cubic splines to produce a continuous representation of a reference signal and then computes an analytical matching function between this reference and a delayed signal. The location of the minima of this function yields estimates of the time delay. In this paper we describe the MUlti-dimensional Spline-based Estimator (MUSE) that allows accurate and precise estimation of multidimensional displacements/strain components from multidimensional data sets. We describe the mathematical formulation for two- and three-dimensional motion/strain estimation and present simulation results to assess the intrinsic bias and standard deviation of this algorithm and compare it to currently available multi-dimensional estimators. In 1000 noise-free simulations of ultrasound data we found that 2D MUSE exhibits maximum bias of 2.6 × 10−4 samples in range and 2.2 × 10−3 samples in azimuth (corresponding to 4.8 and 297 nm, respectively). The maximum simulated standard deviation of estimates in both dimensions was comparable at roughly 2.8 × 10−3 samples (corresponding to 54 nm axially and 378 nm laterally). These results are between two and three orders of magnitude better than currently used 2D tracking methods. Simulation of performance in 3D yielded similar results to those observed in 2D. We also present experimental results obtained using 2D MUSE on data acquired by an Ultrasonix Sonix RP imaging system with an L14-5/38 linear array transducer operating at 6.6 MHz. While our validation of the algorithm was performed using ultrasound data, MUSE

  17. MUlti-Dimensional Spline-Based Estimator (MUSE) for motion estimation: algorithm development and initial results.

    PubMed

    Viola, Francesco; Coe, Ryan L; Owen, Kevin; Guenther, Drake A; Walker, William F

    2008-12-01

    Image registration and motion estimation play central roles in many fields, including RADAR, SONAR, light microscopy, and medical imaging. Because of its central significance, estimator accuracy, precision, and computational cost are of critical importance. We have previously presented a highly accurate, spline-based time delay estimator that directly determines sub-sample time delay estimates from sampled data. The algorithm uses cubic splines to produce a continuous representation of a reference signal and then computes an analytical matching function between this reference and a delayed signal. The location of the minima of this function yields estimates of the time delay. In this paper we describe the MUlti-dimensional Spline-based Estimator (MUSE) that allows accurate and precise estimation of multi-dimensional displacements/strain components from multi-dimensional data sets. We describe the mathematical formulation for two- and three-dimensional motion/strain estimation and present simulation results to assess the intrinsic bias and standard deviation of this algorithm and compare it to currently available multi-dimensional estimators. In 1000 noise-free simulations of ultrasound data we found that 2D MUSE exhibits maximum bias of 2.6 x 10(-4) samples in range and 2.2 x 10(-3) samples in azimuth (corresponding to 4.8 and 297 nm, respectively). The maximum simulated standard deviation of estimates in both dimensions was comparable at roughly 2.8 x 10(-3) samples (corresponding to 54 nm axially and 378 nm laterally). These results are between two and three orders of magnitude better than currently used 2D tracking methods. Simulation of performance in 3D yielded similar results to those observed in 2D. We also present experimental results obtained using 2D MUSE on data acquired by an Ultrasonix Sonix RP imaging system with an L14-5/38 linear array transducer operating at 6.6 MHz. While our validation of the algorithm was performed using ultrasound data, MUSE is

  18. Some Algorithms For Simulating Size-resolved Aerosol Dynamics Models

    NASA Astrophysics Data System (ADS)

    Debry, E.; Sportisse, B.

    Physics, Wiley- 1 interscience, 1998 [2] Binkowski,F.S. and Shankar,U. The regional particulate matter model : Model de- scription and preliminary results Journal of geophysical research, 1995 [3] Whitby,E.R. and McMurry,P.H. Modal Aerosol Dynamics Modeling Aerosol Sci- ence and Technology, 1997 [4] Jacobson,M.Z. and Turco,R.P. and Jensen,E.J. and Toon,O.B. Modeling coagu- lation among particles of different composition and size Atmospheric Environment, 1994, [5] Dhaniyala,S. and Wexler,A.S., Numerical schemes to model condensation and evaporation of aerosols, Atmospheric environment,1995, [6] Sandu, A. A Spectral Method for Solving Aerosol Dynamics Submitted to Applied Numerical Mathematics, August 2001 [7] Debry, E. and Jourdain, B. and Sportisse, B. Modelling aerosol dynamics : a stochastic algorithm article in preparation, 2001

  19. Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales

    SciTech Connect

    E, Weinan; Liu, Di . E-mail: diliu@math.msu.edu; Vanden-Eijnden, Eric

    2007-01-20

    We present an efficient numerical algorithm for simulating chemical kinetic systems with multiple time scales. This algorithm is an improvement of the traditional stochastic simulation algorithm (SSA), also known as Gillespie's algorithm. It is in the form of a nested SSA and uses an outer SSA to simulate the slow reactions with rates computed from realizations of inner SSAs that simulate the fast reactions. The algorithm itself is quite general and seamless, and it amounts to a small modification of the original SSA. Our analysis of such multi-scale chemical kinetic systems allows us to identify the slow variables in the system, derive effective dynamics on the slow time scale, and provide error estimates for the nested SSA. Efficiency of the nested SSA is discussed using these error estimates, and illustrated through several numerical examples.

  20. Comparison of simulated quenching algorithms for design of diffractive optical elements.

    PubMed

    Liu, J S; Caley, A J; Waddie, A J; Taghizadeh, M R

    2008-02-20

    We compare the performance of very fast simulated quenching; generalized simulated quenching, which unifies classical Boltzmann simulated quenching and Cauchy fast simulated quenching; and variable step size simulated quenching. The comparison is carried out by applying these algorithms to the design of diffractive optical elements for beam shaping of monochromatic, spatially incoherent light to a tightly focused image spot, whose central lobe should be smaller than the geometrical-optics limit. For generalized simulated quenching we choose values of visiting and acceptance shape parameters recommended by other investigators and use both a one-dimensional and a multidimensional Tsallis random number generator. We find that, under our test conditions, variable step size simulated quenching, which generates each parameter's new states based on the acceptance ratio instead of a certain theoretical probability distribution, produces the best results. Finally, we demonstrate experimentally a tightly focused image spot, with a central lobe 0.22-0.68 times the geometrical-optics limit and a relative sidelobe intensity 55%-60% that of the central maximum intensity.

  1. Neutron spectrum unfolding using genetic algorithm in a Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Suman, Vitisha; Sarkar, P. K.

    2014-02-01

    A spectrum unfolding technique GAMCD (Genetic Algorithm and Monte Carlo based spectrum Deconvolution) has been developed using the genetic algorithm methodology within the framework of Monte Carlo simulations. Each Monte Carlo history starts with initial solution vectors (population) as randomly generated points in the hyper dimensional solution space that are related to the measured data by the response matrix of the detection system. The transition of the solution points in the solution space from one generation to another are governed by the genetic algorithm methodology using the techniques of cross-over (mating) and mutation in a probabilistic manner adding new solution points to the population. The population size is kept constant by discarding solutions having lesser fitness values (larger differences between measured and calculated results). Solutions having the highest fitness value at the end of each Monte Carlo history are averaged over all histories to obtain the final spectral solution. The present method shows promising results in neutron spectrum unfolding for both under-determined and over-determined problems with simulated test data as well as measured data when compared with some existing unfolding codes. An attractive advantage of the present method is the independence of the final spectra from the initial guess spectra.

  2. Macro-micro interlocked simulation algorithm: an exemplification for aurora arc evolution

    NASA Astrophysics Data System (ADS)

    Sato, Tetsuya; Hasegawa, Hiroki; Ohno, Nobuaki

    2009-01-01

    Using an innovative holistic simulation algorithm that can self-consistently treat a system that evolves as cooperation between macroscopic and microscopic processes, the evolution of a colorful aurora arc is beautifully reproduced as the result of cooperation between the global field-aligned feedback instability of the coupled magnetosphere-ionosphere system and the ensuing microscopic ion-acoustic instability that generates electric double layers and accelerates aurora electrons. These results are in agreement with rocket and satellite observations. This shows that the proposed holistic algorithm could be a reliable tool to reveal complex real dramatic events and become, in the near future, a viable scientifically secure prediction tool for natural disasters such as earthquakes, landslides and floods caused by typhoons.

  3. Design and simulation of imaging algorithm for Fresnel telescopy imaging system

    NASA Astrophysics Data System (ADS)

    Lv, Xiao-yu; Liu, Li-ren; Yan, Ai-min; Sun, Jian-feng; Dai, En-wen; Li, Bing

    2011-06-01

    Fresnel telescopy (short for Fresnel telescopy full-aperture synthesized imaging ladar) is a new high resolution active laser imaging technique. This technique is a variant of Fourier telescopy and optical scanning holography, which uses Fresnel zone plates to scan target. Compare with synthetic aperture imaging ladar(SAIL), Fresnel telescopy avoids problem of time synchronization and space synchronization, which decreasing technical difficulty. In one-dimensional (1D) scanning operational mode for moving target, after time-to-space transformation, spatial distribution of sampling data is non-uniform because of the relative motion between target and scanning beam. However, as we use fast Fourier transform (FFT) in the following imaging algorithm of matched filtering, distribution of data should be regular and uniform. We use resampling interpolation to transform the data into two-dimensional (2D) uniform distribution, and accuracy of resampling interpolation process mainly affects the reconstruction results. Imaging algorithms with different resampling interpolation algorithms have been analysis and computer simulation are also given. We get good reconstruction results of the target, which proves that the designed imaging algorithm for Fresnel telescopy imaging system is effective. This work is found to have substantial practical value and offers significant benefit for high resolution imaging system of Fresnel telescopy laser imaging ladar.

  4. Simulation and experiment research of face recognition with modified multi-method morphological correlation algorithm

    NASA Astrophysics Data System (ADS)

    Yang, Yu; Xuping, Zhang

    2007-03-01

    Morphological definition of similarity degree of gray-scale image and general definition of morphological correlation (GMC) are proposed. Hardware and software design for a compact joint transform correlator are presented in order to implement GMC. Two kinds of modified general morphological correlation algorithm are proposed. The gray-scale image is decomposed into a set of binary image slices in certain decomposition method. In the first algorithm, the edge of each binary joint image slice is detected, width adjustability of which is investigated, and the joint power spectrum of the edge is summed. In the second algorithm, the joint power spectrum of each pair is binarized or thinned and then summed in one situation, and the summation of the joint power spectrums of these pairs is binarized or thinned in the other situation. Computer-simulation results and real face image recognition results indicate that the modified algorithm can improve the discrimination capabilities with respect to the gray-scale face images of high similarity.

  5. A fast algorithm for voxel-based deterministic simulation of X-ray imaging

    NASA Astrophysics Data System (ADS)

    Li, Ning; Zhao, Hua-Xia; Cho, Sang-Hyun; Choi, Jung-Gil; Kim, Myoung-Hee

    2008-04-01

    Deterministic method based on ray tracing technique is known as a powerful alternative to the Monte Carlo approach for virtual X-ray imaging. The algorithm speed is a critical issue in the perspective of simulating hundreds of images, notably to simulate tomographic acquisition or even more, to simulate X-ray radiographic video recordings. We present an algorithm for voxel-based deterministic simulation of X-ray imaging using voxel-driven forward and backward perspective projection operations and minimum bounding rectangles (MBRs). The algorithm is fast, easy to implement, and creates high-quality simulated radiographs. As a result, simulated radiographs can typically be obtained in split seconds with a simple personal computer. Program summaryProgram title: X-ray Catalogue identifier: AEAD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 416 257 No. of bytes in distributed program, including test data, etc.: 6 018 263 Distribution format: tar.gz Programming language: C (Visual C++) Computer: Any PC. Tested on DELL Precision 380 based on a Pentium D 3.20 GHz processor with 3.50 GB of RAM Operating system: Windows XP Classification: 14, 21.1 Nature of problem: Radiographic simulation of voxelized objects based on ray tracing technique. Solution method: The core of the simulation is a fast routine for the calculation of ray-box intersections and minimum bounding rectangles, together with voxel-driven forward and backward perspective projection operations. Restrictions: Memory constraints. There are three programs in all. A. Program for test 3.1(1): Object and detector have axis-aligned orientation; B. Program for test 3.1(2): Object in arbitrary orientation; C. Program for test 3.2: Simulation of X-ray video

  6. [Research on optimization of lower limb parameters of cardiopulmonary resuscitation simulation model based on genetic algorithm].

    PubMed

    Xu, Lin

    2014-10-01

    Sudden cardiac arrest is one of the critical clinical syndromes in emergency situations. A cardiopulmonary resuscitation (CPR) is a necessary curing means for those patients with sudden cardiac arrest. In order to simulate effectively the hemodynamic effects of human under AEI-CPR, which is active compression-decompression CPR coupled with enhanced external counter-pulsation and inspiratory impedance threshold valve, and research physiological parameters of each part of lower limbs in more detail, a CPR simulation model established by Babbs was refined. The part of lower limbs was divided into iliac, thigh and calf, which had 15 physiological parameters. Then, these 15 physiological parameters based on genetic algorithm were optimized, and ideal simulation results were obtained finally.

  7. SPORT: An Algorithm for Divisible Load Scheduling with Result Collection on Heterogeneous Systems

    NASA Astrophysics Data System (ADS)

    Ghatpande, Abhay; Nakazato, Hidenori; Beaumont, Olivier; Watanabe, Hiroshi

    Divisible Load Theory (DLT) is an established mathematical framework to study Divisible Load Scheduling (DLS). However, traditional DLT does not address the scheduling of results back to source (i. e., result collection), nor does it comprehensively deal with system heterogeneity. In this paper, the DLSRCHETS (DLS with Result Collection on HET-erogeneous Systems) problem is addressed. The few papers to date that have dealt with DLSRCHETS, proposed simplistic LIFO (Last In, First Out) and FIFO (First In, First Out) type of schedules as solutions to DLSRCHETS. In this paper, a new polynomial time heuristic algorithm, SPORT (System Parameters based Optimized Result Transfer), is proposed as a solution to the DLSRCHETS problem. With the help of simulations, it is proved that the performance of SPORT is significantly better than existing algorithms. The other major contributions of this paper include, for the first time ever, (a) the derivation of the condition to identify the presence of idle time in a FIFO schedule for two processors, (b) the identification of the limiting condition for the optimality of FIFO and LIFO schedules for two processors, and (c) the introduction of the concept of equivalent processor in DLS for heterogeneous systems with result collection.

  8. 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.

  9. A fast and efficient algorithm for Slater determinant updates in quantum Monte Carlo simulations.

    PubMed

    Nukala, Phani K V V; Kent, P R C

    2009-05-28

    We present an efficient low-rank updating algorithm for updating the trial wave functions used in quantum Monte Carlo (QMC) simulations. The algorithm is based on low-rank updating of the Slater determinants. In particular, the computational complexity of the algorithm is O(kN) during the kth step compared to traditional algorithms that require O(N(2)) computations, where N is the system size. For single determinant trial wave functions the new algorithm is faster than the traditional O(N(2)) Sherman-Morrison algorithm for up to O(N) updates. For multideterminant configuration-interaction-type trial wave functions of M+1 determinants, the new algorithm is significantly more efficient, saving both O(MN(2)) work and O(MN(2)) storage. The algorithm enables more accurate and significantly more efficient QMC calculations using configuration-interaction-type wave functions.

  10. Synchronization Algorithms for Co-Simulation of Power Grid and Communication Networks

    SciTech Connect

    Ciraci, Selim; Daily, Jeffrey A.; Agarwal, Khushbu; Fuller, Jason C.; Marinovici, Laurentiu D.; Fisher, Andrew R.

    2014-09-11

    The ongoing modernization of power grids consists of integrating them with communication networks in order to achieve robust and resilient control of grid operations. To understand the operation of the new smart grid, one approach is to use simulation software. Unfortunately, current power grid simulators at best utilize inadequate approximations to simulate communication networks, if at all. Cooperative simulation of specialized power grid and communication network simulators promises to more accurately reproduce the interactions of real smart grid deployments. However, co-simulation is a challenging problem. A co-simulation must manage the exchange of informa- tion, including the synchronization of simulator clocks, between all simulators while maintaining adequate computational perfor- mance. This paper describes two new conservative algorithms for reducing the overhead of time synchronization, namely Active Set Conservative and Reactive Conservative. We provide a detailed analysis of their performance characteristics with respect to the current state of the art including both conservative and optimistic synchronization algorithms. In addition, we provide guidelines for selecting the appropriate synchronization algorithm based on the requirements of the co-simulation. The newly proposed algorithms are shown to achieve as much as 14% and 63% im- provement, respectively, over the existing conservative algorithm.

  11. Use of a novel Hill-climbing genetic algorithm in protein folding simulations.

    PubMed

    Cooper, Lee R; Corne, David W; Crabbe, M James C

    2003-12-01

    We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 A with an optimised hydrophobic term in the fitness function.

  12. Simulating Future GPS Clock Scenarios with Two Composite Clock Algorithms

    DTIC Science & Technology

    2010-11-01

    Alexandria, Virginia), pp. 223-242. [8] C. A. Greenhall, 2007, “A Kalman filter clock ensemble algorithm that admits measurement noise,” Metrologia ...43, S311-S321. [9] J. A. Davis, C. A. Greenhall, and P. W. Stacey, 2005, “A Kalman filter clock algorithm for use in the presence of flicker frequency modulation noise,” Metrologia , 42, 1-10.

  13. Different genetic algorithms and the evolution of specialization: a study with groups of simulated neural robots.

    PubMed

    Ferrauto, Tomassino; Parisi, Domenico; Di Stefano, Gabriele; Baldassarre, Gianluca

    2013-01-01

    Organisms that live in groups, from microbial symbionts to social insects and schooling fish, exhibit a number of highly efficient cooperative behaviors, often based on role taking and specialization. These behaviors are relevant not only for the biologist but also for the engineer interested in decentralized collective robotics. We address these phenomena by carrying out experiments with groups of two simulated robots controlled by neural networks whose connection weights are evolved by using genetic algorithms. These algorithms and controllers are well suited to autonomously find solutions for decentralized collective robotic tasks based on principles of self-organization. The article first presents a taxonomy of role-taking and specialization mechanisms related to evolved neural network controllers. Then it introduces two cooperation tasks, which can be accomplished by either role taking or specialization, and uses these tasks to compare four different genetic algorithms to evaluate their capacity to evolve a suitable behavioral strategy, which depends on the task demands. Interestingly, only one of the four algorithms, which appears to have more biological plausibility, is capable of evolving role taking or specialization when they are needed. The results are relevant for both collective robotics and biology, as they can provide useful hints on the different processes that can lead to the emergence of specialization in robots and organisms.

  14. Memetic algorithm for real-time combinatorial stochastic simulation optimization problems with performance analysis.

    PubMed

    Horng, Shih-Cheng; Lin, Shin-Yeu; Lee, Loo Hay; Chen, Chun-Hung

    2013-10-01

    A three-phase memetic algorithm (MA) is proposed to find a suboptimal solution for real-time combinatorial stochastic simulation optimization (CSSO) problems with large discrete solution space. In phase 1, a genetic algorithm assisted by an offline global surrogate model is applied to find N good diversified solutions. In phase 2, a probabilistic local search method integrated with an online surrogate model is used to search for the approximate corresponding local optimum of each of the N solutions resulted from phase 1. In phase 3, the optimal computing budget allocation technique is employed to simulate and identify the best solution among the N local optima from phase 2. The proposed MA is applied to an assemble-to-order problem, which is a real-world CSSO problem. Extensive simulations were performed to demonstrate its superior performance, and results showed that the obtained solution is within 1% of the true optimum with a probability of 99%. We also provide a rigorous analysis to evaluate the performance of the proposed MA.

  15. Algorithmic scalability in globally constrained conservative parallel discrete event simulations of asynchronous systems.

    PubMed

    Kolakowska, A; Novotny, M A; Korniss, G

    2003-04-01

    We consider parallel simulations for asynchronous systems employing L processing elements that are arranged on a ring. Processors communicate only among the nearest neighbors and advance their local simulated time only if it is guaranteed that this does not violate causality. In simulations with no constraints, in the infinite L limit the utilization scales [Korniss et al., Phys. Rev. Lett. 84, 1351 (2000)]; but, the width of the virtual time horizon diverges (i.e., the measurement phase of the algorithm does not scale). In this work, we introduce a moving Delta-window global constraint, which modifies the algorithm so that the measurement phase scales as well. We present results of systematic studies in which the system size (i.e., L and the volume load per processor) as well as the constraint are varied. The Delta constraint eliminates the extreme fluctuations in the virtual time horizon, provides a bound on its width, and controls the average progress rate. The width of the Delta window can serve as a tuning parameter that, for a given volume load per processor, could be adjusted to optimize the utilization, so as to maximize the efficiency. This result may find numerous applications in modeling the evolution of general spatially extended short-range interacting systems with asynchronous dynamics, including dynamic Monte Carlo studies.

  16. New Algorithms for Computing the Time-to-Collision in Freeway Traffic Simulation Models

    PubMed Central

    Hou, Jia; List, George F.; Guo, Xiucheng

    2014-01-01

    Ways to estimate the time-to-collision are explored. In the context of traffic simulation models, classical lane-based notions of vehicle location are relaxed and new, fast, and efficient algorithms are examined. With trajectory conflicts being the main focus, computational procedures are explored which use a two-dimensional coordinate system to track the vehicle trajectories and assess conflicts. Vector-based kinematic variables are used to support the calculations. Algorithms based on boxes, circles, and ellipses are considered. Their performance is evaluated in the context of computational complexity and solution time. Results from these analyses suggest promise for effective and efficient analyses. A combined computation process is found to be very effective. PMID:25628650

  17. Assessment of Rainfall-Runoff Simulation Model Based on Satellite Algorithm

    NASA Astrophysics Data System (ADS)

    Nemati, A. R.; Zakeri Niri, M.; Moazami, S.

    2015-12-01

    Simulation of rainfall-runoff process is one of the most important research fields in hydrology and water resources. Generally, the models used in this section are divided into two conceptual and data-driven categories. In this study, a conceptual model and two data-driven models have been used to simulate rainfall-runoff process in Tamer sub-catchment located in Gorganroud watershed in Iran. The conceptual model used is HEC-HMS, and data-driven models are neural network model of multi-layer Perceptron (MLP) and support vector regression (SVR). In addition to simulation of rainfall-runoff process using the recorded land precipitation, the performance of four satellite algorithms of precipitation, that is, CMORPH, PERSIANN, TRMM 3B42 and TRMM 3B42RT were studied. In simulation of rainfall-runoff process, calibration and accuracy of the models were done based on satellite data. The results of the research based on three criteria of correlation coefficient (R), root mean square error (RMSE) and mean absolute error (MAE) showed that in this part the two models of SVR and MLP could perform the simulation of runoff in a relatively appropriate way, but in simulation of the maximum values of the flow, the error of models increased.

  18. Preliminary result of GeoKompsat-2A/AMI land surface temperature retrieval algorithm using Himawari-8/AHI data

    NASA Astrophysics Data System (ADS)

    Choi, Youn-Young; Suh, Myoung-Seok; Park, Gwan-Young

    2017-04-01

    In this study, we developed the prototype of GeoKompsat-2A/AMI land surface temperature retrieval algorithm using proxy data of Himawari-8/AHI data. In order to develop the LST retrieval algorithm, we simulated spectral radiance at the top of atmosphere (TOA) using MODTRAN4.0 based on the satellite viewing angle, atmospheric profile, emissivity, and diurnal temperature range of LST and air temperature of GeoKompsat-2A/AMI observing area. The TOA radiances are transferred into brightness temperature of each channel using the spectral response function of Himawari/AHI IR channels and inverse Planck function. Using the pseudo-match up database from the RTM simulations, the LST retrieval equations were derived according to the day/night and atmospheric conditions (wet/normal/dry). The LST estimated by the developed algorithm showed a strong correlation (0.995) with the prescribed LST and relatively small bias (0.007 K) and root mean square error (RMSE: 1.145 K). However, the LST retrieval algorithm showed a large RMSE when the brightness temperature difference is greater than 5K and the lapse rate condition is superadiabatic. We are plan to improve the LST retrieval algorithm through the reclassification of LST retrieval equation based on the evaluation results. And the LST algorithm was able to reasonably retrieve the LST from Himawari-8/AHI data compared to the MODIS LST version 5. The preliminary validation results showed that the LST retrieved from Himawari/AHI data was slightly warmer (+1.9 K) than that of the collocated MODIS LST. In this presentation, we will show the detailed results of LST retrieval algorithm including validation results according to the day/night and other impacting factors.

  19. Parallel simulations of Grover's algorithm for closest match search in neutron monitor data

    NASA Astrophysics Data System (ADS)

    Kussainov, Arman; White, Yelena

    We are studying the parallel implementations of Grover's closest match search algorithm for neutron monitor data analysis. This includes data formatting, and matching quantum parameters to a conventional structure of a chosen programming language and selected experimental data type. We have employed several workload distribution models based on acquired data and search parameters. As a result of these simulations, we have an understanding of potential problems that may arise during configuration of real quantum computational devices and the way they could run tasks in parallel. The work was supported by the Science Committee of the Ministry of Science and Education of the Republic of Kazakhstan Grant #2532/GF3.

  20. Effectiveness of Intravenous Infusion Algorithms for Glucose Control in Diabetic Patients Using Different Simulation Models

    PubMed Central

    Farmer, Terry G.; Edgar, Thomas F.

    2009-01-01

    The effectiveness of closed-loop insulin infusion algorithms is assessed for three different mathematical models describing insulin and glucose dynamics within a Type I diabetes patient. Simulations are performed to assess the effectiveness of proportional plus integral plus derivative (PID) control, feedforward control, and a physiologically-based control system with respect to maintaining normal glucose levels during a meal and during exercise. Control effectiveness is assessed by comparing the simulated response to a simulation of a healthy patient during both a meal and exercise and establishing maximum and minimum glucose levels and insulin infusion levels, as well as maximum duration of hyperglycemia. Controller effectiveness is assessed within the minimal model, the Sorensen model, and the Hovorka model. Results showed that no type of control was able to maintain normal conditions when simulations were performed using the minimal model. For both the Sorensen model and the Hovorka model, proportional control was sufficient to maintain normal glucose levels. Given published clinical data showing the ineffectiveness of PID control in patients, the work demonstrates that controller success based on simulation results can be misleading, and that future work should focus on addressing the model discrepancies. PMID:20161147

  1. The Research on Web-Based Testing Environment Using Simulated Annealing Algorithm

    PubMed Central

    2014-01-01

    The computerized evaluation is now one of the most important methods to diagnose learning; with the application of artificial intelligence techniques in the field of evaluation, the computerized adaptive testing gradually becomes one of the most important evaluation methods. In this test, the computer dynamic updates the learner's ability level and selects tailored items from the item pool. In order to meet the needs of the test it requires that the system has a relatively high efficiency of the implementation. To solve this problem, we proposed a novel method of web-based testing environment based on simulated annealing algorithm. In the development of the system, through a series of experiments, we compared the simulated annealing method and other methods of the efficiency and efficacy. The experimental results show that this method ensures choosing nearly optimal items from the item bank for learners, meeting a variety of assessment needs, being reliable, and having valid judgment in the ability of learners. In addition, using simulated annealing algorithm to solve the computing complexity of the system greatly improves the efficiency of select items from system and near-optimal solutions. PMID:24959600

  2. A Linked Simulation-Optimization (LSO) Model for Conjunctive Irrigation Management using Clonal Selection Algorithm

    NASA Astrophysics Data System (ADS)

    Islam, Sirajul; Talukdar, Bipul

    2016-09-01

    A Linked Simulation-Optimization (LSO) model based on a Clonal Selection Algorithm (CSA) was formulated for application in conjunctive irrigation management. A series of measures were considered for reducing the computational burden associated with the LSO approach. Certain modifications were incurred to the formulated CSA, so as to decrease the number of function evaluations. In addition, a simple problem specific code for a two dimensional groundwater flow simulation model was developed. The flow model was further simplified by a novel approach of area reduction, in order to save computational time in simulation. The LSO model was applied in the irrigation command of the Pagladiya Dam Project in Assam, India. With a view to evaluate the performance of the CSA, a Genetic Algorithm (GA) was used as a comparison base. The results from the CSA compared well with those from the GA. In fact, the CSA was found to consume less computational time than the GA while converging to the optimal solution, due to the modifications incurred in it.

  3. Detection of water quality using simulated satellite data and semi-empirical algorithms in Finland.

    PubMed

    Härmä, P; Vepsäläinen, J; Hannonen, T; Pyhälahti, T; Kämäri, J; Kallio, K; Eloheimo, K; Koponen, S

    2001-03-14

    The aim of the study was to test the feasibility of the band combination of the TERRA MODIS and ENVISAT MERIS instruments for operational monitoring of lakes and coastal waters in Finland. Also simulated LANDSAT TM data were tested. Satellite bands were simulated using airborne measurements with AISA imaging spectrometer. Semi-empirical algorithms with simulated satellite data were tested against field observations using regression analysis. Interpretation of chlorophyll a, suspended matter, turbidity and secchi-disk depth was included in the analyses. The data for this study were gathered in campaigns carried out in May and August 1997 and August 1998 both for lakes in southern Finland and coastal waters of the Baltic Sea. The data set included 85 in situ observations for lakes and 107 for coastal waters. Our results show that the band combination to be included in the ENVISAT MERIS instrument enables the interpretation of water quality, including chlorophyll a concentration using semi-empirical algorithms both for lakes and coastal waters. MERIS band 9 centred at 705 nm is proven to be of vital importance for the detection of chlorophyll a in local surface waters.

  4. Thermoluminescence curves simulation using genetic algorithm with factorial design

    NASA Astrophysics Data System (ADS)

    Popko, E. A.; Weinstein, I. A.

    2016-05-01

    The evolutionary approach is an effective optimization tool for numeric analysis of thermoluminescence (TL) processes to assess the microparameters of kinetic models and to determine its effects on the shape of TL peaks. In this paper, the procedure for tuning of genetic algorithm (GA) is presented. This approach is based on multifactorial experiment and allows choosing intrinsic mechanisms of evolutionary operators which provide the most efficient algorithm performance. The proposed method is tested by considering the “one trap-one recombination center” (OTOR) model as an example and advantages for approximation of experimental TL curves are shown.

  5. Cross-comparison of three electromyogram decomposition algorithms assessed with experimental and simulated data.

    PubMed

    Dai, Chenyun; Li, Yejin; Christie, Anita; Bonato, Paolo; McGill, Kevin C; Clancy, Edward A

    2015-01-01

    The reliability of clinical and scientific information provided by algorithms that automatically decompose the electromyogram (EMG) depends on the algorithms' accuracies. We used experimental and simulated data to assess the agreement and accuracy of three publicly available decomposition algorithms-EMGlab (McGill , 2005) (single channel data only), Fuzzy Expert (Erim and Lim, 2008) and Montreal (Florestal , 2009). Data consisted of quadrifilar needle EMGs from the tibialis anterior of 12 subjects at 10%, 20% and 50% maximum voluntary contraction (MVC); single channel needle EMGs from the biceps brachii of 10 controls and 10 patients during contractions just above threshold; and matched simulated data. Performance was assessed via agreement between pairs of algorithms for experimental data and accuracy with respect to the known decomposition for simulated data. For the quadrifilar experimental data, median agreements between the Montreal and Fuzzy Expert algorithms at 10%, 20%, and 50% MVC were 95%, 86%, and 64%, respectively. For the single channel control and patient data, median agreements between the three algorithm pairs were statistically similar at ∼ 97% and ∼ 92%, respectively. Accuracy on the simulated data exceeded this performance. Agreement/accuracy was strongly related to the Decomposability Index (Florestal , 2009). When agreement was high between algorithm pairs applied to simulated data, so was accuracy.

  6. Superspreading: molecular dynamics simulations and experimental results

    NASA Astrophysics Data System (ADS)

    Theodorakis, Panagiotis; Kovalchuk, Nina; Starov, Victor; Muller, Erich; Craster, Richard; Matar, Omar

    2015-11-01

    The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Recently, we have observed that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. Here, we present the structural characteristics and kinetics of the droplet spreading during the different stages of this process, and we compare our results with experimental data for trisiloxane and poly oxy ethylene surfactants. In this way, we highlight and explore the differences between surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting. EPSRC Platform Grant MACIPh (EP/L020564/).

  7. Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks.

    PubMed

    Vestergaard, Christian L; Génois, Mathieu

    2015-10-01

    Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling.

  8. Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks

    PubMed Central

    Vestergaard, Christian L.; Génois, Mathieu

    2015-01-01

    Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling. PMID:26517860

  9. Inrush Current Simulation of Power Transformer using Machine Parameters Estimated by Design Procedure of Winding Structure and Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Tokunaga, Yoshitaka

    This paper presents estimation techniques of machine parameters for power transformer using design procedure of transformer and genetic algorithm with real coding. Especially, it is very difficult to obtain machine parameters for transformers in customers' facilities. Using estimation techniques, machine parameters could be calculated from the only nameplate data of these transformers. Subsequently, EMTP-ATP simulation of the inrush current was carried out using machine parameters estimated by techniques developed in this study and simulation results were reproduced measured waveforms.

  10. DESIGNING SUSTAINABLE PROCESSES WITH SIMULATION: THE WASTE REDUCTION (WAR) ALGORITHM

    EPA Science Inventory

    The WAR Algorithm, a methodology for determining the potential environmental impact (PEI) of a chemical process, is presented with modifications that account for the PEI of the energy consumed within that process. From this theory, four PEI indexes are used to evaluate the envir...

  11. DESIGNING SUSTAINABLE PROCESSES WITH SIMULATION: THE WASTE REDUCTION (WAR) ALGORITHM

    EPA Science Inventory

    The WAR Algorithm, a methodology for determining the potential environmental impact (PEI) of a chemical process, is presented with modifications that account for the PEI of the energy consumed within that process. From this theory, four PEI indexes are used to evaluate the envir...

  12. Simulated annealing algorithm for solving chambering student-case assignment problem

    NASA Astrophysics Data System (ADS)

    Ghazali, Saadiah; Abdul-Rahman, Syariza

    2015-12-01

    The problem related to project assignment problem is one of popular practical problem that appear nowadays. The challenge of solving the problem raise whenever the complexity related to preferences, the existence of real-world constraints and problem size increased. This study focuses on solving a chambering student-case assignment problem by using a simulated annealing algorithm where this problem is classified under project assignment problem. The project assignment problem is considered as hard combinatorial optimization problem and solving it using a metaheuristic approach is an advantage because it could return a good solution in a reasonable time. The problem of assigning chambering students to cases has never been addressed in the literature before. For the proposed problem, it is essential for law graduates to peruse in chambers before they are qualified to become legal counselor. Thus, assigning the chambering students to cases is a critically needed especially when involving many preferences. Hence, this study presents a preliminary study of the proposed project assignment problem. The objective of the study is to minimize the total completion time for all students in solving the given cases. This study employed a minimum cost greedy heuristic in order to construct a feasible initial solution. The search then is preceded with a simulated annealing algorithm for further improvement of solution quality. The analysis of the obtained result has shown that the proposed simulated annealing algorithm has greatly improved the solution constructed by the minimum cost greedy heuristic. Hence, this research has demonstrated the advantages of solving project assignment problem by using metaheuristic techniques.

  13. Stochastic simulation of reaction subnetworks: Exploiting synergy between the chemical master equation and the Gillespie algorithm

    NASA Astrophysics Data System (ADS)

    Albert, J.

    2016-12-01

    Stochastic simulation of reaction networks is limited by two factors: accuracy and time. The Gillespie algorithm (GA) is a Monte Carlo-type method for constructing probability distribution functions (pdf) from statistical ensembles. Its accuracy is therefore a function of the computing time. The chemical master equation (CME) is a more direct route to obtaining the pdfs, however, solving the CME is generally very difficult for large networks. We propose a method that combines both approaches in order to simulate stochastically a part of a network. The network is first divided into two parts: A and B. Part A is simulated using the GA, while the solution of the CME for part B, with initial conditions imposed by simulation results of part A, is fed back into the GA. This cycle is then repeated a desired number of times. The advantage of this synergy between the two approaches is: 1) the GA needs to simulate only a part of the whole network, and hence is faster, and 2) the CME is necessarily simpler to solve, as the part of the network it describes is smaller. We will demonstrate on two examples - a positive feedback (genetic switch) and oscillations driven by a negative feedback - the utility of this approach.

  14. Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation

    PubMed Central

    Joldes, Grand Roman; Wittek, Adam; Miller, Karol

    2008-01-01

    Real time computation of soft tissue deformation is important for the use of augmented reality devices and for providing haptic feedback during operation or surgeon training. This requires algorithms that are fast, accurate and can handle material nonlinearities and large deformations. A set of such algorithms is presented in this paper, starting with the finite element formulation and the integration scheme used and addressing common problems such as hourglass control and locking. The computation examples presented prove that by using these algorithms, real time computations become possible without sacrificing the accuracy of the results. For a brain model having more than 7000 degrees of freedom, we computed the reaction forces due to indentation with frequency of around 1000 Hz using a standard dual core PC. Similarly, we conducted simulation of brain shift using a model with more than 50 000 degrees of freedom in less than a minute. The speed benefits of our models results from combining the Total Lagrangian formulation with explicit time integration and low order finite elements. PMID:19152791

  15. A Modified Shake Algorithm for Maintaining Rigid Bonds in Molecular Dynamics Simulations of Large Molecules

    NASA Astrophysics Data System (ADS)

    Lambrakos, S. G.; Boris, J. P.; Oran, E. S.; Chandrasekhar, I.; Nagumo, M.

    1989-12-01

    We present a new modification of the SHAKE algorithm, MSHAKE, that maintains fixed distances in molecular dynamics simulations of polyatomic molecules. The MSHAKE algorithm, which is applied by modifying the leapfrog algorithm to include forces of constraint, computes an initial estimate of constraint forces, then iteratively corrects the constraint forces required to maintain the fixed distances. Thus MSHAKE should always converge more rapidly than SHAKE. Further, the explicit determination of the constraint forces at each timestep makes MSHAKE convenient for use in molecular dynamics simulations where bond stress is a significant dynamical quantity.

  16. A Linac Simulation Code for Macro-Particles Tracking and Steering Algorithm Implementation

    SciTech Connect

    sun, yipeng

    2012-05-03

    In this paper, a linac simulation code written in Fortran90 is presented and several simulation examples are given. This code is optimized to implement linac alignment and steering algorithms, and evaluate the accelerator errors such as RF phase and acceleration gradient, quadrupole and BPM misalignment. It can track a single particle or a bunch of particles through normal linear accelerator elements such as quadrupole, RF cavity, dipole corrector and drift space. One-to-one steering algorithm and a global alignment (steering) algorithm are implemented in this code.

  17. Mechanobiological simulations of peri-acetabular bone ingrowth: a comparative analysis of cell-phenotype specific and phenomenological algorithms.

    PubMed

    Mukherjee, Kaushik; Gupta, Sanjay

    2017-03-01

    Several mechanobiology algorithms have been employed to simulate bone ingrowth around porous coated implants. However, there is a scarcity of quantitative comparison between the efficacies of commonly used mechanoregulatory algorithms. The objectives of this study are: (1) to predict peri-acetabular bone ingrowth using cell-phenotype specific algorithm and to compare these predictions with those obtained using phenomenological algorithm and (2) to investigate the influences of cellular parameters on bone ingrowth. The variation in host bone material property and interfacial micromotion of the implanted pelvis were mapped onto the microscale model of implant-bone interface. An overall variation of 17-88 % in peri-acetabular bone ingrowth was observed. Despite differences in predicted tissue differentiation patterns during the initial period, both the algorithms predicted similar spatial distribution of neo-tissue layer, after attainment of equilibrium. Results indicated that phenomenological algorithm, being computationally faster than the cell-phenotype specific algorithm, might be used to predict peri-prosthetic bone ingrowth. The cell-phenotype specific algorithm, however, was found to be useful in numerically investigating the influence of alterations in cellular activities on bone ingrowth, owing to biologically related factors. Amongst the host of cellular activities, matrix production rate of bone tissue was found to have predominant influence on peri-acetabular bone ingrowth.

  18. LMS learning algorithms: misconceptions and new results on converence.

    PubMed

    Wang, Z Q; Manry, M T; Schiano, J L

    2000-01-01

    The Widrow-Hoff delta rule is one of the most popular rules used in training neural networks. It was originally proposed for the ADALINE, but has been successfully applied to a few nonlinear neural networks as well. Despite its popularity, there exist a few misconceptions on its convergence properties. In this paper we consider repetitive learning (i.e., a fixed set of samples are used for training) and provide an in-depth analysis in the least mean square (LMS) framework. Our main result is that contrary to common belief, the nonbatch Widrow-Hoff rule does not converge in general. It converges only to a limit cycle.

  19. PENELOPE: An algorithm for Monte Carlo simulation of the penetration and energy loss of electrons and positrons in matter

    NASA Astrophysics Data System (ADS)

    Baró, J.; Sempau, J.; Fernández-Varea, J. M.; Salvat, F.

    1995-05-01

    A mixed algorithm for Monte Carlo simulation of relativistic electron and positron transport in matter is described. Cross sections for the different interaction mechanisms are approximated by expressions that permit the generation of random tracks by using purely analytical methods. Hard elastic collisions, with scattering angle greater than a preselected cutoff value, and hard inelastic collisions and radiative events, with energy loss larger than given cutoff values, are simulated in detail. Soft interactions, with scattering angle or energy loss less than the corresponding cutoffs, are simulated by means of multiple scattering approaches. This algorithm handles lateral displacements correctly and completely avoids difficulties related with interface crossing. The simulation is shown to be stable under variations of the adopted cutoffs; these can be made quite large, thus speeding up the simulation considerably, without altering the results. The reliability of the algorithm is demonstrated through a comparison of simulation results with experimental data. Good agreement is found for electrons and positrons with kinetic energies down to a few keV.

  20. Aerosol retrieval algorithm for MERIS: Description of concept and presenting results

    NASA Astrophysics Data System (ADS)

    Kosmale, Miriam; Kolmonen, Pekka; Popp, Thomas

    2017-04-01

    The Medium Resolution Imaging Spectrometer (MERIS) has been launched in 2002 onboard the ESA Envisat satellite and was providing data until Envisat's end in 2012. The MERIS spectrometer was designed primarily for surface and land scientific applications and measured reflected solar radiation in 15 channels from 400-900nm. Based on the work of Sayer and Hsu for SeaWiFS, an aerosol retrieval for MERIS was developed as part of the ESA Aerosol_cci project. The high spectral resolution of the instrument provides capability for retrieving aerosols. The algorithm can be transferred also to the OLCI measurements operating onboard the Sentinel-3 satellites since 2015. The retrieval code uses a Look-Up-Table (LUT) approach to speed up the calculations. The LUTs are calculated with the radiative transfer code LibRadtran (Meyer und Kylling, 2005). In minimizing the differences of satellite measurements with forward simulations, with Levenberg-Marquardt as the mathematical approach, the aerosol loading of the satellite measurement is inferred. As basis for the algorithm, a MERIS new cloud detection system (exploiting blue to near infrared channels) was defined, as well as a 16-day moving average surface albedo database. The presentation will describe the general concept of the retrieval algorithm and show results of aerosol properties retrieved from the MERIS measurements. An information content analysis is used to assess the general capability of retrieving aerosol optical depth (AOD) from the MERIS channels. Challenges concerning the retrieval algorithm and its input data will be discussed. Comparisons with external datasets will be given, either for the cloud mask, the surface database as well as the final AOD product. Results of the aerosol product will be presented together with a discussion on its quality triggered by validation with AERONET measurements. Mayer, B. & Kylling, A. Technical note: The libRadtran software package for radiative transfer calculations

  1. An object localization optimization technique in medical images using plant growth simulation algorithm.

    PubMed

    Bhattacharjee, Deblina; Paul, Anand; Kim, Jeong Hong; Kim, Mucheol

    2016-01-01

    The analysis of leukocyte images has drawn interest from fields of both medicine and computer vision for quite some time where different techniques have been applied to automate the process of manual analysis and classification of such images. Manual analysis of blood samples to identify leukocytes is time-consuming and susceptible to error due to the different morphological features of the cells. In this article, the nature-inspired plant growth simulation algorithm has been applied to optimize the image processing technique of object localization of medical images of leukocytes. This paper presents a random bionic algorithm for the automated detection of white blood cells embedded in cluttered smear and stained images of blood samples that uses a fitness function that matches the resemblances of the generated candidate solution to an actual leukocyte. The set of candidate solutions evolves via successive iterations as the proposed algorithm proceeds, guaranteeing their fit with the actual leukocytes outlined in the edge map of the image. The higher precision and sensitivity of the proposed scheme from the existing methods is validated with the experimental results of blood cell images. The proposed method reduces the feasible sets of growth points in each iteration, thereby reducing the required run time of load flow, objective function evaluation, thus reaching the goal state in minimum time and within the desired constraints.

  2. State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events

    NASA Astrophysics Data System (ADS)

    Roh, Min K.; Daigle, Bernie J.; Gillespie, Dan T.; Petzold, Linda R.

    2011-12-01

    In recent years there has been substantial growth in the development of algorithms for characterizing rare events in stochastic biochemical systems. Two such algorithms, the state-dependent weighted stochastic simulation algorithm (swSSA) and the doubly weighted SSA (dwSSA) are extensions of the weighted SSA (wSSA) by H. Kuwahara and I. Mura [J. Chem. Phys. 129, 165101 (2008)], 10.1063/1.2987701. The swSSA substantially reduces estimator variance by implementing system state-dependent importance sampling (IS) parameters, but lacks an automatic parameter identification strategy. In contrast, the dwSSA provides for the automatic determination of state-independent IS parameters, thus it is inefficient for systems whose states vary widely in time. We present a novel modification of the dwSSA—the state-dependent doubly weighted SSA (sdwSSA)—that combines the strengths of the swSSA and the dwSSA without inheriting their weaknesses. The sdwSSA automatically computes state-dependent IS parameters via the multilevel cross-entropy method. We apply the method to three examples: a reversible isomerization process, a yeast polarization model, and a lac operon model. Our results demonstrate that the sdwSSA offers substantial improvements over previous methods in terms of both accuracy and efficiency.

  3. State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events.

    PubMed

    Roh, Min K; Daigle, Bernie J; Gillespie, Dan T; Petzold, Linda R

    2011-12-21

    In recent years there has been substantial growth in the development of algorithms for characterizing rare events in stochastic biochemical systems. Two such algorithms, the state-dependent weighted stochastic simulation algorithm (swSSA) and the doubly weighted SSA (dwSSA) are extensions of the weighted SSA (wSSA) by H. Kuwahara and I. Mura [J. Chem. Phys. 129, 165101 (2008)]. The swSSA substantially reduces estimator variance by implementing system state-dependent importance sampling (IS) parameters, but lacks an automatic parameter identification strategy. In contrast, the dwSSA provides for the automatic determination of state-independent IS parameters, thus it is inefficient for systems whose states vary widely in time. We present a novel modification of the dwSSA--the state-dependent doubly weighted SSA (sdwSSA)--that combines the strengths of the swSSA and the dwSSA without inheriting their weaknesses. The sdwSSA automatically computes state-dependent IS parameters via the multilevel cross-entropy method. We apply the method to three examples: a reversible isomerization process, a yeast polarization model, and a lac operon model. Our results demonstrate that the sdwSSA offers substantial improvements over previous methods in terms of both accuracy and efficiency.

  4. Simulation of Anderson localization in a random fiber using a fast Fresnel diffraction algorithm

    NASA Astrophysics Data System (ADS)

    Davis, Jeffrey A.; Cottrell, Don M.

    2016-06-01

    Anderson localization has been previously demonstrated both theoretically and experimentally for transmission of a Gaussian beam through long distances in an optical fiber consisting of a random array of smaller fibers, each having either a higher or lower refractive index. However, the computational times were extremely long. We show how to simulate these results using a fast Fresnel diffraction algorithm. In each iteration of this approach, the light passes through a phase mask, undergoes Fresnel diffraction over a small distance, and then passes through the same phase mask. We also show results where we use a binary amplitude mask at the input that selectively illuminates either the higher or the lower index fibers. Additionally, we examine imaging of various sized objects through these fibers. In all cases, our results are consistent with other computational methods and experimental results, but with a much reduced computational time.

  5. On the rejection-based algorithm for simulation and analysis of large-scale reaction networks

    NASA Astrophysics Data System (ADS)

    Thanh, Vo Hong; Zunino, Roberto; Priami, Corrado

    2015-06-01

    Stochastic simulation for in silico studies of large biochemical networks requires a great amount of computational time. We recently proposed a new exact simulation algorithm, called the rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)], to improve simulation performance by postponing and collapsing as much as possible the propensity updates. In this paper, we analyze the performance of this algorithm in detail, and improve it for simulating large-scale biochemical reaction networks. We also present a new algorithm, called simultaneous RSSA (SRSSA), which generates many independent trajectories simultaneously for the analysis of the biochemical behavior. SRSSA improves simulation performance by utilizing a single data structure across simulations to select reaction firings and forming trajectories. The memory requirement for building and storing the data structure is thus independent of the number of trajectories. The updating of the data structure when needed is performed collectively in a single operation across the simulations. The trajectories generated by SRSSA are exact and independent of each other by exploiting the rejection-based mechanism. We test our new improvement on real biological systems with a wide range of reaction networks to demonstrate its applicability and efficiency.

  6. On the rejection-based algorithm for simulation and analysis of large-scale reaction networks

    SciTech Connect

    Thanh, Vo Hong; Zunino, Roberto; Priami, Corrado

    2015-06-28

    Stochastic simulation for in silico studies of large biochemical networks requires a great amount of computational time. We recently proposed a new exact simulation algorithm, called the rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)], to improve simulation performance by postponing and collapsing as much as possible the propensity updates. In this paper, we analyze the performance of this algorithm in detail, and improve it for simulating large-scale biochemical reaction networks. We also present a new algorithm, called simultaneous RSSA (SRSSA), which generates many independent trajectories simultaneously for the analysis of the biochemical behavior. SRSSA improves simulation performance by utilizing a single data structure across simulations to select reaction firings and forming trajectories. The memory requirement for building and storing the data structure is thus independent of the number of trajectories. The updating of the data structure when needed is performed collectively in a single operation across the simulations. The trajectories generated by SRSSA are exact and independent of each other by exploiting the rejection-based mechanism. We test our new improvement on real biological systems with a wide range of reaction networks to demonstrate its applicability and efficiency.

  7. Designing a binary Fourier-phase-only correlation filter using a simulated annealing algorithm

    NASA Astrophysics Data System (ADS)

    Nomura, Takanori; Nagase, Takamitsu; Itoh, Kazuyoshi; Ichioka, Yoshiki

    1990-11-01

    A method of designing a multiple-object recognition filter using a simulated annealing algorithm is presented. This filter has only binary phase information and is correlated with a binary Fourier-phase component of a test object. The filter is used in an incoherent-optical/digital-electric hybrid system. Computer simulations confirm the superior performance of this filter.

  8. Developing a Moving-Solid Algorithm for Simulating Tsunamis Induced by Rock Sliding

    NASA Astrophysics Data System (ADS)

    Chuang, M.; Wu, T.; Huang, C.; Wang, C.; Chu, C.; Chen, M.

    2012-12-01

    The landslide generated tsunami is one of the most devastating nature hazards. However, the involvement of the moving obstacle and dynamic free-surface movement makes the numerical simulation a difficult task. To describe the fluid motion, we use modified two-step projection method to decouple the velocity and pressure fields with 3D LES turbulent model. The free-surface movement is tracked by volume of fluid (VOF) method (Wu, 2004). To describe the effect from the moving obstacle on the fluid, a newly developed moving-solid algorithm (MSA) is developed. We combine the ideas from immersed boundary method (IBM) and partial-cell treatment (PCT) for specifying the contacting speed on the solid face and for presenting the obstacle blocking effect, respectively. By using the concept of IBM, the cell-center and cell-face velocities can be specified arbitrarily. And because we move the solid obstacle on a fixed grid, the boundary of the solid seldom coincides with the cell faces, which makes it inappropriate to assign the solid boundary velocity to the cell faces. To overcome this problem, the PCT is adopted. Using this algorithm, the solid surface is conceptually coincided with the cell faces, and the cell face velocity is able to be specified as the obstacle velocity. The advantage of using this algorithm is obtaining the stable pressure field which is extremely important for coupling with a force-balancing model which describes the solid motion. This model is therefore able to simulate incompressible high-speed fluid motion. In order to describe the solid motion, the DEM (Discrete Element Method) is adopted. The new-time solid movement can be predicted and divided into translation and rotation based on the Newton's equations and Euler's equations respectively. The detail of the moving-solid algorithm is presented in this paper. This model is then applied to studying the rock-slide generated tsunami. The results are validated with the laboratory data (Liu and Wu, 2005

  9. Fast Plasma Instrument for MMS: Data Compression Simulation Results

    NASA Technical Reports Server (NTRS)

    Barrie, A.; Adrian, Mark L.; Yeh, P.-S.; Winkert, G. E.; Lobell, J. V.; Vinas, A.F.; Simpson, D. J.; Moore, T. E.

    2008-01-01

    Magnetospheric Multiscale (MMS) mission will study small-scale reconnection structures and their rapid motions from closely spaced platforms using instruments capable of high angular, energy, and time resolution measurements. To meet these requirements, the Fast Plasma Instrument (FPI) consists of eight (8) identical half top-hat electron sensors and eights (8) identical ion sensors and an Instrument Data Processing Unit (IDPU). The sensors (electron or ion) are grouped into pairs whose 6 deg x 180 deg fields-of-view (FOV) are set 90 deg apart. Each sensor is equipped with electrostatic aperture steering to allow the sensor to scan a 45 deg x 180 deg fan about its nominal viewing (0 deg deflection) direction. Each pair of sensors, known as the Dual Electron Spectrometer (DES) and the Dual Ion Spectrometer (DIS), occupies a quadrant on the MMS spacecraft and the combination of the eight electron/ion sensors, employing aperture steering, image the full-sky every 30-ms (electrons) and 150-ms (ions), respectively. To probe the results in the DES complement of a given spacecraft generating 6.5-Mbs(exp -1) of electron data while the DIS generates 1.1-Mbs(exp -1) of ion data yielding an FPI total data rate of 6.6-MBs(exp -1). The FPI electron/ion data is collected by the IDPU then transmitted to the Central Data Instrument Processor (CIDP) on the spacecraft for science interest ranking. Only data sequences that contain the greatest amount of temporal/spatial structure will be intelligently down-linked by the spacecraft. Currently, the FPI data rate allocation to the CIDP is 1.5-Mbs(exp -1). Consequently, the FPI-IDPU must employ data/image compression to meet this CIDP telemetry allocation. Here, we present simulations of the CCSDS 122.0-B-1 algorithm-based compression of the FPI-DES electron data. Compression analysis is based upon a seed of re-processed Cluster/PEACE electron measurements. Topics to be discussed include: review of compression algorithm; data quality

  10. Fast Plasma Instrument for MMS: Data Compression Simulation Results

    NASA Technical Reports Server (NTRS)

    Barrie, A.; Adrian, Mark L.; Yeh, P.-S.; Winkert, G. E.; Lobell, J. V.; Vinas, A.F.; Simpson, D. J.; Moore, T. E.

    2008-01-01

    Magnetospheric Multiscale (MMS) mission will study small-scale reconnection structures and their rapid motions from closely spaced platforms using instruments capable of high angular, energy, and time resolution measurements. To meet these requirements, the Fast Plasma Instrument (FPI) consists of eight (8) identical half top-hat electron sensors and eights (8) identical ion sensors and an Instrument Data Processing Unit (IDPU). The sensors (electron or ion) are grouped into pairs whose 6 deg x 180 deg fields-of-view (FOV) are set 90 deg apart. Each sensor is equipped with electrostatic aperture steering to allow the sensor to scan a 45 deg x 180 deg fan about its nominal viewing (0 deg deflection) direction. Each pair of sensors, known as the Dual Electron Spectrometer (DES) and the Dual Ion Spectrometer (DIS), occupies a quadrant on the MMS spacecraft and the combination of the eight electron/ion sensors, employing aperture steering, image the full-sky every 30-ms (electrons) and 150-ms (ions), respectively. To probe the results in the DES complement of a given spacecraft generating 6.5-Mbs(exp -1) of electron data while the DIS generates 1.1-Mbs(exp -1) of ion data yielding an FPI total data rate of 6.6-MBs(exp -1). The FPI electron/ion data is collected by the IDPU then transmitted to the Central Data Instrument Processor (CIDP) on the spacecraft for science interest ranking. Only data sequences that contain the greatest amount of temporal/spatial structure will be intelligently down-linked by the spacecraft. Currently, the FPI data rate allocation to the CIDP is 1.5-Mbs(exp -1). Consequently, the FPI-IDPU must employ data/image compression to meet this CIDP telemetry allocation. Here, we present simulations of the CCSDS 122.0-B-1 algorithm-based compression of the FPI-DES electron data. Compression analysis is based upon a seed of re-processed Cluster/PEACE electron measurements. Topics to be discussed include: review of compression algorithm; data quality

  11. Fast Plasma Instrument for MMS: Data Compression Simulation Results

    NASA Astrophysics Data System (ADS)

    Barrie, A.; Adrian, M. L.; Yeh, P.; Winkert, G.; Lobell, J.; Vinas, A. F.; Simpson, D. G.

    2009-12-01

    Magnetospheric Multiscale (MMS) mission will study small-scale reconnection structures and their rapid motions from closely spaced platforms using instruments capable of high angular, energy, and time resolution measurements. To meet these requirements, the Fast Plasma Instrument (FPI) consists of eight (8) identical half top-hat electron sensors and eight (8) identical ion sensors and an Instrument Data Processing Unit (IDPU). The sensors (electron or ion) are grouped into pairs whose 6° x 180° fields-of-view (FOV) are set 90° apart. Each sensor is equipped with electrostatic aperture steering to allow the sensor to scan a 45° x 180° fan about the its nominal viewing (0° deflection) direction. Each pair of sensors, known as the Dual Electron Spectrometer (DES) and the Dual Ion Spectrometer (DIS), occupies a quadrant on the MMS spacecraft and the combination of the eight electron/ion sensors, employing aperture steering, image the full-sky every 30-ms (electrons) and 150-ms (ions), respectively. To probe the diffusion regions of reconnection, the highest temporal/spatial resolution mode of FPI results in the DES complement of a given spacecraft generating 6.5-Mb s-1 of electron data while the DIS generates 1.1-Mb s-1 of ion data yielding an FPI total data rate of 6.6-Mb s-1. The FPI electron/ion data is collected by the IDPU then transmitted to the Central Data Instrument Processor (CIDP) on the spacecraft for science interest ranking. Only data sequences that contain the greatest amount of temporal/spatial structure will be intelligently down-linked by the spacecraft. Currently, the FPI data rate allocation to the CIDP is 1.5-Mb s-1. Consequently, the FPI-IDPU must employ data/image compression to meet this CIDP telemetry allocation. Here, we present updated simulations of the CCSDS 122.0-B-1 algorithm-based compression of the FPI-DES electron data as well as the FPI-DIS ion data. Compression analysis is based upon a seed of re-processed Cluster

  12. Fast Plasma Instrument for MMS: Data Compression Simulation Results

    NASA Astrophysics Data System (ADS)

    Barrie, A. C.; Adrian, M. L.; Yeh, P.; Winkert, G. E.; Lobell, J. V.; Viňas, A. F.; Simpson, D. G.; Moore, T. E.

    2008-12-01

    Magnetospheric Multiscale (MMS) mission will study small-scale reconnection structures and their rapid motions from closely spaced platforms using instruments capable of high angular, energy, and time resolution measurements. To meet these requirements, the Fast Plasma Instrument (FPI) consists of eight (8) identical half top-hat electron sensors and eight (8) identical ion sensors and an Instrument Data Processing Unit (IDPU). The sensors (electron or ion) are grouped into pairs whose 6° × 180° fields-of-view (FOV) are set 90° apart. Each sensor is equipped with electrostatic aperture steering to allow the sensor to scan a 45° × 180° fan about the its nominal viewing (0° deflection) direction. Each pair of sensors, known as the Dual Electron Spectrometer (DES) and the Dual Ion Spectrometer (DIS), occupies a quadrant on the MMS spacecraft and the combination of the eight electron/ion sensors, employing aperture steering, image the full-sky every 30-ms (electrons) and 150-ms (ions), respectively. To probe the diffusion regions of reconnection, the highest temporal/spatial resolution mode of FPI results in the DES complement of a given spacecraft generating 6.5-Mb s-1 of electron data while the DIS generates 1.1-Mb s-1 of ion data yielding an FPI total data rate of 7.6-Mb s-1. The FPI electron/ion data is collected by the IDPU then transmitted to the Central Data Instrument Processor (CIDP) on the spacecraft for science interest ranking. Only data sequences that contain the greatest amount of temporal/spatial structure will be intelligently down-linked by the spacecraft. Currently, the FPI data rate allocation to the CIDP is 1.5-Mb s-1. Consequently, the FPI-IDPU must employ data/image compression to meet this CIDP telemetry allocation. Here, we present simulations of the CCSDS 122.0-B-1 algorithm- based compression of the FPI-DES electron data. Compression analysis is based upon a seed of re- processed Cluster/PEACE electron measurements. Topics to be

  13. Numerical stability of relativistic beam multidimensional PIC simulations employing the Esirkepov algorithm

    SciTech Connect

    Godfrey, Brendan B.; Vay, Jean-Luc

    2013-09-01

    Rapidly growing numerical instabilities routinely occur in multidimensional particle-in-cell computer simulations of plasma-based particle accelerators, astrophysical phenomena, and relativistic charged particle beams. Reducing instability growth to acceptable levels has necessitated higher resolution grids, high-order field solvers, current filtering, etc. except for certain ratios of the time step to the axial cell size, for which numerical growth rates and saturation levels are reduced substantially. This paper derives and solves the cold beam dispersion relation for numerical instabilities in multidimensional, relativistic, electromagnetic particle-in-cell programs employing either the standard or the Cole–Karkkainnen finite difference field solver on a staggered mesh and the common Esirkepov current-gathering algorithm. Good overall agreement is achieved with previously reported results of the WARP code. In particular, the existence of select time steps for which instabilities are minimized is explained. Additionally, an alternative field interpolation algorithm is proposed for which instabilities are almost completely eliminated for a particular time step in ultra-relativistic simulations.

  14. Reconstruction of the vertical electron density profile based on vertical TEC using the simulated annealing algorithm

    NASA Astrophysics Data System (ADS)

    Jiang, Chunhua; Yang, Guobin; Zhu, Peng; Nishioka, Michi; Yokoyama, Tatsuhiro; Zhou, Chen; Song, Huan; Lan, Ting; Zhao, Zhengyu; Zhang, Yuannong

    2016-05-01

    This paper presents a new method to reconstruct the vertical electron density profile based on vertical Total Electron Content (TEC) using the simulated annealing algorithm. The present technique used the Quasi-parabolic segments (QPS) to model the bottomside ionosphere. The initial parameters of the ionosphere model were determined from both International Reference Ionosphere (IRI) (Bilitza et al., 2014) and vertical TEC (vTEC). Then, the simulated annealing algorithm was used to search the best-fit parameters of the ionosphere model by comparing with the GPS-TEC. The performance and robust of this technique were verified by ionosonde data. The critical frequency (foF2) and peak height (hmF2) of the F2 layer obtained from ionograms recorded at different locations and on different days were compared with those calculated by the proposed method. The analysis of results shows that the present method is inspiring for obtaining foF2 from vTEC. However, the accuracy of hmF2 needs to be improved in the future work.

  15. Physics and Algorithm Enhancements for a Validated MCNP/X Monte Carlo Simulation Tool, Phase VII

    SciTech Connect

    McKinney, Gregg W

    2012-07-17

    Currently the US lacks an end-to-end (i.e., source-to-detector) radiation transport simulation code with predictive capability for the broad range of DHS nuclear material detection applications. For example, gaps in the physics, along with inadequate analysis algorithms, make it difficult for Monte Carlo simulations to provide a comprehensive evaluation, design, and optimization of proposed interrogation systems. With the development and implementation of several key physics and algorithm enhancements, along with needed improvements in evaluated data and benchmark measurements, the MCNP/X Monte Carlo codes will provide designers, operators, and systems analysts with a validated tool for developing state-of-the-art active and passive detection systems. This project is currently in its seventh year (Phase VII). This presentation will review thirty enhancements that have been implemented in MCNPX over the last 3 years and were included in the 2011 release of version 2.7.0. These improvements include 12 physics enhancements, 4 source enhancements, 8 tally enhancements, and 6 other enhancements. Examples and results will be provided for each of these features. The presentation will also discuss the eight enhancements that will be migrated into MCNP6 over the upcoming year.

  16. Blind decorrelation and deconvolution algorithm for multiple-input multiple-output system: II. Analysis and simulation

    NASA Astrophysics Data System (ADS)

    Chen, Da-Ching; Yu, Tommy; Yao, Kung; Pottie, Gregory J.

    1999-11-01

    For single-input multiple-output (SIMO) systems blind deconvolution based on second-order statistics has been shown promising given that the sources and channels meet certain assumptions. In our previous paper we extend the work to multiple-input multiple-output (MIMO) systems by introducing a blind deconvolution algorithm to remove all channel dispersion followed by a blind decorrelation algorithm to separate different sources from their instantaneous mixture. In this paper we first explore more details embedded in our algorithm. Then we present simulation results to show that our algorithm is applicable to MIMO systems excited by a broad class of signals such as speech, music and digitally modulated symbols.

  17. Room Acoustical Simulation Algorithm Based on the Free Path Distribution

    NASA Astrophysics Data System (ADS)

    VORLÄNDER, M.

    2000-04-01

    A new algorithm is presented which provides estimates of impulse responses in rooms. It is applicable to arbitrary shaped rooms, thus including non-diffuse spaces like workrooms or offices. In the latter cases, for instance, sound propagation curves are of interest to be applied in noise control. In the case of concert halls and opera houses, the method enables very fast predictions of room acoustical criteria like reverberation time, strength or clarity. The method is based on a low-resolved ray tracing and recording of the free paths. Estimates of impulse responses are derived from evaluation of the free path distribution and of the free path transition probabilities.

  18. The EM/MPM algorithm for segmentation of textured images: analysis and further experimental results.

    PubMed

    Comer, M L; Delp, E J

    2000-01-01

    In this paper we present new results relative to the "expectation-maximization/maximization of the posterior marginals" (EM/MPM) algorithm for simultaneous parameter estimation and segmentation of textured images. The EM/MPM algorithm uses a Markov random field model for the pixel class labels and alternately approximates the MPM estimate of the pixel class labels and estimates parameters of the observed image model. The goal of the EM/MPM algorithm is to minimize the expected value of the number of misclassified pixels. We present new theoretical results in this paper which show that the algorithm can be expected to achieve this goal, to the extent that the EM estimates of the model parameters are close to the true values of the model parameters. We also present new experimental results demonstrating the performance of the EM/MPM algorithm.

  19. Experimental Results in the Comparison of Search Algorithms Used with Room Temperature Detectors

    SciTech Connect

    Guss, P., Yuan, D., Cutler, M., Beller, D.

    2010-11-01

    Analysis of time sequence data was run for several higher resolution scintillation detectors using a variety of search algorithms, and results were obtained in predicting the relative performance for these detectors, which included a slightly superior performance by CeBr{sub 3}. Analysis of several search algorithms shows that inclusion of the RSPRT methodology can improve sensitivity.

  20. A new cut-cell algorithm for DSMC simulations of rarefied gas flows around immersed moving objects

    NASA Astrophysics Data System (ADS)

    Jin, Wenjie; Ommen, J. Ruud van; Kleijn, Chris R.

    2017-03-01

    Direct Simulation Monte Carlo (DSMC) is a widely applied numerical technique to simulate rarefied gas flows. For flows around immersed moving objects, the use of body fitted meshes is inefficient, whereas published methods using cut-cells in a fixed background mesh have important limitations. We present a novel cut-cell algorithm, which allows for accurate DSMC simulations around arbitrarily shaped moving objects. The molecule-surface interaction occurs exactly at the instantaneous collision point on the moving body surface, and accounts for its instantaneous velocity, thus precisely imposing the desired boundary conditions. A simple algorithm to calculate the effective volume of cut cells is presented and shown to converge linearly with grid refinement. The potential and efficiency of method is demonstrated by calculating rarefied gas flow drag forces on steady and moving immersed spheres. The obtained results are in excellent agreement with results obtained with a body-fitted mesh, and with analytical approximations for high-Knudsen number flows.

  1. Cell light scattering characteristic numerical simulation research based on FDTD algorithm

    NASA Astrophysics Data System (ADS)

    Lin, Xiaogang; Wan, Nan; Zhu, Hao; Weng, Lingdong

    2017-01-01

    In this study, finite-difference time-domain (FDTD) algorithm has been used to work out the cell light scattering problem. Before beginning to do the simulation contrast, finding out the changes or the differences between normal cells and abnormal cells which may be cancerous or maldevelopment is necessary. The preparation of simulation are building up the simple cell model of cell which consists of organelles, nucleus and cytoplasm and setting up the suitable precision of mesh. Meanwhile, setting up the total field scattering field source as the excitation source and far field projection analysis group is also important. Every step need to be explained by the principles of mathematic such as the numerical dispersion, perfect matched layer boundary condition and near-far field extrapolation. The consequences of simulation indicated that the position of nucleus changed will increase the back scattering intensity and the significant difference on the peak value of scattering intensity may result from the changes of the size of cytoplasm. The study may help us find out the regulations based on the simulation consequences and the regulations can be meaningful for early diagnosis of cancers.

  2. Wavelet Monte Carlo dynamics: A new algorithm for simulating the hydrodynamics of interacting Brownian particles.

    PubMed

    Dyer, Oliver T; Ball, Robin C

    2017-03-28

    We develop a new algorithm for the Brownian dynamics of soft matter systems that evolves time by spatially correlated Monte Carlo moves. The algorithm uses vector wavelets as its basic moves and produces hydrodynamics in the low Reynolds number regime propagated according to the Oseen tensor. When small moves are removed, the correlations closely approximate the Rotne-Prager tensor, itself widely used to correct for deficiencies in Oseen. We also include plane wave moves to provide the longest range correlations, which we detail for both infinite and periodic systems. The computational cost of the algorithm scales competitively with the number of particles simulated, N, scaling as N In N in homogeneous systems and as N in dilute systems. In comparisons to established lattice Boltzmann and Brownian dynamics algorithms, the wavelet method was found to be only a factor of order 1 times more expensive than the cheaper lattice Boltzmann algorithm in marginally semi-dilute simulations, while it is significantly faster than both algorithms at large N in dilute simulations. We also validate the algorithm by checking that it reproduces the correct dynamics and equilibrium properties of simple single polymer systems, as well as verifying the effect of periodicity on the mobility tensor.

  3. A fast algorithm for the simulation of arterial pulse waves

    NASA Astrophysics Data System (ADS)

    Du, Tao; Hu, Dan; Cai, David

    2016-06-01

    One-dimensional models have been widely used in studies of the propagation of blood pulse waves in large arterial trees. Under a periodic driving of the heartbeat, traditional numerical methods, such as the Lax-Wendroff method, are employed to obtain asymptotic periodic solutions at large times. However, these methods are severely constrained by the CFL condition due to large pulse wave speed. In this work, we develop a new numerical algorithm to overcome this constraint. First, we reformulate the model system of pulse wave propagation using a set of Riemann variables and derive a new form of boundary conditions at the inlet, the outlets, and the bifurcation points of the arterial tree. The new form of the boundary conditions enables us to design a convergent iterative method to enforce the boundary conditions. Then, after exchanging the spatial and temporal coordinates of the model system, we apply the Lax-Wendroff method in the exchanged coordinate system, which turns the large pulse wave speed from a liability to a benefit, to solve the wave equation in each artery of the model arterial system. Our numerical studies show that our new algorithm is stable and can perform ∼15 times faster than the traditional implementation of the Lax-Wendroff method under the requirement that the relative numerical error of blood pressure be smaller than one percent, which is much smaller than the modeling error.

  4. An extended molecular statics algorithm simulating the electromechanical continuum response of ferroelectric materials

    NASA Astrophysics Data System (ADS)

    Endres, F.; Steinmann, P.

    2014-12-01

    Molecular dynamics (MD) simulations of ferroelectric materials have improved tremendously over the last few decades. Specifically, the core-shell model has been commonly used for the simulation of ferroelectric materials such as barium titanate. However, due to the computational costs of MD, the calculation of ferroelectric hysteresis behaviour, and especially the stress-strain relation, has been a computationally intense task. In this work a molecular statics algorithm, similar to a finite element method for nonlinear trusses, has been implemented. From this, an algorithm to calculate the stress dependent continuum deformation of a discrete particle system, such as a ferroelectric crystal, has been devised. Molecular statics algorithms for the atomistic simulation of ferroelectric materials have been previously described. However, in contrast to the prior literature the algorithm proposed in this work is also capable of effectively computing the macroscopic ferroelectric butterfly hysteresis behaviour. Therefore the advocated algorithm is able to calculate the piezoelectric effect as well as the converse piezoelectric effect simultaneously on atomistic and continuum length scales. Barium titanate has been simulated using the core-shell model to validate the developed algorithm.

  5. Multiobjective optimization with a modified simulated annealing algorithm for external beam radiotherapy treatment planning

    SciTech Connect

    Aubry, Jean-Francois; Beaulieu, Frederic; Sevigny, Caroline; Beaulieu, Luc; Tremblay, Daniel

    2006-12-15

    Inverse planning in external beam radiotherapy often requires a scalar objective function that incorporates importance factors to mimic the planner's preferences between conflicting objectives. Defining those importance factors is not straightforward, and frequently leads to an iterative process in which the importance factors become variables of the optimization problem. In order to avoid this drawback of inverse planning, optimization using algorithms more suited to multiobjective optimization, such as evolutionary algorithms, has been suggested. However, much inverse planning software, including one based on simulated annealing developed at our institution, does not include multiobjective-oriented algorithms. This work investigates the performance of a modified simulated annealing algorithm used to drive aperture-based intensity-modulated radiotherapy inverse planning software in a multiobjective optimization framework. For a few test cases involving gastric cancer patients, the use of this new algorithm leads to an increase in optimization speed of a little more than a factor of 2 over a conventional simulated annealing algorithm, while giving a close approximation of the solutions produced by a standard simulated annealing. A simple graphical user interface designed to facilitate the decision-making process that follows an optimization is also presented.

  6. An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks

    PubMed Central

    2014-01-01

    Background Motif mining has always been a hot research topic in bioinformatics. Most of current research on biological networks focuses on exact motif mining. However, due to the inevitable experimental error and noisy data, biological network data represented as the probability model could better reflect the authenticity and biological significance, therefore, it is more biological meaningful to discover probability motif in uncertain biological networks. One of the key steps in probability motif mining is frequent pattern discovery which is usually based on the possible world model having a relatively high computational complexity. Methods In this paper, we present a novel method for detecting frequent probability patterns based on circuit simulation in the uncertain biological networks. First, the partition based efficient search is applied to the non-tree like subgraph mining where the probability of occurrence in random networks is small. Then, an algorithm of probability isomorphic based on circuit simulation is proposed. The probability isomorphic combines the analysis of circuit topology structure with related physical properties of voltage in order to evaluate the probability isomorphism between probability subgraphs. The circuit simulation based probability isomorphic can avoid using traditional possible world model. Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters. Results The experiment results on data sets of the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae show that the proposed method can efficiently discover the frequent probability subgraphs. The discovered subgraphs in our study contain all probability motifs reported in the experiments published in other related papers. Conclusions The algorithm of probability graph isomorphism

  7. Conduct of an algorithm in quantifying simulated palatal surface tooth erosion.

    PubMed

    Chadwick, R G; Mitchell, H L

    2001-05-01

    In order to test the ability of an algorithm to quantify simulated palatal erosion, a total of 10 extracted permanent upper central incisors were mounted in brass blocks. Baseline impressions were recorded using an addition cured silicone impression material in a metal impression tray. Once set and removed from the teeth, the impressions were coated twice with a high silver content electroconductive paint, applied using a brush, before being backed up with die stone to form an electroconductive replica. Each tooth was then subject to three treatments: application of phosphoric acid etchant gel for 60 s, application of etchant gel for 120 s and immersion for 3 h in Diet Coca-Cola*. After each one the replication process was repeated. Thereafter all replicas were mapped using a computer controlled electrical probe and the resultant digital terrain models (DTMS) compared using a surface matching and difference detection algorithm (SMADDA). Surface matching was unsuccessful only in one instance. As the duration of the insult increased, so did the proportion of the surface that underwent change to a maximum of 33.3%. Anatomical site was significantly (P < 0.05) associated with the susceptibility to erosion. The cingulum periphery appeared most resistant to this. The algorithmic approach offers much scope for monitoring dental erosion as acid dissolution of the tooth's surface appears to occur gradually. The cingulum region appears relatively more resistant to this process than other tooth sites and thus facilitates the process of surface matching. Further testing is however, required to determine precisely the algorithm's upper tolerance level.

  8. Development and evaluation of a micro-macro algorithm for the simulation of polymer flow

    SciTech Connect

    Feigl, Kathleen . E-mail: feigl@mtu.edu; Tanner, Franz X.

    2006-07-20

    A micro-macro algorithm for the calculation of polymer flow is developed and numerically evaluated. The system being solved consists of the momentum and mass conservation equations from continuum mechanics coupled with a microscopic-based rheological model for polymer stress. Standard finite element techniques are used to solve the conservation equations for velocity and pressure, while stochastic simulation techniques are used to compute polymer stress from the simulated polymer dynamics in the rheological model. The rheological model considered combines aspects of reptation, network and continuum models. Two types of spatial approximation are considered for the configuration fields defining the dynamics in the model: piecewise constant and piecewise linear. The micro-macro algorithm is evaluated by simulating the abrupt planar die entry flow of a polyisobutylene solution described in the literature. The computed velocity and stress fields are found to be essentially independent of mesh size and ensemble size, while there is some dependence of the results on the order of spatial approximation to the configuration fields close to the die entry. Comparison with experimental data shows that the piecewise linear approximation leads to better predictions of the centerline first normal stress difference. Finally, the computational time associated with the piecewise constant spatial approximation is found to be about 2.5 times lower than that associated with the piecewise linear approximation. This is the result of the more efficient time integration scheme that is possible with the former type of approximation due to the pointwise incompressibility guaranteed by the choice of velocity-pressure finite element.

  9. Simulating Multivariate Nonnormal Data Using an Iterative Algorithm

    ERIC Educational Resources Information Center

    Ruscio, John; Kaczetow, Walter

    2008-01-01

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

  10. A process-based algorithm for simulating terraces in SWAT

    USDA-ARS?s Scientific Manuscript database

    Terraces in crop fields are one of the most important soil and water conservation measures that affect runoff and erosion processes in a watershed. In large hydrological programs such as the Soil and Water Assessment Tool (SWAT), terrace effects are simulated by adjusting the slope length and the US...

  11. Simulating Multivariate Nonnormal Data Using an Iterative Algorithm

    ERIC Educational Resources Information Center

    Ruscio, John; Kaczetow, Walter

    2008-01-01

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

  12. GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

    PubMed

    Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

    2015-07-01

    GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

  13. GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

    PubMed Central

    Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

    2015-01-01

    GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 PMID:26753008

  14. Parallel Algorithms for Monte Carlo Particle Transport Simulation on Exascale Computing Architectures

    NASA Astrophysics Data System (ADS)

    Romano, Paul Kollath

    Monte Carlo particle transport methods are being considered as a viable option for high-fidelity simulation of nuclear reactors. While Monte Carlo methods offer several potential advantages over deterministic methods, there are a number of algorithmic shortcomings that would prevent their immediate adoption for full-core analyses. In this thesis, algorithms are proposed both to ameliorate the degradation in parallel efficiency typically observed for large numbers of processors and to offer a means of decomposing large tally data that will be needed for reactor analysis. A nearest-neighbor fission bank algorithm was proposed and subsequently implemented in the OpenMC Monte Carlo code. A theoretical analysis of the communication pattern shows that the expected cost is O( N ) whereas traditional fission bank algorithms are O(N) at best. The algorithm was tested on two supercomputers, the Intrepid Blue Gene/P and the Titan Cray XK7, and demonstrated nearly linear parallel scaling up to 163,840 processor cores on a full-core benchmark problem. An algorithm for reducing network communication arising from tally reduction was analyzed and implemented in OpenMC. The proposed algorithm groups only particle histories on a single processor into batches for tally purposes---in doing so it prevents all network communication for tallies until the very end of the simulation. The algorithm was tested, again on a full-core benchmark, and shown to reduce network communication substantially. A model was developed to predict the impact of load imbalances on the performance of domain decomposed simulations. The analysis demonstrated that load imbalances in domain decomposed simulations arise from two distinct phenomena: non-uniform particle densities and non-uniform spatial leakage. The dominant performance penalty for domain decomposition was shown to come from these physical effects rather than insufficient network bandwidth or high latency. The model predictions were verified with

  15. A Super-Resolution Algorithm for Enhancement of FLASH LIDAR Data: Flight Test Results

    NASA Technical Reports Server (NTRS)

    Bulyshev, Alexander; Amzajerdian, Farzin; Roback, Eric; Reisse Robert

    2014-01-01

    This paper describes the results of a 3D super-resolution algorithm applied to the range data obtained from a recent Flash Lidar helicopter flight test. The flight test was conducted by the NASA's Autonomous Landing and Hazard Avoidance Technology (ALHAT) project over a simulated lunar terrain facility at NASA Kennedy Space Center. ALHAT is developing the technology for safe autonomous landing on the surface of celestial bodies: Moon, Mars, asteroids. One of the test objectives was to verify the ability of 3D super-resolution technique to generate high resolution digital elevation models (DEMs) and to determine time resolved relative positions and orientations of the vehicle. 3D super-resolution algorithm was developed earlier and tested in computational modeling, and laboratory experiments, and in a few dynamic experiments using a moving truck. Prior to the helicopter flight test campaign, a 100mX100m hazard field was constructed having most of the relevant extraterrestrial hazard: slopes, rocks, and craters with different sizes. Data were collected during the flight and then processed by the super-resolution code. The detailed DEM of the hazard field was constructed using independent measurement to be used for comparison. ALHAT navigation system data were used to verify abilities of super-resolution method to provide accurate relative navigation information. Namely, the 6 degree of freedom state vector of the instrument as a function of time was restored from super-resolution data. The results of comparisons show that the super-resolution method can construct high quality DEMs and allows for identifying hazards like rocks and craters within the accordance of ALHAT requirements.

  16. A super-resolution algorithm for enhancement of flash lidar data: flight test results

    NASA Astrophysics Data System (ADS)

    Bulyshev, Alexander; Amzajerdian, Farzin; Roback, Eric; Reisse, Robert

    2013-03-01

    This paper describes the results of a 3D super-resolution algorithm applied to the range data obtained from a recent Flash Lidar helicopter flight test. The flight test was conducted by the NASA's Autonomous Landing and Hazard Avoidance Technology (ALHAT) project over a simulated lunar terrain facility at NASA Kennedy Space Center. ALHAT is developing the technology for safe autonomous landing on the surface of celestial bodies: Moon, Mars, asteroids. One of the test objectives was to verify the ability of 3D super-resolution technique to generate high resolution digital elevation models (DEMs) and to determine time resolved relative positions and orientations of the vehicle. 3D super-resolution algorithm was developed earlier and tested in computational modeling, and laboratory experiments, and in a few dynamic experiments using a moving truck. Prior to the helicopter flight test campaign, a 100mX100m hazard field was constructed having most of the relevant extraterrestrial hazard: slopes, rocks, and craters with different sizes. Data were collected during the flight and then processed by the super-resolution code. The detailed DEM of the hazard field was constructed using independent measurement to be used for comparison. ALHAT navigation system data were used to verify abilities of super-resolution method to provide accurate relative navigation information. Namely, the 6 degree of freedom state vector of the instrument as a function of time was restored from super-resolution data. The results of comparisons show that the super-resolution method can construct high quality DEMs and allows for identifying hazards like rocks and craters within the accordance of ALHAT requirements.

  17. Spatial independent component analysis of functional MRI time-series: to what extent do results depend on the algorithm used?

    PubMed

    Esposito, Fabrizio; Formisano, Elia; Seifritz, Erich; Goebel, Rainer; Morrone, Renato; Tedeschi, Gioacchino; Di Salle, Francesco

    2002-07-01

    Independent component analysis (ICA) has been successfully employed to decompose functional MRI (fMRI) time-series into sets of activation maps and associated time-courses. Several ICA algorithms have been proposed in the neural network literature. Applied to fMRI, these algorithms might lead to different spatial or temporal readouts of brain activation. We compared the two ICA algorithms that have been used so far for spatial ICA (sICA) of fMRI time-series: the Infomax (Bell and Sejnowski [1995]: Neural Comput 7:1004-1034) and the Fixed-Point (Hyvärinen [1999]: Adv Neural Inf Proc Syst 10:273-279) algorithms. We evaluated the Infomax- and Fixed Point-based sICA decompositions of simulated motor, and real motor and visual activation fMRI time-series using an ensemble of measures. Log-likelihood (McKeown et al. [1998]: Hum Brain Mapp 6:160-188) was used as a measure of how significantly the estimated independent sources fit the statistical structure of the data; receiver operating characteristics (ROC) and linear correlation analyses were used to evaluate the algorithms' accuracy of estimating the spatial layout and the temporal dynamics of simulated and real activations; cluster sizing calculations and an estimation of a residual gaussian noise term within the components were used to examine the anatomic structure of ICA components and for the assessment of noise reduction capabilities. Whereas both algorithms produced highly accurate results, the Fixed-Point outperformed the Infomax in terms of spatial and temporal accuracy as long as inferential statistics were employed as benchmarks. Conversely, the Infomax sICA was superior in terms of global estimation of the ICA model and noise reduction capabilities. Because of its adaptive nature, the Infomax approach appears to be better suited to investigate activation phenomena that are not predictable or adequately modelled by inferential techniques. Copyright 2002 Wiley-Liss, Inc.

  18. An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks.

    PubMed

    He, Jieyue; Wang, Chunyan; Qiu, Kunpu; Zhong, Wei

    2014-01-01

    Motif mining has always been a hot research topic in bioinformatics. Most of current research on biological networks focuses on exact motif mining. However, due to the inevitable experimental error and noisy data, biological network data represented as the probability model could better reflect the authenticity and biological significance, therefore, it is more biological meaningful to discover probability motif in uncertain biological networks. One of the key steps in probability motif mining is frequent pattern discovery which is usually based on the possible world model having a relatively high computational complexity. In this paper, we present a novel method for detecting frequent probability patterns based on circuit simulation in the uncertain biological networks. First, the partition based efficient search is applied to the non-tree like subgraph mining where the probability of occurrence in random networks is small. Then, an algorithm of probability isomorphic based on circuit simulation is proposed. The probability isomorphic combines the analysis of circuit topology structure with related physical properties of voltage in order to evaluate the probability isomorphism between probability subgraphs. The circuit simulation based probability isomorphic can avoid using traditional possible world model. Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters. The experiment results on data sets of the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae show that the proposed method can efficiently discover the frequent probability subgraphs. The discovered subgraphs in our study contain all probability motifs reported in the experiments published in other related papers. The algorithm of probability graph isomorphism evaluation based on circuit simulation

  19. Building a LiDAR point cloud simulator: Testing algorithms for high resolution topographic change

    NASA Astrophysics Data System (ADS)

    Carrea, Dario; Abellán, Antonio; Derron, Marc-Henri; Jaboyedoff, Michel

    2014-05-01

    (erosion, landslide monitoring, etc) and we then tested the use of filtering techniques using 3D moving windows along the space and time, which considerably reduces data scattering due to the benefits of data redundancy. In conclusion, the simulator allowed us to improve our different algorithms and to understand how instrumental error affects final results. And also, improve the methodology of scans acquisition to find the best compromise between point density, positioning and acquisition time with the best accuracy possible to characterize the topographic change.

  20. Advanced time integration algorithms for dislocation dynamics simulations of work hardening

    NASA Astrophysics Data System (ADS)

    Sills, Ryan B.; Aghaei, Amin; Cai, Wei

    2016-05-01

    Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank-Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relative to traditional schemes. Subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.

  1. Parallel algorithms for simulating continuous time Markov chains

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Heidelberger, Philip

    1992-01-01

    We have previously shown that the mathematical technique of uniformization can serve as the basis of synchronization for the parallel simulation of continuous-time Markov chains. This paper reviews the basic method and compares five different methods based on uniformization, evaluating their strengths and weaknesses as a function of problem characteristics. The methods vary in their use of optimism, logical aggregation, communication management, and adaptivity. Performance evaluation is conducted on the Intel Touchstone Delta multiprocessor, using up to 256 processors.

  2. Direct dynamics simulations using Hessian-based predictor-corrector integration algorithms.

    PubMed

    Lourderaj, Upakarasamy; Song, Kihyung; Windus, Theresa L; Zhuang, Yu; Hase, William L

    2007-01-28

    In previous research [J. Chem. Phys. 111, 3800 (1999)] a Hessian-based integration algorithm was derived for performing direct dynamics simulations. In the work presented here, improvements to this algorithm are described. The algorithm has a predictor step based on a local second-order Taylor expansion of the potential in Cartesian coordinates, within a trust radius, and a fifth-order correction to this predicted trajectory. The current algorithm determines the predicted trajectory in Cartesian coordinates, instead of the instantaneous normal mode coordinates used previously, to ensure angular momentum conservation. For the previous algorithm the corrected step was evaluated in rotated Cartesian coordinates. Since the local potential expanded in Cartesian coordinates is not invariant to rotation, the constants of motion are not necessarily conserved during the corrector step. An approximate correction to this shortcoming was made by projecting translation and rotation out of the rotated coordinates. For the current algorithm unrotated Cartesian coordinates are used for the corrected step to assure the constants of motion are conserved. An algorithm is proposed for updating the trust radius to enhance the accuracy and efficiency of the numerical integration. This modified Hessian-based integration algorithm, with its new components, has been implemented into the VENUS/NWChem software package and compared with the velocity-Verlet algorithm for the H(2)CO-->H(2)+CO, O(3)+C(3)H(6), and F(-)+CH(3)OOH chemical reactions.

  3. Engineering phase shifter domains for multiple QPM using simulated annealing algorithm

    NASA Astrophysics Data System (ADS)

    Siva, Chellappa; Sunder Meetei, Toijam; Shiva, Prabhakar; Narayanan, Balaji; Arvind, Ganesh; Boomadevi, Shanmugam; Pandiyan, Krishnamoorthy

    2017-10-01

    We have utilized the general algorithm of simulated annealing (SA) to engineer the phase shifter domains in a quasi-phase-matching (QPM) device to generate multiple frequency conversion. SA is an algorithm generally used to find the global maxima or minima in a given random function. Here, we have utilized this algorithm to generate multiple QPM second harmonic generation (SHG) by distributing phase shifters suitably. In general, phase shifters are distributed in a QPM device with some specific profile along the length to generate multiple QPM SHG. Using the SA algorithm, the location of these phase shifters can be easily identified to have the desired multiple QPM with higher conversion efficiency. The methodology to generate the desired multiple QPM SHG using the SA algorithm has been discussed in detail.

  4. Simulation of rat behavior by a reinforcement learning algorithm in consideration of appearance probabilities of reinforcement signals.

    PubMed

    Murakoshi, Kazushi; Noguchi, Takuya

    2005-04-01

    Brown and Wanger [Brown, R.T., Wanger, A.R., 1964. Resistance to punishment and extinction following training with shock or nonreinforcement. J. Exp. Psychol. 68, 503-507] investigated rat behaviors with the following features: (1) rats were exposed to reward and punishment at the same time, (2) environment changed and rats relearned, and (3) rats were stochastically exposed to reward and punishment. The results are that exposure to nonreinforcement produces resistance to the decremental effects of behavior after stochastic reward schedule and that exposure to both punishment and reinforcement produces resistance to the decremental effects of behavior after stochastic punishment schedule. This paper aims to simulate the rat behaviors by a reinforcement learning algorithm in consideration of appearance probabilities of reinforcement signals. The former algorithms of reinforcement learning were unable to simulate the behavior of the feature (3). We improve the former reinforcement learning algorithms by controlling learning parameters in consideration of the acquisition probabilities of reinforcement signals. The proposed algorithm qualitatively simulates the result of the animal experiment of Brown and Wanger.

  5. A research on short-term hydro-wind economic dispatch problem simulated with a modified differential evolution algorithm

    NASA Astrophysics Data System (ADS)

    Xuemin, Wang; Anqiang, Li; Rui, Zhang

    2017-05-01

    Due to the wide construction of wind power and the difficulty for it to join the power grid, a short-term hydro-wind economic dispatch (WHED) problem is proposed. WHED system contains several wind power units and hydropower plants, which are renewable and clean. Combined with hydropower plants, the wind power units can join the power grid stably. Then, a WHED system with four cascaded hydropower plants and two wind units is established, and a modified differential evolution (DE) algorithm with chaotic perturbation is proposed for optimizing. Finally, two cases are simulated and analysed, the dispatch results show that the presented model and algorithm are feasible and effective.

  6. A syncopated leap-frog algorithm for orbit consistent plasma simulation of materials processing reactors

    SciTech Connect

    Cobb, J.W.; Leboeuf, J.N.

    1994-10-01

    The authors present a particle algorithm to extend simulation capabilities for plasma based materials processing reactors. The orbit integrator uses a syncopated leap-frog algorithm in cylindrical coordinates, which maintains second order accuracy, and minimizes computational complexity. Plasma source terms are accumulated orbit consistently directly in the frequency and azimuthal mode domains. Finally they discuss the numerical analysis of this algorithm. Orbit consistency greatly reduces the computational cost for a given level of precision. The computational cost is independent of the degree of time scale separation.

  7. Parallel implementation of the FETI-DPEM algorithm for general 3D EM simulations

    NASA Astrophysics Data System (ADS)

    Li, Yu-Jia; Jin, Jian-Ming

    2009-05-01

    A parallel implementation of the electromagnetic dual-primal finite element tearing and interconnecting algorithm (FETI-DPEM) is designed for general three-dimensional (3D) electromagnetic large-scale simulations. As a domain decomposition implementation of the finite element method, the FETI-DPEM algorithm provides fully decoupled subdomain problems and an excellent numerical scalability, and thus is well suited for parallel computation. The parallel implementation of the FETI-DPEM algorithm on a distributed-memory system using the message passing interface (MPI) is discussed in detail along with a few practical guidelines obtained from numerical experiments. Numerical examples are provided to demonstrate the efficiency of the parallel implementation.

  8. Multi-Rate Digital Control Systems with Simulation Applications. Volume II. Computer Algorithms

    DTIC Science & Technology

    1980-09-01

    34 ~AFWAL-TR-80-31 01 • • Volume II L IL MULTI-RATE DIGITAL CONTROL SYSTEMS WITH SIMULATiON APPLICATIONS Volume II: Computer Algorithms DENNIS G. J...29 Ma -8 - Volume II. Computer Algorithms ~ / ’+ 44MWLxkQT N Uwe ~~ 4 ~jjskYIF336l5-79-C-369~ 9. PER~rORMING ORGANIZATION NAME AND ADDRESS IPROG AMEL...additional options. The analytical basis for the computer algorithms is discussed in Ref. 12. However, to provide a complete description of the program, some

  9. An EM algorithm for nonparametric estimation of the cumulative incidence function from repeated imperfect test results.

    PubMed

    Witte, Birgit I; Berkhof, Johannes; Jonker, Marianne A

    2017-09-20

    In screening and surveillance studies, event times are interval censored. Besides, screening tests are imperfect so that the interval at which an event takes place may be uncertain. We describe an expectation-maximization algorithm to find the nonparametric maximum likelihood estimator of the cumulative incidence function of an event based on screening test data. Our algorithm has a closed-form solution for the combined expectation and maximization step and is computationally undemanding. A simulation study indicated that the bias of the estimator tends to zero for large sample size, and its mean squared error is in general lower than the mean squared error of the estimator that assumes the screening test is perfect. We apply the algorithm to follow-up data from women treated for cervical precancer. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  10. Measurement and Simulation Results of Ti Coated Microwave Absorber

    SciTech Connect

    Sun, Ding; McGinnis, Dave; /Fermilab

    1998-11-01

    When microwave absorbers are put in a waveguide, a layer of resistive coating can change the distribution of the E-M fields and affect the attenuation of the signal within the microwave absorbers. In order to study such effect, microwave absorbers (TT2-111) were coated with titanium thin film. This report is a document on the coating process and measurement results. The measurement results have been used to check the simulation results from commercial software HFSS (High Frequency Structure Simulator.)

  11. An End-to-End simulator for the development of atmospheric corrections and temperature - emissivity separation algorithms in the TIR spectral domain

    NASA Astrophysics Data System (ADS)

    Rock, Gilles; Fischer, Kim; Schlerf, Martin; Gerhards, Max; Udelhoven, Thomas

    2017-04-01

    The development and optimization of image processing algorithms requires the availability of datasets depicting every step from earth surface to the sensor's detector. The lack of ground truth data obliges to develop algorithms on simulated data. The simulation of hyperspectral remote sensing data is a useful tool for a variety of tasks such as the design of systems, the understanding of the image formation process, and the development and validation of data processing algorithms. An end-to-end simulator has been set up consisting of a forward simulator, a backward simulator and a validation module. The forward simulator derives radiance datasets based on laboratory sample spectra, applies atmospheric contributions using radiative transfer equations, and simulates the instrument response using configurable sensor models. This is followed by the backward simulation branch, consisting of an atmospheric correction (AC), a temperature and emissivity separation (TES) or a hybrid AC and TES algorithm. An independent validation module allows the comparison between input and output dataset and the benchmarking of different processing algorithms. In this study, hyperspectral thermal infrared scenes of a variety of surfaces have been simulated to analyze existing AC and TES algorithms. The ARTEMISS algorithm was optimized and benchmarked against the original implementations. The errors in TES were found to be related to incorrect water vapor retrieval. The atmospheric characterization could be optimized resulting in increasing accuracies in temperature and emissivity retrieval. Airborne datasets of different spectral resolutions were simulated from terrestrial HyperCam-LW measurements. The simulated airborne radiance spectra were subjected to atmospheric correction and TES and further used for a plant species classification study analyzing effects related to noise and mixed pixels.

  12. Adaptive particle-cell algorithm for Fokker-Planck based rarefied gas flow simulations

    NASA Astrophysics Data System (ADS)

    Pfeiffer, M.; Gorji, M. H.

    2017-04-01

    Recently, the Fokker-Planck (FP) kinetic model has been devised on the basis of the Boltzmann equation (Jenny et al., 2010; Gorji et al., 2011). Particle Monte-Carlo schemes are then introduced for simulations of rarefied gas flows based on the FP kinetics. Here the particles follow independent stochastic paths and thus a spatio-temporal resolution coarser than the collisional scales becomes possible. In contrast to the direct simulation Monte-Carlo (DSMC), the computational cost is independent of the Knudsen number resulting in efficient simulations at moderate/low Knudsen flows. In order to further exploit the efficiency of the FP method, the required particle-cell resolutions should be found, and a cell refinement strategy has to be developed accordingly. In this study, an adaptive particle-cell scheme applicable to a general unstructured mesh is derived for the FP model. Virtual sub cells are introduced for the adaptive mesh refinement. Moreover a sub cell-merging algorithm is provided to honor the minimum required number of particles per cell. For assessments, the 70 degree blunted cone reentry flow (Allgre et al., 1997) is studied. Excellent agreement between the introduced adaptive FP method and DSMC is achieved.

  13. Turning Simulation into Estimation: Generalized Exchange Algorithms for Exponential Family Models

    PubMed Central

    Maris, Gunter; Bechger, Timo; Glas, Cees

    2017-01-01

    The Single Variable Exchange algorithm is based on a simple idea; any model that can be simulated can be estimated by producing draws from the posterior distribution. We build on this simple idea by framing the Exchange algorithm as a mixture of Metropolis transition kernels and propose strategies that automatically select the more efficient transition kernels. In this manner we achieve significant improvements in convergence rate and autocorrelation of the Markov chain without relying on more than being able to simulate from the model. Our focus will be on statistical models in the Exponential Family and use two simple models from educational measurement to illustrate the contribution. PMID:28076429

  14. Aggressively Parallel Algorithms of Collision and Nearest Neighbor Detection for GPU Planetesimal Disk Simulation

    NASA Astrophysics Data System (ADS)

    Quillen, Alice C.; Moore, A.

    2008-09-01

    Planetesimal and dust dynamical simulations require collision and nearest neighbor detection. A brute force implementation for sorting interparticle distances requires O(N2) computations for N particles, limiting the numbers of particles that have been simulated. Parallel algorithms recently developed for the GPU (graphics processing unit), such as the radix sort, can run as fast as O(N) and sort distances between a million particles in a few hundred milliseconds. We introduce improvements in collision and nearest neighbor detection algorithms and how we have incorporated them into our efficient parallel 2nd order democratic heliocentric method symplectic integrator written in NVIDIA's CUDA for the GPU.

  15. Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems

    SciTech Connect

    Cao Yang . E-mail: ycao@cs.ucsb.edu; Gillespie, Dan . E-mail: GillespieDT@mailaps.org; Petzold, Linda . E-mail: petzold@engineering.ucsb.edu

    2005-07-01

    In this paper, we introduce a multiscale stochastic simulation algorithm (MSSA) which makes use of Gillespie's stochastic simulation algorithm (SSA) together with a new stochastic formulation of the partial equilibrium assumption (PEA). This method is much more efficient than SSA alone. It works even with a very small population of fast species. Implementation details are discussed, and an application to the modeling of the heat shock response of E. Coli is presented which demonstrates the excellent efficiency and accuracy obtained with the new method.

  16. Modeling Signal Transduction Networks: A comparison of two Stochastic Kinetic Simulation Algorithms

    SciTech Connect

    Pettigrew, Michel F.; Resat, Haluk

    2005-09-15

    Simulations of a scalable four compartment reaction model based on the well known epidermal growth factor receptor (EGFR) signal transduction system are used to compare two stochastic algorithms ? StochSim and the Gibson-Gillespie. It is concluded that the Gibson-Gillespie is the algorithm of choice for most realistic cases with the possible exception of signal transduction networks characterized by a moderate number (< 100) of complex types, each with a very small population, but with a high degree of connectivity amongst the complex types. Keywords: Signal transduction networks, Stochastic simulation, StochSim, Gillespie

  17. A sweep algorithm for massively parallel simulation of circuit-switched networks

    NASA Technical Reports Server (NTRS)

    Gaujal, Bruno; Greenberg, Albert G.; Nicol, David M.

    1992-01-01

    A new massively parallel algorithm is presented for simulating large asymmetric circuit-switched networks, controlled by a randomized-routing policy that includes trunk-reservation. A single instruction multiple data (SIMD) implementation is described, and corresponding experiments on a 16384 processor MasPar parallel computer are reported. A multiple instruction multiple data (MIMD) implementation is also described, and corresponding experiments on an Intel IPSC/860 parallel computer, using 16 processors, are reported. By exploiting parallelism, our algorithm increases the possible execution rate of such complex simulations by as much as an order of magnitude.

  18. Simulation of Biochemical Pathway Adaptability Using Evolutionary Algorithms

    SciTech Connect

    Bosl, W J

    2005-01-26

    The systems approach to genomics seeks quantitative and predictive descriptions of cells and organisms. However, both the theoretical and experimental methods necessary for such studies still need to be developed. We are far from understanding even the simplest collective behavior of biomolecules, cells or organisms. A key aspect to all biological problems, including environmental microbiology, evolution of infectious diseases, and the adaptation of cancer cells is the evolvability of genomes. This is particularly important for Genomes to Life missions, which tend to focus on the prospect of engineering microorganisms to achieve desired goals in environmental remediation and climate change mitigation, and energy production. All of these will require quantitative tools for understanding the evolvability of organisms. Laboratory biodefense goals will need quantitative tools for predicting complicated host-pathogen interactions and finding counter-measures. In this project, we seek to develop methods to simulate how external and internal signals cause the genetic apparatus to adapt and organize to produce complex biochemical systems to achieve survival. This project is specifically directed toward building a computational methodology for simulating the adaptability of genomes. This project investigated the feasibility of using a novel quantitative approach to studying the adaptability of genomes and biochemical pathways. This effort was intended to be the preliminary part of a larger, long-term effort between key leaders in computational and systems biology at Harvard University and LLNL, with Dr. Bosl as the lead PI. Scientific goals for the long-term project include the development and testing of new hypotheses to explain the observed adaptability of yeast biochemical pathways when the myosin-II gene is deleted and the development of a novel data-driven evolutionary computation as a way to connect exploratory computational simulation with hypothesis

  19. Algorithmic Extensions of Low-Dispersion Scheme and Modeling Effects for Acoustic Wave Simulation. Revised

    NASA Technical Reports Server (NTRS)

    Kaushik, Dinesh K.; Baysal, Oktay

    1997-01-01

    Accurate computation of acoustic wave propagation may be more efficiently performed when their dispersion relations are considered. Consequently, computational algorithms which attempt to preserve these relations have been gaining popularity in recent years. In the present paper, the extensions to one such scheme are discussed. By solving the linearized, 2-D Euler and Navier-Stokes equations with such a method for the acoustic wave propagation, several issues were investigated. Among them were higher-order accuracy, choice of boundary conditions and differencing stencils, effects of viscosity, low-storage time integration, generalized curvilinear coordinates, periodic series, their reflections and interference patterns from a flat wall and scattering from a circular cylinder. The results were found to be promising en route to the aeroacoustic simulations of realistic engineering problems.

  20. Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins

    NASA Astrophysics Data System (ADS)

    Aina, A.; Wallin, S.

    2017-09-01

    We consider a generalized-ensemble algorithm for coarse-grained simulations of biomolecules which allows the thermodynamic behavior of two or more sequences to be determined in a single multisequence run. By carrying out a random walk in sequence space, the method also enhances conformational sampling. Escape from local energy minima is accelerated by visiting sequences for which the minima are more shallow or absent. We test the method on an intermediate-resolution coarse-grained model for protein folding with 3 amino acid types and explore the potential for a large-scale coverage of sequence space by applying the method to sets of more than 1000 sequences. The resulting thermodynamic data are used to analyze the structures and stability properties of sequences covering the space between folds with different secondary structures.

  1. Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins.

    PubMed

    Aina, A; Wallin, S

    2017-09-07

    We consider a generalized-ensemble algorithm for coarse-grained simulations of biomolecules which allows the thermodynamic behavior of two or more sequences to be determined in a single multisequence run. By carrying out a random walk in sequence space, the method also enhances conformational sampling. Escape from local energy minima is accelerated by visiting sequences for which the minima are more shallow or absent. We test the method on an intermediate-resolution coarse-grained model for protein folding with 3 amino acid types and explore the potential for a large-scale coverage of sequence space by applying the method to sets of more than 1000 sequences. The resulting thermodynamic data are used to analyze the structures and stability properties of sequences covering the space between folds with different secondary structures.

  2. [The utility boiler low NOx combustion optimization based on ANN and simulated annealing algorithm].

    PubMed

    Zhou, Hao; Qian, Xinping; Zheng, Ligang; Weng, Anxin; Cen, Kefa

    2003-11-01

    With the developing restrict environmental protection demand, more attention was paid on the low NOx combustion optimizing technology for its cheap and easy property. In this work, field experiments on the NOx emissions characteristics of a 600 MW coal-fired boiler were carried out, on the base of the artificial neural network (ANN) modeling, the simulated annealing (SA) algorithm was employed to optimize the boiler combustion to achieve a low NOx emissions concentration, and the combustion scheme was obtained. Two sets of SA parameters were adopted to find a better SA scheme, the result show that the parameters of T0 = 50 K, alpha = 0.6 can lead to a better optimizing process. This work can give the foundation of the boiler low NOx combustion on-line control technology.

  3. Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm.

    PubMed

    Ramírez, Claudia L; Zeida, Ari; Jara, Gabriel E; Roitberg, Adrián E; Martí, Marcelo A

    2014-10-14

    The fundamental object for studying a (bio)chemical reaction obtained from simulations is the free energy profile, which can be directly related to experimentally determined properties. Although quite accurate hybrid quantum (DFT based)-classical methods are available, achieving statistically accurate and well converged results at a moderate computational cost is still an open challenge. Here, we present and thoroughly test a hybrid differential relaxation algorithm (HyDRA), which allows faster equilibration of the classical environment during the nonequilibrium steering of a (bio)chemical reaction. We show and discuss why (in the context of Jarzynski's Relationship) this method allows obtaining accurate free energy profiles with smaller number of independent trajectories and/or faster pulling speeds, thus reducing the overall computational cost. Moreover, due to the availability and straightforward implementation of the method, we expect that it will foster theoretical studies of key enzymatic processes.

  4. Algorithmic Extensions of Low-Dispersion Scheme and Modeling Effects for Acoustic Wave Simulation. Revised

    NASA Technical Reports Server (NTRS)

    Kaushik, Dinesh K.; Baysal, Oktay

    1997-01-01

    Accurate computation of acoustic wave propagation may be more efficiently performed when their dispersion relations are considered. Consequently, computational algorithms which attempt to preserve these relations have been gaining popularity in recent years. In the present paper, the extensions to one such scheme are discussed. By solving the linearized, 2-D Euler and Navier-Stokes equations with such a method for the acoustic wave propagation, several issues were investigated. Among them were higher-order accuracy, choice of boundary conditions and differencing stencils, effects of viscosity, low-storage time integration, generalized curvilinear coordinates, periodic series, their reflections and interference patterns from a flat wall and scattering from a circular cylinder. The results were found to be promising en route to the aeroacoustic simulations of realistic engineering problems.

  5. Algorithm for calculating turbine cooling flow and the resulting decrease in turbine efficiency

    NASA Technical Reports Server (NTRS)

    Gauntner, J. W.

    1980-01-01

    An algorithm is presented for calculating both the quantity of compressor bleed flow required to cool the turbine and the decrease in turbine efficiency caused by the injection of cooling air into the gas stream. The algorithm, which is intended for an axial flow, air routine in a properly written thermodynamic cycle code. Ten different cooling configurations are available for each row of cooled airfoils in the turbine. Results from the algorithm are substantiated by comparison with flows predicted by major engine manufacturers for given bulk metal temperatures and given cooling configurations. A list of definitions for the terms in the subroutine is presented.

  6. Simulated performance of remote sensing ocean colour algorithms during the 1996 PRIME cruise

    NASA Astrophysics Data System (ADS)

    Westbrook, A. G.; Pinkerton, M. H.; Aiken, J.; Pilgrim, D. A.

    Coincident pigment and underwater radiometric data were collected during a cruise along the 20°W meridian from 60°N to 37°N in the north-eastern Atlantic Ocean as part of the Natural Environment Research Council (NERC) thematic programme: plankton reactivity in the marine environment (PRIME). These data were used to simulate the retrieval of two bio-optical variables from remotelysensed measurements of ocean colour (for example by the NASA Sea-viewing wide field-of-view sensor, SeaWiFS), using two-band semi-empirical algorithms. The variables considered were the diffuse attenuation coefficient at 490 nm, ( Kd(490), units: m -1) and the phytoplankton pigment concentration expressed as optically-weighted chlorophyll- a concentration [ Ca, units: mg m -3]. There was good agreement between the measured and the retrieved bio-optical values. Algorithms based on the PRIME data were generated to compare the performance of local algorithms (algorithms which apply to a restricted area and/or season) with global algorithms (algorithms developed on data from a wide variety of water masses). The use of local algorithms improved the average accuracy, but not the precision, of the retrievals: errors were still ±36% ( Kd) and ±117% ( Ca) using local algorithms.

  7. Efficient Constant-Time Complexity Algorithm for Stochastic Simulation of Large Reaction Networks.

    PubMed

    Thanh, Vo Hong; Zunino, Roberto; Priami, Corrado

    2017-01-01

    Exact stochastic simulation is an indispensable tool for a quantitative study of biochemical reaction networks. The simulation realizes the time evolution of the model by randomly choosing a reaction to fire and update the system state according to a probability that is proportional to the reaction propensity. Two computationally expensive tasks in simulating large biochemical networks are the selection of next reaction firings and the update of reaction propensities due to state changes. We present in this work a new exact algorithm to optimize both of these simulation bottlenecks. Our algorithm employs the composition-rejection on the propensity bounds of reactions to select the next reaction firing. The selection of next reaction firings is independent of the number reactions while the update of propensities is skipped and performed only when necessary. It therefore provides a favorable scaling for the computational complexity in simulating large reaction networks. We benchmark our new algorithm with the state of the art algorithms available in literature to demonstrate its applicability and efficiency.

  8. Electron-cloud simulation results for the SPS and recent results for the LHC

    SciTech Connect

    Furman, M.A.; Pivi, M.T.F.

    2002-06-19

    We present an update of computer simulation results for some features of the electron cloud at the Large Hadron Collider (LHC) and recent simulation results for the Super Proton Synchrotron (SPS). We focus on the sensitivity of the power deposition on the LHC beam screen to the emitted electron spectrum, which we study by means of a refined secondary electron (SE) emission model recently included in our simulation code.

  9. Physical formulation and numerical algorithm for simulating N immiscible incompressible fluids involving general order parameters

    SciTech Connect

    Dong, S.

    2015-02-15

    We present a family of physical formulations, and a numerical algorithm, based on a class of general order parameters for simulating the motion of a mixture of N (N⩾2) immiscible incompressible fluids with given densities, dynamic viscosities, and pairwise surface tensions. The N-phase formulations stem from a phase field model we developed in a recent work based on the conservations of mass/momentum, and the second law of thermodynamics. The introduction of general order parameters leads to an extremely strongly-coupled system of (N−1) phase field equations. On the other hand, the general form enables one to compute the N-phase mixing energy density coefficients in an explicit fashion in terms of the pairwise surface tensions. We show that the increased complexity in the form of the phase field equations associated with general order parameters in actuality does not cause essential computational difficulties. Our numerical algorithm reformulates the (N−1) strongly-coupled phase field equations for general order parameters into 2(N−1) Helmholtz-type equations that are completely de-coupled from one another. This leads to a computational complexity comparable to that for the simplified phase field equations associated with certain special choice of the order parameters. We demonstrate the capabilities of the method developed herein using several test problems involving multiple fluid phases and large contrasts in densities and viscosities among the multitude of fluids. In particular, by comparing simulation results with the Langmuir–de Gennes theory of floating liquid lenses we show that the method using general order parameters produces physically accurate results for multiple fluid phases.

  10. Computer simulation results of attitude estimation of earth orbiting satellites

    NASA Technical Reports Server (NTRS)

    Kou, S. R.

    1976-01-01

    Computer simulation results of attitude estimation of Earth-orbiting satellites (including Space Telescope) subjected to environmental disturbances and noises are presented. Decomposed linear recursive filter and Kalman filter were used as estimation tools. Six programs were developed for this simulation, and all were written in the basic language and were run on HP 9830A and HP 9866A computers. Simulation results show that a decomposed linear recursive filter is accurate in estimation and fast in response time. Furthermore, for higher order systems, this filter has computational advantages (i.e., less integration errors and roundoff errors) over a Kalman filter.

  11. Electron-cloud simulation results for the PSR and SNS

    SciTech Connect

    Pivi, M.; Furman, M.A.

    2002-07-08

    We present recent simulation results for the main features of the electron cloud in the storage ring of the Spallation Neutron Source (SNS) at Oak Ridge, and updated results for the Proton Storage Ring (PSR) at Los Alamos. In particular, a complete refined model for the secondary emission process including the so called true secondary, rediffused and backscattered electrons has been included in the simulation code.

  12. A novel coupling of noise reduction algorithms for particle flow simulations

    SciTech Connect

    Zimoń, M.J.; Reese, J.M.; Emerson, D.R.

    2016-09-15

    Proper orthogonal decomposition (POD) and its extension based on time-windows have been shown to greatly improve the effectiveness of recovering smooth ensemble solutions from noisy particle data. However, to successfully de-noise any molecular system, a large number of measurements still need to be provided. In order to achieve a better efficiency in processing time-dependent fields, we have combined POD with a well-established signal processing technique, wavelet-based thresholding. In this novel hybrid procedure, the wavelet filtering is applied within the POD domain and referred to as WAVinPOD. The algorithm exhibits promising results when applied to both synthetically generated signals and particle data. In this work, the simulations compare the performance of our new approach with standard POD or wavelet analysis in extracting smooth profiles from noisy velocity and density fields. Numerical examples include molecular dynamics and dissipative particle dynamics simulations of unsteady force- and shear-driven liquid flows, as well as phase separation phenomenon. Simulation results confirm that WAVinPOD preserves the dimensionality reduction obtained using POD, while improving its filtering properties through the sparse representation of data in wavelet basis. This paper shows that WAVinPOD outperforms the other estimators for both synthetically generated signals and particle-based measurements, achieving a higher signal-to-noise ratio from a smaller number of samples. The new filtering methodology offers significant computational savings, particularly for multi-scale applications seeking to couple continuum informations with atomistic models. It is the first time that a rigorous analysis has compared de-noising techniques for particle-based fluid simulations.

  13. A novel coupling of noise reduction algorithms for particle flow simulations

    NASA Astrophysics Data System (ADS)

    Zimoń, M. J.; Reese, J. M.; Emerson, D. R.

    2016-09-01

    Proper orthogonal decomposition (POD) and its extension based on time-windows have been shown to greatly improve the effectiveness of recovering smooth ensemble solutions from noisy particle data. However, to successfully de-noise any molecular system, a large number of measurements still need to be provided. In order to achieve a better efficiency in processing time-dependent fields, we have combined POD with a well-established signal processing technique, wavelet-based thresholding. In this novel hybrid procedure, the wavelet filtering is applied within the POD domain and referred to as WAVinPOD. The algorithm exhibits promising results when applied to both synthetically generated signals and particle data. In this work, the simulations compare the performance of our new approach with standard POD or wavelet analysis in extracting smooth profiles from noisy velocity and density fields. Numerical examples include molecular dynamics and dissipative particle dynamics simulations of unsteady force- and shear-driven liquid flows, as well as phase separation phenomenon. Simulation results confirm that WAVinPOD preserves the dimensionality reduction obtained using POD, while improving its filtering properties through the sparse representation of data in wavelet basis. This paper shows that WAVinPOD outperforms the other estimators for both synthetically generated signals and particle-based measurements, achieving a higher signal-to-noise ratio from a smaller number of samples. The new filtering methodology offers significant computational savings, particularly for multi-scale applications seeking to couple continuum informations with atomistic models. It is the first time that a rigorous analysis has compared de-noising techniques for particle-based fluid simulations.

  14. Comparative Study of Algorithms for the Numerical Simulation of Lattice QCD

    SciTech Connect

    Luz, Fernando H. P.; Mendes, Tereza

    2010-11-12

    Large-scale numerical simulations are the prime method for a nonperturbative study of QCD from first principles. Although the lattice simulation of the pure-gauge (or quenched-QCD) case may be performed very efficiently on parallel machines, there are several additional difficulties in the simulation of the full-QCD case, i.e. when dynamical quark effects are taken into account. We discuss the main aspects of full-QCD simulations, describing the most common algorithms. We present a comparative analysis of performance for two versions of the hybrid Monte Carlo method (the so-called R and RHMC algorithms), as provided in the MILC software package. We consider two degenerate flavors of light quarks in the staggered formulation, having in mind the case of finite-temperature QCD.

  15. A fast sorting algorithm for a hypersonic rarefied flow particle simulation on the connection machine

    NASA Technical Reports Server (NTRS)

    Dagum, Leonardo

    1989-01-01

    The data parallel implementation of a particle simulation for hypersonic rarefied flow described by Dagum associates a single parallel data element with each particle in the simulation. The simulated space is divided into discrete regions called cells containing a variable and constantly changing number of particles. The implementation requires a global sort of the parallel data elements so as to arrange them in an order that allows immediate access to the information associated with cells in the simulation. Described here is a very fast algorithm for performing the necessary ranking of the parallel data elements. The performance of the new algorithm is compared with that of the microcoded instruction for ranking on the Connection Machine.

  16. A memory structure adapted simulated annealing algorithm for a green vehicle routing problem.

    PubMed

    Küçükoğlu, İlker; Ene, Seval; Aksoy, Aslı; Öztürk, Nursel

    2015-03-01

    Currently, reduction of carbon dioxide (CO2) emissions and fuel consumption has become a critical environmental problem and has attracted the attention of both academia and the industrial sector. Government regulations and customer demands are making environmental responsibility an increasingly important factor in overall supply chain operations. Within these operations, transportation has the most hazardous effects on the environment, i.e., CO2 emissions, fuel consumption, noise and toxic effects on the ecosystem. This study aims to construct vehicle routes with time windows that minimize the total fuel consumption and CO2 emissions. The green vehicle routing problem with time windows (G-VRPTW) is formulated using a mixed integer linear programming model. A memory structure adapted simulated annealing (MSA-SA) meta-heuristic algorithm is constructed due to the high complexity of the proposed problem and long solution times for practical applications. The proposed models are integrated with a fuel consumption and CO2 emissions calculation algorithm that considers the vehicle technical specifications, vehicle load, and transportation distance in a green supply chain environment. The proposed models are validated using well-known instances with different numbers of customers. The computational results indicate that the MSA-SA heuristic is capable of obtaining good G-VRPTW solutions within a reasonable amount of time by providing reductions in fuel consumption and CO2 emissions.

  17. Proposal of a brand-new gyrokinetic algorithm for global MHD simulation

    NASA Astrophysics Data System (ADS)

    Naitou, Hiroshi; Kobayashi, Kenichi; Hashimoto, Hiroki; Andachi, Takehisa; Lee, Wei-Li; Tokuda, Shinji; Yagi, Masatoshi

    2009-11-01

    A new algorithm for the gyrokinetic PIC code is proposed. The basic equations are energy conserving and composed of (1) the gyrokinetic Vlasov (GKV) equation, (2) the Vortex equation, and (3) the generalized Ohm's law along the magnetic field. Equation (2) is used to advance electrostatic potential in time. Equation (3) is used to advance longitudinal component of vector potential in time as well as estimating longitudinal induced electric field to accelerate charged particles. The particle information is used to estimate pressure terms in equation (3). The idea was obtained in the process of reviewing the split-weight-scheme formalism. This algorithm was incorporated in the Gpic-MHD code. Preliminary results for the m=1/n=1 internal kink mode simulation in the cylindrical geometry indicate good energy conservation, quite low noise due to particle discreteness, and applicability to larger spatial scale and higher beta regimes. The advantage of new Gpic-MHD is that the lower order moments of the GKV equation are estimated by the moment equation while the particle information is used to evaluate the second order moment.

  18. Clustering of tethered satellite system simulation data by an adaptive neuro-fuzzy algorithm

    NASA Technical Reports Server (NTRS)

    Mitra, Sunanda; Pemmaraju, Surya

    1992-01-01

    Recent developments in neuro-fuzzy systems indicate that the concepts of adaptive pattern recognition, when used to identify appropriate control actions corresponding to clusters of patterns representing system states in dynamic nonlinear control systems, may result in innovative designs. A modular, unsupervised neural network architecture, in which fuzzy learning rules have been embedded is used for on-line identification of similar states. The architecture and control rules involved in Adaptive Fuzzy Leader Clustering (AFLC) allow this system to be incorporated in control systems for identification of system states corresponding to specific control actions. We have used this algorithm to cluster the simulation data of Tethered Satellite System (TSS) to estimate the range of delta voltages necessary to maintain the desired length rate of the tether. The AFLC algorithm is capable of on-line estimation of the appropriate control voltages from the corresponding length error and length rate error without a priori knowledge of their membership functions and familarity with the behavior of the Tethered Satellite System.

  19. 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.

  20. Shuttle Entry Air Data System (SEADS) - Optimization of preflight algorithms based on flight results

    NASA Technical Reports Server (NTRS)

    Wolf, H.; Henry, M. W.; Siemers, Paul M., III

    1988-01-01

    The SEADS pressure model algorithm results were tested against other sources of air data, in particular, the Shuttle Best Estimated Trajectory (BET). The algorithm basis was also tested through a comparison of flight-measured pressure distribution vs the wind tunnel database. It is concluded that the successful flight of SEADS and the subsequent analysis of the data shows good agreement between BET and SEADS air data.

  1. Mitigating Multipath Bias Using a Dual-Polarization Antenna: Theoretical Performance, Algorithm Design, and Simulation

    PubMed Central

    Xie, Lin; Cui, Xiaowei; Zhao, Sihao; Lu, Mingquan

    2017-01-01

    It is well known that multipath effect remains a dominant error source that affects the positioning accuracy of Global Navigation Satellite System (GNSS) receivers. Significant efforts have been made by researchers and receiver manufacturers to mitigate multipath error in the past decades. Recently, a multipath mitigation technique using dual-polarization antennas has become a research hotspot for it provides another degree of freedom to distinguish the line-of-sight (LOS) signal from the LOS and multipath composite signal without extensively increasing the complexity of the receiver. Numbers of multipath mitigation techniques using dual-polarization antennas have been proposed and all of them report performance improvement over the single-polarization methods. However, due to the unpredictability of multipath, multipath mitigation techniques based on dual-polarization are not always effective while few studies discuss the condition under which the multipath mitigation using a dual-polarization antenna can outperform that using a single-polarization antenna, which is a fundamental question for dual-polarization multipath mitigation (DPMM) and the design of multipath mitigation algorithms. In this paper we analyze the characteristics of the signal received by a dual-polarization antenna and use the maximum likelihood estimation (MLE) to assess the theoretical performance of DPMM in different received signal cases. Based on the assessment we answer this fundamental question and find the dual-polarization antenna’s capability in mitigating short delay multipath—the most challenging one among all types of multipath for the majority of the multipath mitigation techniques. Considering these effective conditions, we propose a dual-polarization sequential iterative maximum likelihood estimation (DP-SIMLE) algorithm for DPMM. The simulation results verify our theory and show superior performance of the proposed DP-SIMLE algorithm over the traditional one using only an

  2. Mitigating Multipath Bias Using a Dual-Polarization Antenna: Theoretical Performance, Algorithm Design, and Simulation.

    PubMed

    Xie, Lin; Cui, Xiaowei; Zhao, Sihao; Lu, Mingquan

    2017-02-13

    It is well known that multipath effect remains a dominant error source that affects the positioning accuracy of Global Navigation Satellite System (GNSS) receivers. Significant efforts have been made by researchers and receiver manufacturers to mitigate multipath error in the past decades. Recently, a multipath mitigation technique using dual-polarization antennas has become a research hotspot for it provides another degree of freedom to distinguish the line-of-sight (LOS) signal from the LOS and multipath composite signal without extensively increasing the complexity of the receiver. Numbers of multipath mitigation techniques using dual-polarization antennas have been proposed and all of them report performance improvement over the single-polarization methods. However, due to the unpredictability of multipath, multipath mitigation techniques based on dual-polarization are not always effective while few studies discuss the condition under which the multipath mitigation using a dual-polarization antenna can outperform that using a single-polarization antenna, which is a fundamental question for dual-polarization multipath mitigation (DPMM) and the design of multipath mitigation algorithms. In this paper we analyze the characteristics of the signal received by a dual-polarization antenna and use the maximum likelihood estimation (MLE) to assess the theoretical performance of DPMM in different received signal cases. Based on the assessment we answer this fundamental question and find the dual-polarization antenna's capability in mitigating short delay multipath-the most challenging one among all types of multipath for the majority of the multipath mitigation techniques. Considering these effective conditions, we propose a dual-polarization sequential iterative maximum likelihood estimation (DP-SIMLE) algorithm for DPMM. The simulation results verify our theory and show superior performance of the proposed DP-SIMLE algorithm over the traditional one using only an RHCP

  3. Obtaining Identical Results on Varying Numbers of Processors In Domain Decomposed particle Monte Carlo Simulations

    SciTech Connect

    Gentile, N A; Kalos, M H; Brunner, T A

    2005-03-22

    Domain decomposed Monte Carlo codes, like other domain-decomposed codes, are difficult to debug. Domain decomposition is prone to error, and interactions between the domain decomposition code and the rest of the algorithm often produces subtle bugs. These bugs are particularly difficult to find in a Monte Carlo algorithm, in which the results have statistical noise. Variations in the results due to statistical noise can mask errors when comparing the results to other simulations or analytic results. If a code can get the same result on one domain as on many, debugging the whole code is easier. This reproducibility property is also desirable when comparing results done on different numbers of processors and domains. We describe how reproducibility, to machine precision, is obtained on different numbers of domains in an Implicit Monte Carlo photonics code.

  4. MIA computer simulation test results report. [space shuttle avionics

    NASA Technical Reports Server (NTRS)

    Unger, G. E.

    1974-01-01

    Results of the first noise susceptibility computer simulation tests of the complete MIA receiver analytical model are presented. Computer simulation tests were conducted with both Gaussian and pulse noise inputs. The results of the Gaussian noise tests were compared to results predicted previously and were found to be in substantial agreement. The results of the pulse noise tests will be compared to the results of planned analogous tests in the Data Bus Evaluation Laboratory at a later time. The MIA computer model is considered to be fully operational at this time.

  5. Simulation of a navigator algorithm for a low-cost GPS receiver

    NASA Technical Reports Server (NTRS)

    Hodge, W. F.

    1980-01-01

    The analytical structure of an existing navigator algorithm for a low cost global positioning system receiver is described in detail to facilitate its implementation on in-house digital computers and real-time simulators. The material presented includes a simulation of GPS pseudorange measurements, based on a two-body representation of the NAVSTAR spacecraft orbits, and a four component model of the receiver bias errors. A simpler test for loss of pseudorange measurements due to spacecraft shielding is also noted.

  6. An enhanced simulated annealing routing algorithm for semi-diagonal torus network

    NASA Astrophysics Data System (ADS)

    Adzhar, Noraziah; Salleh, Shaharuddin

    2017-09-01

    Multiprocessor is another great technology that helps in advancing human civilization due to high demands for solving complex problems. A multiprocessing system can have a lot of replicated processor-memory pairs (henceforth regard as net) or also called as processing nodes. Each of these nodes is connected to each other through interconnection networks and passes message using a standard message passing mechanism. In this paper, we present a routing algorithm based on enhanced simulated annealing technique to provide the connection between nodes in a semi-diagonal torus (SD-Torus) network. This network is both symmetric and regular; thus, make it very beneficial in the implementation process. The main objective is to maximize the number of established connection between nodes in this SD-Torus network. In order to achieve this objective, each node must be connected in its shortest way as possible. We start our algorithm by designing shortest path algorithm based on Dijkstra’s method. While this algorithm guarantees to find the shortest path for each single net, if it exists, each routed net will form obstacle for later paths. This increases the complexity to route later nets and makes routing longer than optimal, or sometimes impossible to complete. The solution is further refined by re-routing all nets in different orders using simulated annealing method. Through simulation program, our proposed algorithm succeeded in performing complete routing up to 81 nodes with 40 nets in 9×9 SD-Torus network size.

  7. Hierarchical tree algorithm for collisional N-body simulations on GRAPE

    NASA Astrophysics Data System (ADS)

    Fukushige, Toshiyuki; Kawai, Atsushi

    2016-06-01

    We present an implementation of the hierarchical tree algorithm on the individual timestep algorithm (the Hermite scheme) for collisional N-body simulations, running on the GRAPE-9 system, a special-purpose hardware accelerator for gravitational many-body simulations. Such a combination of the tree algorithm and the individual timestep algorithm was not easy on the previous GRAPE system mainly because its memory addressing scheme was limited only to sequential access to a full set of particle data. The present GRAPE-9 system has an indirect memory addressing unit and a particle memory large enough to store all the particle data and also the tree node data. The indirect memory addressing unit stores interaction lists for the tree algorithm, which is constructed on the host computer, and, according to the interaction lists, force pipelines calculate only the interactions necessary. In our implementation, the interaction calculations are significantly reduced compared to direct N2 summation in the original Hermite scheme. For example, we can achieve about a factor 30 of speedup (equivalent to about 17 teraflops) against the Hermite scheme for a simulation of an N = 106 system, using hardware of a peak speed of 0.6 teraflops for the Hermite scheme.

  8. A Physics-based Algorithm for Real-time Simulation of Electrosurgery Procedures in Minimally Invasive Surgery

    PubMed Central

    Lu, Zhonghua; Arikatla, Venkata S; Han, Zhongqing; Allen, Brian F.; De, Suvranu

    2014-01-01

    Background High-frequency electricity is used in a majority of surgical interventions. However, modern computer-based training and simulation systems rely on physically unrealistic models that fail to capture the interplay of the electrical, mechanical and thermal properties of biological tissue. Methods We present a real-time and physically realistic simulation of electrosurgery, by modeling the electrical, thermal and mechanical properties as three iteratively solved finite element models. To provide sub-finite-element graphical rendering of vaporized tissue, a dual mesh dynamic triangulation algorithm based on isotherms is proposed. The block compressed row storage (BCRS) structure is shown to be critical in allowing computationally efficient changes in the tissue topology due to vaporization. Results We have demonstrated our physics based electrosurgery cutting algorithm through various examples. Our matrix manipulation algorithms designed for topology changes have shown low computational cost. Conclusions Our simulator offers substantially greater physical fidelity compared to previous simulators that use simple geometry-based heat characterization. PMID:24357156

  9. Semirigorous synchronous sublattice algorithm for parallel kinetic Monte Carlo simulations of thin film growth

    NASA Astrophysics Data System (ADS)

    Shim, Yunsic; Amar, Jacques G.

    2005-03-01

    The standard kinetic Monte Carlo algorithm is an extremely efficient method to carry out serial simulations of dynamical processes such as thin film growth. However, in some cases it is necessary to study systems over extended time and length scales, and therefore a parallel algorithm is desired. Here we describe an efficient, semirigorous synchronous sublattice algorithm for parallel kinetic Monte Carlo simulations. The accuracy and parallel efficiency are studied as a function of diffusion rate, processor size, and number of processors for a variety of simple models of epitaxial growth. The effects of fluctuations on the parallel efficiency are also studied. Since only local communications are required, linear scaling behavior is observed, e.g., the parallel efficiency is independent of the number of processors for fixed processor size.

  10. Simulating the time-dependent Schr"odinger equation with a quantum lattice-gas algorithm

    NASA Astrophysics Data System (ADS)

    Prezkuta, Zachary; Coffey, Mark

    2007-03-01

    Quantum computing algorithms promise remarkable improvements in speed or memory for certain applications. Currently, the Type II (or hybrid) quantum computer is the most feasible to build. This consists of a large number of small Type I (pure) quantum computers that compute with quantum logic, but communicate with nearest neighbors in a classical way. The arrangement thus formed is suitable for computations that execute a quantum lattice gas algorithm (QLGA). We report QLGA simulations for both the linear and nonlinear time-dependent Schr"odinger equation. These evidence the stable, efficient, and at least second order convergent properties of the algorithm. The simulation capability provides a computational tool for applications in nonlinear optics, superconducting and superfluid materials, Bose-Einstein condensates, and elsewhere.

  11. Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

    SciTech Connect

    Thanh, Vo Hong; Priami, Corrado

    2015-08-07

    We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reaction rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness.

  12. A novel algorithm for non-bonded-list updating in molecular simulations.

    PubMed

    Maximova, Tatiana; Keasar, Chen

    2006-06-01

    Simulations of molecular systems typically handle interactions within non-bonded pairs. Generating and updating a list of these pairs can be the most time-consuming part of energy calculations for large systems. Thus, efficient non-bonded list processing can speed up the energy calculations significantly. While the asymptotic complexity of current algorithms (namely O(N), where N is the number of particles) is probably the lowest possible, a wide space for optimization is still left. This article offers a heuristic extension to the previously suggested grid based algorithms. We show that, when the average particle movements are slow, simulation time can be reduced considerably. The proposed algorithm has been implemented in the DistanceMatrix class of the molecular modeling package MESHI. MESHI is freely available at .

  13. Aerosol kinetic code "AERFORM": Model, validation and simulation results

    NASA Astrophysics Data System (ADS)

    Gainullin, K. G.; Golubev, A. I.; Petrov, A. M.; Piskunov, V. N.

    2016-06-01

    The aerosol kinetic code "AERFORM" is modified to simulate droplet and ice particle formation in mixed clouds. The splitting method is used to calculate condensation and coagulation simultaneously. The method is calibrated with analytic solutions of kinetic equations. Condensation kinetic model is based on cloud particle growth equation, mass and heat balance equations. The coagulation kinetic model includes Brownian, turbulent and precipitation effects. The real values are used for condensation and coagulation growth of water droplets and ice particles. The model and the simulation results for two full-scale cloud experiments are presented. The simulation model and code may be used autonomously or as an element of another code.

  14. Experimental and simulational result multipactors in 112 MHz QWR injector

    SciTech Connect

    Xin, T.; Ben-Zvi, I.; Belomestnykh, S.; Brutus, J. C.; Skaritka, J.; Wu, Q.; Xiao, B.

    2015-05-03

    The first RF commissioning of 112 MHz QWR superconducting electron gun was done in late 2014. The coaxial Fundamental Power Coupler (FPC) and Cathode Stalk (stalk) were installed and tested for the first time. During this experiment, we observed several multipacting barriers at different gun voltage levels. The simulation work was done within the same range. The comparison between the experimental observation and the simulation results are presented in this paper. The observations during the test are consisted with the simulation predictions. We were able to overcome most of the multipacting barriers and reach 1.8 MV gun voltage under pulsed mode after several round of conditioning processes.

  15. Golfing with protons: using research grade simulation algorithms for online games

    NASA Astrophysics Data System (ADS)

    Harold, J.

    2004-12-01

    Scientists have long known the power of simulations. By modeling a system in a computer, researchers can experiment at will, developing an intuitive sense of how a system behaves. The rapid increase in the power of personal computers, combined with technologies such as Flash, Shockwave and Java, allow us to bring research simulations into the education world by creating exploratory environments for the public. This approach is illustrated by a project funded by a small grant from NSF's Informal Science Education program, through an opportunity that provides education supplements to existing research awards. Using techniques adapted from a magnetospheric research program, several Flash based interactives have been developed that allow web site visitors to explore the motion of particles in the Earth's magnetosphere. These pieces were folded into a larger Space Weather Center web project at the Space Science Institute (www.spaceweathercenter.org). Rather than presenting these interactives as plasma simulations per se, the research algorithms were used to create games such as "Magneto Mini Golf", where the balls are protons moving in combined electric and magnetic fields. The "holes" increase in complexity, beginning with no fields and progressing towards a simple model of Earth's magnetosphere. The emphasis of the activity is gameplay, but because it is at its core a plasma simulation, the user develops an intuitive sense of charged particle motion as they progress. Meanwhile, the pieces contain embedded assessments that are measurable through a database driven tracking system. Mining that database not only provides helpful usability information, but allows us to examine whether users are meeting the learning goals of the activities. We will discuss the development and evaluation results of the project, as well as the potential for these types of activities to shift the expectations of what a web site can and should provide educationally.

  16. SIMULATION OF AEROSOL DYNAMICS: A COMPARATIVE REVIEW OF ALGORITHMS USED IN AIR QUALITY MODELS

    EPA Science Inventory

    A comparative review of algorithms currently used in air quality models to simulate aerosol dynamics is presented. This review addresses coagulation, condensational growth, nucleation, and gas/particle mass transfer. Two major approaches are used in air quality models to repres...

  17. An algorithm to help design fire simulation and other data base work

    Treesearch

    Romain Mees

    1974-01-01

    The data necessary for fire simulation may be made available through an algorithm based on tracing of boundaries composed of straight-line segments. Useful assumptions are that if a closed boundary does not contain a given point, then any other closed boundary contained within the former one does not contain the location; and that a given location will be contained in...

  18. SIMULATION OF AEROSOL DYNAMICS: A COMPARATIVE REVIEW OF ALGORITHMS USED IN AIR QUALITY MODELS

    EPA Science Inventory

    A comparative review of algorithms currently used in air quality models to simulate aerosol dynamics is presented. This review addresses coagulation, condensational growth, nucleation, and gas/particle mass transfer. Two major approaches are used in air quality models to repres...

  19. A three-dimensional spectral algorithm for simulations of transition and turbulence

    NASA Technical Reports Server (NTRS)

    Zang, T. A.; Hussaini, M. Y.

    1985-01-01

    A spectral algorithm for simulating three dimensional, incompressible, parallel shear flows is described. It applies to the channel, to the parallel boundary layer, and to other shear flows with one wall bounded and two periodic directions. Representative applications to the channel and to the heated boundary layer are presented.

  20. A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms.

    PubMed

    Lai, Fu-Jou; Chang, Hong-Tsun; Huang, Yueh-Min; Wu, Wei-Sheng

    2014-01-01

    Eukaryotic transcriptional regulation is known to be highly connected through the networks of cooperative transcription factors (TFs). Measuring the cooperativity of TFs is helpful for understanding the biological relevance of these TFs in regulating genes. The recent advances in computational techniques led to various predictions of cooperative TF pairs in yeast. As each algorithm integrated different data resources and was developed based on different rationales, it possessed its own merit and claimed outperforming others. However, the claim was prone to subjectivity because each algorithm compared with only a few other algorithms and only used a small set of performance indices for comparison. This motivated us to propose a series of indices to objectively evaluate the prediction performance of existing algorithms. And based on the proposed performance indices, we conducted a comprehensive performance evaluation. We collected 14 sets of predicted cooperative TF pairs (PCTFPs) in yeast from 14 existing algorithms in the literature. Using the eight performance indices we adopted/proposed, the cooperativity of each PCTFP was measured and a ranking score according to the mean cooperativity of the set was given to each set of PCTFPs under evaluation for each performance index. It was seen that the ranking scores of a set of PCTFPs vary with different performance indices, implying that an algorithm used in predicting cooperative TF pairs is of strength somewhere but may be of weakness elsewhere. We finally made a comprehensive ranking for these 14 sets. The results showed that Wang J's study obtained the best performance evaluation on the prediction of cooperative TF pairs in yeast. In this study, we adopted/proposed eight performance indices to make a comprehensive performance evaluation on the prediction results of 14 existing cooperative TFs identification algorithms. Most importantly, these proposed indices can be easily applied to measure the performance of new

  1. A combined Event-Driven/Time-Driven molecular dynamics algorithm for the simulation of shock waves in rarefied gases

    SciTech Connect

    Valentini, Paolo Schwartzentruber, Thomas E.

    2009-12-10

    A novel combined Event-Driven/Time-Driven (ED/TD) algorithm to speed-up the Molecular Dynamics simulation of rarefied gases using realistic spherically symmetric soft potentials is presented. Due to the low density regime, the proposed method correctly identifies the time that must elapse before the next interaction occurs, similarly to Event-Driven Molecular Dynamics. However, each interaction is treated using Time-Driven Molecular Dynamics, thereby integrating Newton's Second Law using the sufficiently small time step needed to correctly resolve the atomic motion. Although infrequent, many-body interactions are also accounted for with a small approximation. The combined ED/TD method is shown to correctly reproduce translational relaxation in argon, described using the Lennard-Jones potential. For densities between {rho}=10{sup -4}kg/m{sup 3} and {rho}=10{sup -1}kg/m{sup 3}, comparisons with kinetic theory, Direct Simulation Monte Carlo, and pure Time-Driven Molecular Dynamics demonstrate that the ED/TD algorithm correctly reproduces the proper collision rates and the evolution toward thermal equilibrium. Finally, the combined ED/TD algorithm is applied to the simulation of a Mach 9 shock wave in rarefied argon. Density and temperature profiles as well as molecular velocity distributions accurately match DSMC results, and the shock thickness is within the experimental uncertainty. For the problems considered, the ED/TD algorithm ranged from several hundred to several thousand times faster than conventional Time-Driven MD. Moreover, the force calculation to integrate the molecular trajectories is found to contribute a negligible amount to the overall ED/TD simulation time. Therefore, this method could pave the way for the application of much more refined and expensive interatomic potentials, either classical or first-principles, to Molecular Dynamics simulations of shock waves in rarefied gases, involving vibrational nonequilibrium and chemical reactivity.

  2. Forward-Masked Frequency Selectivity Improvements in Simulated and Actual Cochlear Implant Users Using a Preprocessing Algorithm

    PubMed Central

    Jürgens, Tim

    2016-01-01

    Frequency selectivity can be quantified using masking paradigms, such as psychophysical tuning curves (PTCs). Normal-hearing (NH) listeners show sharp PTCs that are level- and frequency-dependent, whereas frequency selectivity is strongly reduced in cochlear implant (CI) users. This study aims at (a) assessing individual shapes of PTCs in CI users, (b) comparing these shapes to those of simulated CI listeners (NH listeners hearing through a CI simulation), and (c) increasing the sharpness of PTCs using a biologically inspired dynamic compression algorithm, BioAid, which has been shown to sharpen the PTC shape in hearing-impaired listeners. A three-alternative-forced-choice forward-masking technique was used to assess PTCs in 8 CI users (with their own speech processor) and 11 NH listeners (with and without listening through a vocoder to simulate electric hearing). CI users showed flat PTCs with large interindividual variability in shape, whereas simulated CI listeners had PTCs of the same average flatness, but more homogeneous shapes across listeners. The algorithm BioAid was used to process the stimuli before entering the CI users’ speech processor or the vocoder simulation. This algorithm was able to partially restore frequency selectivity in both groups, particularly in seven out of eight CI users, meaning significantly sharper PTCs than in the unprocessed condition. The results indicate that algorithms can improve the large-scale sharpness of frequency selectivity in some CI users. This finding may be useful for the design of sound coding strategies particularly for situations in which high frequency selectivity is desired, such as for music perception. PMID:27604785

  3. Cardiovascular system and microgravity simulation and inflight results

    NASA Astrophysics Data System (ADS)

    Pottier, J. M.; Patat, F.; Arbeille, P.; Pourcelot, L.; Massabuau, P.; Guell, A.; Gharib, C.

    Main results of cardiovascular investigation, performed with ultrasound methods during the common French/Soviet flight aboard Salyut VII in June 1982, are compared to variations of the same parameters studied during ground-based simulations on the same subject or observed by other investigators during various ground-based experiences. The antiorthostatic bed rest simulation partly reproduces microgravity conditions and seems to be better adaptated to cardiac hemodynamics, despite some differences, and to the cerebral circulation, than to the inferior limb circulation.

  4. Hyper-X Stage Separation: Simulation Development and Results

    NASA Technical Reports Server (NTRS)

    Reubush, David E.; Martin, John G.; Robinson, Jeffrey S.; Bose, David M.; Strovers, Brian K.

    2001-01-01

    This paper provides an overview of stage separation simulation development and results for NASA's Hyper-X program; a focused hypersonic technology effort designed to move hypersonic, airbreathing vehicle technology from the laboratory environment to the flight environment. This paper presents an account of the development of the current 14 degree of freedom stage separation simulation tool (SepSim) and results from use of the tool in a Monte Carlo analysis to evaluate the risk of failure for the separation event. Results from use of the tool show that there is only a very small risk of failure in the separation event.

  5. Flight test results of failure detection and isolation algorithms for a redundant strapdown inertial measurement unit

    NASA Technical Reports Server (NTRS)

    Morrell, F. R.; Motyka, P. R.; Bailey, M. L.

    1990-01-01

    Flight test results for two sensor fault-tolerant algorithms developed for a redundant strapdown inertial measurement unit are presented. The inertial measurement unit (IMU) consists of four two-degrees-of-freedom gyros and accelerometers mounted on the faces of a semi-octahedron. Fault tolerance is provided by edge vector test and generalized likelihood test algorithms, each of which can provide dual fail-operational capability for the IMU. To detect the wide range of failure magnitudes in inertial sensors, which provide flight crucial information for flight control and navigation, failure detection and isolation are developed in terms of a multi level structure. Threshold compensation techniques, developed to enhance the sensitivity of the failure detection process to navigation level failures, are presented. Four flight tests were conducted in a commercial transport-type environment to compare and determine the performance of the failure detection and isolation methods. Dual flight processors enabled concurrent tests for the algorithms. Failure signals such as hard-over, null, or bias shift, were added to the sensor outputs as simple or multiple failures during the flights. Both algorithms provided timely detection and isolation of flight control level failures. The generalized likelihood test algorithm provided more timely detection of low-level sensor failures, but it produced one false isolation. Both algorithms demonstrated the capability to provide dual fail-operational performance for the skewed array of inertial sensors.

  6. Flight test results of failure detection and isolation algorithms for a redundant strapdown inertial measurement unit

    NASA Technical Reports Server (NTRS)

    Morrell, F. R.; Motyka, P. R.; Bailey, M. L.

    1990-01-01

    Flight test results for two sensor fault-tolerant algorithms developed for a redundant strapdown inertial measurement unit are presented. The inertial measurement unit (IMU) consists of four two-degrees-of-freedom gyros and accelerometers mounted on the faces of a semi-octahedron. Fault tolerance is provided by edge vector test and generalized likelihood test algorithms, each of which can provide dual fail-operational capability for the IMU. To detect the wide range of failure magnitudes in inertial sensors, which provide flight crucial information for flight control and navigation, failure detection and isolation are developed in terms of a multi level structure. Threshold compensation techniques, developed to enhance the sensitivity of the failure detection process to navigation level failures, are presented. Four flight tests were conducted in a commercial transport-type environment to compare and determine the performance of the failure detection and isolation methods. Dual flight processors enabled concurrent tests for the algorithms. Failure signals such as hard-over, null, or bias shift, were added to the sensor outputs as simple or multiple failures during the flights. Both algorithms provided timely detection and isolation of flight control level failures. The generalized likelihood test algorithm provided more timely detection of low-level sensor failures, but it produced one false isolation. Both algorithms demonstrated the capability to provide dual fail-operational performance for the skewed array of inertial sensors.

  7. Improving Simulation-Based Algorithms for Fitting ERGMs

    PubMed Central

    Hummel, Ruth M.; Hunter, David R.; Handcock, Mark S.

    2015-01-01

    Markov chain Monte Carlo methods can be used to approximate the intractable normalizing constants that arise in likelihood calculations for many exponential family random graph models for networks. However, in practice, the resulting approximations degrade as parameter values move away from the value used to define the Markov chain, even in cases where the chain produces perfectly efficient samples. We introduce a new approximation method along with a novel method of moving toward a maximum likelihood estimator (MLE) from an arbitrary starting parameter value in a series of steps based on alternating between the canonical exponential family parameterization and the mean-value parameterization. This technique enables us to find an approximate MLE in many cases where this was previously not possible. We illustrate these methods on a model for a transcriptional regulation network for E. coli, an example where previous attempts to approximate an MLE had failed, and a model for a well-known social network dataset involving friendships among workers in a tailor shop. These methods are implemented in the publicly available ergm package for R, and computer code to duplicate the results of this paper is included in the Supplemental Materials. PMID:26120266

  8. Structural optimization and segregation behavior of quaternary alloy nanoparticles based on simulated annealing algorithm

    NASA Astrophysics Data System (ADS)

    Xin-Ze, Lu; Gui-Fang, Shao; Liang-You, Xu; Tun-Dong, Liu; Yu-Hua, Wen

    2016-05-01

    Alloy nanoparticles exhibit higher catalytic activity than monometallic nanoparticles, and their stable structures are of importance to their applications. We employ the simulated annealing algorithm to systematically explore the stable structure and segregation behavior of tetrahexahedral Pt-Pd-Cu-Au quaternary alloy nanoparticles. Three alloy nanoparticles consisting of 443 atoms, 1417 atoms, and 3285 atoms are considered and compared. The preferred positions of atoms in the nanoparticles are analyzed. The simulation results reveal that Cu and Au atoms tend to occupy the surface, Pt atoms preferentially occupy the middle layers, and Pd atoms tend to segregate to the inner layers. Furthermore, Au atoms present stronger surface segregation than Cu ones. This study provides a fundamental understanding on the structural features and segregation phenomena of multi-metallic nanoparticles. Project supported by the National Natural Science Foundation of China (Grant Nos. 51271156, 11474234, and 61403318) and the Natural Science Foundation of Fujian Province of China (Grant Nos. 2013J01255 and 2013J06002).

  9. Algorithm for Building a Spectrum for NREL's One-Sun Multi-Source Simulator: Preprint

    SciTech Connect

    Moriarty, T.; Emery, K.; Jablonski, J.

    2012-06-01

    Historically, the tools used at NREL to compensate for the difference between a reference spectrum and a simulator spectrum have been well-matched reference cells and the application of a calculated spectral mismatch correction factor, M. This paper describes the algorithm for adjusting the spectrum of a 9-channel fiber-optic-based solar simulator with a uniform beam size of 9 cm square at 1-sun. The combination of this algorithm and the One-Sun Multi-Source Simulator (OSMSS) hardware reduces NREL's current vs. voltage measurement time for a typical three-junction device from man-days to man-minutes. These time savings may be significantly greater for devices with more junctions.

  10. Space-based Doppler lidar sampling strategies: Algorithm development and simulated observation experiments

    NASA Technical Reports Server (NTRS)

    Emmitt, G. D.; Wood, S. A.; Morris, M.

    1990-01-01

    Lidar Atmospheric Wind Sounder (LAWS) Simulation Models (LSM) were developed to evaluate the potential impact of global wind observations on the basic understanding of the Earth's atmosphere and on the predictive skills of current forecast models (GCM and regional scale). Fully integrated top to bottom LAWS Simulation Models for global and regional scale simulations were developed. The algorithm development incorporated the effects of aerosols, water vapor, clouds, terrain, and atmospheric turbulence into the models. Other additions include a new satellite orbiter, signal processor, line of sight uncertainty model, new Multi-Paired Algorithm and wind error analysis code. An atmospheric wind field library containing control fields, meteorological fields, phenomena fields, and new European Center for Medium Range Weather Forecasting (ECMWF) data was also added. The LSM was used to address some key LAWS issues and trades such as accuracy and interpretation of LAWS information, data density, signal strength, cloud obscuration, and temporal data resolution.

  11. Speeding up simulation of diffusion in zeolites by a parallel synchronous kinetic Monte Carlo algorithm.

    PubMed

    Gabrieli, Andrea; Demontis, Pierfranco; Pazzona, Federico G; Suffritti, Giuseppe B

    2011-05-01

    Understanding the behaviors of molecules in tight confinement is a challenging task. Standard simulation tools like kinetic Monte Carlo have proven to be very effective in the study of adsorption and diffusion phenomena in microporous materials, but they turn out to be very inefficient when simulation time and length scales are extended. In this paper we have explored the possibility of application of a discrete version of the synchronous parallel kinetic Monte Carlo algorithm introduced by Martínez et al. [J. Comput. Phys. 227, 3804 (2008)] to the study of aromatic hydrocarbons diffusion in zeolites. The efficiency of this algorithm is investigated as a function of the number of processors and domain size. We show that with an accurate choice of domains size it is possible to achieve very good efficiencies thus permitting us to effectively extend space and time scales of the simulated system. © 2011 American Physical Society

  12. Direct Dynamics Simulations using Hessian-based Predictor-corrector Integration Algorithms

    SciTech Connect

    Lourderaj, Upakarasamy; Song, Kihyung; Windus, Theresa L; Zhuang, Yu; Hase, William L

    2007-01-29

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. In previous research (J. Chem. Phys. 111, 3800 (1999)) a Hessian-based integration algorithm was derived for performing direct dynamics simulations. In the work presented here, improvements to this algorithm are described. The algorithm has a predictor step based on a local second-order Taylor expansion of the potential in Cartesian coordinates, within a trust radius, and a fifth-order correction to this predicted trajectory. The current algorithm determines the predicted trajectory in Cartesian coordinates, instead of the instantaneous normal mode coordinates used previously, to ensure angular momentum conservation. For the previous algorithm the corrected step was evaluated in rotated Cartesian coordinates. Since the local potential expanded in Cartesian coordinates is not invariant to rotation, the constants of motion are not necessarily conserved during the corrector step. An approximate correction to this shortcoming was made by projecting translation and rotation out of the rotated coordinates. For the current algorithm unrotated Cartesian coordinates are used for the corrected step to assure the constants of motion are conserved. An algorithm is proposed for updating the trust radius to enhance the accuracy and efficiency of the numerical integration. This modified Hessian-based integration algorithm, with its new components, has been implemented into the VENUS/NWChem software package and compared with the velocity-Verlet algorithm for the H₂CO→H₂+CO, O₃+C₃H₆, and F-+CH₃OOH chemical reactions.

  13. Presenting simulation results in a nested loop plot.

    PubMed

    Rücker, Gerta; Schwarzer, Guido

    2014-12-12

    Statisticians investigate new methods in simulations to evaluate their properties for future real data applications. Results are often presented in a number of figures, e.g., Trellis plots. We had conducted a simulation study on six statistical methods for estimating the treatment effect in binary outcome meta-analyses, where selection bias (e.g., publication bias) was suspected because of apparent funnel plot asymmetry. We varied five simulation parameters: true treatment effect, extent of selection, event proportion in control group, heterogeneity parameter, and number of studies in meta-analysis. In combination, this yielded a total number of 768 scenarios. To present all results using Trellis plots, 12 figures were needed. Choosing bias as criterion of interest, we present a 'nested loop plot', a diagram type that aims to have all simulation results in one plot. The idea was to bring all scenarios into a lexicographical order and arrange them consecutively on the horizontal axis of a plot, whereas the treatment effect estimate is presented on the vertical axis. The plot illustrates how parameters simultaneously influenced the estimate. It can be combined with a Trellis plot in a so-called hybrid plot. Nested loop plots may also be applied to other criteria such as the variance of estimation. The nested loop plot, similar to a time series graph, summarizes all information about the results of a simulation study with respect to a chosen criterion in one picture and provides a suitable alternative or an addition to Trellis plots.

  14. A Systematic Evaluation of Feature Selection and Classification Algorithms Using Simulated and Real miRNA Sequencing Data.

    PubMed

    Yang, Sheng; Guo, Li; Shao, Fang; Zhao, Yang; Chen, Feng

    2015-01-01

    Sequencing is widely used to discover associations between microRNAs (miRNAs) and diseases. However, the negative binomial distribution (NB) and high dimensionality of data obtained using sequencing can lead to low-power results and low reproducibility. Several statistical learning algorithms have been proposed to address sequencing data, and although evaluation of these methods is essential, such studies are relatively rare. The performance of seven feature selection (FS) algorithms, including baySeq, DESeq, edgeR, the rank sum test, lasso, particle swarm optimistic decision tree, and random forest (RF), was compared by simulation under different conditions based on the difference of the mean, the dispersion parameter of the NB, and the signal to noise ratio. Real data were used to evaluate the performance of RF, logistic regression, and support vector machine. Based on the simulation and real data, we discuss the behaviour of the FS and classification algorithms. The Apriori algorithm identified frequent item sets (mir-133a, mir-133b, mir-183, mir-937, and mir-96) from among the deregulated miRNAs of six datasets from The Cancer Genomics Atlas. Taking these findings altogether and considering computational memory requirements, we propose a strategy that combines edgeR and DESeq for large sample sizes.

  15. Simulation and experimental design of a new advanced variable step size Incremental Conductance MPPT algorithm for PV systems.

    PubMed

    Loukriz, Abdelhamid; Haddadi, Mourad; Messalti, Sabir

    2016-05-01

    Improvement of the efficiency of photovoltaic system based on new maximum power point tracking (MPPT) algorithms is the most promising solution due to its low cost and its easy implementation without equipment updating. Many MPPT methods with fixed step size have been developed. However, when atmospheric conditions change rapidly , the performance of conventional algorithms is reduced. In this paper, a new variable step size Incremental Conductance IC MPPT algorithm has been proposed. Modeling and simulation of different operational conditions of conventional Incremental Conductance IC and proposed methods are presented. The proposed method was developed and tested successfully on a photovoltaic system based on Flyback converter and control circuit using dsPIC30F4011. Both, simulation and experimental design are provided in several aspects. A comparative study between the proposed variable step size and fixed step size IC MPPT method under similar operating conditions is presented. The obtained results demonstrate the efficiency of the proposed MPPT algorithm in terms of speed in MPP tracking and accuracy.

  16. A Systematic Evaluation of Feature Selection and Classification Algorithms Using Simulated and Real miRNA Sequencing Data

    PubMed Central

    Yang, Sheng; Guo, Li; Shao, Fang; Zhao, Yang; Chen, Feng

    2015-01-01

    Sequencing is widely used to discover associations between microRNAs (miRNAs) and diseases. However, the negative binomial distribution (NB) and high dimensionality of data obtained using sequencing can lead to low-power results and low reproducibility. Several statistical learning algorithms have been proposed to address sequencing data, and although evaluation of these methods is essential, such studies are relatively rare. The performance of seven feature selection (FS) algorithms, including baySeq, DESeq, edgeR, the rank sum test, lasso, particle swarm optimistic decision tree, and random forest (RF), was compared by simulation under different conditions based on the difference of the mean, the dispersion parameter of the NB, and the signal to noise ratio. Real data were used to evaluate the performance of RF, logistic regression, and support vector machine. Based on the simulation and real data, we discuss the behaviour of the FS and classification algorithms. The Apriori algorithm identified frequent item sets (mir-133a, mir-133b, mir-183, mir-937, and mir-96) from among the deregulated miRNAs of six datasets from The Cancer Genomics Atlas. Taking these findings altogether and considering computational memory requirements, we propose a strategy that combines edgeR and DESeq for large sample sizes. PMID:26508990

  17. The Geometric Cluster Algorithm: Rejection-Free Monte Carlo Simulation of Complex Fluids

    NASA Astrophysics Data System (ADS)

    Luijten, Erik

    2005-03-01

    The study of complex fluids is an area of intense research activity, in which exciting and counter-intuitive behavior continue to be uncovered. Ironically, one of the very factors responsible for such interesting properties, namely the presence of multiple relevant time and length scales, often greatly complicates accurate theoretical calculations and computer simulations that could explain the observations. We have recently developed a new Monte Carlo simulation methodootnotetextJ. Liu and E. Luijten, Phys. Rev. Lett.92, 035504 (2004); see also Physics Today, March 2004, pp. 25--27. that overcomes this problem for several classes of complex fluids. Our approach can accelerate simulations by orders of magnitude by introducing nonlocal, collective moves of the constituents. Strikingly, these cluster Monte Carlo moves are proposed in such a manner that the algorithm is rejection-free. The identification of the clusters is based upon geometric symmetries and can be considered as the off-latice generalization of the widely-used Swendsen--Wang and Wolff algorithms for lattice spin models. While phrased originally for complex fluids that are governed by the Boltzmann distribution, the geometric cluster algorithm can be used to efficiently sample configurations from an arbitrary underlying distribution function and may thus be applied in a variety of other areas. In addition, I will briefly discuss various extensions of the original algorithm, including methods to influence the size of the clusters that are generated and ways to introduce density fluctuations.

  18. Comparison of Reconstruction and Control algorithms on the ESO end-to-end simulator OCTOPUS

    NASA Astrophysics Data System (ADS)

    Montilla, I.; Béchet, C.; Lelouarn, M.; Correia, C.; Tallon, M.; Reyes, M.; Thiébaut, É.

    Extremely Large Telescopes are very challenging concerning their Adaptive Optics requirements. Their diameters, the specifications demanded by the science for which they are being designed for, and the planned use of Extreme Adaptive Optics systems, imply a huge increment in the number of degrees of freedom in the deformable mirrors. It is necessary to study new reconstruction algorithms to implement the real time control in Adaptive Optics at the required speed. We have studied the performance, applied to the case of the European ELT, of three different algorithms: the matrix-vector multiplication (MVM) algorithm, considered as a reference; the Fractal Iterative Method (FrIM); and the Fourier Transform Reconstructor (FTR). The algorithms have been tested on ESO's OCTOPUS software, which simulates the atmosphere, the deformable mirror, the sensor and the closed-loop control. The MVM is the default reconstruction and control method implemented in OCTOPUS, but it scales in O(N2) operations per loop so it is not considered as a fast algorithm for wave-front reconstruction and control on an Extremely Large Telescope. The two other methods are the fast algorithms studied in the E-ELT Design Study. The performance, as well as their response in the presence of noise and with various atmospheric conditions, has been compared using a Single Conjugate Adaptive Optics configuration for a 42 m diameter ELT, with a total amount of 5402 actuators. Those comparisons made on a common simulator allow to enhance the pros and cons of the various methods, and give us a better understanding of the type of reconstruction algorithm that an ELT demands.

  19. Advanced Thermal Simulator Testing: Thermal Analysis and Test Results

    NASA Technical Reports Server (NTRS)

    Bragg-Sitton, Shannon M.; Dickens, Ricky; Dixon, David; Reid, Robert; Adams, Mike; Davis, Joe

    2008-01-01

    Work at the NASA Marshall Space Flight Center seeks to develop high fidelity, electrically heated thermal simulators that represent fuel elements in a nuclear reactor design to support non-nuclear testing applicable to the development of a space nuclear power or propulsion system. Comparison between the fuel pins and thermal simulators is made at the outer fuel clad surface, which corresponds to the outer sheath surface in the thermal simulator. The thermal simulators that are currently being tested correspond to a SNAP derivative reactor design that could be applied for Lunar surface power. These simulators are designed to meet the geometric and power requirements of a proposed surface power reactor design, accommodate testing of various axial power profiles, and incorporate imbedded instrumentation. This paper reports the results of thermal simulator analysis and testing in a bare element configuration, which does not incorporate active heat removal, and testing in a water-cooled calorimeter designed to mimic the heat removal that would be experienced in a reactor core.

  20. Advanced Thermal Simulator Testing: Thermal Analysis and Test Results

    SciTech Connect

    Bragg-Sitton, Shannon M.; Dickens, Ricky; Dixon, David; Reid, Robert; Adams, Mike; Davis, Joe

    2008-01-21

    Work at the NASA Marshall Space Flight Center seeks to develop high fidelity, electrically heated thermal simulators that represent fuel elements in a nuclear reactor design to support non-nuclear testing applicable to the potential development of a space nuclear power or propulsion system. Comparison between the fuel pins and thermal simulators is made at the outer fuel clad surface, which corresponds to the outer sheath surface in the thermal simulator. The thermal simulators that are currently being tested correspond to a liquid metal cooled reactor design that could be applied for Lunar surface power. These simulators are designed to meet the geometric and power requirements of a proposed surface power reactor design, accommodate testing of various axial power profiles, and incorporate imbedded instrumentation. This paper reports the results of thermal simulator analysis and testing in a bare element configuration, which does not incorporate active heat removal, and testing in a water-cooled calorimeter designed to mimic the heat removal that would be experienced in a reactor core.

  1. Advancements of in-flight mass moment of inertia and structural deflection algorithms for satellite attitude simulators

    NASA Astrophysics Data System (ADS)

    Wright, Jonathan W.

    Experimental satellite attitude simulators have long been used to test and analyze control algorithms in order to drive down risk before implementation on an operational satellite. Ideally, the dynamic response of a terrestrial-based experimental satellite attitude simulator would be similar to that of an on-orbit satellite. Unfortunately, gravitational disturbance torques and poorly characterized moments of inertia introduce uncertainty into the system dynamics leading to questionable attitude control algorithm experimental results. This research consists of three distinct, but related contributions to the field of developing robust satellite attitude simulators. In the first part of this research, existing approaches to estimate mass moments and products of inertia are evaluated followed by a proposition and evaluation of a new approach that increases both the accuracy and precision of these estimates using typical on-board satellite sensors. Next, in order to better simulate the micro-torque environment of space, a new approach to mass balancing satellite attitude simulator is presented, experimentally evaluated, and verified. Finally, in the third area of research, we capitalize on the platform improvements to analyze a control moment gyroscope (CMG) singularity avoidance steering law. Several successful experiments were conducted with the CMG array at near-singular configurations. An evaluation process was implemented to verify that the platform remained near the desired test momentum, showing that the first two components of this research were effective in allowing us to conduct singularity avoidance experiments in a representative space-like test environment.

  2. Circuit model of the ITER-like antenna for JET and simulation of its control algorithms

    NASA Astrophysics Data System (ADS)

    Durodié, Frédéric; Dumortier, Pierre; Helou, Walid; Křivská, Alena; Lerche, Ernesto

    2015-12-01

    The ITER-like Antenna (ILA) for JET [1] is a 2 toroidal by 2 poloidal array of Resonant Double Loops (RDL) featuring in-vessel matching capacitors feeding RF current straps in conjugate-T manner, a low impedance quarter-wave impedance transformer, a service stub allowing hydraulic actuator and water cooling services to reach the aforementioned capacitors and a 2nd stage phase-shifter-stub matching circuit allowing to correct/choose the conjugate-T working impedance. Toroidally adjacent RDLs are fed from a 3dB hybrid splitter. It has been operated at 33, 42 and 47MHz on plasma (2008-2009) while it presently estimated frequency range is from 29 to 49MHz. At the time of the design (2001-2004) as well as the experiments the circuit models of the ILA were quite basic. The ILA front face and strap array Topica model was relatively crude and failed to correctly represent the poloidal central septum, Faraday Screen attachment as well as the segmented antenna central septum limiter. The ILA matching capacitors, T-junction, Vacuum Transmission Line (VTL) and Service Stubs were represented by lumped circuit elements and simple transmission line models. The assessment of the ILA results carried out to decide on the repair of the ILA identified that achieving routine full array operation requires a better understanding of the RF circuit, a feedback control algorithm for the 2nd stage matching as well as tighter calibrations of RF measurements. The paper presents the progress in modelling of the ILA comprising a more detailed Topica model of the front face for various plasma Scrape Off Layer profiles, a comprehensive HFSS model of the matching capacitors including internal bellows and electrode cylinders, 3D-EM models of the VTL including vacuum ceramic window, Service stub, a transmission line model of the 2nd stage matching circuit and main transmission lines including the 3dB hybrid splitters. A time evolving simulation using the improved circuit model allowed to design and

  3. Circuit model of the ITER-like antenna for JET and simulation of its control algorithms

    SciTech Connect

    Durodié, Frédéric Křivská, Alena; Helou, Walid; Collaboration: EUROfusion Consortium

    2015-12-10

    The ITER-like Antenna (ILA) for JET [1] is a 2 toroidal by 2 poloidal array of Resonant Double Loops (RDL) featuring in-vessel matching capacitors feeding RF current straps in conjugate-T manner, a low impedance quarter-wave impedance transformer, a service stub allowing hydraulic actuator and water cooling services to reach the aforementioned capacitors and a 2nd stage phase-shifter-stub matching circuit allowing to correct/choose the conjugate-T working impedance. Toroidally adjacent RDLs are fed from a 3dB hybrid splitter. It has been operated at 33, 42 and 47MHz on plasma (2008-2009) while it presently estimated frequency range is from 29 to 49MHz. At the time of the design (2001-2004) as well as the experiments the circuit models of the ILA were quite basic. The ILA front face and strap array Topica model was relatively crude and failed to correctly represent the poloidal central septum, Faraday Screen attachment as well as the segmented antenna central septum limiter. The ILA matching capacitors, T-junction, Vacuum Transmission Line (VTL) and Service Stubs were represented by lumped circuit elements and simple transmission line models. The assessment of the ILA results carried out to decide on the repair of the ILA identified that achieving routine full array operation requires a better understanding of the RF circuit, a feedback control algorithm for the 2nd stage matching as well as tighter calibrations of RF measurements. The paper presents the progress in modelling of the ILA comprising a more detailed Topica model of the front face for various plasma Scrape Off Layer profiles, a comprehensive HFSS model of the matching capacitors including internal bellows and electrode cylinders, 3D-EM models of the VTL including vacuum ceramic window, Service stub, a transmission line model of the 2nd stage matching circuit and main transmission lines including the 3dB hybrid splitters. A time evolving simulation using the improved circuit model allowed to design and

  4. DSMC moving-boundary algorithms for simulating MEMS geometries with opening and closing gaps.

    SciTech Connect

    Gallis, Michail A.; Rader, Daniel John; Torczynski, John Robert

    2010-06-01

    Moving-boundary algorithms for the Direct Simulation Monte Carlo (DSMC) method are investigated for a microbeam that moves toward and away from a parallel substrate. The simpler but analogous one-dimensional situation of a piston moving between two parallel walls is investigated using two moving-boundary algorithms. In the first, molecules are reflected rigorously from the moving piston by performing the reflections in the piston frame of reference. In the second, molecules are reflected approximately from the moving piston by moving the piston and subsequently moving all molecules and reflecting them from the moving piston at its new or old position.

  5. An evaluation of the Gauss-Radau algorithm for the simulation of chemical dynamics

    SciTech Connect

    Bolton, K.; Nordholm, S. Chalmers Univ. of Technology, Goeteborg )

    1994-08-01

    The Verlet, Verlet leap frog, Gear fixed time step, Gear variable time step, Runge-Kutta, and Gauss-Radau algorithms have been compared using trajectory data obtained from the integration of a one-dimensional diatomic chain under constant pressure. Investigation into the times of local and normal mode relaxation and conservation of the constants of the motion facilitated comparison of the integration techniques. It has been found that the Gauss-Radau algorithm, which is not widely used in the simulation of chemical dynamics, generally affords a higher accuracy at an improved efficiency. 14 refs., 10 figs., 11 tabs.

  6. Monte Carlo algorithm for efficient simulation of time-resolved fluorescence in layered turbid media.

    PubMed

    Liebert, A; Wabnitz, H; Zołek, N; Macdonald, R

    2008-08-18

    We present an efficient Monte Carlo algorithm for simulation of time-resolved fluorescence in a layered turbid medium. It is based on the propagation of excitation and fluorescence photon bundles and the assumption of equal reduced scattering coefficients at the excitation and emission wavelengths. In addition to distributions of times of arrival of fluorescence photons at the detector, 3-D spatial generation probabilities were calculated. The algorithm was validated by comparison with the analytical solution of the diffusion equation for time-resolved fluorescence from a homogeneous semi-infinite turbid medium. It was applied to a two-layered model mimicking intra- and extracerebral compartments of the adult human head.

  7. Simulation and experimental tests on active mass damper control system based on Model Reference Adaptive Control algorithm

    NASA Astrophysics Data System (ADS)

    Tu, Jianwei; Lin, Xiaofeng; Tu, Bo; Xu, Jiayun; Tan, Dongmei

    2014-09-01

    In the process of sudden natural disasters (such as earthquake or typhoon), the active mass damper (AMD) system can reduce the structural vibration response optimally, which serves as a frequently applied but less mature vibration-reducing technology in wind and earthquake resistance of high-rise buildings. As the core of this technology, the selection of control algorithm is extremely challenging due to the uncertainty of structural parameters and the randomness of external loads. It is not necessary for the Model Reference Adaptive Control (MRAC) based on the Minimal Controller Synthesis (MCS) algorithm to know in advance the structural parameters, which produces special advantages in conditions of real-time change of system parameters, uncertain external disturbance, and the nonlinear dynamic system. This paper studies the application of the MRAC into the AMD active control system. The principle of MRAC algorithm is recommended and the dynamic model and the motion differential equation of AMD system based on MRAC is established under seismic excitation. The simulation analysis for linear and nonlinear structures when the structural stiffness is degenerated is performed under AMD system controlled by MRAC algorithm. To verify the validity of the MRAC over the AMD system, experimental tests are carried out on a linear structure and a structure with variable stiffness with the AMD system under seismic excitation on the shake table, and the experimental results are compared with those of the traditional pole assignment control algorithm.

  8. Use of a machine learning algorithm to classify expertise: analysis of hand motion patterns during a simulated surgical task.

    PubMed

    Watson, Robert A

    2014-08-01

    To test the hypothesis that machine learning algorithms increase the predictive power to classify surgical expertise using surgeons' hand motion patterns. In 2012 at the University of North Carolina at Chapel Hill, 14 surgical attendings and 10 first- and second-year surgical residents each performed two bench model venous anastomoses. During the simulated tasks, the participants wore an inertial measurement unit on the dorsum of their dominant (right) hand to capture their hand motion patterns. The pattern from each bench model task performed was preprocessed into a symbolic time series and labeled as expert (attending) or novice (resident). The labeled hand motion patterns were processed and used to train a Support Vector Machine (SVM) classification algorithm. The trained algorithm was then tested for discriminative/predictive power against unlabeled (blinded) hand motion patterns from tasks not used in the training. The Lempel-Ziv (LZ) complexity metric was also measured from each hand motion pattern, with an optimal threshold calculated to separately classify the patterns. The LZ metric classified unlabeled (blinded) hand motion patterns into expert and novice groups with an accuracy of 70% (sensitivity 64%, specificity 80%). The SVM algorithm had an accuracy of 83% (sensitivity 86%, specificity 80%). The results confirmed the hypothesis. The SVM algorithm increased the predictive power to classify blinded surgical hand motion patterns into expert versus novice groups. With further development, the system used in this study could become a viable tool for low-cost, objective assessment of procedural proficiency in a competency-based curriculum.

  9. Evaluating intraspecific "network" construction methods using simulated sequence data: do existing algorithms outperform the global maximum parsimony approach?

    PubMed

    Cassens, Insa; Mardulyn, Patrick; Milinkovitch, Michel C

    2005-06-01

    In intraspecific studies, reticulated graphs are valuable tools for visualization, within a single figure, of alternative genealogical pathways among haplotypes. As available software packages implementing the global maximum parsimony (MP) approach only give the possibility to merge resulting topologies into less-resolved consensus trees, MP has often been neglected as an alternative approach to purely algorithmic (i.e., methods defined solely on the basis of an algorithm) "network" construction methods. Here, we propose to search tree space using the MP criterion and present a new algorithm for uniting all equally most parsimonious trees into a single (possibly reticulated) graph. Using simulated sequence data, we compare our method with three purely algorithmic and widely used graph construction approaches (minimum-spanning network, statistical parsimony, and median-joining network). We demonstrate that the combination of MP trees into a single graph provides a good estimate of the true genealogy. Moreover, our analyses indicate that, when internal node haplotypes are not sampled, the median-joining and MP methods provide the best estimate of the true genealogy whereas the minimum-spanning algorithm shows very poor performances.

  10. Respiratory rate detection algorithm based on RGB-D camera: theoretical background and experimental results.

    PubMed

    Benetazzo, Flavia; Freddi, Alessandro; Monteriù, Andrea; Longhi, Sauro

    2014-09-01

    Both the theoretical background and the experimental results of an algorithm developed to perform human respiratory rate measurements without any physical contact are presented. Based on depth image sensing techniques, the respiratory rate is derived by measuring morphological changes of the chest wall. The algorithm identifies the human chest, computes its distance from the camera and compares this value with the instantaneous distance, discerning if it is due to the respiratory act or due to a limited movement of the person being monitored. To experimentally validate the proposed algorithm, the respiratory rate measurements coming from a spirometer were taken as a benchmark and compared with those estimated by the algorithm. Five tests were performed, with five different persons sat in front of the camera. The first test aimed to choose the suitable sampling frequency. The second test was conducted to compare the performances of the proposed system with respect to the gold standard in ideal conditions of light, orientation and clothing. The third, fourth and fifth tests evaluated the algorithm performances under different operating conditions. The experimental results showed that the system can correctly measure the respiratory rate, and it is a viable alternative to monitor the respiratory activity of a person without using invasive sensors.

  11. Respiratory rate detection algorithm based on RGB-D camera: theoretical background and experimental results

    PubMed Central

    Freddi, Alessandro; Monteriù, Andrea; Longhi, Sauro

    2014-01-01

    Both the theoretical background and the experimental results of an algorithm developed to perform human respiratory rate measurements without any physical contact are presented. Based on depth image sensing techniques, the respiratory rate is derived by measuring morphological changes of the chest wall. The algorithm identifies the human chest, computes its distance from the camera and compares this value with the instantaneous distance, discerning if it is due to the respiratory act or due to a limited movement of the person being monitored. To experimentally validate the proposed algorithm, the respiratory rate measurements coming from a spirometer were taken as a benchmark and compared with those estimated by the algorithm. Five tests were performed, with five different persons sat in front of the camera. The first test aimed to choose the suitable sampling frequency. The second test was conducted to compare the performances of the proposed system with respect to the gold standard in ideal conditions of light, orientation and clothing. The third, fourth and fifth tests evaluated the algorithm performances under different operating conditions. The experimental results showed that the system can correctly measure the respiratory rate, and it is a viable alternative to monitor the respiratory activity of a person without using invasive sensors. PMID:26609383

  12. Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms.

    PubMed

    Mori, Yoshiharu; Okumura, Hisashi

    2015-12-05

    Simulated tempering (ST) is a useful method to enhance sampling of molecular simulations. When ST is used, the Metropolis algorithm, which satisfies the detailed balance condition, is usually applied to calculate the transition probability. Recently, an alternative method that satisfies the global balance condition instead of the detailed balance condition has been proposed by Suwa and Todo. In this study, ST method with the Suwa-Todo algorithm is proposed. Molecular dynamics simulations with ST are performed with three algorithms (the Metropolis, heat bath, and Suwa-Todo algorithms) to calculate the transition probability. Among the three algorithms, the Suwa-Todo algorithm yields the highest acceptance ratio and the shortest autocorrelation time. These suggest that sampling by a ST simulation with the Suwa-Todo algorithm is most efficient. In addition, because the acceptance ratio of the Suwa-Todo algorithm is higher than that of the Metropolis algorithm, the number of temperature states can be reduced by 25% for the Suwa-Todo algorithm when compared with the Metropolis algorithm.

  13. Relationships between driving simulator performance and driving test results.

    PubMed

    de Winter, J C F; de Groot, S; Mulder, M; Wieringa, P A; Dankelman, J; Mulder, J A

    2009-02-01

    This article is considered relevant because: 1) car driving is an everyday and safety-critical task; 2) simulators are used to an increasing extent for driver training (related topics: training, virtual reality, human-machine interaction); 3) the article addresses relationships between performance in the simulator and driving test results--a relevant topic for those involved in driver training and the virtual reality industries; 4) this article provides new insights about individual differences in young drivers' behaviour. Simulators are being used to an increasing extent for driver training, allowing for the possibility of collecting objective data on driver proficiency under standardised conditions. However, relatively little is known about how learner drivers' simulator measures relate to on-road driving. This study proposes a theoretical framework that quantifies driver proficiency in terms of speed of task execution, violations and errors. This study investigated the relationships between these three measures of learner drivers' (n=804) proficiency during initial simulation-based training and the result of the driving test on the road, occurring an average of 6 months later. A higher chance of passing the driving test the first time was associated with making fewer steering errors on the simulator and could be predicted in regression analysis with a correlation of 0.18. Additionally, in accordance with the theoretical framework, a shorter duration of on-road training corresponded with faster task execution, fewer violations and fewer steering errors (predictive correlation 0.45). It is recommended that researchers conduct more large-scale studies into the reliability and validity of simulator measures and on-road driving tests.

  14. Results from Binary Black Hole Simulations in Astrophysics Applications

    NASA Technical Reports Server (NTRS)

    Baker, John G.

    2007-01-01

    Present and planned gravitational wave observatories are opening a new astronomical window to the sky. A key source of gravitational waves is the merger of two black holes. The Laser Interferometer Space Antenna (LISA), in particular, is expected to observe these events with signal-to-noise ratio's in the thousands. To fully reap the scientific benefits of these observations requires a detailed understanding, based on numerical simulations, of the predictions of General Relativity for the waveform signals. New techniques for simulating binary black hole mergers, introduced two years ago, have led to dramatic advances in applied numerical simulation work. Over the last two years, numerical relativity researchers have made tremendous strides in understanding the late stages of binary black hole mergers. Simulations have been applied to test much of the basic physics of binary black hole interactions, showing robust results for merger waveform predictions, and illuminating such phenomena as spin-precession. Calculations have shown that merging systems can be kicked at up to 2500 km/s by the thrust from asymmetric emission. Recently, long lasting simulations of ten or more orbits allow tests of post-Newtonian (PN) approximation results for radiation from the last orbits of the binary's inspiral. Already, analytic waveform models based PN techniques with incorporated information from numerical simulations may be adequate for observations with current ground based observatories. As new advances in simulations continue to rapidly improve our theoretical understanding of the systems, it seems certain that high-precision predictions will be available in time for LISA and other advanced ground-based instruments. Future gravitational wave observatories are expected to make precision.

  15. Results from Binary Black Hole Simulations in Astrophysics Applications

    NASA Technical Reports Server (NTRS)

    Baker, John G.

    2007-01-01

    Present and planned gravitational wave observatories are opening a new astronomical window to the sky. A key source of gravitational waves is the merger of two black holes. The Laser Interferometer Space Antenna (LISA), in particular, is expected to observe these events with signal-to-noise ratio's in the thousands. To fully reap the scientific benefits of these observations requires a detailed understanding, based on numerical simulations, of the predictions of General Relativity for the waveform signals. New techniques for simulating binary black hole mergers, introduced two years ago, have led to dramatic advances in applied numerical simulation work. Over the last two years, numerical relativity researchers have made tremendous strides in understanding the late stages of binary black hole mergers. Simulations have been applied to test much of the basic physics of binary black hole interactions, showing robust results for merger waveform predictions, and illuminating such phenomena as spin-precession. Calculations have shown that merging systems can be kicked at up to 2500 km/s by the thrust from asymmetric emission. Recently, long lasting simulations of ten or more orbits allow tests of post-Newtonian (PN) approximation results for radiation from the last orbits of the binary's inspiral. Already, analytic waveform models based PN techniques with incorporated information from numerical simulations may be adequate for observations with current ground based observatories. As new advances in simulations continue to rapidly improve our theoretical understanding of the systems, it seems certain that high-precision predictions will be available in time for LISA and other advanced ground-based instruments. Future gravitational wave observatories are expected to make precision.

  16. Comparative Evaluation of Registration Algorithms in Different Brain Databases With Varying Difficulty: Results and Insights

    PubMed Central

    Akbari, Hamed; Bilello, Michel; Da, Xiao; Davatzikos, Christos

    2015-01-01

    Evaluating various algorithms for the inter-subject registration of brain magnetic resonance images (MRI) is a necessary topic receiving growing attention. Existing studies evaluated image registration algorithms in specific tasks or using specific databases (e.g., only for skull-stripped images, only for single-site images, etc.). Consequently, the choice of registration algorithms seems task- and usage/parameter-dependent. Nevertheless, recent large-scale, often multi-institutional imaging-related studies create the need and raise the question whether some registration algorithms can 1) generally apply to various tasks/databases posing various challenges; 2) perform consistently well, and while doing so, 3) require minimal or ideally no parameter tuning. In seeking answers to this question, we evaluated 12 general-purpose registration algorithms, for their generality, accuracy and robustness. We fixed their parameters at values suggested by algorithm developers as reported in the literature. We tested them in 7 databases/tasks, which present one or more of 4 commonly-encountered challenges: 1) inter-subject anatomical variability in skull-stripped images; 2) intensity homogeneity, noise and large structural differences in raw images; 3) imaging protocol and field-of-view (FOV) differences in multi-site data; and 4) missing correspondences in pathology-bearing images. Totally 7,562 registrations were performed. Registration accuracies were measured by (multi-)expert-annotated landmarks or regions of interest (ROIs). To ensure reproducibility, we used public software tools, public databases (whenever possible), and we fully disclose the parameter settings. We show evaluation results, and discuss the performances in light of algorithms’ similarity metrics, transformation models and optimization strategies. We also discuss future directions for the algorithm development and evaluations. PMID:24951685

  17. Simulation of diurnal thermal energy storage systems: Preliminary results

    NASA Astrophysics Data System (ADS)

    Katipamula, S.; Somasundaram, S.; Williams, H. R.

    1994-12-01

    This report describes the results of a simulation of thermal energy storage (TES) integrated with a simple-cycle gas turbine cogeneration system. Integrating TES with cogeneration can serve the electrical and thermal loads independently while firing all fuel in the gas turbine. The detailed engineering and economic feasibility of diurnal TES systems integrated with cogeneration systems has been described in two previous PNL reports. The objective of this study was to lay the ground work for optimization of the TES system designs using a simulation tool called TRNSYS (TRaNsient SYstem Simulation). TRNSYS is a transient simulation program with a sequential-modular structure developed at the Solar Energy Laboratory, University of Wisconsin-Madison. The two TES systems selected for the base-case simulations were: (1) a one-tank storage model to represent the oil/rock TES system; and (2) a two-tank storage model to represent the molten nitrate salt TES system. Results of the study clearly indicate that an engineering optimization of the TES system using TRNSYS is possible. The one-tank stratified oil/rock storage model described here is a good starting point for parametric studies of a TES system. Further developments to the TRNSYS library of available models (economizer, evaporator, gas turbine, etc.) are recommended so that the phase-change processes is accurately treated.

  18. Accelerating the Gillespie Exact Stochastic Simulation Algorithm using hybrid parallel execution on graphics processing units.

    PubMed

    Komarov, Ivan; D'Souza, Roshan M

    2012-01-01

    The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differential equations. The inherent limitations of the GSSA include the time required for executing a single run and the need for multiple runs for parameter sweep exercises due to the stochastic nature of the simulation. Even very efficient variants of GSSA are prohibitively expensive to compute and perform parameter sweeps. Here we present a novel variant of the exact GSSA that is amenable to acceleration by using graphics processing units (GPUs). We parallelize the execution of a single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, which is the bottleneck in computing the GSSA. Our benchmarks show an 8×-120× performance gain over various state-of-the-art serial algorithms when simulating different types of models.

  19. Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units

    PubMed Central

    Komarov, Ivan; D'Souza, Roshan M.

    2012-01-01

    The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differential equations. The inherent limitations of the GSSA include the time required for executing a single run and the need for multiple runs for parameter sweep exercises due to the stochastic nature of the simulation. Even very efficient variants of GSSA are prohibitively expensive to compute and perform parameter sweeps. Here we present a novel variant of the exact GSSA that is amenable to acceleration by using graphics processing units (GPUs). We parallelize the execution of a single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, which is the bottleneck in computing the GSSA. Our benchmarks show an 8×−120× performance gain over various state-of-the-art serial algorithms when simulating different types of models. PMID:23152751

  20. Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining

    SciTech Connect

    Khasin, M.; Kosloff, R.

    2010-04-15

    An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables--the elements of the spectrum-generating algebra--is simulated by a surrogate open-system dynamics, which can be interpreted as weak measurement of the target observables, performed on the evolving system. The open-system state can be represented by a mixture of pure states, localized in the phase space. The localization reduces the scaling of the computational resources with the Hilbert-space dimension n by factor n{sup 3/2}(ln n){sup -1} compared to conventional sparse-matrix methods. The guidelines for the choice of parameters for the simulation are presented and the scaling of the computational resources with the Hilbert-space dimension of the system is estimated. The algorithm is applied to the simulation of the dynamics of systems of 2x10{sup 4} and 2x10{sup 6} cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.

  1. Automated Algorithms for Quantum-Level Accuracy in Atomistic Simulations: LDRD Final Report.

    SciTech Connect

    Thompson, Aidan Patrick; Schultz, Peter Andrew; Crozier, Paul; Moore, Stan Gerald; Swiler, Laura Painton; Stephens, John Adam; Trott, Christian Robert; Foiles, Stephen Martin; Tucker, Garritt J.

    2014-09-01

    This report summarizes the result of LDRD project 12-0395, titled "Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations." During the course of this LDRD, we have developed an interatomic potential for solids and liquids called Spectral Neighbor Analysis Poten- tial (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The SNAP coef- ficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. Global optimization methods in the DAKOTA software package are used to seek out good choices of hyperparameters that define the overall structure of the SNAP potential. FitSnap.py, a Python-based software pack- age interfacing to both LAMMPS and DAKOTA is used to formulate the linear regression problem, solve it, and analyze the accuracy of the resultant SNAP potential. We describe a SNAP potential for tantalum that accurately reproduces a variety of solid and liquid properties. Most significantly, in contrast to existing tantalum potentials, SNAP correctly predicts the Peierls barrier for screw dislocation motion. We also present results from SNAP potentials generated for indium phosphide (InP) and silica (SiO 2 ). We describe efficient algorithms for calculating SNAP forces and energies in molecular dynamics simulations using massively parallel computers

  2. Simulation results for the electron-cloud at the PSR

    SciTech Connect

    Furman, M.A.; Pivi, M.

    2001-06-26

    We present a first set of computer simulations for the main features of the electron cloud at the Proton Storage Ring (PSR), particularly its energy spectrum. We compare our results with recent measurements, which have been obtained by means of dedicated probes.

  3. Boundary pint corrections for variable radius plots - simulation results

    Treesearch

    Margaret Penner; Sam Otukol

    2000-01-01

    The boundary plot problem is encountered when a forest inventory plot includes two or more forest conditions. Depending on the correction method used, the resulting estimates can be biased. The various correction alternatives are reviewed. No correction, area correction, half sweep, and toss-back methods are evaluated using simulation on an actual data set. Based on...

  4. Image Artifacts Resulting from Gamma-Ray Tracking Algorithms Used with Compton Imagers

    SciTech Connect

    Seifert, Carolyn E.; He, Zhong

    2005-10-01

    For Compton imaging it is necessary to determine the sequence of gamma-ray interactions in a single detector or array of detectors. This can be done by time-of-flight measurements if the interactions are sufficiently far apart. However, in small detectors the time between interactions can be too small to measure, and other means of gamma-ray sequencing must be used. In this work, several popular sequencing algorithms are reviewed for sequences with two observed events and three or more observed events in the detector. These algorithms can result in poor imaging resolution and introduce artifacts in the backprojection images. The effects of gamma-ray tracking algorithms on Compton imaging are explored in the context of the 4π Compton imager built by the University of Michigan.

  5. Initial Data Analysis Results for ATD-2 ISAS HITL Simulation

    NASA Technical Reports Server (NTRS)

    Lee, Hanbong

    2017-01-01

    To evaluate the operational procedures and information requirements for the core functional capabilities of the ATD-2 project, such as tactical surface metering tool, APREQ-CFR procedure, and data element exchanges between ramp and tower, human-in-the-loop (HITL) simulations were performed in March, 2017. This presentation shows the initial data analysis results from the HITL simulations. With respect to the different runway configurations and metering values in tactical surface scheduler, various airport performance metrics were analyzed and compared. These metrics include gate holding time, taxi-out in time, runway throughput, queue size and wait time in queue, and TMI flight compliance. In addition to the metering value, other factors affecting the airport performance in the HITL simulation, including run duration, runway changes, and TMI constraints, are also discussed.

  6. Multi-frequency Imaging Algorithms and Simulation of Space VLBI Using the VLA

    NASA Astrophysics Data System (ADS)

    Likhachev, S.; Kogan, L.; Fomalont, E.; Owen, F.

    2009-08-01

    New Multi-Frequency Synthesis (MFS) algorithms were developed and implemented in the Astro Space Locator (ASL) operating under MS Windows system. In November 2005 multi-frequency VLA observations of the radio source M87 were carried out at the following frequencies: 14.7, 15.2 21.3, 22.2, 23.0, and 23.4 GHz. We used the new MFS algorithms to determine the structure of M87 at the central frequency (19 GHz) and obtained both the image and spectral index map of the source. Comparison with more straight-forward imaging techniques (with single frequency images) shows that the new MFS algorithms increase the fidelity of the image by at least a factor of two and provides accurate spectral indices across the emission. Application to simulated Radioastron data is also shown.

  7. Use of a simulated annealing algorithm to fit compartmental models with an application to fractal pharmacokinetics.

    PubMed

    Marsh, Rebeccah E; Riauka, Terence A; McQuarrie, Steve A

    2007-01-01

    Increasingly, fractals are being incorporated into pharmacokinetic models to describe transport and chemical kinetic processes occurring in confined and heterogeneous spaces. However, fractal compartmental models lead to differential equations with power-law time-dependent kinetic rate coefficients that currently are not accommodated by common commercial software programs. This paper describes a parameter optimization method for fitting individual pharmacokinetic curves based on a simulated annealing (SA) algorithm, which always converged towards the global minimum and was independent of the initial parameter values and parameter bounds. In a comparison using a classical compartmental model, similar fits by the Gauss-Newton and Nelder-Mead simplex algorithms required stringent initial estimates and ranges for the model parameters. The SA algorithm is ideal for fitting a wide variety of pharmacokinetic models to clinical data, especially those for which there is weak prior knowledge of the parameter values, such as the fractal models.

  8. A comparison of various algorithms to extract Magic Formula tyre model coefficients for vehicle dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vijay Alagappan, A.; Narasimha Rao, K. V.; Krishna Kumar, R.

    2015-02-01

    Tyre models are a prerequisite for any vehicle dynamics simulation. Tyre models range from the simplest mathematical models that consider only the cornering stiffness to a complex set of formulae. Among all the steady-state tyre models that are in use today, the Magic Formula tyre model is unique and most popular. Though the Magic Formula tyre model is widely used, obtaining the model coefficients from either the experimental or the simulation data is not straightforward due to its nonlinear nature and the presence of a large number of coefficients. A common procedure used for this extraction is the least-squares minimisation that requires considerable experience for initial guesses. Various researchers have tried different algorithms, namely, gradient and Newton-based methods, differential evolution, artificial neural networks, etc. The issues involved in all these algorithms are setting bounds or constraints, sensitivity of the parameters, the features of the input data such as the number of points, noisy data, experimental procedure used such as slip angle sweep or tyre measurement (TIME) procedure, etc. The extracted Magic Formula coefficients are affected by these variants. This paper highlights the issues that are commonly encountered in obtaining these coefficients with different algorithms, namely, least-squares minimisation using trust region algorithms, Nelder-Mead simplex, pattern search, differential evolution, particle swarm optimisation, cuckoo search, etc. A key observation is that not all the algorithms give the same Magic Formula coefficients for a given data. The nature of the input data and the type of the algorithm decide the set of the Magic Formula tyre model coefficients.

  9. Initial Evaluations of LoC Prediction Algorithms Using the NASA Vertical Motion Simulator

    NASA Technical Reports Server (NTRS)

    Krishnakumar, Kalmanje; Stepanyan, Vahram; Barlow, Jonathan; Hardy, Gordon; Dorais, Greg; Poolla, Chaitanya; Reardon, Scott; Soloway, Donald

    2014-01-01

    Flying near the edge of the safe operating envelope is an inherently unsafe proposition. Edge of the envelope here implies that small changes or disturbances in system state or system dynamics can take the system out of the safe envelope in a short time and could result in loss-of-control events. This study evaluated approaches to predicting loss-of-control safety margins as the aircraft gets closer to the edge of the safe operating envelope. The goal of the approach is to provide the pilot aural, visual, and tactile cues focused on maintaining the pilot's control action within predicted loss-of-control boundaries. Our predictive architecture combines quantitative loss-of-control boundaries, an adaptive prediction method to estimate in real-time Markov model parameters and associated stability margins, and a real-time data-based predictive control margins estimation algorithm. The combined architecture is applied to a nonlinear transport class aircraft. Evaluations of various feedback cues using both test and commercial pilots in the NASA Ames Vertical Motion-base Simulator (VMS) were conducted in the summer of 2013. The paper presents results of this evaluation focused on effectiveness of these approaches and the cues in preventing the pilots from entering a loss-of-control event.

  10. ANOVA parameters influence in LCF experimental data and simulation results

    NASA Astrophysics Data System (ADS)

    Delprete, C.; Sesanaa, R.; Vercelli, A.

    2010-06-01

    The virtual design of components undergoing thermo mechanical fatigue (TMF) and plastic strains is usually run in many phases. The numerical finite element method gives a useful instrument which becomes increasingly effective as the geometrical and numerical modelling gets more accurate. The constitutive model definition plays an important role in the effectiveness of the numerical simulation [1, 2] as, for example, shown in Figure 1. In this picture it is shown how a good cyclic plasticity constitutive model can simulate a cyclic load experiment. The component life estimation is the subsequent phase and it needs complex damage and life estimation models [3-5] which take into account of several parameters and phenomena contributing to damage and life duration. The calibration of these constitutive and damage models requires an accurate testing activity. In the present paper the main topic of the research activity is to investigate whether the parameters, which result to be influent in the experimental activity, influence the numerical simulations, thus defining the effectiveness of the models in taking into account of all the phenomena actually influencing the life of the component. To obtain this aim a procedure to tune the parameters needed to estimate the life of mechanical components undergoing TMF and plastic strains is presented for commercial steel. This procedure aims to be easy and to allow calibrating both material constitutive model (for the numerical structural simulation) and the damage and life model (for life assessment). The procedure has been applied to specimens. The experimental activity has been developed on three sets of tests run at several temperatures: static tests, high cycle fatigue (HCF) tests, low cycle fatigue (LCF) tests. The numerical structural FEM simulations have been run on a commercial non linear solver, ABAQUS®6.8. The simulations replied the experimental tests. The stress, strain, thermal results from the thermo structural FEM

  11. First results of coupled IPS/NIMROD/GENRAY simulations

    NASA Astrophysics Data System (ADS)

    Jenkins, Thomas; Kruger, S. E.; Held, E. D.; Harvey, R. W.; Elwasif, W. R.; Schnack, D. D.

    2010-11-01

    The Integrated Plasma Simulator (IPS) framework, developed by the SWIM Project Team, facilitates self-consistent simulations of complicated plasma behavior via the coupling of various codes modeling different spatial/temporal scales in the plasma. Here, we apply this capability to investigate the stabilization of tearing modes by ECCD. Under IPS control, the NIMROD code (MHD) evolves fluid equations to model bulk plasma behavior, while the GENRAY code (RF) calculates the self-consistent propagation and deposition of RF power in the resulting plasma profiles. GENRAY data is then used to construct moments of the quasilinear diffusion tensor (induced by the RF) which influence the dynamics of momentum/energy evolution in NIMROD's equations. We present initial results from these coupled simulations and demonstrate that they correctly capture the physics of magnetic island stabilization [Jenkins et al, PoP 17, 012502 (2010)] in the low-beta limit. We also discuss the process of code verification in these simulations, demonstrating good agreement between NIMROD and GENRAY predictions for the flux-surface-averaged, RF-induced currents. An overview of ongoing model development (synthetic diagnostics/plasma control systems; neoclassical effects; etc.) is also presented. Funded by US DoE.

  12. New exclusive CHIPS-TPT algorithms for simulation of neutron-nuclear reactions

    NASA Astrophysics Data System (ADS)

    Kosov, M.; Savin, D.

    2015-05-01

    The CHIPS-TPT physics library for simulation of neutron-nuclear reactions on the new exclusive level is being developed in CFAR VNIIA. The exclusive modeling conserves energy, momentum and quantum numbers in each neutron-nuclear interaction. The CHIPS-TPT algorithms are based on the exclusive CHIPS library, which is compatible with Geant4. Special CHIPS-TPT physics lists in the Geant4 format are provided. The calculation time for an exclusive CHIPS-TPT simulation is comparable to the time of the corresponding Geant4- HP simulation. In addition to the reduction of the deposited energy fluctuations, which is a consequence of the energy conservation, the CHIPS-TPT libraries provide a possibility of simulation of the secondary particles correlation, e.g. secondary gammas, and of the Doppler broadening of gamma lines in the spectrum, which can be measured by germanium detectors.

  13. A Simulated Annealing Algorithm for the Optimization of Multistage Depressed Collector Efficiency

    NASA Technical Reports Server (NTRS)

    Vaden, Karl R.; Wilson, Jeffrey D.; Bulson, Brian A.

    2002-01-01

    The microwave traveling wave tube amplifier (TWTA) is widely used as a high-power transmitting source for space and airborne communications. One critical factor in designing a TWTA is the overall efficiency. However, overall efficiency is highly dependent upon collector efficiency; so collector design is critical to the performance of a TWTA. Therefore, NASA Glenn Research Center has developed an optimization algorithm based on Simulated Annealing to quickly design highly efficient multi-stage depressed collectors (MDC).

  14. A Fourier analysis for a fast simulation algorithm. [for switching converters

    NASA Technical Reports Server (NTRS)

    King, Roger J.

    1988-01-01

    This paper presents a derivation of compact expressions for the Fourier series analysis of the steady-state solution of a typical switching converter. The modeling procedure for the simulation and the steady-state solution is described, and some desirable traits for its matrix exponential subroutine are discussed. The Fourier analysis algorithm was tested on a phase-controlled parallel-loaded resonant converter, providing an experimental confirmation.

  15. Broadband diffusion metasurface based on a single anisotropic element and optimized by the Simulated Annealing algorithm.

    PubMed

    Zhao, Yi; Cao, Xiangyu; Gao, Jun; Sun, Yu; Yang, Huanhuan; Liu, Xiao; Zhou, Yulong; Han, Tong; Chen, Wei

    2016-04-01

    We propose a new strategy to design broadband and wide angle diffusion metasurfaces. An anisotropic structure which has opposite phases under x- and y-polarized incidence is employed as the "0" and "1" elements base on the concept of coding metamaterial. To obtain a uniform backward scattering under normal incidence, Simulated Annealing algorithm is utilized in this paper to calculate the optimal layout. The proposed method provides an efficient way to design diffusion metasurface with a simple structure, which has been proved by both simulations and measurements.

  16. Broadband diffusion metasurface based on a single anisotropic element and optimized by the Simulated Annealing algorithm

    PubMed Central

    Zhao, Yi; Cao, Xiangyu; Gao, Jun; Sun, Yu; Yang, Huanhuan; Liu, Xiao; Zhou, Yulong; Han, Tong; Chen, Wei

    2016-01-01

    We propose a new strategy to design broadband and wide angle diffusion metasurfaces. An anisotropic structure which has opposite phases under x- and y-polarized incidence is employed as the “0” and “1” elements base on the concept of coding metamaterial. To obtain a uniform backward scattering under normal incidence, Simulated Annealing algorithm is utilized in this paper to calculate the optimal layout. The proposed method provides an efficient way to design diffusion metasurface with a simple structure, which has been proved by both simulations and measurements. PMID:27034110

  17. Effective algorithm for ray-tracing simulations of lobster eye and similar reflective optical systems

    NASA Astrophysics Data System (ADS)

    Tichý, Vladimír; Hudec, René; Němcová, Šárka

    2016-06-01

    The algorithm presented is intended mainly for lobster eye optics. This type of optics (and some similar types) allows for a simplification of the classical ray-tracing procedure that requires great many rays to simulate. The method presented performs the simulation of a only few rays; therefore it is extremely effective. Moreover, to simplify the equations, a specific mathematical formalism is used. Only a few simple equations are used, therefore the program code can be simple as well. The paper also outlines how to apply the method to some other reflective optical systems.

  18. A novel Monte Carlo algorithm for simulating crystals with McStas

    NASA Astrophysics Data System (ADS)

    Alianelli, L.; Sánchez del Río, M.; Felici, R.; Andersen, K. H.; Farhi, E.

    2004-07-01

    We developed an original Monte Carlo algorithm for the simulation of Bragg diffraction by mosaic, bent and gradient crystals. It has practical applications, as it can be used for simulating imperfect crystals (monochromators, analyzers and perhaps samples) in neutron ray-tracing packages, like McStas. The code we describe here provides a detailed description of the particle interaction with the microscopic homogeneous regions composing the crystal, therefore it can be used also for the calculation of quantities having a conceptual interest, as multiple scattering, or for the interpretation of experiments aiming at characterizing crystals, like diffraction topographs.

  19. A Comprehensive Study of Three Delay Compensation Algorithms for Flight Simulators

    NASA Technical Reports Server (NTRS)

    Guo, Liwen; Cardullo, Frank M.; Houck, Jacob A.; Kelly, Lon C.; Wolters, Thomas E.

    2005-01-01

    This paper summarizes a comprehensive study of three predictors used for compensating the transport delay in a flight simulator; The McFarland, Adaptive and State Space Predictors. The paper presents proof that the stochastic approximation algorithm can achieve the best compensation among all four adaptive predictors, and intensively investigates the relationship between the state space predictor s compensation quality and its reference model. Piloted simulation tests show that the adaptive predictor and state space predictor can achieve better compensation of transport delay than the McFarland predictor.

  20. 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

    2017-06-21

    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.

  1. Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data.

    PubMed

    Montaseri, Soheila; Ganjtabesh, Mohammad; Zare-Mirakabad, Fatemeh

    2016-01-01

    Non-coding RNAs perform a wide range of functions inside the living cells that are related to their structures. Several algorithms have been proposed to predict RNA secondary structure based on minimum free energy. Low prediction accuracy of these algorithms indicates that free energy alone is not sufficient to predict the functional secondary structure. Recently, the obtained information from the SHAPE experiment greatly improves the accuracy of RNA secondary structure prediction by adding this information to the thermodynamic free energy as pseudo-free energy. In this paper, a new method is proposed to predict RNA secondary structure based on both free energy and SHAPE pseudo-free energy. For each RNA sequence, a population of secondary structures is constructed and their SHAPE data are simulated. Then, an evolutionary algorithm is used to improve each structure based on both free and pseudo-free energies. Finally, a structure with minimum summation of free and pseudo-free energies is considered as the predicted RNA secondary structure. Computationally simulating the SHAPE data for a given RNA sequence requires its secondary structure. Here, we overcome this limitation by employing a population of secondary structures. This helps us to simulate the SHAPE data for any RNA sequence and consequently improves the accuracy of RNA secondary structure prediction as it is confirmed by our experiments. The source code and web server of our proposed method are freely available at http://mostafa.ut.ac.ir/ESD-Fold/.

  2. Efficient classical simulation of the Deutsch-Jozsa and Simon's algorithms

    NASA Astrophysics Data System (ADS)

    Johansson, Niklas; Larsson, Jan-Åke

    2017-09-01

    A long-standing aim of quantum information research is to understand what gives quantum computers their advantage. This requires separating problems that need genuinely quantum resources from those for which classical resources are enough. Two examples of quantum speed-up are the Deutsch-Jozsa and Simon's problem, both efficiently solvable on a quantum Turing machine, and both believed to lack efficient classical solutions. Here we present a framework that can simulate both quantum algorithms efficiently, solving the Deutsch-Jozsa problem with probability 1 using only one oracle query, and Simon's problem using linearly many oracle queries, just as expected of an ideal quantum computer. The presented simulation framework is in turn efficiently simulatable in a classical probabilistic Turing machine. This shows that the Deutsch-Jozsa and Simon's problem do not require any genuinely quantum resources, and that the quantum algorithms show no speed-up when compared with their corresponding classical simulation. Finally, this gives insight into what properties are needed in the two algorithms and calls for further study of oracle separation between quantum and classical computation.

  3. A new warfarin dosing algorithm including VKORC1 3730 G > A polymorphism: comparison with results obtained by other published algorithms.

    PubMed

    Cini, Michela; Legnani, Cristina; Cosmi, Benilde; Guazzaloca, Giuliana; Valdrè, Lelia; Frascaro, Mirella; Palareti, Gualtiero

    2012-08-01

    Warfarin dosing is affected by clinical and genetic variants, but the contribution of the genotype associated with warfarin resistance in pharmacogenetic algorithms has not been well assessed yet. We developed a new dosing algorithm including polymorphisms associated both with warfarin sensitivity and resistance in the Italian population, and its performance was compared with those of eight previously published algorithms. Clinical and genetic data (CYP2C9*2, CYP2C9*3, VKORC1 -1639 G > A, and VKORC1 3730 G > A) were used to elaborate the new algorithm. Derivation and validation groups comprised 55 (58.2% men, mean age 69 years) and 40 (57.5% men, mean age 70 years) patients, respectively, who were on stable anticoagulation therapy for at least 3 months with different oral anticoagulation therapy (OAT) indications. Performance of the new algorithm, evaluated with mean absolute error (MAE) defined as the absolute value of the difference between observed daily maintenance dose and predicted daily dose, correlation with the observed dose and R(2) value, was comparable with or slightly lower than that obtained using the other algorithms. The new algorithm could correctly assign 53.3%, 50.0%, and 57.1% of patients to the low (≤25 mg/week), intermediate (26-44 mg/week) and high (≥ 45 mg/week) dosing range, respectively. Our data showed a significant increase in predictive accuracy among patients requiring high warfarin dose compared with the other algorithms (ranging from 0% to 28.6%). The algorithm including VKORC1 3730 G > A, associated with warfarin resistance, allowed a more accurate identification of resistant patients who require higher warfarin dosage.

  4. Enhanced vision systems: results of simulation and operational tests

    NASA Astrophysics Data System (ADS)

    Hecker, Peter; Doehler, Hans-Ullrich

    1998-07-01

    Today's aircrews have to handle more and more complex situations. Most critical tasks in the field of civil aviation are landing approaches and taxiing. Especially under bad weather conditions the crew has to handle a tremendous workload. Therefore DLR's Institute of Flight Guidance has developed a concept for an enhanced vision system (EVS), which increases performance and safety of the aircrew and provides comprehensive situational awareness. In previous contributions some elements of this concept have been presented, i.e. the 'Simulation of Imaging Radar for Obstacle Detection and Enhanced Vision' by Doehler and Bollmeyer 1996. Now the presented paper gives an overview about the DLR's enhanced vision concept and research approach, which consists of two main components: simulation and experimental evaluation. In a first step the simulational environment for enhanced vision research with a pilot-in-the-loop is introduced. An existing fixed base flight simulator is supplemented by real-time simulations of imaging sensors, i.e. imaging radar and infrared. By applying methods of data fusion an enhanced vision display is generated combining different levels of information, such as terrain model data, processed images acquired by sensors, aircraft state vectors and data transmitted via datalink. The second part of this contribution presents some experimental results. In cooperation with Daimler Benz Aerospace Sensorsystems Ulm, a test van and a test aircraft were equipped with a prototype of an imaging millimeter wave radar. This sophisticated HiVision Radar is up to now one of the most promising sensors for all weather operations. Images acquired by this sensor are shown as well as results of data fusion processes based on digital terrain models. The contribution is concluded by a short video presentation.

  5. Multiple Frequency Contrast Source Inversion Method for Vertical Electromagnetic Profiling: 2D Simulation Results and Analyses

    NASA Astrophysics Data System (ADS)

    Li, Jinghe; Song, Linping; Liu, Qing Huo

    2016-02-01

    A simultaneous multiple frequency contrast source inversion (CSI) method is applied to reconstructing hydrocarbon reservoir targets in a complex multilayered medium in two dimensions. It simulates the effects of a salt dome sedimentary formation in the context of reservoir monitoring. In this method, the stabilized biconjugate-gradient fast Fourier transform (BCGS-FFT) algorithm is applied as a fast solver for the 2D volume integral equation for the forward computation. The inversion technique with CSI combines the efficient FFT algorithm to speed up the matrix-vector multiplication and the stable convergence of the simultaneous multiple frequency CSI in the iteration process. As a result, this method is capable of making quantitative conductivity image reconstruction effectively for large-scale electromagnetic oil exploration problems, including the vertical electromagnetic profiling (VEP) survey investigated here. A number of numerical examples have been demonstrated to validate the effectiveness and capacity of the simultaneous multiple frequency CSI method for a limited array view in VEP.

  6. ENTROPY PRODUCTION IN COLLISIONLESS SYSTEMS. III. RESULTS FROM SIMULATIONS

    SciTech Connect

    Barnes, Eric I.; Egerer, Colin P. E-mail: egerer.coli@uwlax.edu

    2015-05-20

    The equilibria formed by the self-gravitating, collisionless collapse of simple initial conditions have been investigated for decades. We present the results of our attempts to describe the equilibria formed in N-body simulations using thermodynamically motivated models. Previous work has suggested that it is possible to define distribution functions for such systems that describe maximum entropy states. These distribution functions are used to create radial density and velocity distributions for comparison to those from simulations. A wide variety of N-body code conditions are used to reduce the chance that results are biased by numerical issues. We find that a subset of initial conditions studied lead to equilibria that can be accurately described by these models, and that direct calculation of the entropy shows maximum values being achieved.

  7. Entropy Production in Collisionless Systems. III. Results from Simulations

    NASA Astrophysics Data System (ADS)

    Barnes, Eric I.; Egerer, Colin P.

    2015-05-01

    The equilibria formed by the self-gravitating, collisionless collapse of simple initial conditions have been investigated for decades. We present the results of our attempts to describe the equilibria formed in N-body simulations using thermodynamically motivated models. Previous work has suggested that it is possible to define distribution functions for such systems that describe maximum entropy states. These distribution functions are used to create radial density and velocity distributions for comparison to those from simulations. A wide variety of N-body code conditions are used to reduce the chance that results are biased by numerical issues. We find that a subset of initial conditions studied lead to equilibria that can be accurately described by these models, and that direct calculation of the entropy shows maximum values being achieved.

  8. Windblown sand on Venus - Preliminary results of laboratory simulations

    NASA Technical Reports Server (NTRS)

    Greeley, R.; Iversen, J.; Leach, R.; Marshall, J.; Williams, S.; White, B.

    1984-01-01

    Small particles and winds of sufficient strength to move them have been detected from Venera and Pioneer-Venus data and suggest the existence of aeolian processes on Venus. The Venus wind tunnel (VWT) was fabricated in order to investigate the behavior of windblown particles in a simulated Venusian environment. Preliminary results show that sand-size material is readily entrained at the wind speeds detected on Venus and that saltating grains achieve velocities closely matching those of the wind. Measurements of saltation threshold and particle flux for various particle sizes have been compared with theoretical models which were developed by extrapolation of findings from Martian and terrestrial simulations. Results are in general agreement with theory, although certain discrepancies are apparent which may be attributed to experimental and/or theoretical-modeling procedures. Present findings enable a better understanding of Venusian surface processes and suggest that aeolian processes are important in the geological evolution of Venus.

  9. Key results from SB8 simulant flowsheet studies

    SciTech Connect

    Koopman, D. C.

    2013-04-26

    Key technically reviewed results are presented here in support of the Defense Waste Processing Facility (DWPF) acceptance of Sludge Batch 8 (SB8). This report summarizes results from simulant flowsheet studies of the DWPF Chemical Process Cell (CPC). Results include: Hydrogen generation rate for the Sludge Receipt and Adjustment Tank (SRAT) and Slurry Mix Evaporator (SME) cycles of the CPC on a 6,000 gallon basis; Volume percent of nitrous oxide, N2O, produced during the SRAT cycle; Ammonium ion concentrations recovered from the SRAT and SME off-gas; and, Dried weight percent solids (insoluble, soluble, and total) measurements and density.

  10. Comprehensive simulation of the middle atmospheric climate: some recent results

    NASA Astrophysics Data System (ADS)

    Hamilton, Kevin

    1995-05-01

    This study discusses the results of comprehensive time-dependent, three-dimensional numerical modelling of the circulation in the middle atmosphere obtained with the GFDL “SKYHI” troposphere-stratosphere-mesosphere general circulation model (GCM). The climate in a long control simulation with an intermediate resolution version (≈3° in horizontal) is briefly reviewed. While many aspects of the simulation are quite realistic, the focus in this study is on remaining first-order problems with the modelled middle atmospheric general circulation, notably the very cold high latitude temperatures in the Southern Hemisphere (SH) winter/spring, and the virtual absence of a quasi-biennial oscillation (QBO) in the tropical stratosphere. These problems are shared by other extant GCMs. It was noted that the SH cold pole problem is somewhat ameliorated with increasing horizontal resolution in the model. This suggests that improved resolution increases the vertical momentum fluxes from the explicitly resolved gravity waves in the model, a point confirmed by detailed analysis of the spectrum of vertical eddy momentum flux in the winter SH extratropics. This result inspired a series of experiments with the 3° SKYHI model modified by adding a prescribed zonally-symmetric zonal drag on the SH winter westerlies. The form of the imposed momentum source was based on the simple assumption that the mean flow drag produced by unresolved waves has a spatial distribution similar to that of the Eliassen-Palm flux divergence associated with explicitly resolved gravity waves. It was found that an appropriately-chosen drag confined to the top six model levels (above 0.35 mb) can lead to quite realistic simulations of the SH winter flow (including even the stationary wave fields) through August, but that problems still remain in the late-winter/springtime simulation. While the imposed momentum source was largely confined to the extratropics, it produced considerable improvement in the

  11. On the near space population from simulation results

    NASA Astrophysics Data System (ADS)

    Tischenko, V. I.

    A new computer technology module for studying meteoroid complexes is proposed. Space structure is represented by orbital fragments with their visualization from simulated cometary nucleus disintegration. The modelled section in the ecliptic is shown which presents the complex form and its inner structure. This representation can be used for analysing space filling to establish potentially dangerous regions near the complex and the concrete planet's orbits or other object routes. Main results for specific comets are given.

  12. Real-time dynamics simulation of the Cassini spacecraft using DARTS. Part 1: Functional capabilities and the spatial algebra algorithm

    NASA Technical Reports Server (NTRS)

    Jain, A.; Man, G. K.

    1993-01-01

    This paper describes the Dynamics Algorithms for Real-Time Simulation (DARTS) real-time hardware-in-the-loop dynamics simulator for the National Aeronautics and Space Administration's Cassini spacecraft. The spacecraft model consists of a central flexible body with a number of articulated rigid-body appendages. The demanding performance requirements from the spacecraft control system require the use of a high fidelity simulator for control system design and testing. The DARTS algorithm provides a new algorithmic and hardware approach to the solution of this hardware-in-the-loop simulation problem. It is based upon the efficient spatial algebra dynamics for flexible multibody systems. A parallel and vectorized version of this algorithm is implemented on a low-cost, multiprocessor computer to meet the simulation timing requirements.

  13. Advanced Discontinuous Galerkin Algorithms and First Open-Field Line Turbulence Simulations

    NASA Astrophysics Data System (ADS)

    Hammett, G. W.; Hakim, A.; Shi, E. L.

    2016-10-01

    New versions of Discontinuous Galerkin (DG) algorithms have interesting features that may help with challenging problems of higher-dimensional kinetic problems. We are developing the gyrokinetic code Gkeyll based on DG. DG also has features that may help with the next generation of Exascale computers. Higher-order methods do more FLOPS to extract more information per byte, thus reducing memory and communications costs (which are a bottleneck at exascale). DG uses efficient Gaussian quadrature like finite elements, but keeps the calculation local for the kinetic solver, also reducing communication. Sparse grid methods might further reduce the cost significantly in higher dimensions. The inner product norm can be chosen to preserve energy conservation with non-polynomial basis functions (such as Maxwellian-weighted bases), which can be viewed as a Petrov-Galerkin method. This allows a full- F code to benefit from similar Gaussian quadrature as used in popular δf gyrokinetic codes. Consistent basis functions avoid high-frequency numerical modes from electromagnetic terms. We will show our first results of 3 x + 2 v simulations of open-field line/SOL turbulence in a simple helical geometry (like Helimak/TORPEX), with parameters from LAPD, TORPEX, and NSTX. Supported by the Max-Planck/Princeton Center for Plasma Physics, the SciDAC Center for the Study of Plasma Microturbulence, and DOE Contract DE-AC02-09CH11466.

  14. Speed-up hyperspheres homotopic path tracking algorithm for PWL circuits simulations.

    PubMed

    Ramirez-Pinero, A; Vazquez-Leal, H; Jimenez-Fernandez, V M; Sedighi, H M; Rashidi, M M; Filobello-Nino, U; Castaneda-Sheissa, R; Huerta-Chua, J; Sarmiento-Reyes, L A; Laguna-Camacho, J R; Castro-Gonzalez, F

    2016-01-01

    In the present work, we introduce an improved version of the hyperspheres path tracking method adapted for piecewise linear (PWL) circuits. This enhanced version takes advantage of the PWL characteristics from the homotopic curve, achieving faster path tracking and improving the performance of the homotopy continuation method (HCM). Faster computing time allows the study of complex circuits with higher complexity; the proposed method also decrease, significantly, the probability of having a diverging problem when using the Newton-Raphson method because it is applied just twice per linear region on the homotopic path. Equilibrium equations of the studied circuits are obtained applying the modified nodal analysis; this method allows to propose an algorithm for nonlinear circuit analysis. Besides, a starting point criteria is proposed to obtain better performance of the HCM and a technique for avoiding the reversion phenomenon is also proposed. To prove the efficiency of the path tracking method, several cases study with bipolar (BJT) and CMOS transistors are provided. Simulation results show that the proposed approach can be up to twelve times faster than the original path tracking method and also helps to avoid several reversion cases that appears when original hyperspheres path tracking scheme was employed.

  15. Combined Simulated Annealing and Genetic Algorithm Approach to Bus Network Design

    NASA Astrophysics Data System (ADS)

    Liu, Li; Olszewski, Piotr; Goh, Pong-Chai

    A new method - combined simulated annealing (SA) and genetic algorithm (GA) approach is proposed to solve the problem of bus route design and frequency setting for a given road network with fixed bus stop locations and fixed travel demand. The method involves two steps: a set of candidate routes is generated first and then the best subset of these routes is selected by the combined SA and GA procedure. SA is the main process to search for a better solution to minimize the total system cost, comprising user and operator costs. GA is used as a sub-process to generate new solutions. Bus demand assignment on two alternative paths is performed at the solution evaluation stage. The method was implemented on four theoretical grid networks of different size and a benchmark network. Several GA operators (crossover and mutation) were utilized and tested for their effectiveness. The results show that the proposed method can efficiently converge to the optimal solution on a small network but computation time increases significantly with network size. The method can also be used for other transport operation management problems.

  16. Control of Boolean networks: hardness results and algorithms for tree structured networks.

    PubMed

    Akutsu, Tatsuya; Hayashida, Morihiro; Ching, Wai-Ki; Ng, Michael K

    2007-02-21

    Finding control strategies of cells is a challenging and important problem in the post-genomic era. This paper considers theoretical aspects of the control problem using the Boolean network (BN), which is a simplified model of genetic networks. It is shown that finding a control strategy leading to the desired global state is computationally intractable (NP-hard) in general. Furthermore, this hardness result is extended for BNs with considerably restricted network structures. These results justify existing exponential time algorithms for finding control strategies for probabilistic Boolean networks (PBNs). On the other hand, this paper shows that the control problem can be solved in polynomial time if the network has a tree structure. Then, this algorithm is extended for the case where the network has a few loops and the number of time steps is small. Though this paper focuses on theoretical aspects, biological implications of the theoretical results are also discussed.

  17. Algorithms for personalized therapy of type 2 diabetes: results of a web-based international survey.

    PubMed

    Gallo, Marco; Mannucci, Edoardo; De Cosmo, Salvatore; Gentile, Sandro; Candido, Riccardo; De Micheli, Alberto; Di Benedetto, Antonino; Esposito, Katherine; Genovese, Stefano; Medea, Gerardo; Ceriello, Antonio

    2015-01-01

    In recent years increasing interest in the issue of treatment personalization for type 2 diabetes (T2DM) has emerged. This international web-based survey aimed to evaluate opinions of physicians about tailored therapeutic algorithms developed by the Italian Association of Diabetologists (AMD) and available online, and to get suggestions for future developments. Another aim of this initiative was to assess whether the online advertising and the survey would have increased the global visibility of the AMD algorithms. The web-based survey, which comprised five questions, has been available from the homepage of the web-version of the journal Diabetes Care throughout the month of December 2013, and on the AMD website between December 2013 and September 2014. Participation was totally free and responders were anonymous. Overall, 452 physicians (M=58.4%) participated in the survey. Diabetologists accounted for 76.8% of responders. The results of the survey show wide agreement (>90%) by participants on the utility of the algorithms proposed, even if they do not cover all possible needs of patients with T2DM for a personalized therapeutic approach. In the online survey period and in the months after its conclusion, a relevant and durable increase in the number of unique users who visited the websites was registered, compared to the period preceding the survey. Patients with T2DM are heterogeneous, and there is interest toward accessible and easy to use personalized therapeutic algorithms. Responders opinions probably reflect the peculiar organization of diabetes care in each country.

  18. A novel algorithm for solving the true coincident counting issues in Monte Carlo simulations for radiation spectroscopy.

    PubMed

    Guan, Fada; Johns, Jesse M; Vasudevan, Latha; Zhang, Guoqing; Tang, Xiaobin; Poston, John W; Braby, Leslie A

    2015-06-01

    Coincident counts can be observed in experimental radiation spectroscopy. Accurate quantification of the radiation source requires the detection efficiency of the spectrometer, which is often experimentally determined. However, Monte Carlo analysis can be used to supplement experimental approaches to determine the detection efficiency a priori. The traditional Monte Carlo method overestimates the detection efficiency as a result of omitting coincident counts caused mainly