Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

PubMed Central

Ando, Tadashi; Chow, Edmond; Saad, Yousef; Skolnick, Jeffrey

2012-01-01

Hydrodynamic interactions play an important role in the dynamics of macromolecules. The most common way to take into account hydrodynamic effects in molecular simulations is in the context of a Brownian dynamics simulation. However, the calculation of correlated Brownian noise vectors in these simulations is computationally very demanding and alternative methods are desirable. This paper studies methods based on Krylov subspaces for computing Brownian noise vectors. These methods are related to Chebyshev polynomial approximations, but do not require eigenvalue estimates. We show that only low accuracy is required in the Brownian noise vectors to accurately compute values of dynamic and static properties of polymer and monodisperse suspension models. With this level of accuracy, the computational time of Krylov subspace methods scales very nearly as O(N2) for the number of particles N up to 10 000, which was the limit tested. The performance of the Krylov subspace methods, especially the “block” version, is slightly better than that of the Chebyshev method, even without taking into account the additional cost of eigenvalue estimates required by the latter. Furthermore, at N = 10 000, the Krylov subspace method is 13 times faster than the exact Cholesky method. Thus, Krylov subspace methods are recommended for performing large-scale Brownian dynamics simulations with hydrodynamic interactions. PMID:22897254

Fast Learning for Immersive Engagement in Energy Simulations

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

Bush, Brian W; Bugbee, Bruce; Gruchalla, Kenny M

The fast computation which is critical for immersive engagement with and learning from energy simulations would be furthered by developing a general method for creating rapidly computed simplified versions of NREL's computation-intensive energy simulations. Created using machine learning techniques, these 'reduced form' simulations can provide statistically sound estimates of the results of the full simulations at a fraction of the computational cost with response times - typically less than one minute of wall-clock time - suitable for real-time human-in-the-loop design and analysis. Additionally, uncertainty quantification techniques can document the accuracy of the approximate models and their domain of validity. Approximationmore » methods are applicable to a wide range of computational models, including supply-chain models, electric power grid simulations, and building models. These reduced-form representations cannot replace or re-implement existing simulations, but instead supplement them by enabling rapid scenario design and quality assurance for large sets of simulations. We present an overview of the framework and methods we have implemented for developing these reduced-form representations.« less

Physical Principle for Generation of Randomness

NASA Technical Reports Server (NTRS)

Zak, Michail

2009-01-01

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

Comparison of meaningful learning characteristics in simulated nursing practice after traditional versus computer-based simulation method: a qualitative videography study.

PubMed

Poikela, Paula; Ruokamo, Heli; Teräs, Marianne

2015-02-01

Nursing educators must ensure that nursing students acquire the necessary competencies; finding the most purposeful teaching methods and encouraging learning through meaningful learning opportunities is necessary to meet this goal. We investigated student learning in a simulated nursing practice using videography. The purpose of this paper is to examine how two different teaching methods presented students' meaningful learning in a simulated nursing experience. The 6-hour study was divided into three parts: part I, general information; part II, training; and part III, simulated nursing practice. Part II was delivered by two different methods: a computer-based simulation and a lecture. The study was carried out in the simulated nursing practice in two universities of applied sciences, in Northern Finland. The participants in parts II and I were 40 first year nursing students; 12 student volunteers continued to part III. Qualitative analysis method was used. The data were collected using video recordings and analyzed by videography. The students who used a computer-based simulation program were more likely to report meaningful learning themes than those who were first exposed to lecture method. Educators should be encouraged to use computer-based simulation teaching in conjunction with other teaching methods to ensure that nursing students are able to receive the greatest educational benefits. Copyright © 2014 Elsevier Ltd. All rights reserved.

The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.

PubMed

Drawert, Brian; Lawson, Michael J; Petzold, Linda; Khammash, Mustafa

2010-02-21

We have developed a computational framework for accurate and efficient simulation of stochastic spatially inhomogeneous biochemical systems. The new computational method employs a fractional step hybrid strategy. A novel formulation of the finite state projection (FSP) method, called the diffusive FSP method, is introduced for the efficient and accurate simulation of diffusive transport. Reactions are handled by the stochastic simulation algorithm.

Icing simulation: A survey of computer models and experimental facilities

NASA Technical Reports Server (NTRS)

Potapczuk, M. G.; Reinmann, J. J.

1991-01-01

A survey of the current methods for simulation of the response of an aircraft or aircraft subsystem to an icing encounter is presented. The topics discussed include a computer code modeling of aircraft icing and performance degradation, an evaluation of experimental facility simulation capabilities, and ice protection system evaluation tests in simulated icing conditions. Current research focussed on upgrading simulation fidelity of both experimental and computational methods is discussed. The need for increased understanding of the physical processes governing ice accretion, ice shedding, and iced airfoil aerodynamics is examined.

Icing simulation: A survey of computer models and experimental facilities

NASA Technical Reports Server (NTRS)

Potapczuk, M. G.; Reinmann, J. J.

1991-01-01

A survey of the current methods for simulation of the response of an aircraft or aircraft subsystem to an icing encounter is presented. The topics discussed include a computer code modeling of aircraft icing and performance degradation, an evaluation of experimental facility simulation capabilities, and ice protection system evaluation tests in simulated icing conditions. Current research focused on upgrading simulation fidelity of both experimental and computational methods is discussed. The need for the increased understanding of the physical processes governing ice accretion, ice shedding, and iced aerodynamics is examined.

Computer Simulation as an Aid for Management of an Information System.

ERIC Educational Resources Information Center

Simmonds, W. H.; And Others

The aim of this study was to develop methods, based upon computer simulation, of designing information systems and illustrate the use of these methods by application to an information service. The method developed is based upon Monte Carlo and discrete event simulation techniques and is described in an earlier report - Sira report R412 Organizing…

Data-driven train set crash dynamics simulation

NASA Astrophysics Data System (ADS)

Tang, Zhao; Zhu, Yunrui; Nie, Yinyu; Guo, Shihui; Liu, Fengjia; Chang, Jian; Zhang, Jianjun

2017-02-01

Traditional finite element (FE) methods are arguably expensive in computation/simulation of the train crash. High computational cost limits their direct applications in investigating dynamic behaviours of an entire train set for crashworthiness design and structural optimisation. On the contrary, multi-body modelling is widely used because of its low computational cost with the trade-off in accuracy. In this study, a data-driven train crash modelling method is proposed to improve the performance of a multi-body dynamics simulation of train set crash without increasing the computational burden. This is achieved by the parallel random forest algorithm, which is a machine learning approach that extracts useful patterns of force-displacement curves and predicts a force-displacement relation in a given collision condition from a collection of offline FE simulation data on various collision conditions, namely different crash velocities in our analysis. Using the FE simulation results as a benchmark, we compared our method with traditional multi-body modelling methods and the result shows that our data-driven method improves the accuracy over traditional multi-body models in train crash simulation and runs at the same level of efficiency.

Verifying the Simulation Hypothesis via Infinite Nested Universe Simulacrum Loops

NASA Astrophysics Data System (ADS)

Sharma, Vikrant

2017-01-01

The simulation hypothesis proposes that local reality exists as a simulacrum within a hypothetical computer's dimension. More specifically, Bostrom's trilemma proposes that the number of simulations an advanced 'posthuman' civilization could produce makes the proposition very likely. In this paper a hypothetical method to verify the simulation hypothesis is discussed using infinite regression applied to a new type of infinite loop. Assign dimension n to any computer in our present reality, where dimension signifies the hierarchical level in nested simulations our reality exists in. A computer simulating known reality would be dimension (n-1), and likewise a computer simulating an artificial reality, such as a video game, would be dimension (n +1). In this method, among others, four key assumptions are made about the nature of the original computer dimension n. Summations show that regressing such a reality infinitely will create convergence, implying that the verification of whether local reality is a grand simulation is feasible to detect with adequate compute capability. The action of reaching said convergence point halts the simulation of local reality. Sensitivities to the four assumptions and implications are discussed.

High Performance Parallel Computational Nanotechnology

NASA Technical Reports Server (NTRS)

Saini, Subhash; Craw, James M. (Technical Monitor)

1995-01-01

At a recent press conference, NASA Administrator Dan Goldin encouraged NASA Ames Research Center to take a lead role in promoting research and development of advanced, high-performance computer technology, including nanotechnology. Manufacturers of leading-edge microprocessors currently perform large-scale simulations in the design and verification of semiconductor devices and microprocessors. Recently, the need for this intensive simulation and modeling analysis has greatly increased, due in part to the ever-increasing complexity of these devices, as well as the lessons of experiences such as the Pentium fiasco. Simulation, modeling, testing, and validation will be even more important for designing molecular computers because of the complex specification of millions of atoms, thousands of assembly steps, as well as the simulation and modeling needed to ensure reliable, robust and efficient fabrication of the molecular devices. The software for this capacity does not exist today, but it can be extrapolated from the software currently used in molecular modeling for other applications: semi-empirical methods, ab initio methods, self-consistent field methods, Hartree-Fock methods, molecular mechanics; and simulation methods for diamondoid structures. In as much as it seems clear that the application of such methods in nanotechnology will require powerful, highly powerful systems, this talk will discuss techniques and issues for performing these types of computations on parallel systems. We will describe system design issues (memory, I/O, mass storage, operating system requirements, special user interface issues, interconnects, bandwidths, and programming languages) involved in parallel methods for scalable classical, semiclassical, quantum, molecular mechanics, and continuum models; molecular nanotechnology computer-aided designs (NanoCAD) techniques; visualization using virtual reality techniques of structural models and assembly sequences; software required to control mini robotic manipulators for positional control; scalable numerical algorithms for reliability, verifications and testability. There appears no fundamental obstacle to simulating molecular compilers and molecular computers on high performance parallel computers, just as the Boeing 777 was simulated on a computer before manufacturing it.

Filters for Improvement of Multiscale Data from Atomistic Simulations

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

Gardner, David J.; Reynolds, Daniel R.

Multiscale computational models strive to produce accurate and efficient numerical simulations of systems involving interactions across multiple spatial and temporal scales that typically differ by several orders of magnitude. Some such models utilize a hybrid continuum-atomistic approach combining continuum approximations with first-principles-based atomistic models to capture multiscale behavior. By following the heterogeneous multiscale method framework for developing multiscale computational models, unknown continuum scale data can be computed from an atomistic model. Concurrently coupling the two models requires performing numerous atomistic simulations which can dominate the computational cost of the method. Furthermore, when the resulting continuum data is noisy due tomore » sampling error, stochasticity in the model, or randomness in the initial conditions, filtering can result in significant accuracy gains in the computed multiscale data without increasing the size or duration of the atomistic simulations. In this work, we demonstrate the effectiveness of spectral filtering for increasing the accuracy of noisy multiscale data obtained from atomistic simulations. Moreover, we present a robust and automatic method for closely approximating the optimum level of filtering in the case of additive white noise. By improving the accuracy of this filtered simulation data, it leads to a dramatic computational savings by allowing for shorter and smaller atomistic simulations to achieve the same desired multiscale simulation precision.« less

Filters for Improvement of Multiscale Data from Atomistic Simulations

DOE PAGES

Gardner, David J.; Reynolds, Daniel R.

2017-01-05

Multiscale computational models strive to produce accurate and efficient numerical simulations of systems involving interactions across multiple spatial and temporal scales that typically differ by several orders of magnitude. Some such models utilize a hybrid continuum-atomistic approach combining continuum approximations with first-principles-based atomistic models to capture multiscale behavior. By following the heterogeneous multiscale method framework for developing multiscale computational models, unknown continuum scale data can be computed from an atomistic model. Concurrently coupling the two models requires performing numerous atomistic simulations which can dominate the computational cost of the method. Furthermore, when the resulting continuum data is noisy due tomore » sampling error, stochasticity in the model, or randomness in the initial conditions, filtering can result in significant accuracy gains in the computed multiscale data without increasing the size or duration of the atomistic simulations. In this work, we demonstrate the effectiveness of spectral filtering for increasing the accuracy of noisy multiscale data obtained from atomistic simulations. Moreover, we present a robust and automatic method for closely approximating the optimum level of filtering in the case of additive white noise. By improving the accuracy of this filtered simulation data, it leads to a dramatic computational savings by allowing for shorter and smaller atomistic simulations to achieve the same desired multiscale simulation precision.« less

Nonequilibrium hypersonic flows simulations with asymptotic-preserving Monte Carlo methods

NASA Astrophysics Data System (ADS)

Ren, Wei; Liu, Hong; Jin, Shi

2014-12-01

In the rarefied gas dynamics, the DSMC method is one of the most popular numerical tools. It performs satisfactorily in simulating hypersonic flows surrounding re-entry vehicles and micro-/nano- flows. However, the computational cost is expensive, especially when Kn → 0. Even for flows in the near-continuum regime, pure DSMC simulations require a number of computational efforts for most cases. Albeit several DSMC/NS hybrid methods are proposed to deal with this, those methods still suffer from the boundary treatment, which may cause nonphysical solutions. Filbet and Jin [1] proposed a framework of new numerical methods of Boltzmann equation, called asymptotic preserving schemes, whose computational costs are affordable as Kn → 0. Recently, Ren et al. [2] realized the AP schemes with Monte Carlo methods (AP-DSMC), which have better performance than counterpart methods. In this paper, AP-DSMC is applied in simulating nonequilibrium hypersonic flows. Several numerical results are computed and analyzed to study the efficiency and capability of capturing complicated flow characteristics.

A Computer Simulation of Community Pharmacy Practice for Educational Use.

PubMed

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

2014-11-15

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

Modelling and Simulation as a Recognizing Method in Education

ERIC Educational Resources Information Center

Stoffa, Veronika

2004-01-01

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

Theoretical and computational foundations of management class simulation

Treesearch

Denie Gerold

1978-01-01

Investigations on complicated, complex, and not well-ordered systems are possible only with the aid of mathematical methods and electronic data processing. Simulation as a method of operations research is particularly suitable for this purpose. Theoretical and computational foundations of management class simulation must be integrated into the planning systems of...

Computer Simulation for Pain Management Education: A Pilot Study.

PubMed

Allred, Kelly; Gerardi, Nicole

2017-10-01

Effective pain management is an elusive concept in acute care. Inadequate knowledge has been identified as a barrier to providing optimal pain management. This study aimed to determine student perceptions of an interactive computer simulation as a potential method for learning pain management, as a motivator to read and learn more about pain management, preference over traditional lecture, and its potential to change nursing practice. A post-computer simulation survey with a mixed-methods descriptive design was used in this study. A college of nursing in a large metropolitan university in the Southeast United States. A convenience sample of 30 nursing students in a Bachelor of Science nursing program. An interactive computer simulation was developed as a potential alternative method of teaching pain management to nursing students. Increases in educational gain as well as its potential to change practice were explored. Each participant was asked to complete a survey consisting of 10 standard 5-point Likert scale items and 5 open-ended questions. The survey was used to evaluate the students' perception of the simulation, specifically related to educational benefit, preference compared with traditional teaching methods, and perceived potential to change nursing practice. Data provided descriptive statistics for initial evaluation of the computer simulation. The responses on the survey suggest nursing students perceive the computer simulation to be entertaining, fun, educational, occasionally preferred over regular lecture, and with potential to change practice. Preliminary data support the use of computer simulation in educating nursing students about pain management. Copyright © 2017 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.

Evaluation of Computer Simulations for Teaching Apparel Merchandising Concepts.

ERIC Educational Resources Information Center

Jolly, Laura D.; Sisler, Grovalynn

1988-01-01

The study developed and evaluated computer simulations for teaching apparel merchandising concepts. Evaluation results indicated that teaching method (computer simulation versus case study) does not significantly affect cognitive learning. Student attitudes varied, however, according to topic (profitable merchandising analysis versus retailing…

A hybrid parallel architecture for electrostatic interactions in the simulation of dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Yang, Sheng-Chun; Lu, Zhong-Yuan; Qian, Hu-Jun; Wang, Yong-Lei; Han, Jie-Ping

2017-11-01

In this work, we upgraded the electrostatic interaction method of CU-ENUF (Yang, et al., 2016) which first applied CUNFFT (nonequispaced Fourier transforms based on CUDA) to the reciprocal-space electrostatic computation and made the computation of electrostatic interaction done thoroughly in GPU. The upgraded edition of CU-ENUF runs concurrently in a hybrid parallel way that enables the computation parallelizing on multiple computer nodes firstly, then further on the installed GPU in each computer. By this parallel strategy, the size of simulation system will be never restricted to the throughput of a single CPU or GPU. The most critical technical problem is how to parallelize a CUNFFT in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Furthermore, the upgraded method is capable of computing electrostatic interactions for both the atomistic molecular dynamics (MD) and the dissipative particle dynamics (DPD). Finally, the benchmarks conducted for validation and performance indicate that the upgraded method is able to not only present a good precision when setting suitable parameters, but also give an efficient way to compute electrostatic interactions for huge simulation systems. Program Files doi:http://dx.doi.org/10.17632/zncf24fhpv.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: C, C++, and CUDA C Supplementary material: The program is designed for effective electrostatic interactions of large-scale simulation systems, which runs on particular computers equipped with NVIDIA GPUs. It has been tested on (a) single computer node with Intel(R) Core(TM) i7-3770@ 3.40 GHz (CPU) and GTX 980 Ti (GPU), and (b) MPI parallel computer nodes with the same configurations. Nature of problem: For molecular dynamics simulation, the electrostatic interaction is the most time-consuming computation because of its long-range feature and slow convergence in simulation space, which approximately take up most of the total simulation time. Although the parallel method CU-ENUF (Yang et al., 2016) based on GPU has achieved a qualitative leap compared with previous methods in electrostatic interactions computation, the computation capability is limited to the throughput capacity of a single GPU for super-scale simulation system. Therefore, we should look for an effective method to handle the calculation of electrostatic interactions efficiently for a simulation system with super-scale size. Solution method: We constructed a hybrid parallel architecture, in which CPU and GPU are combined to accelerate the electrostatic computation effectively. Firstly, the simulation system is divided into many subtasks via domain-decomposition method. Then MPI (Message Passing Interface) is used to implement the CPU-parallel computation with each computer node corresponding to a particular subtask, and furthermore each subtask in one computer node will be executed in GPU in parallel efficiently. In this hybrid parallel method, the most critical technical problem is how to parallelize a CUNFFT (nonequispaced fast Fourier transform based on CUDA) in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Restrictions: The HP-ENUF is mainly oriented to super-scale system simulations, in which the performance superiority is shown adequately. However, for a small simulation system containing less than 106 particles, the mode of multiple computer nodes has no apparent efficiency advantage or even lower efficiency due to the serious network delay among computer nodes, than the mode of single computer node. References: (1) S.-C. Yang, H.-J. Qian, Z.-Y. Lu, Appl. Comput. Harmon. Anal. 2016, http://dx.doi.org/10.1016/j.acha.2016.04.009. (2) S.-C. Yang, Y.-L. Wang, G.-S. Jiao, H.-J. Qian, Z.-Y. Lu, J. Comput. Chem. 37 (2016) 378. (3) S.-C. Yang, Y.-L. Zhu, H.-J. Qian, Z.-Y. Lu, Appl. Chem. Res. Chin. Univ., 2017, http://dx.doi.org/10.1007/s40242-016-6354-5. (4) Y.-L. Zhu, H. Liu, Z.-W. Li, H.-J. Qian, G. Milano, Z.-Y. Lu, J. Comput. Chem. 34 (2013) 2197.

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

NASA Astrophysics Data System (ADS)

Furuichi, M.; Nishiura, D.

2015-12-01

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

Acceleration of discrete stochastic biochemical simulation using GPGPU.

PubMed

Sumiyoshi, Kei; Hirata, Kazuki; Hiroi, Noriko; Funahashi, Akira

2015-01-01

For systems made up of a small number of molecules, such as a biochemical network in a single cell, a simulation requires a stochastic approach, instead of a deterministic approach. The stochastic simulation algorithm (SSA) simulates the stochastic behavior of a spatially homogeneous system. Since stochastic approaches produce different results each time they are used, multiple runs are required in order to obtain statistical results; this results in a large computational cost. We have implemented a parallel method for using SSA to simulate a stochastic model; the method uses a graphics processing unit (GPU), which enables multiple realizations at the same time, and thus reduces the computational time and cost. During the simulation, for the purpose of analysis, each time course is recorded at each time step. A straightforward implementation of this method on a GPU is about 16 times faster than a sequential simulation on a CPU with hybrid parallelization; each of the multiple simulations is run simultaneously, and the computational tasks within each simulation are parallelized. We also implemented an improvement to the memory access and reduced the memory footprint, in order to optimize the computations on the GPU. We also implemented an asynchronous data transfer scheme to accelerate the time course recording function. To analyze the acceleration of our implementation on various sizes of model, we performed SSA simulations on different model sizes and compared these computation times to those for sequential simulations with a CPU. When used with the improved time course recording function, our method was shown to accelerate the SSA simulation by a factor of up to 130.

Acceleration of discrete stochastic biochemical simulation using GPGPU

PubMed Central

Sumiyoshi, Kei; Hirata, Kazuki; Hiroi, Noriko; Funahashi, Akira

2015-01-01

For systems made up of a small number of molecules, such as a biochemical network in a single cell, a simulation requires a stochastic approach, instead of a deterministic approach. The stochastic simulation algorithm (SSA) simulates the stochastic behavior of a spatially homogeneous system. Since stochastic approaches produce different results each time they are used, multiple runs are required in order to obtain statistical results; this results in a large computational cost. We have implemented a parallel method for using SSA to simulate a stochastic model; the method uses a graphics processing unit (GPU), which enables multiple realizations at the same time, and thus reduces the computational time and cost. During the simulation, for the purpose of analysis, each time course is recorded at each time step. A straightforward implementation of this method on a GPU is about 16 times faster than a sequential simulation on a CPU with hybrid parallelization; each of the multiple simulations is run simultaneously, and the computational tasks within each simulation are parallelized. We also implemented an improvement to the memory access and reduced the memory footprint, in order to optimize the computations on the GPU. We also implemented an asynchronous data transfer scheme to accelerate the time course recording function. To analyze the acceleration of our implementation on various sizes of model, we performed SSA simulations on different model sizes and compared these computation times to those for sequential simulations with a CPU. When used with the improved time course recording function, our method was shown to accelerate the SSA simulation by a factor of up to 130. PMID:25762936

Fast Multipole Methods for Three-Dimensional N-body Problems

NASA Technical Reports Server (NTRS)

Koumoutsakos, P.

1995-01-01

We are developing computational tools for the simulations of three-dimensional flows past bodies undergoing arbitrary motions. High resolution viscous vortex methods have been developed that allow for extended simulations of two-dimensional configurations such as vortex generators. Our objective is to extend this methodology to three dimensions and develop a robust computational scheme for the simulation of such flows. A fundamental issue in the use of vortex methods is the ability of employing efficiently large numbers of computational elements to resolve the large range of scales that exist in complex flows. The traditional cost of the method scales as Omicron (N(sup 2)) as the N computational elements/particles induce velocities at each other, making the method unacceptable for simulations involving more than a few tens of thousands of particles. In the last decade fast methods have been developed that have operation counts of Omicron (N log N) or Omicron (N) (referred to as BH and GR respectively) depending on the details of the algorithm. These methods are based on the observation that the effect of a cluster of particles at a certain distance may be approximated by a finite series expansion. In order to exploit this observation we need to decompose the element population spatially into clusters of particles and build a hierarchy of clusters (a tree data structure) - smaller neighboring clusters combine to form a cluster of the next size up in the hierarchy and so on. This hierarchy of clusters allows one to determine efficiently when the approximation is valid. This algorithm is an N-body solver that appears in many fields of engineering and science. Some examples of its diverse use are in astrophysics, molecular dynamics, micro-magnetics, boundary element simulations of electromagnetic problems, and computer animation. More recently these N-body solvers have been implemented and applied in simulations involving vortex methods. Koumoutsakos and Leonard (1995) implemented the GR scheme in two dimensions for vector computer architectures allowing for simulations of bluff body flows using millions of particles. Winckelmans presented three-dimensional, viscous simulations of interacting vortex rings, using vortons and an implementation of a BH scheme for parallel computer architectures. Bhatt presented a vortex filament method to perform inviscid vortex ring interactions, with an alternative implementation of a BH scheme for a Connection Machine parallel computer architecture.

Quantum simulator review

NASA Astrophysics Data System (ADS)

Bednar, Earl; Drager, Steven L.

2007-04-01

Quantum information processing's objective is to utilize revolutionary computing capability based on harnessing the paradigm shift offered by quantum computing to solve classically hard and computationally challenging problems. Some of our computationally challenging problems of interest include: the capability for rapid image processing, rapid optimization of logistics, protecting information, secure distributed simulation, and massively parallel computation. Currently, one important problem with quantum information processing is that the implementation of quantum computers is difficult to realize due to poor scalability and great presence of errors. Therefore, we have supported the development of Quantum eXpress and QuIDD Pro, two quantum computer simulators running on classical computers for the development and testing of new quantum algorithms and processes. This paper examines the different methods used by these two quantum computing simulators. It reviews both simulators, highlighting each simulators background, interface, and special features. It also demonstrates the implementation of current quantum algorithms on each simulator. It concludes with summary comments on both simulators.

Computer simulation of reconstructed image for computer-generated holograms

NASA Astrophysics Data System (ADS)

Yasuda, Tomoki; Kitamura, Mitsuru; Watanabe, Masachika; Tsumuta, Masato; Yamaguchi, Takeshi; Yoshikawa, Hiroshi

2009-02-01

This report presents the results of computer simulation images for image-type Computer-Generated Holograms (CGHs) observable under white light fabricated with an electron beam lithography system. The simulated image is obtained by calculating wavelength and intensity of diffracted light traveling toward the viewing point from the CGH. Wavelength and intensity of the diffracted light are calculated using FFT image generated from interference fringe data. Parallax image of CGH corresponding to the viewing point can be easily obtained using this simulation method. Simulated image from interference fringe data was compared with reconstructed image of real CGH with an Electron Beam (EB) lithography system. According to the result, the simulated image resembled the reconstructed image of the CGH closely in shape, parallax, coloring and shade. And, in accordance with the shape of the light sources the simulated images which were changed in chroma saturation and blur by using two kinds of simulations: the several light sources method and smoothing method. In addition, as the applications of the CGH, full-color CGH and CGH with multiple images were simulated. The result was that the simulated images of those CGHs closely resembled the reconstructed image of real CGHs.

Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

PubMed

Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

2018-02-01

Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.

Physics Computing '92: Proceedings of the 4th International Conference

NASA Astrophysics Data System (ADS)

de Groot, Robert A.; Nadrchal, Jaroslav

1993-04-01

The Table of Contents for the book is as follows: * Preface * INVITED PAPERS * Ab Initio Theoretical Approaches to the Structural, Electronic and Vibrational Properties of Small Clusters and Fullerenes: The State of the Art * Neural Multigrid Methods for Gauge Theories and Other Disordered Systems * Multicanonical Monte Carlo Simulations * On the Use of the Symbolic Language Maple in Physics and Chemistry: Several Examples * Nonequilibrium Phase Transitions in Catalysis and Population Models * Computer Algebra, Symmetry Analysis and Integrability of Nonlinear Evolution Equations * The Path-Integral Quantum Simulation of Hydrogen in Metals * Digital Optical Computing: A New Approach of Systolic Arrays Based on Coherence Modulation of Light and Integrated Optics Technology * Molecular Dynamics Simulations of Granular Materials * Numerical Implementation of a K.A.M. Algorithm * Quasi-Monte Carlo, Quasi-Random Numbers and Quasi-Error Estimates * What Can We Learn from QMC Simulations * Physics of Fluctuating Membranes * Plato, Apollonius, and Klein: Playing with Spheres * Steady States in Nonequilibrium Lattice Systems * CONVODE: A REDUCE Package for Differential Equations * Chaos in Coupled Rotators * Symplectic Numerical Methods for Hamiltonian Problems * Computer Simulations of Surfactant Self Assembly * High-dimensional and Very Large Cellular Automata for Immunological Shape Space * A Review of the Lattice Boltzmann Method * Electronic Structure of Solids in the Self-interaction Corrected Local-spin-density Approximation * Dedicated Computers for Lattice Gauge Theory Simulations * Physics Education: A Survey of Problems and Possible Solutions * Parallel Computing and Electronic-Structure Theory * High Precision Simulation Techniques for Lattice Field Theory * CONTRIBUTED PAPERS * Case Study of Microscale Hydrodynamics Using Molecular Dynamics and Lattice Gas Methods * Computer Modelling of the Structural and Electronic Properties of the Supported Metal Catalysis * Ordered Particle Simulations for Serial and MIMD Parallel Computers * "NOLP" -- Program Package for Laser Plasma Nonlinear Optics * Algorithms to Solve Nonlinear Least Square Problems * Distribution of Hydrogen Atoms in Pd-H Computed by Molecular Dynamics * A Ray Tracing of Optical System for Protein Crystallography Beamline at Storage Ring-SIBERIA-2 * Vibrational Properties of a Pseudobinary Linear Chain with Correlated Substitutional Disorder * Application of the Software Package Mathematica in Generalized Master Equation Method * Linelist: An Interactive Program for Analysing Beam-foil Spectra * GROMACS: A Parallel Computer for Molecular Dynamics Simulations * GROMACS Method of Virial Calculation Using a Single Sum * The Interactive Program for the Solution of the Laplace Equation with the Elimination of Singularities for Boundary Functions * Random-Number Generators: Testing Procedures and Comparison of RNG Algorithms * Micro-TOPIC: A Tokamak Plasma Impurities Code * Rotational Molecular Scattering Calculations * Orthonormal Polynomial Method for Calibrating of Cryogenic Temperature Sensors * Frame-based System Representing Basis of Physics * The Role of Massively Data-parallel Computers in Large Scale Molecular Dynamics Simulations * Short-range Molecular Dynamics on a Network of Processors and Workstations * An Algorithm for Higher-order Perturbation Theory in Radiative Transfer Computations * Hydrostochastics: The Master Equation Formulation of Fluid Dynamics * HPP Lattice Gas on Transputers and Networked Workstations * Study on the Hysteresis Cycle Simulation Using Modeling with Different Functions on Intervals * Refined Pruning Techniques for Feed-forward Neural Networks * Random Walk Simulation of the Motion of Transient Charges in Photoconductors * The Optical Hysteresis in Hydrogenated Amorphous Silicon * Diffusion Monte Carlo Analysis of Modern Interatomic Potentials for He * A Parallel Strategy for Molecular Dynamics Simulations of Polar Liquids on Transputer Arrays * Distribution of Ions Reflected on Rough Surfaces * The Study of Step Density Distribution During Molecular Beam Epitaxy Growth: Monte Carlo Computer Simulation * Towards a Formal Approach to the Construction of Large-scale Scientific Applications Software * Correlated Random Walk and Discrete Modelling of Propagation through Inhomogeneous Media * Teaching Plasma Physics Simulation * A Theoretical Determination of the Au-Ni Phase Diagram * Boson and Fermion Kinetics in One-dimensional Lattices * Computational Physics Course on the Technical University * Symbolic Computations in Simulation Code Development and Femtosecond-pulse Laser-plasma Interaction Studies * Computer Algebra and Integrated Computing Systems in Education of Physical Sciences * Coordinated System of Programs for Undergraduate Physics Instruction * Program Package MIRIAM and Atomic Physics of Extreme Systems * High Energy Physics Simulation on the T_Node * The Chapman-Kolmogorov Equation as Representation of Huygens' Principle and the Monolithic Self-consistent Numerical Modelling of Lasers * Authoring System for Simulation Developments * Molecular Dynamics Study of Ion Charge Effects in the Structure of Ionic Crystals * A Computational Physics Introductory Course * Computer Calculation of Substrate Temperature Field in MBE System * Multimagnetical Simulation of the Ising Model in Two and Three Dimensions * Failure of the CTRW Treatment of the Quasicoherent Excitation Transfer * Implementation of a Parallel Conjugate Gradient Method for Simulation of Elastic Light Scattering * Algorithms for Study of Thin Film Growth * Algorithms and Programs for Physics Teaching in Romanian Technical Universities * Multicanonical Simulation of 1st order Transitions: Interface Tension of the 2D 7-State Potts Model * Two Numerical Methods for the Calculation of Periodic Orbits in Hamiltonian Systems * Chaotic Behavior in a Probabilistic Cellular Automata? * Wave Optics Computing by a Networked-based Vector Wave Automaton * Tensor Manipulation Package in REDUCE * Propagation of Electromagnetic Pulses in Stratified Media * The Simple Molecular Dynamics Model for the Study of Thermalization of the Hot Nucleon Gas * Electron Spin Polarization in PdCo Alloys Calculated by KKR-CPA-LSD Method * Simulation Studies of Microscopic Droplet Spreading * A Vectorizable Algorithm for the Multicolor Successive Overrelaxation Method * Tetragonality of the CuAu I Lattice and Its Relation to Electronic Specific Heat and Spin Susceptibility * Computer Simulation of the Formation of Metallic Aggregates Produced by Chemical Reactions in Aqueous Solution * Scaling in Growth Models with Diffusion: A Monte Carlo Study * The Nucleus as the Mesoscopic System * Neural Network Computation as Dynamic System Simulation * First-principles Theory of Surface Segregation in Binary Alloys * Data Smooth Approximation Algorithm for Estimating the Temperature Dependence of the Ice Nucleation Rate * Genetic Algorithms in Optical Design * Application of 2D-FFT in the Study of Molecular Exchange Processes by NMR * Advanced Mobility Model for Electron Transport in P-Si Inversion Layers * Computer Simulation for Film Surfaces and its Fractal Dimension * Parallel Computation Techniques and the Structure of Catalyst Surfaces * Educational SW to Teach Digital Electronics and the Corresponding Text Book * Primitive Trinomials (Mod 2) Whose Degree is a Mersenne Exponent * Stochastic Modelisation and Parallel Computing * Remarks on the Hybrid Monte Carlo Algorithm for the ∫4 Model * An Experimental Computer Assisted Workbench for Physics Teaching * A Fully Implicit Code to Model Tokamak Plasma Edge Transport * EXPFIT: An Interactive Program for Automatic Beam-foil Decay Curve Analysis * Mapping Technique for Solving General, 1-D Hamiltonian Systems * Freeway Traffic, Cellular Automata, and Some (Self-Organizing) Criticality * Photonuclear Yield Analysis by Dynamic Programming * Incremental Representation of the Simply Connected Planar Curves * Self-convergence in Monte Carlo Methods * Adaptive Mesh Technique for Shock Wave Propagation * Simulation of Supersonic Coronal Streams and Their Interaction with the Solar Wind * The Nature of Chaos in Two Systems of Ordinary Nonlinear Differential Equations * Considerations of a Window-shopper * Interpretation of Data Obtained by RTP 4-Channel Pulsed Radar Reflectometer Using a Multi Layer Perceptron * Statistics of Lattice Bosons for Finite Systems * Fractal Based Image Compression with Affine Transformations * Algorithmic Studies on Simulation Codes for Heavy-ion Reactions * An Energy-Wise Computer Simulation of DNA-Ion-Water Interactions Explains the Abnormal Structure of Poly[d(A)]:Poly[d(T)] * Computer Simulation Study of Kosterlitz-Thouless-Like Transitions * Problem-oriented Software Package GUN-EBT for Computer Simulation of Beam Formation and Transport in Technological Electron-Optical Systems * Parallelization of a Boundary Value Solver and its Application in Nonlinear Dynamics * The Symbolic Classification of Real Four-dimensional Lie Algebras * Short, Singular Pulses Generation by a Dye Laser at Two Wavelengths Simultaneously * Quantum Monte Carlo Simulations of the Apex-Oxygen-Model * Approximation Procedures for the Axial Symmetric Static Einstein-Maxwell-Higgs Theory * Crystallization on a Sphere: Parallel Simulation on a Transputer Network * FAMULUS: A Software Product (also) for Physics Education * MathCAD vs. FAMULUS -- A Brief Comparison * First-principles Dynamics Used to Study Dissociative Chemisorption * A Computer Controlled System for Crystal Growth from Melt * A Time Resolved Spectroscopic Method for Short Pulsed Particle Emission * Green's Function Computation in Radiative Transfer Theory * Random Search Optimization Technique for One-criteria and Multi-criteria Problems * Hartley Transform Applications to Thermal Drift Elimination in Scanning Tunneling Microscopy * Algorithms of Measuring, Processing and Interpretation of Experimental Data Obtained with Scanning Tunneling Microscope * Time-dependent Atom-surface Interactions * Local and Global Minima on Molecular Potential Energy Surfaces: An Example of N3 Radical * Computation of Bifurcation Surfaces * Symbolic Computations in Quantum Mechanics: Energies in Next-to-solvable Systems * A Tool for RTP Reactor and Lamp Field Design * Modelling of Particle Spectra for the Analysis of Solid State Surface * List of Participants

Some issues related to simulation of the tracking and communications computer network

NASA Technical Reports Server (NTRS)

Lacovara, Robert C.

1989-01-01

The Communications Performance and Integration branch of the Tracking and Communications Division has an ongoing involvement in the simulation of its flight hardware for Space Station Freedom. Specifically, the communication process between central processor(s) and orbital replaceable units (ORU's) is simulated with varying degrees of fidelity. The results of investigations into three aspects of this simulation effort are given. The most general area involves the use of computer assisted software engineering (CASE) tools for this particular simulation. The second area of interest is simulation methods for systems of mixed hardware and software. The final area investigated is the application of simulation methods to one of the proposed computer network protocols for space station, specifically IEEE 802.4.

Some issues related to simulation of the tracking and communications computer network

NASA Astrophysics Data System (ADS)

Lacovara, Robert C.

1989-12-01

The Communications Performance and Integration branch of the Tracking and Communications Division has an ongoing involvement in the simulation of its flight hardware for Space Station Freedom. Specifically, the communication process between central processor(s) and orbital replaceable units (ORU's) is simulated with varying degrees of fidelity. The results of investigations into three aspects of this simulation effort are given. The most general area involves the use of computer assisted software engineering (CASE) tools for this particular simulation. The second area of interest is simulation methods for systems of mixed hardware and software. The final area investigated is the application of simulation methods to one of the proposed computer network protocols for space station, specifically IEEE 802.4.

Methods of parallel computation applied on granular simulations

NASA Astrophysics Data System (ADS)

Martins, Gustavo H. B.; Atman, Allbens P. F.

2017-06-01

Every year, parallel computing has becoming cheaper and more accessible. As consequence, applications were spreading over all research areas. Granular materials is a promising area for parallel computing. To prove this statement we study the impact of parallel computing in simulations of the BNE (Brazil Nut Effect). This property is due the remarkable arising of an intruder confined to a granular media when vertically shaken against gravity. By means of DEM (Discrete Element Methods) simulations, we study the code performance testing different methods to improve clock time. A comparison between serial and parallel algorithms, using OpenMP® is also shown. The best improvement was obtained by optimizing the function that find contacts using Verlet's cells.

Fast Particle Methods for Multiscale Phenomena Simulations

NASA Technical Reports Server (NTRS)

Koumoutsakos, P.; Wray, A.; Shariff, K.; Pohorille, Andrew

2000-01-01

We are developing particle methods oriented at improving computational modeling capabilities of multiscale physical phenomena in : (i) high Reynolds number unsteady vortical flows, (ii) particle laden and interfacial flows, (iii)molecular dynamics studies of nanoscale droplets and studies of the structure, functions, and evolution of the earliest living cell. The unifying computational approach involves particle methods implemented in parallel computer architectures. The inherent adaptivity, robustness and efficiency of particle methods makes them a multidisciplinary computational tool capable of bridging the gap of micro-scale and continuum flow simulations. Using efficient tree data structures, multipole expansion algorithms, and improved particle-grid interpolation, particle methods allow for simulations using millions of computational elements, making possible the resolution of a wide range of length and time scales of these important physical phenomena.The current challenges in these simulations are in : [i] the proper formulation of particle methods in the molecular and continuous level for the discretization of the governing equations [ii] the resolution of the wide range of time and length scales governing the phenomena under investigation. [iii] the minimization of numerical artifacts that may interfere with the physics of the systems under consideration. [iv] the parallelization of processes such as tree traversal and grid-particle interpolations We are conducting simulations using vortex methods, molecular dynamics and smooth particle hydrodynamics, exploiting their unifying concepts such as : the solution of the N-body problem in parallel computers, highly accurate particle-particle and grid-particle interpolations, parallel FFT's and the formulation of processes such as diffusion in the context of particle methods. This approach enables us to transcend among seemingly unrelated areas of research.

Overview of Computer Simulation Modeling Approaches and Methods

Treesearch

Robert E. Manning; Robert M. Itami; David N. Cole; Randy Gimblett

2005-01-01

The field of simulation modeling has grown greatly with recent advances in computer hardware and software. Much of this work has involved large scientific and industrial applications for which substantial financial resources are available. However, advances in object-oriented programming and simulation methodology, concurrent with dramatic increases in computer...

Patient flow within UK emergency departments: a systematic review of the use of computer simulation modelling methods

PubMed Central

Mohiuddin, Syed; Busby, John; Savović, Jelena; Richards, Alison; Northstone, Kate; Hollingworth, William; Donovan, Jenny L; Vasilakis, Christos

2017-01-01

Objectives Overcrowding in the emergency department (ED) is common in the UK as in other countries worldwide. Computer simulation is one approach used for understanding the causes of ED overcrowding and assessing the likely impact of changes to the delivery of emergency care. However, little is known about the usefulness of computer simulation for analysis of ED patient flow. We undertook a systematic review to investigate the different computer simulation methods and their contribution for analysis of patient flow within EDs in the UK. Methods We searched eight bibliographic databases (MEDLINE, EMBASE, COCHRANE, WEB OF SCIENCE, CINAHL, INSPEC, MATHSCINET and ACM DIGITAL LIBRARY) from date of inception until 31 March 2016. Studies were included if they used a computer simulation method to capture patient progression within the ED of an established UK National Health Service hospital. Studies were summarised in terms of simulation method, key assumptions, input and output data, conclusions drawn and implementation of results. Results Twenty-one studies met the inclusion criteria. Of these, 19 used discrete event simulation and 2 used system dynamics models. The purpose of many of these studies (n=16; 76%) centred on service redesign. Seven studies (33%) provided no details about the ED being investigated. Most studies (n=18; 86%) used specific hospital models of ED patient flow. Overall, the reporting of underlying modelling assumptions was poor. Nineteen studies (90%) considered patient waiting or throughput times as the key outcome measure. Twelve studies (57%) reported some involvement of stakeholders in the simulation study. However, only three studies (14%) reported on the implementation of changes supported by the simulation. Conclusions We found that computer simulation can provide a means to pretest changes to ED care delivery before implementation in a safe and efficient manner. However, the evidence base is small and poorly developed. There are some methodological, data, stakeholder, implementation and reporting issues, which must be addressed by future studies. PMID:28487459

Oxygen transport properties estimation by DSMC-CT simulations

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

Bruno, Domenico; Frezzotti, Aldo; Ghiroldi, Gian Pietro

Coupling DSMC simulations with classical trajectories calculations is emerging as a powerful tool to improve predictive capabilities of computational rarefied gas dynamics. The considerable increase of computational effort outlined in the early application of the method (Koura,1997) can be compensated by running simulations on massively parallel computers. In particular, GPU acceleration has been found quite effective in reducing computing time (Ferrigni,2012; Norman et al.,2013) of DSMC-CT simulations. The aim of the present work is to study rarefied Oxygen flows by modeling binary collisions through an accurate potential energy surface, obtained by molecular beams scattering (Aquilanti, et al.,1999). The accuracy ofmore » the method is assessed by calculating molecular Oxygen shear viscosity and heat conductivity following three different DSMC-CT simulation methods. In the first one, transport properties are obtained from DSMC-CT simulations of spontaneous fluctuation of an equilibrium state (Bruno et al, Phys. Fluids, 23, 093104, 2011). In the second method, the collision trajectory calculation is incorporated in a Monte Carlo integration procedure to evaluate the Taxman’s expressions for the transport properties of polyatomic gases (Taxman,1959). In the third, non-equilibrium zero and one-dimensional rarefied gas dynamic simulations are adopted and the transport properties are computed from the non-equilibrium fluxes of momentum and energy. The three methods provide close values of the transport properties, their estimated statistical error not exceeding 3%. The experimental values are slightly underestimated, the percentage deviation being, again, few percent.« less

Symplectic molecular dynamics simulations on specially designed parallel computers.

PubMed

Borstnik, Urban; Janezic, Dusanka

2005-01-01

We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

Coarse-Grained Lattice Model Simulations of Sequence-Structure Fitness of a Ribosome-Inactivating Protein

DTIC Science & Technology

2007-11-05

limits of what is considered practical when applying all-atom molecular - dynamics simulation methods. Lattice models provide computationally robust...of expectation values from the density of states. All-atom molecular - dynamics simulations provide the most rigorous sampling method to generate con... molecular - dynamics simulations of protein folding,6–9 reported studies of computing a heat capacity or other calorimetric observables have been limited to

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

PubMed Central

Greenberg, David A.

2011-01-01

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

Technical Evaluation Report for Symposium AVT-147: Computational Uncertainty in Military Vehicle Design

NASA Technical Reports Server (NTRS)

Radespiel, Rolf; Hemsch, Michael J.

2007-01-01

The complexity of modern military systems, as well as the cost and difficulty associated with experimentally verifying system and subsystem design makes the use of high-fidelity based simulation a future alternative for design and development. The predictive ability of such simulations such as computational fluid dynamics (CFD) and computational structural mechanics (CSM) have matured significantly. However, for numerical simulations to be used with confidence in design and development, quantitative measures of uncertainty must be available. The AVT 147 Symposium has been established to compile state-of-the art methods of assessing computational uncertainty, to identify future research and development needs associated with these methods, and to present examples of how these needs are being addressed and how the methods are being applied. Papers were solicited that address uncertainty estimation associated with high fidelity, physics-based simulations. The solicitation included papers that identify sources of error and uncertainty in numerical simulation from either the industry perspective or from the disciplinary or cross-disciplinary research perspective. Examples of the industry perspective were to include how computational uncertainty methods are used to reduce system risk in various stages of design or development.

Numerical Simulation of Transit-Time Ultrasonic Flowmeters by a Direct Approach.

PubMed

Luca, Adrian; Marchiano, Regis; Chassaing, Jean-Camille

2016-06-01

This paper deals with the development of a computational code for the numerical simulation of wave propagation through domains with a complex geometry consisting in both solids and moving fluids. The emphasis is on the numerical simulation of ultrasonic flowmeters (UFMs) by modeling the wave propagation in solids with the equations of linear elasticity (ELE) and in fluids with the linearized Euler equations (LEEs). This approach requires high performance computing because of the high number of degrees of freedom and the long propagation distances. Therefore, the numerical method should be chosen with care. In order to minimize the numerical dissipation which may occur in this kind of configuration, the numerical method employed here is the nodal discontinuous Galerkin (DG) method. Also, this method is well suited for parallel computing. To speed up the code, almost all the computational stages have been implemented to run on graphical processing unit (GPU) by using the compute unified device architecture (CUDA) programming model from NVIDIA. This approach has been validated and then used for the two-dimensional simulation of gas UFMs. The large contrast of acoustic impedance characteristic to gas UFMs makes their simulation a real challenge.

Computer animation challenges for computational fluid dynamics

NASA Astrophysics Data System (ADS)

Vines, Mauricio; Lee, Won-Sook; Mavriplis, Catherine

2012-07-01

Computer animation requirements differ from those of traditional computational fluid dynamics (CFD) investigations in that visual plausibility and rapid frame update rates trump physical accuracy. We present an overview of the main techniques for fluid simulation in computer animation, starting with Eulerian grid approaches, the Lattice Boltzmann method, Fourier transform techniques and Lagrangian particle introduction. Adaptive grid methods, precomputation of results for model reduction, parallelisation and computation on graphical processing units (GPUs) are reviewed in the context of accelerating simulation computations for animation. A survey of current specific approaches for the application of these techniques to the simulation of smoke, fire, water, bubbles, mixing, phase change and solid-fluid coupling is also included. Adding plausibility to results through particle introduction, turbulence detail and concentration on regions of interest by level set techniques has elevated the degree of accuracy and realism of recent animations. Basic approaches are described here. Techniques to control the simulation to produce a desired visual effect are also discussed. Finally, some references to rendering techniques and haptic applications are mentioned to provide the reader with a complete picture of the challenges of simulating fluids in computer animation.

A Machine Learning Method for the Prediction of Receptor Activation in the Simulation of Synapses

PubMed Central

Montes, Jesus; Gomez, Elena; Merchán-Pérez, Angel; DeFelipe, Javier; Peña, Jose-Maria

2013-01-01

Chemical synaptic transmission involves the release of a neurotransmitter that diffuses in the extracellular space and interacts with specific receptors located on the postsynaptic membrane. Computer simulation approaches provide fundamental tools for exploring various aspects of the synaptic transmission under different conditions. In particular, Monte Carlo methods can track the stochastic movements of neurotransmitter molecules and their interactions with other discrete molecules, the receptors. However, these methods are computationally expensive, even when used with simplified models, preventing their use in large-scale and multi-scale simulations of complex neuronal systems that may involve large numbers of synaptic connections. We have developed a machine-learning based method that can accurately predict relevant aspects of the behavior of synapses, such as the percentage of open synaptic receptors as a function of time since the release of the neurotransmitter, with considerably lower computational cost compared with the conventional Monte Carlo alternative. The method is designed to learn patterns and general principles from a corpus of previously generated Monte Carlo simulations of synapses covering a wide range of structural and functional characteristics. These patterns are later used as a predictive model of the behavior of synapses under different conditions without the need for additional computationally expensive Monte Carlo simulations. This is performed in five stages: data sampling, fold creation, machine learning, validation and curve fitting. The resulting procedure is accurate, automatic, and it is general enough to predict synapse behavior under experimental conditions that are different to the ones it has been trained on. Since our method efficiently reproduces the results that can be obtained with Monte Carlo simulations at a considerably lower computational cost, it is suitable for the simulation of high numbers of synapses and it is therefore an excellent tool for multi-scale simulations. PMID:23894367

[The research on bidirectional reflectance computer simulation of forest canopy at pixel scale].

PubMed

Song, Jin-Ling; Wang, Jin-Di; Shuai, Yan-Min; Xiao, Zhi-Qiang

2009-08-01

Computer simulation is based on computer graphics to generate the realistic 3D structure scene of vegetation, and to simulate the canopy regime using radiosity method. In the present paper, the authors expand the computer simulation model to simulate forest canopy bidirectional reflectance at pixel scale. But usually, the trees are complex structures, which are tall and have many branches. So there is almost a need for hundreds of thousands or even millions of facets to built up the realistic structure scene for the forest It is difficult for the radiosity method to compute so many facets. In order to make the radiosity method to simulate the forest scene at pixel scale, in the authors' research, the authors proposed one idea to simplify the structure of forest crowns, and abstract the crowns to ellipsoids. And based on the optical characteristics of the tree component and the characteristics of the internal energy transmission of photon in real crown, the authors valued the optical characteristics of ellipsoid surface facets. In the computer simulation of the forest, with the idea of geometrical optics model, the gap model is considered to get the forest canopy bidirectional reflectance at pixel scale. Comparing the computer simulation results with the GOMS model, and Multi-angle Imaging SpectroRadiometer (MISR) multi-angle remote sensing data, the simulation results are in agreement with the GOMS simulation result and MISR BRF. But there are also some problems to be solved. So the authors can conclude that the study has important value for the application of multi-angle remote sensing and the inversion of vegetation canopy structure parameters.

NMR diffusion simulation based on conditional random walk.

PubMed

Gudbjartsson, H; Patz, S

1995-01-01

The authors introduce here a new, very fast, simulation method for free diffusion in a linear magnetic field gradient, which is an extension of the conventional Monte Carlo (MC) method or the convolution method described by Wong et al. (in 12th SMRM, New York, 1993, p.10). In earlier NMR-diffusion simulation methods, such as the finite difference method (FD), the Monte Carlo method, and the deterministic convolution method, the outcome of the calculations depends on the simulation time step. In the authors' method, however, the results are independent of the time step, although, in the convolution method the step size has to be adequate for spins to diffuse to adjacent grid points. By always selecting the largest possible time step the computation time can therefore be reduced. Finally the authors point out that in simple geometric configurations their simulation algorithm can be used to reduce computation time in the simulation of restricted diffusion.

Remote control system for high-perfomance computer simulation of crystal growth by the PFC method

NASA Astrophysics Data System (ADS)

Pavlyuk, Evgeny; Starodumov, Ilya; Osipov, Sergei

2017-04-01

Modeling of crystallization process by the phase field crystal method (PFC) - one of the important directions of modern computational materials science. In this paper, the practical side of the computer simulation of the crystallization process by the PFC method is investigated. To solve problems using this method, it is necessary to use high-performance computing clusters, data storage systems and other often expensive complex computer systems. Access to such resources is often limited, unstable and accompanied by various administrative problems. In addition, the variety of software and settings of different computing clusters sometimes does not allow researchers to use unified program code. There is a need to adapt the program code for each configuration of the computer complex. The practical experience of the authors has shown that the creation of a special control system for computing with the possibility of remote use can greatly simplify the implementation of simulations and increase the performance of scientific research. In current paper we show the principal idea of such a system and justify its efficiency.

Tutorial: Parallel Computing of Simulation Models for Risk Analysis.

PubMed

Reilly, Allison C; Staid, Andrea; Gao, Michael; Guikema, Seth D

2016-10-01

Simulation models are widely used in risk analysis to study the effects of uncertainties on outcomes of interest in complex problems. Often, these models are computationally complex and time consuming to run. This latter point may be at odds with time-sensitive evaluations or may limit the number of parameters that are considered. In this article, we give an introductory tutorial focused on parallelizing simulation code to better leverage modern computing hardware, enabling risk analysts to better utilize simulation-based methods for quantifying uncertainty in practice. This article is aimed primarily at risk analysts who use simulation methods but do not yet utilize parallelization to decrease the computational burden of these models. The discussion is focused on conceptual aspects of embarrassingly parallel computer code and software considerations. Two complementary examples are shown using the languages MATLAB and R. A brief discussion of hardware considerations is located in the Appendix. © 2016 Society for Risk Analysis.

Temporal acceleration of spatially distributed kinetic Monte Carlo simulations

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

Chatterjee, Abhijit; Vlachos, Dionisios G.

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

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

PubMed

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

2017-01-08

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

Hierarchical optimization for neutron scattering problems

DOE PAGES

Bao, Feng; Archibald, Rick; Bansal, Dipanshu; ...

2016-03-14

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Hierarchical optimization for neutron scattering problems

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

Bao, Feng; Archibald, Rick; Bansal, Dipanshu

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Particle behavior simulation in thermophoresis phenomena by direct simulation Monte Carlo method

NASA Astrophysics Data System (ADS)

Wada, Takao

2014-07-01

A particle motion considering thermophoretic force is simulated by using direct simulation Monte Carlo (DSMC) method. Thermophoresis phenomena, which occur for a particle size of 1 μm, are treated in this paper. The problem of thermophoresis simulation is computation time which is proportional to the collision frequency. Note that the time step interval becomes much small for the simulation considering the motion of large size particle. Thermophoretic forces calculated by DSMC method were reported, but the particle motion was not computed because of the small time step interval. In this paper, the molecule-particle collision model, which computes the collision between a particle and multi molecules in a collision event, is considered. The momentum transfer to the particle is computed with a collision weight factor, where the collision weight factor means the number of molecules colliding with a particle in a collision event. The large time step interval is adopted by considering the collision weight factor. Furthermore, the large time step interval is about million times longer than the conventional time step interval of the DSMC method when a particle size is 1 μm. Therefore, the computation time becomes about one-millionth. We simulate the graphite particle motion considering thermophoretic force by DSMC-Neutrals (Particle-PLUS neutral module) with above the collision weight factor, where DSMC-Neutrals is commercial software adopting DSMC method. The size and the shape of the particle are 1 μm and a sphere, respectively. The particle-particle collision is ignored. We compute the thermophoretic forces in Ar and H2 gases of a pressure range from 0.1 to 100 mTorr. The results agree well with Gallis' analytical results. Note that Gallis' analytical result for continuum limit is the same as Waldmann's result.

KU-Band rendezvous radar performance computer simulation model

NASA Technical Reports Server (NTRS)

Griffin, J. W.

1980-01-01

The preparation of a real time computer simulation model of the KU band rendezvous radar to be integrated into the shuttle mission simulator (SMS), the shuttle engineering simulator (SES), and the shuttle avionics integration laboratory (SAIL) simulator is described. To meet crew training requirements a radar tracking performance model, and a target modeling method were developed. The parent simulation/radar simulation interface requirements, and the method selected to model target scattering properties, including an application of this method to the SPAS spacecraft are described. The radar search and acquisition mode performance model and the radar track mode signal processor model are examined and analyzed. The angle, angle rate, range, and range rate tracking loops are also discussed.

On the "Exchangeability" of Hands-On and Computer-Simulated Science Performance Assessments. CSE Technical Report.

ERIC Educational Resources Information Center

Rosenquist, Anders; Shavelson, Richard J.; Ruiz-Primo, Maria Araceli

Inconsistencies in scores from computer-simulated and "hands-on" science performance assessments have led to questions about the exchangeability of these two methods in spite of the highly touted potential of computer-simulated performance assessment. This investigation considered possible explanations for students' inconsistent performances: (1)…

Effective description of a 3D object for photon transportation in Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Suganuma, R.; Ogawa, K.

2000-06-01

Photon transport simulation by means of the Monte Carlo method is an indispensable technique for examining scatter and absorption correction methods in SPECT and PET. The authors have developed a method for object description with maximum size regions (maximum rectangular regions: MRRs) to speed up photon transport simulation, and compared the computation time with that for conventional object description methods, a voxel-based (VB) method and an octree method, in the simulations of two kinds of phantoms. The simulation results showed that the computation time with the proposed method became about 50% of that with the VD method and about 70% of that with the octree method for a high resolution MCAT phantom. Here, details of the expansion of the MRR method to three dimensions are given. Moreover, the effectiveness of the proposed method was compared with the VB and octree methods.

Helical gears with circular arc teeth: Generation, geometry, precision and adjustment to errors, computer aided simulation of conditions of meshing and bearing contact

NASA Technical Reports Server (NTRS)

Litvin, Faydor L.; Tsay, Chung-Biau

1987-01-01

The authors have proposed a method for the generation of circular arc helical gears which is based on the application of standard equipment, worked out all aspects of the geometry of the gears, proposed methods for the computer aided simulation of conditions of meshing and bearing contact, investigated the influence of manufacturing and assembly errors, and proposed methods for the adjustment of gears to these errors. The results of computer aided solutions are illustrated with computer graphics.

Computer Laboratory for Multi-scale Simulations of Novel Nanomaterials

DTIC Science & Technology

2014-09-15

schemes for multiscale modeling of polymers. Permselective ion-exchange membranes for protective clothing, fuel cells , and batteries are of special...polyelectrolyte membranes ( PEM ) with chemical warfare agents (CWA) and their simulants and (2) development of new simulation methods and computational...chemical potential using gauge cell method and calculation of density profiles. However, the code does not run in parallel environments. For mesoscale

Interval sampling methods and measurement error: a computer simulation.

PubMed

Wirth, Oliver; Slaven, James; Taylor, Matthew A

2014-01-01

A simulation study was conducted to provide a more thorough account of measurement error associated with interval sampling methods. A computer program simulated the application of momentary time sampling, partial-interval recording, and whole-interval recording methods on target events randomly distributed across an observation period. The simulation yielded measures of error for multiple combinations of observation period, interval duration, event duration, and cumulative event duration. The simulations were conducted up to 100 times to yield measures of error variability. Although the present simulation confirmed some previously reported characteristics of interval sampling methods, it also revealed many new findings that pertain to each method's inherent strengths and weaknesses. The analysis and resulting error tables can help guide the selection of the most appropriate sampling method for observation-based behavioral assessments. © Society for the Experimental Analysis of Behavior.

The Structure and Properties of Silica Glass Nanostructures using Novel Computational Systems

NASA Astrophysics Data System (ADS)

Doblack, Benjamin N.

The structure and properties of silica glass nanostructures are examined using computational methods in this work. Standard synthesis methods of silica and its associated material properties are first discussed in brief. A review of prior experiments on this amorphous material is also presented. Background and methodology for the simulation of mechanical tests on amorphous bulk silica and nanostructures are later presented. A new computational system for the accurate and fast simulation of silica glass is also presented, using an appropriate interatomic potential for this material within the open-source molecular dynamics computer program LAMMPS. This alternative computational method uses modern graphics processors, Nvidia CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model select materials, this enhancement allows the addition of accelerated molecular dynamics simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal of this project is to investigate the structure and size dependent mechanical properties of silica glass nanohelical structures under tensile MD conditions using the innovative computational system. Specifically, silica nanoribbons and nanosprings are evaluated which revealed unique size dependent elastic moduli when compared to the bulk material. For the nanoribbons, the tensile behavior differed widely between the models simulated, with distinct characteristic extended elastic regions. In the case of the nanosprings simulated, more clear trends are observed. In particular, larger nanospring wire cross-sectional radii (r) lead to larger Young's moduli, while larger helical diameters (2R) resulted in smaller Young's moduli. Structural transformations and theoretical models are also analyzed to identify possible factors which might affect the mechanical response of silica nanostructures under tension. The work presented outlines an innovative simulation methodology, and discusses how results can be validated against prior experimental and simulation findings. The ultimate goal is to develop new computational methods for the study of nanostructures which will make the field of materials science more accessible, cost effective and efficient.

Computer simulation of surface and film processes

NASA Technical Reports Server (NTRS)

Tiller, W. A.; Halicioglu, M. T.

1983-01-01

Adequate computer methods, based on interactions between discrete particles, provide information leading to an atomic level understanding of various physical processes. The success of these simulation methods, however, is related to the accuracy of the potential energy function representing the interactions among the particles. The development of a potential energy function for crystalline SiO2 forms that can be employed in lengthy computer modelling procedures was investigated. In many of the simulation methods which deal with discrete particles, semiempirical two body potentials were employed to analyze energy and structure related properties of the system. Many body interactions are required for a proper representation of the total energy for many systems. Many body interactions for simulations based on discrete particles are discussed.

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

PubMed Central

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

2011-01-01

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

A Comparison of Four Simulation and Instructional Methods for Endodontic Review.

ERIC Educational Resources Information Center

Sandoval, Victor A.; And Others

1987-01-01

The effects of four different endodontic self-instructional review formats (slide-tape, latent-image simulation, computer text simulation, and computer-assisted video interactive simulation) on senior clinical endodontic performance are compared. Student evaluations, as well as comparative developmental expenditures, are discussed. (Author/MLW)

Advances in free-energy-based simulations of protein folding and ligand binding.

PubMed

Perez, Alberto; Morrone, Joseph A; Simmerling, Carlos; Dill, Ken A

2016-02-01

Free-energy-based simulations are increasingly providing the narratives about the structures, dynamics and biological mechanisms that constitute the fabric of protein science. Here, we review two recent successes. It is becoming practical: first, to fold small proteins with free-energy methods without knowing substructures and second, to compute ligand-protein binding affinities, not just their binding poses. Over the past 40 years, the timescales that can be simulated by atomistic MD are doubling every 1.3 years--which is faster than Moore's law. Thus, these advances are not simply due to the availability of faster computers. Force fields, solvation models and simulation methodology have kept pace with computing advancements, and are now quite good. At the tip of the spear recently are GPU-based computing, improved fast-solvation methods, continued advances in force fields, and conformational sampling methods that harness external information. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cost efficient CFD simulations: Proper selection of domain partitioning strategies

NASA Astrophysics Data System (ADS)

Haddadi, Bahram; Jordan, Christian; Harasek, Michael

2017-10-01

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

Iterative load-balancing method with multigrid level relaxation for particle simulation with short-range interactions

NASA Astrophysics Data System (ADS)

Furuichi, Mikito; Nishiura, Daisuke

2017-10-01

We developed dynamic load-balancing algorithms for Particle Simulation Methods (PSM) involving short-range interactions, such as Smoothed Particle Hydrodynamics (SPH), Moving Particle Semi-implicit method (MPS), and Discrete Element method (DEM). These are needed to handle billions of particles modeled in large distributed-memory computer systems. Our method utilizes flexible orthogonal domain decomposition, allowing the sub-domain boundaries in the column to be different for each row. The imbalances in the execution time between parallel logical processes are treated as a nonlinear residual. Load-balancing is achieved by minimizing the residual within the framework of an iterative nonlinear solver, combined with a multigrid technique in the local smoother. Our iterative method is suitable for adjusting the sub-domain frequently by monitoring the performance of each computational process because it is computationally cheaper in terms of communication and memory costs than non-iterative methods. Numerical tests demonstrated the ability of our approach to handle workload imbalances arising from a non-uniform particle distribution, differences in particle types, or heterogeneous computer architecture which was difficult with previously proposed methods. We analyzed the parallel efficiency and scalability of our method using Earth simulator and K-computer supercomputer systems.

A method for three-dimensional modeling of wind-shear environments for flight simulator applications

NASA Technical Reports Server (NTRS)

Bray, R. S.

1984-01-01

A computational method for modeling severe wind shears of the type that have been documented during severe convective atmospheric conditions is offered for use in research and training flight simulation. The procedure was developed with the objectives of operational flexibility and minimum computer load. From one to five, simple down burst wind models can be configured and located to produce the wind field desired for specific simulated flight scenarios. A definition of related turbulence parameters is offered as an additional product of the computations. The use of the method to model several documented examples of severe wind shear is demonstrated.

Efficiency analysis of numerical integrations for finite element substructure in real-time hybrid simulation

NASA Astrophysics Data System (ADS)

Wang, Jinting; Lu, Liqiao; Zhu, Fei

2018-01-01

Finite element (FE) is a powerful tool and has been applied by investigators to real-time hybrid simulations (RTHSs). This study focuses on the computational efficiency, including the computational time and accuracy, of numerical integrations in solving FE numerical substructure in RTHSs. First, sparse matrix storage schemes are adopted to decrease the computational time of FE numerical substructure. In this way, the task execution time (TET) decreases such that the scale of the numerical substructure model increases. Subsequently, several commonly used explicit numerical integration algorithms, including the central difference method (CDM), the Newmark explicit method, the Chang method and the Gui-λ method, are comprehensively compared to evaluate their computational time in solving FE numerical substructure. CDM is better than the other explicit integration algorithms when the damping matrix is diagonal, while the Gui-λ (λ = 4) method is advantageous when the damping matrix is non-diagonal. Finally, the effect of time delay on the computational accuracy of RTHSs is investigated by simulating structure-foundation systems. Simulation results show that the influences of time delay on the displacement response become obvious with the mass ratio increasing, and delay compensation methods may reduce the relative error of the displacement peak value to less than 5% even under the large time-step and large time delay.

An Investigation of High-Order Shock-Capturing Methods for Computational Aeroacoustics

NASA Technical Reports Server (NTRS)

Casper, Jay; Baysal, Oktay

1997-01-01

Topics covered include: Low-dispersion scheme for nonlinear acoustic waves in nonuniform flow; Computation of acoustic scattering by a low-dispersion scheme; Algorithmic extension of low-dispersion scheme and modeling effects for acoustic wave simulation; The accuracy of shock capturing in two spatial dimensions; Using high-order methods on lower-order geometries; and Computational considerations for the simulation of discontinuous flows.

Comparison of competing segmentation standards for X-ray computed topographic imaging using Lattice Boltzmann techniques

NASA Astrophysics Data System (ADS)

Larsen, J. D.; Schaap, M. G.

2013-12-01

Recent advances in computing technology and experimental techniques have made it possible to observe and characterize fluid dynamics at the micro-scale. Many computational methods exist that can adequately simulate fluid flow in porous media. Lattice Boltzmann methods provide the distinct advantage of tracking particles at the microscopic level and returning macroscopic observations. While experimental methods can accurately measure macroscopic fluid dynamics, computational efforts can be used to predict and gain insight into fluid dynamics by utilizing thin sections or computed micro-tomography (CMT) images of core sections. Although substantial effort have been made to advance non-invasive imaging methods such as CMT, fluid dynamics simulations, and microscale analysis, a true three dimensional image segmentation technique has not been developed until recently. Many competing segmentation techniques are utilized in industry and research settings with varying results. In this study lattice Boltzmann method is used to simulate stokes flow in a macroporous soil column. Two dimensional CMT images were used to reconstruct a three dimensional representation of the original sample. Six competing segmentation standards were used to binarize the CMT volumes which provide distinction between solid phase and pore space. The permeability of the reconstructed samples was calculated, with Darcy's Law, from lattice Boltzmann simulations of fluid flow in the samples. We compare simulated permeability from differing segmentation algorithms to experimental findings.

Computational Methods Development at Ames

NASA Technical Reports Server (NTRS)

Kwak, Dochan; Smith, Charles A. (Technical Monitor)

1998-01-01

This viewgraph presentation outlines the development at Ames Research Center of advanced computational methods to provide appropriate fidelity computational analysis/design capabilities. Current thrusts of the Ames research include: 1) methods to enhance/accelerate viscous flow simulation procedures, and the development of hybrid/polyhedral-grid procedures for viscous flow; 2) the development of real time transonic flow simulation procedures for a production wind tunnel, and intelligent data management technology; and 3) the validation of methods and the flow physics study gives historical precedents to above research, and speculates on its future course.

A Fast Synthetic Aperture Radar Raw Data Simulation Using Cloud Computing

PubMed Central

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

2017-01-01

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

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running

PubMed Central

Zhu, Hao; Sun, Yan; Rajagopal, Gunaretnam; Mondry, Adrian; Dhar, Pawan

2004-01-01

Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described. PMID:15339335

Using a Computer Simulation To Teach Science Process Skills to College Biology and Elementary Education Majors.

ERIC Educational Resources Information Center

Lee, Aimee T.; Hairston, Rosalina V.; Thames, Rachel; Lawrence, Tonya; Herron, Sherry S.

2002-01-01

Describes the Lateblight computer simulation implemented in the general biology laboratory and science methods course for elementary teachers to reinforce the processes of science and allow students to engage, explore, explain, elaborate, and evaluate the methods of building concepts in science. (Author/KHR)

Quake Final Video

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

None

Critical infrastructures of the world are at constant risks for earthquakes. Most of these critical structures are designed using archaic, seismic, simulation methods that were built from early digital computers from the 1970s. Idaho National Laboratory’s Seismic Research Group are working to modernize the simulation methods through computational research and large-scale laboratory experiments.

Paper simulation techniques in user requirements analysis for interactive computer systems

NASA Technical Reports Server (NTRS)

Ramsey, H. R.; Atwood, M. E.; Willoughby, J. K.

1979-01-01

This paper describes the use of a technique called 'paper simulation' in the analysis of user requirements for interactive computer systems. In a paper simulation, the user solves problems with the aid of a 'computer', as in normal man-in-the-loop simulation. In this procedure, though, the computer does not exist, but is simulated by the experimenters. This allows simulated problem solving early in the design effort, and allows the properties and degree of structure of the system and its dialogue to be varied. The technique, and a method of analyzing the results, are illustrated with examples from a recent paper simulation exercise involving a Space Shuttle flight design task

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures. It is structured to mainly supplement, complement, and whenever possible replace, costly experimental efforts which are unavoidable during engineering research and development programs. Specific objectives include: investigate unique advantages of parallel and multiprocesses for: reformulating/solving structural mechanics and formulating/solving multidisciplinary mechanics and develop integrated structural system computational simulators for: predicting structural performances, evaluating newly developed methods, and for identifying and prioritizing improved/missing methods needed. Herein the CSM program is summarized with emphasis on the Engine Structures Computational Simulator (ESCS). Typical results obtained using ESCS are described to illustrate its versatility.

Understanding Emergency Care Delivery Through Computer Simulation Modeling.

PubMed

Laker, Lauren F; Torabi, Elham; France, Daniel J; Froehle, Craig M; Goldlust, Eric J; Hoot, Nathan R; Kasaie, Parastu; Lyons, Michael S; Barg-Walkow, Laura H; Ward, Michael J; Wears, Robert L

2018-02-01

In 2017, Academic Emergency Medicine convened a consensus conference entitled, "Catalyzing System Change through Health Care Simulation: Systems, Competency, and Outcomes." This article, a product of the breakout session on "understanding complex interactions through systems modeling," explores the role that computer simulation modeling can and should play in research and development of emergency care delivery systems. This article discusses areas central to the use of computer simulation modeling in emergency care research. The four central approaches to computer simulation modeling are described (Monte Carlo simulation, system dynamics modeling, discrete-event simulation, and agent-based simulation), along with problems amenable to their use and relevant examples to emergency care. Also discussed is an introduction to available software modeling platforms and how to explore their use for research, along with a research agenda for computer simulation modeling. Through this article, our goal is to enhance adoption of computer simulation, a set of methods that hold great promise in addressing emergency care organization and design challenges. © 2017 by the Society for Academic Emergency Medicine.

Simulation Insights Using "R"

ERIC Educational Resources Information Center

Kostadinov, Boyan

2013-01-01

This article attempts to introduce the reader to computational thinking and solving problems involving randomness. The main technique being employed is the Monte Carlo method, using the freely available software "R for Statistical Computing." The author illustrates the computer simulation approach by focusing on several problems of…

Methods for simulation-based analysis of fluid-structure interaction.

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

Barone, Matthew Franklin; Payne, Jeffrey L.

2005-10-01

Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonalmore » decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.« less

Multiple shooting shadowing for sensitivity analysis of chaotic dynamical systems

NASA Astrophysics Data System (ADS)

Blonigan, Patrick J.; Wang, Qiqi

2018-02-01

Sensitivity analysis methods are important tools for research and design with simulations. Many important simulations exhibit chaotic dynamics, including scale-resolving turbulent fluid flow simulations. Unfortunately, conventional sensitivity analysis methods are unable to compute useful gradient information for long-time-averaged quantities in chaotic dynamical systems. Sensitivity analysis with least squares shadowing (LSS) can compute useful gradient information for a number of chaotic systems, including simulations of chaotic vortex shedding and homogeneous isotropic turbulence. However, this gradient information comes at a very high computational cost. This paper presents multiple shooting shadowing (MSS), a more computationally efficient shadowing approach than the original LSS approach. Through an analysis of the convergence rate of MSS, it is shown that MSS can have lower memory usage and run time than LSS.

Examining Information Problem-Solving, Knowledge, and Application Gains within Two Instructional Methods: Problem-Based and Computer-Mediated Participatory Simulation

ERIC Educational Resources Information Center

Newell, Terrance S.

2008-01-01

This study compared the effectiveness of two instructional methods--problem-based instruction within a face-to-face context and computer-mediated participatory simulation--in increasing students' content knowledge and application gains in the area of information problem-solving. The instructional methods were implemented over a four-week period. A…

Finite Element Methods for real-time Haptic Feedback of Soft-Tissue Models in Virtual Reality Simulators

NASA Technical Reports Server (NTRS)

Frank, Andreas O.; Twombly, I. Alexander; Barth, Timothy J.; Smith, Jeffrey D.; Dalton, Bonnie P. (Technical Monitor)

2001-01-01

We have applied the linear elastic finite element method to compute haptic force feedback and domain deformations of soft tissue models for use in virtual reality simulators. Our results show that, for virtual object models of high-resolution 3D data (>10,000 nodes), haptic real time computations (>500 Hz) are not currently possible using traditional methods. Current research efforts are focused in the following areas: 1) efficient implementation of fully adaptive multi-resolution methods and 2) multi-resolution methods with specialized basis functions to capture the singularity at the haptic interface (point loading). To achieve real time computations, we propose parallel processing of a Jacobi preconditioned conjugate gradient method applied to a reduced system of equations resulting from surface domain decomposition. This can effectively be achieved using reconfigurable computing systems such as field programmable gate arrays (FPGA), thereby providing a flexible solution that allows for new FPGA implementations as improved algorithms become available. The resulting soft tissue simulation system would meet NASA Virtual Glovebox requirements and, at the same time, provide a generalized simulation engine for any immersive environment application, such as biomedical/surgical procedures or interactive scientific applications.

Computer simulation to predict energy use, greenhouse gas emissions and costs for production of fluid milk using alternative processing methods

USDA-ARS?s Scientific Manuscript database

Computer simulation is a useful tool for benchmarking the electrical and fuel energy consumption and water use in a fluid milk plant. In this study, a computer simulation model of the fluid milk process based on high temperature short time (HTST) pasteurization was extended to include models for pr...

Particle-In-Cell simulations of high pressure plasmas using graphics processing units

NASA Astrophysics Data System (ADS)

Gebhardt, Markus; Atteln, Frank; Brinkmann, Ralf Peter; Mussenbrock, Thomas; Mertmann, Philipp; Awakowicz, Peter

2009-10-01

Particle-In-Cell (PIC) simulations are widely used to understand the fundamental phenomena in low-temperature plasmas. Particularly plasmas at very low gas pressures are studied using PIC methods. The inherent drawback of these methods is that they are very time consuming -- certain stability conditions has to be satisfied. This holds even more for the PIC simulation of high pressure plasmas due to the very high collision rates. The simulations take up to very much time to run on standard computers and require the help of computer clusters or super computers. Recent advances in the field of graphics processing units (GPUs) provides every personal computer with a highly parallel multi processor architecture for very little money. This architecture is freely programmable and can be used to implement a wide class of problems. In this paper we present the concepts of a fully parallel PIC simulation of high pressure plasmas using the benefits of GPU programming.

Programmable Quantum Photonic Processor Using Silicon Photonics

DTIC Science & Technology

2017-04-01

quantum information processing and quantum sensing, ranging from linear optics quantum computing and quantum simulation to quantum ...transformers have driven experimental and theoretical advances in quantum simulation, cluster-state quantum computing , all-optical quantum repeaters...neuromorphic computing , and other applications. In addition, we developed new schemes for ballistic quantum computation , new methods for

Incremental update of electrostatic interactions in adaptively restrained particle simulations.

PubMed

Edorh, Semeho Prince A; Redon, Stéphane

2018-04-06

The computation of long-range potentials is one of the demanding tasks in Molecular Dynamics. During the last decades, an inventive panoply of methods was developed to reduce the CPU time of this task. In this work, we propose a fast method dedicated to the computation of the electrostatic potential in adaptively restrained systems. We exploit the fact that, in such systems, only some particles are allowed to move at each timestep. We developed an incremental algorithm derived from a multigrid-based alternative to traditional Fourier-based methods. Our algorithm was implemented inside LAMMPS, a popular molecular dynamics simulation package. We evaluated the method on different systems. We showed that the new algorithm's computational complexity scales with the number of active particles in the simulated system, and is able to outperform the well-established Particle Particle Particle Mesh (P3M) for adaptively restrained simulations. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

A new unconditionally stable and consistent quasi-analytical in-stream water quality solution scheme for CSTR-based water quality simulators

NASA Astrophysics Data System (ADS)

Woldegiorgis, Befekadu Taddesse; van Griensven, Ann; Pereira, Fernando; Bauwens, Willy

2017-06-01

Most common numerical solutions used in CSTR-based in-stream water quality simulators are susceptible to instabilities and/or solution inconsistencies. Usually, they cope with instability problems by adopting computationally expensive small time steps. However, some simulators use fixed computation time steps and hence do not have the flexibility to do so. This paper presents a novel quasi-analytical solution for CSTR-based water quality simulators of an unsteady system. The robustness of the new method is compared with the commonly used fourth-order Runge-Kutta methods, the Euler method and three versions of the SWAT model (SWAT2012, SWAT-TCEQ, and ESWAT). The performance of each method is tested for different hypothetical experiments. Besides the hypothetical data, a real case study is used for comparison. The growth factors we derived as stability measures for the different methods and the R-factor—considered as a consistency measure—turned out to be very useful for determining the most robust method. The new method outperformed all the numerical methods used in the hypothetical comparisons. The application for the Zenne River (Belgium) shows that the new method provides stable and consistent BOD simulations whereas the SWAT2012 model is shown to be unstable for the standard daily computation time step. The new method unconditionally simulates robust solutions. Therefore, it is a reliable scheme for CSTR-based water quality simulators that use first-order reaction formulations.

Monte Carlo simulation of photon migration in a cloud computing environment with MapReduce

PubMed Central

Pratx, Guillem; Xing, Lei

2011-01-01

Monte Carlo simulation is considered the most reliable method for modeling photon migration in heterogeneous media. However, its widespread use is hindered by the high computational cost. The purpose of this work is to report on our implementation of a simple MapReduce method for performing fault-tolerant Monte Carlo computations in a massively-parallel cloud computing environment. We ported the MC321 Monte Carlo package to Hadoop, an open-source MapReduce framework. In this implementation, Map tasks compute photon histories in parallel while a Reduce task scores photon absorption. The distributed implementation was evaluated on a commercial compute cloud. The simulation time was found to be linearly dependent on the number of photons and inversely proportional to the number of nodes. For a cluster size of 240 nodes, the simulation of 100 billion photon histories took 22 min, a 1258 × speed-up compared to the single-threaded Monte Carlo program. The overall computational throughput was 85,178 photon histories per node per second, with a latency of 100 s. The distributed simulation produced the same output as the original implementation and was resilient to hardware failure: the correctness of the simulation was unaffected by the shutdown of 50% of the nodes. PMID:22191916

High-speed extended-term time-domain simulation for online cascading analysis of power system

NASA Astrophysics Data System (ADS)

Fu, Chuan

A high-speed extended-term (HSET) time domain simulator (TDS), intended to become a part of an energy management system (EMS), has been newly developed for use in online extended-term dynamic cascading analysis of power systems. HSET-TDS includes the following attributes for providing situational awareness of high-consequence events: (i) online analysis, including n-1 and n-k events, (ii) ability to simulate both fast and slow dynamics for 1-3 hours in advance, (iii) inclusion of rigorous protection-system modeling, (iv) intelligence for corrective action ID, storage, and fast retrieval, and (v) high-speed execution. Very fast on-line computational capability is the most desired attribute of this simulator. Based on the process of solving algebraic differential equations describing the dynamics of power system, HSET-TDS seeks to develop computational efficiency at each of the following hierarchical levels, (i) hardware, (ii) strategies, (iii) integration methods, (iv) nonlinear solvers, and (v) linear solver libraries. This thesis first describes the Hammer-Hollingsworth 4 (HH4) implicit integration method. Like the trapezoidal rule, HH4 is symmetrically A-Stable but it possesses greater high-order precision (h4 ) than the trapezoidal rule. Such precision enables larger integration steps and therefore improves simulation efficiency for variable step size implementations. This thesis provides the underlying theory on which we advocate use of HH4 over other numerical integration methods for power system time-domain simulation. Second, motivated by the need to perform high speed extended-term time domain simulation (HSET-TDS) for on-line purposes, this thesis presents principles for designing numerical solvers of differential algebraic systems associated with power system time-domain simulation, including DAE construction strategies (Direct Solution Method), integration methods(HH4), nonlinear solvers(Very Dishonest Newton), and linear solvers(SuperLU). We have implemented a design appropriate for HSET-TDS, and we compare it to various solvers, including the commercial grade PSSE program, with respect to computational efficiency and accuracy, using as examples the New England 39 bus system, the expanded 8775 bus system, and PJM 13029 buses system. Third, we have explored a stiffness-decoupling method, intended to be part of parallel design of time domain simulation software for super computers. The stiffness-decoupling method is able to combine the advantages of implicit methods (A-stability) and explicit method(less computation). With the new stiffness detection method proposed herein, the stiffness can be captured. The expanded 975 buses system is used to test simulation efficiency. Finally, several parallel strategies for super computer deployment to simulate power system dynamics are proposed and compared. Design A partitions the task via scale with the stiffness decoupling method, waveform relaxation, and parallel linear solver. Design B partitions the task via the time axis using a highly precise integration method, the Kuntzmann-Butcher Method - order 8 (KB8). The strategy of partitioning events is designed to partition the whole simulation via the time axis through a simulated sequence of cascading events. For all strategies proposed, a strategy of partitioning cascading events is recommended, since the sub-tasks for each processor are totally independent, and therefore minimum communication time is needed.

A Non-Cut Cell Immersed Boundary Method for Use in Icing Simulations

NASA Technical Reports Server (NTRS)

Sarofeen, Christian M.; Noack, Ralph W.; Kreeger, Richard E.

2013-01-01

This paper describes a computational fluid dynamic method used for modelling changes in aircraft geometry due to icing. While an aircraft undergoes icing, the accumulated ice results in a geometric alteration of the aerodynamic surfaces. In computational simulations for icing, it is necessary that the corresponding geometric change is taken into consideration. The method used, herein, for the representation of the geometric change due to icing is a non-cut cell Immersed Boundary Method (IBM). Computational cells that are in a body fitted grid of a clean aerodynamic geometry that are inside a predicted ice formation are identified. An IBM is then used to change these cells from being active computational cells to having properties of viscous solid bodies. This method has been implemented in the NASA developed node centered, finite volume computational fluid dynamics code, FUN3D. The presented capability is tested for two-dimensional airfoils including a clean airfoil, an iced airfoil, and an airfoil in harmonic pitching motion about its quarter chord. For these simulations velocity contours, pressure distributions, coefficients of lift, coefficients of drag, and coefficients of pitching moment about the airfoil's quarter chord are computed and used for comparison against experimental results, a higher order panel method code with viscous effects, XFOIL, and the results from FUN3D's original solution process. The results of the IBM simulations show that the accuracy of the IBM compares satisfactorily with the experimental results, XFOIL results, and the results from FUN3D's original solution process.

Modeling and simulation of ocean wave propagation using lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Nuraiman, Dian

2017-10-01

In this paper, we present on modeling and simulation of ocean wave propagation from the deep sea to the shoreline. This requires high computational cost for simulation with large domain. We propose to couple a 1D shallow water equations (SWE) model with a 2D incompressible Navier-Stokes equations (NSE) model in order to reduce the computational cost. The coupled model is solved using the lattice Boltzmann method (LBM) with the lattice Bhatnagar-Gross-Krook (BGK) scheme. Additionally, a special method is implemented to treat the complex behavior of free surface close to the shoreline. The result shows the coupled model can reduce computational cost significantly compared to the full NSE model.

Model-free simulations of turbulent reactive flows

NASA Technical Reports Server (NTRS)

Givi, Peyman

1989-01-01

The current computational methods for solving transport equations of turbulent reacting single-phase flows are critically reviewed, with primary attention given to those methods that lead to model-free simulations. In particular, consideration is given to direct numerical simulations using spectral (Galerkin) and pseudospectral (collocation) methods, spectral element methods, and Lagrangian methods. The discussion also covers large eddy simulations and turbulence modeling.

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

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

Pointer, William David

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

A 2.5D Computational Method to Simulate Cylindrical Fluidized Beds

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

Li, Tingwen; Benyahia, Sofiane; Dietiker, Jeff

2015-02-17

In this paper, the limitations of axisymmetric and Cartesian two-dimensional (2D) simulations of cylindrical gas-solid fluidized beds are discussed. A new method has been proposed to carry out pseudo-two-dimensional (2.5D) simulations of a cylindrical fluidized bed by appropriately combining computational domains of Cartesian 2D and axisymmetric simulations. The proposed method was implemented in the open-source code MFIX and applied to the simulation of a lab-scale bubbling fluidized bed with necessary sensitivity study. After a careful grid study to ensure the numerical results are grid independent, detailed comparisons of the flow hydrodynamics were presented against axisymmetric and Cartesian 2D simulations. Furthermore,more » the 2.5D simulation results have been compared to the three-dimensional (3D) simulation for evaluation. This new approach yields better agreement with the 3D simulation results than with axisymmetric and Cartesian 2D simulations.« less

Constraint methods that accelerate free-energy simulations of biomolecules.

PubMed

Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

2015-12-28

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

A Monte Carlo study of Weibull reliability analysis for space shuttle main engine components

NASA Technical Reports Server (NTRS)

Abernethy, K.

1986-01-01

The incorporation of a number of additional capabilities into an existing Weibull analysis computer program and the results of Monte Carlo computer simulation study to evaluate the usefulness of the Weibull methods using samples with a very small number of failures and extensive censoring are discussed. Since the censoring mechanism inherent in the Space Shuttle Main Engine (SSME) data is hard to analyze, it was decided to use a random censoring model, generating censoring times from a uniform probability distribution. Some of the statistical techniques and computer programs that are used in the SSME Weibull analysis are described. The methods documented in were supplemented by adding computer calculations of approximate (using iteractive methods) confidence intervals for several parameters of interest. These calculations are based on a likelihood ratio statistic which is asymptotically a chisquared statistic with one degree of freedom. The assumptions built into the computer simulations are described. The simulation program and the techniques used in it are described there also. Simulation results are tabulated for various combinations of Weibull shape parameters and the numbers of failures in the samples.

Computational simulations of supersonic magnetohydrodynamic flow control, power and propulsion systems

NASA Astrophysics Data System (ADS)

Wan, Tian

This work is motivated by the lack of fully coupled computational tool that solves successfully the turbulent chemically reacting Navier-Stokes equation, the electron energy conservation equation and the electric current Poisson equation. In the present work, the abovementioned equations are solved in a fully coupled manner using fully implicit parallel GMRES methods. The system of Navier-Stokes equations are solved using a GMRES method with combined Schwarz and ILU(0) preconditioners. The electron energy equation and the electric current Poisson equation are solved using a GMRES method with combined SOR and Jacobi preconditioners. The fully coupled method has also been implemented successfully in an unstructured solver, US3D, and convergence test results were presented. This new method is shown two to five times faster than the original DPLR method. The Poisson solver is validated with analytic test problems. Then, four problems are selected; two of them are computed to explore the possibility of onboard MHD control and power generation, and the other two are simulation of experiments. First, the possibility of onboard reentry shock control by a magnetic field is explored. As part of a previous project, MHD power generation onboard a re-entry vehicle is also simulated. Then, the MHD acceleration experiments conducted at NASA Ames research center are simulated. Lastly, the MHD power generation experiments known as the HVEPS project are simulated. For code validation, the scramjet experiments at University of Queensland are simulated first. The generator section of the HVEPS test facility is computed then. The main conclusion is that the computational tool is accurate for different types of problems and flow conditions, and its accuracy and efficiency are necessary when the flow complexity increases.

Computational system identification of continuous-time nonlinear systems using approximate Bayesian computation

NASA Astrophysics Data System (ADS)

Krishnanathan, Kirubhakaran; Anderson, Sean R.; Billings, Stephen A.; Kadirkamanathan, Visakan

2016-11-01

In this paper, we derive a system identification framework for continuous-time nonlinear systems, for the first time using a simulation-focused computational Bayesian approach. Simulation approaches to nonlinear system identification have been shown to outperform regression methods under certain conditions, such as non-persistently exciting inputs and fast-sampling. We use the approximate Bayesian computation (ABC) algorithm to perform simulation-based inference of model parameters. The framework has the following main advantages: (1) parameter distributions are intrinsically generated, giving the user a clear description of uncertainty, (2) the simulation approach avoids the difficult problem of estimating signal derivatives as is common with other continuous-time methods, and (3) as noted above, the simulation approach improves identification under conditions of non-persistently exciting inputs and fast-sampling. Term selection is performed by judging parameter significance using parameter distributions that are intrinsically generated as part of the ABC procedure. The results from a numerical example demonstrate that the method performs well in noisy scenarios, especially in comparison to competing techniques that rely on signal derivative estimation.

Computer simulation of liquid metals

NASA Astrophysics Data System (ADS)

Belashchenko, D. K.

2013-12-01

Methods for and the results of the computer simulation of liquid metals are reviewed. Two basic methods, classical molecular dynamics with known interparticle potentials and the ab initio method, are considered. Most attention is given to the simulated results obtained using the embedded atom model (EAM). The thermodynamic, structural, and diffusion properties of liquid metal models under normal and extreme (shock) pressure conditions are considered. Liquid-metal simulated results for the Groups I - IV elements, a number of transition metals, and some binary systems (Fe - C, Fe - S) are examined. Possibilities for the simulation to account for the thermal contribution of delocalized electrons to energy and pressure are considered. Solidification features of supercooled metals are also discussed.

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

Lai, Jih-Sheng

This paper introduces control system design based softwares, SIMNON and MATLAB/SIMULINK, for power electronics system simulation. A complete power electronics system typically consists of a rectifier bridge along with its smoothing capacitor, an inverter, and a motor. The system components, featuring discrete or continuous, linear or nonlinear, are modeled in mathematical equations. Inverter control methods,such as pulse-width-modulation and hysteresis current control, are expressed in either computer algorithms or digital circuits. After describing component models and control methods, computer programs are then developed for complete systems simulation. Simulation results are mainly used for studying system performances, such as input and outputmore » current harmonics, torque ripples, and speed responses. Key computer programs and simulation results are demonstrated for educational purposes.« less

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

NASA Astrophysics Data System (ADS)

Sartore, Luca; Fabbri, Paolo; Gaetan, Carlo

2016-09-01

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

MUSIDH, multiple use of simulated demographic histories, a novel method to reduce computation time in microsimulation models of infectious diseases.

PubMed

Fischer, E A J; De Vlas, S J; Richardus, J H; Habbema, J D F

2008-09-01

Microsimulation of infectious diseases requires simulation of many life histories of interacting individuals. In particular, relatively rare infections such as leprosy need to be studied in very large populations. Computation time increases disproportionally with the size of the simulated population. We present a novel method, MUSIDH, an acronym for multiple use of simulated demographic histories, to reduce computation time. Demographic history refers to the processes of birth, death and all other demographic events that should be unrelated to the natural course of an infection, thus non-fatal infections. MUSIDH attaches a fixed number of infection histories to each demographic history, and these infection histories interact as if being the infection history of separate individuals. With two examples, mumps and leprosy, we show that the method can give a factor 50 reduction in computation time at the cost of a small loss in precision. The largest reductions are obtained for rare infections with complex demographic histories.

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.

A Novel Method for Characterization of Superconductors: Physical Measurements and Modeling of Thin Films

NASA Technical Reports Server (NTRS)

Kim, B. F.; Moorjani, K.; Phillips, T. E.; Adrian, F. J.; Bohandy, J.; Dolecek, Q. E.

1993-01-01

A method for characterization of granular superconducting thin films has been developed which encompasses both the morphological state of the sample and its fabrication process parameters. The broad scope of this technique is due to the synergism between experimental measurements and their interpretation using numerical simulation. Two novel technologies form the substance of this system: the magnetically modulated resistance method for characterizing superconductors; and a powerful new computer peripheral, the Parallel Information Processor card, which provides enhanced computing capability for PC computers. This enhancement allows PC computers to operate at speeds approaching that of supercomputers. This makes atomic scale simulations possible on low cost machines. The present development of this system involves the integration of these two technologies using mesoscale simulations of thin film growth. A future stage of development will incorporate atomic scale modeling.

Development of an E-Prime Based Computer Simulation of an Interactive Human Rights Violation Negotiation Script (Developpement d’un Programme de Simulation par Ordinateur Fonde sur le Logiciel E Prime pour la Negociation Interactive en cas de Violation des Droits de la Personne)

DTIC Science & Technology

2010-12-01

Base ( CFB ) Kingston. The computer simulation developed in this project is intended to be used for future research and as a possible training platform...DRDC Toronto No. CR 2010-055 Development of an E-Prime based computer simulation of an interactive Human Rights Violation negotiation script...Abstract This report describes the method of developing an E-Prime computer simulation of an interactive Human Rights Violation (HRV) negotiation. An

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

NASA Astrophysics Data System (ADS)

Lejeune, John Van

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

Math modeling and computer mechanization for real time simulation of rotary-wing aircraft

NASA Technical Reports Server (NTRS)

Howe, R. M.

1979-01-01

Mathematical modeling and computer mechanization for real time simulation of rotary wing aircraft is discussed. Error analysis in the digital simulation of dynamic systems, such as rotary wing aircraft is described. The method for digital simulation of nonlinearities with discontinuities, such as exist in typical flight control systems and rotor blade hinges, is discussed.

NASA Workshop on Computational Structural Mechanics 1987, part 2

NASA Technical Reports Server (NTRS)

Sykes, Nancy P. (Editor)

1989-01-01

Advanced methods and testbed/simulator development topics are discussed. Computational Structural Mechanics (CSM) testbed architecture, engine structures simulation, applications to laminate structures, and a generic element processor are among the topics covered.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

Mesoscopic modelling and simulation of soft matter.

PubMed

Schiller, Ulf D; Krüger, Timm; Henrich, Oliver

2017-12-20

The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We review a number of the most popular simulation methods that have emerged, such as Langevin dynamics, dissipative particle dynamics, multi-particle collision dynamics, sometimes also referred to as stochastic rotation dynamics, and the lattice-Boltzmann method. We conclude this review with a short glance at current compute architectures for high-performance computing and community codes for soft matter simulation.

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1988-01-01

The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.

Methods of sound simulation and applications in flight simulators

NASA Technical Reports Server (NTRS)

Gaertner, K. P.

1980-01-01

An overview of methods for electronically synthesizing sounds is presented. A given amount of hardware and computer capacity places an upper limit on the degree and fidelity of realism of sound simulation which is attainable. Good sound realism for aircraft simulators can be especially expensive because of the complexity of flight sounds and their changing patterns through time. Nevertheless, the flight simulator developed at the Research Institute for Human Engineering, West Germany, shows that it is possible to design an inexpensive sound simulator with the required acoustic properties using analog computer elements. The characteristics of the sub-sound elements produced by this sound simulator for take-off, cruise and approach are discussed.

A hybrid FDTD-Rayleigh integral computational method for the simulation of the ultrasound measurement of proximal femur.

PubMed

Cassereau, Didier; Nauleau, Pierre; Bendjoudi, Aniss; Minonzio, Jean-Gabriel; Laugier, Pascal; Bossy, Emmanuel; Grimal, Quentin

2014-07-01

The development of novel quantitative ultrasound (QUS) techniques to measure the hip is critically dependent on the possibility to simulate the ultrasound propagation. One specificity of hip QUS is that ultrasounds propagate through a large thickness of soft tissue, which can be modeled by a homogeneous fluid in a first approach. Finite difference time domain (FDTD) algorithms have been widely used to simulate QUS measurements but they are not adapted to simulate ultrasonic propagation over long distances in homogeneous media. In this paper, an hybrid numerical method is presented to simulate hip QUS measurements. A two-dimensional FDTD simulation in the vicinity of the bone is coupled to the semi-analytic calculation of the Rayleigh integral to compute the wave propagation between the probe and the bone. The method is used to simulate a setup dedicated to the measurement of circumferential guided waves in the cortical compartment of the femoral neck. The proposed approach is validated by comparison with a full FDTD simulation and with an experiment on a bone phantom. For a realistic QUS configuration, the computation time is estimated to be sixty times less with the hybrid method than with a full FDTD approach. Copyright © 2013 Elsevier B.V. All rights reserved.

Research in Distance Education: A System Modeling Approach.

ERIC Educational Resources Information Center

Saba, Farhad; Twitchell, David

1988-01-01

Describes how a computer simulation research method can be used for studying distance education systems. Topics discussed include systems research in distance education; a technique of model development using the System Dynamics approach and DYNAMO simulation language; and a computer simulation of a prototype model. (18 references) (LRW)

TH-E-18A-01: Developments in Monte Carlo Methods for Medical Imaging

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

Badal, A; Zbijewski, W; Bolch, W

Monte Carlo simulation methods are widely used in medical physics research and are starting to be implemented in clinical applications such as radiation therapy planning systems. Monte Carlo simulations offer the capability to accurately estimate quantities of interest that are challenging to measure experimentally while taking into account the realistic anatomy of an individual patient. Traditionally, practical application of Monte Carlo simulation codes in diagnostic imaging was limited by the need for large computational resources or long execution times. However, recent advancements in high-performance computing hardware, combined with a new generation of Monte Carlo simulation algorithms and novel postprocessing methods,more » are allowing for the computation of relevant imaging parameters of interest such as patient organ doses and scatter-to-primaryratios in radiographic projections in just a few seconds using affordable computational resources. Programmable Graphics Processing Units (GPUs), for example, provide a convenient, affordable platform for parallelized Monte Carlo executions that yield simulation times on the order of 10{sup 7} xray/ s. Even with GPU acceleration, however, Monte Carlo simulation times can be prohibitive for routine clinical practice. To reduce simulation times further, variance reduction techniques can be used to alter the probabilistic models underlying the x-ray tracking process, resulting in lower variance in the results without biasing the estimates. Other complementary strategies for further reductions in computation time are denoising of the Monte Carlo estimates and estimating (scoring) the quantity of interest at a sparse set of sampling locations (e.g. at a small number of detector pixels in a scatter simulation) followed by interpolation. Beyond reduction of the computational resources required for performing Monte Carlo simulations in medical imaging, the use of accurate representations of patient anatomy is crucial to the virtual generation of medical images and accurate estimation of radiation dose and other imaging parameters. For this, detailed computational phantoms of the patient anatomy must be utilized and implemented within the radiation transport code. Computational phantoms presently come in one of three format types, and in one of four morphometric categories. Format types include stylized (mathematical equation-based), voxel (segmented CT/MR images), and hybrid (NURBS and polygon mesh surfaces). Morphometric categories include reference (small library of phantoms by age at 50th height/weight percentile), patient-dependent (larger library of phantoms at various combinations of height/weight percentiles), patient-sculpted (phantoms altered to match the patient's unique outer body contour), and finally, patient-specific (an exact representation of the patient with respect to both body contour and internal anatomy). The existence and availability of these phantoms represents a very important advance for the simulation of realistic medical imaging applications using Monte Carlo methods. New Monte Carlo simulation codes need to be thoroughly validated before they can be used to perform novel research. Ideally, the validation process would involve comparison of results with those of an experimental measurement, but accurate replication of experimental conditions can be very challenging. It is very common to validate new Monte Carlo simulations by replicating previously published simulation results of similar experiments. This process, however, is commonly problematic due to the lack of sufficient information in the published reports of previous work so as to be able to replicate the simulation in detail. To aid in this process, the AAPM Task Group 195 prepared a report in which six different imaging research experiments commonly performed using Monte Carlo simulations are described and their results provided. The simulation conditions of all six cases are provided in full detail, with all necessary data on material composition, source, geometry, scoring and other parameters provided. The results of these simulations when performed with the four most common publicly available Monte Carlo packages are also provided in tabular form. The Task Group 195 Report will be useful for researchers needing to validate their Monte Carlo work, and for trainees needing to learn Monte Carlo simulation methods. In this symposium we will review the recent advancements in highperformance computing hardware enabling the reduction in computational resources needed for Monte Carlo simulations in medical imaging. We will review variance reduction techniques commonly applied in Monte Carlo simulations of medical imaging systems and present implementation strategies for efficient combination of these techniques with GPU acceleration. Trade-offs involved in Monte Carlo acceleration by means of denoising and “sparse sampling” will be discussed. A method for rapid scatter correction in cone-beam CT (<5 min/scan) will be presented as an illustration of the simulation speeds achievable with optimized Monte Carlo simulations. We will also discuss the development, availability, and capability of the various combinations of computational phantoms for Monte Carlo simulation of medical imaging systems. Finally, we will review some examples of experimental validation of Monte Carlo simulations and will present the AAPM Task Group 195 Report. Learning Objectives: Describe the advances in hardware available for performing Monte Carlo simulations in high performance computing environments. Explain variance reduction, denoising and sparse sampling techniques available for reduction of computational time needed for Monte Carlo simulations of medical imaging. List and compare the computational anthropomorphic phantoms currently available for more accurate assessment of medical imaging parameters in Monte Carlo simulations. Describe experimental methods used for validation of Monte Carlo simulations in medical imaging. Describe the AAPM Task Group 195 Report and its use for validation and teaching of Monte Carlo simulations in medical imaging.« less

Computer simulation of space charge

NASA Astrophysics Data System (ADS)

Yu, K. W.; Chung, W. K.; Mak, S. S.

1991-05-01

Using the particle-mesh (PM) method, a one-dimensional simulation of the well-known Langmuir-Child's law is performed on an INTEL 80386-based personal computer system. The program is coded in turbo basic (trademark of Borland International, Inc.). The numerical results obtained were in excellent agreement with theoretical predictions and the computational time required is quite modest. This simulation exercise demonstrates that some simple computer simulation using particles may be implemented successfully on PC's that are available today, and hopefully this will provide the necessary incentives for newcomers to the field who wish to acquire a flavor of the elementary aspects of the practice.

Reversible simulation of irreversible computation

NASA Astrophysics Data System (ADS)

Li, Ming; Tromp, John; Vitányi, Paul

1998-09-01

Computer computations are generally irreversible while the laws of physics are reversible. This mismatch is penalized by among other things generating excess thermic entropy in the computation. Computing performance has improved to the extent that efficiency degrades unless all algorithms are executed reversibly, for example by a universal reversible simulation of irreversible computations. All known reversible simulations are either space hungry or time hungry. The leanest method was proposed by Bennett and can be analyzed using a simple ‘reversible’ pebble game. The reachable reversible simulation instantaneous descriptions (pebble configurations) of such pebble games are characterized completely. As a corollary we obtain the reversible simulation by Bennett and, moreover, show that it is a space-optimal pebble game. We also introduce irreversible steps and give a theorem on the tradeoff between the number of allowed irreversible steps and the memory gain in the pebble game. In this resource-bounded setting the limited erasing needs to be performed at precise instants during the simulation. The reversible simulation can be modified so that it is applicable also when the simulated computation time is unknown.

Promoting Systems Thinking through Biology Lessons

NASA Astrophysics Data System (ADS)

Riess, Werner; Mischo, Christoph

2010-04-01

This study's goal was to analyze various teaching approaches within the context of natural science lessons, especially in biology. The main focus of the paper lies on the effectiveness of different teaching methods in promoting systems thinking in the field of Education for Sustainable Development. The following methods were incorporated into the study: special lessons designed to promote systems thinking, a computer-simulated scenario on the topic "ecosystem forest," and a combination of both special lessons and the computer simulation. These groups were then compared to a control group. A questionnaire was used to assess systems thinking skills of 424 sixth-grade students of secondary schools in Germany. The assessment differentiated between a conceptual understanding (measured as achievement score) and a reflexive justification (measured as justification score) of systems thinking. The following control variables were used: logical thinking, grades in school, memory span, and motivational goal orientation. Based on the pretest-posttest control group design, only those students who received both special instruction and worked with the computer simulation showed a significant increase in their achievement scores. The justification score increased in the computer simulation condition as well as in the combination of computer simulation and lesson condition. The possibilities and limits of promoting various forms of systems thinking by using realistic computer simulations are discussed.

Boundary conditions for simulating large SAW devices using ANSYS.

PubMed

Peng, Dasong; Yu, Fengqi; Hu, Jian; Li, Peng

2010-08-01

In this report, we propose improved substrate left and right boundary conditions for simulating SAW devices using ANSYS. Compared with the previous methods, the proposed method can greatly reduce computation time. Furthermore, the longer the distance from the first reflector to the last one, the more computation time can be reduced. To verify the proposed method, a design example is presented with device center frequency 971.14 MHz.

Predicting Flows of Rarefied Gases

NASA Technical Reports Server (NTRS)

LeBeau, Gerald J.; Wilmoth, Richard G.

2005-01-01

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

Massively parallel multicanonical simulations

NASA Astrophysics Data System (ADS)

Gross, Jonathan; Zierenberg, Johannes; Weigel, Martin; Janke, Wolfhard

2018-03-01

Generalized-ensemble Monte Carlo simulations such as the multicanonical method and similar techniques are among the most efficient approaches for simulations of systems undergoing discontinuous phase transitions or with rugged free-energy landscapes. As Markov chain methods, they are inherently serial computationally. It was demonstrated recently, however, that a combination of independent simulations that communicate weight updates at variable intervals allows for the efficient utilization of parallel computational resources for multicanonical simulations. Implementing this approach for the many-thread architecture provided by current generations of graphics processing units (GPUs), we show how it can be efficiently employed with of the order of 104 parallel walkers and beyond, thus constituting a versatile tool for Monte Carlo simulations in the era of massively parallel computing. We provide the fully documented source code for the approach applied to the paradigmatic example of the two-dimensional Ising model as starting point and reference for practitioners in the field.

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

NASA Astrophysics Data System (ADS)

Miao, Linling; Young, Charles D.; Sing, Charles E.

2017-07-01

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.

The Effects of 3D Computer Simulation on Biology Students' Achievement and Memory Retention

ERIC Educational Resources Information Center

Elangovan, Tavasuria; Ismail, Zurida

2014-01-01

A quasi experimental study was conducted for six weeks to determine the effectiveness of two different 3D computer simulation based teaching methods, that is, realistic simulation and non-realistic simulation on Form Four Biology students' achievement and memory retention in Perak, Malaysia. A sample of 136 Form Four Biology students in Perak,…

Remembrance of phases past: An autoregressive method for generating realistic atmospheres in simulations

NASA Astrophysics Data System (ADS)

Srinath, Srikar; Poyneer, Lisa A.; Rudy, Alexander R.; Ammons, S. M.

2014-08-01

The advent of expensive, large-aperture telescopes and complex adaptive optics (AO) systems has strengthened the need for detailed simulation of such systems from the top of the atmosphere to control algorithms. The credibility of any simulation is underpinned by the quality of the atmosphere model used for introducing phase variations into the incident photons. Hitherto, simulations which incorporate wind layers have relied upon phase screen generation methods that tax the computation and memory capacities of the platforms on which they run. This places limits on parameters of a simulation, such as exposure time or resolution, thus compromising its utility. As aperture sizes and fields of view increase the problem will only get worse. We present an autoregressive method for evolving atmospheric phase that is efficient in its use of computation resources and allows for variability in the power contained in frozen flow or stochastic components of the atmosphere. Users have the flexibility of generating atmosphere datacubes in advance of runs where memory constraints allow to save on computation time or of computing the phase at each time step for long exposure times. Preliminary tests of model atmospheres generated using this method show power spectral density and rms phase in accordance with established metrics for Kolmogorov models.

Coarse-grained computation for particle coagulation and sintering processes by linking Quadrature Method of Moments with Monte-Carlo

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

Zou Yu, E-mail: yzou@Princeton.ED; Kavousanakis, Michail E., E-mail: mkavousa@Princeton.ED; Kevrekidis, Ioannis G., E-mail: yannis@Princeton.ED

2010-07-20

The study of particle coagulation and sintering processes is important in a variety of research studies ranging from cell fusion and dust motion to aerosol formation applications. These processes are traditionally simulated using either Monte-Carlo methods or integro-differential equations for particle number density functions. In this paper, we present a computational technique for cases where we believe that accurate closed evolution equations for a finite number of moments of the density function exist in principle, but are not explicitly available. The so-called equation-free computational framework is then employed to numerically obtain the solution of these unavailable closed moment equations bymore » exploiting (through intelligent design of computational experiments) the corresponding fine-scale (here, Monte-Carlo) simulation. We illustrate the use of this method by accelerating the computation of evolving moments of uni- and bivariate particle coagulation and sintering through short simulation bursts of a constant-number Monte-Carlo scheme.« less

Automatic domain updating technique for improving computational efficiency of 2-D flood-inundation simulation

NASA Astrophysics Data System (ADS)

Tanaka, T.; Tachikawa, Y.; Ichikawa, Y.; Yorozu, K.

2017-12-01

Flood is one of the most hazardous disasters and causes serious damage to people and property around the world. To prevent/mitigate flood damage through early warning system and/or river management planning, numerical modelling of flood-inundation processes is essential. In a literature, flood-inundation models have been extensively developed and improved to achieve flood flow simulation with complex topography at high resolution. With increasing demands on flood-inundation modelling, its computational burden is now one of the key issues. Improvements of computational efficiency of full shallow water equations are made from various perspectives such as approximations of the momentum equations, parallelization technique, and coarsening approaches. To support these techniques and more improve the computational efficiency of flood-inundation simulations, this study proposes an Automatic Domain Updating (ADU) method of 2-D flood-inundation simulation. The ADU method traces the wet and dry interface and automatically updates the simulation domain in response to the progress and recession of flood propagation. The updating algorithm is as follow: first, to register the simulation cells potentially flooded at initial stage (such as floodplains nearby river channels), and then if a registered cell is flooded, to register its surrounding cells. The time for this additional process is saved by checking only cells at wet and dry interface. The computation time is reduced by skipping the processing time of non-flooded area. This algorithm is easily applied to any types of 2-D flood inundation models. The proposed ADU method is implemented to 2-D local inertial equations for the Yodo River basin, Japan. Case studies for two flood events show that the simulation is finished within two to 10 times smaller time showing the same result as that without the ADU method.

The Bravyi-Kitaev transformation for quantum computation of electronic structure

NASA Astrophysics Data System (ADS)

Seeley, Jacob T.; Richard, Martin J.; Love, Peter J.

2012-12-01

Quantum simulation is an important application of future quantum computers with applications in quantum chemistry, condensed matter, and beyond. Quantum simulation of fermionic systems presents a specific challenge. The Jordan-Wigner transformation allows for representation of a fermionic operator by O(n) qubit operations. Here, we develop an alternative method of simulating fermions with qubits, first proposed by Bravyi and Kitaev [Ann. Phys. 298, 210 (2002), 10.1006/aphy.2002.6254; e-print arXiv:quant-ph/0003137v2], that reduces the simulation cost to O(log n) qubit operations for one fermionic operation. We apply this new Bravyi-Kitaev transformation to the task of simulating quantum chemical Hamiltonians, and give a detailed example for the simplest possible case of molecular hydrogen in a minimal basis. We show that the quantum circuit for simulating a single Trotter time step of the Bravyi-Kitaev derived Hamiltonian for H2 requires fewer gate applications than the equivalent circuit derived from the Jordan-Wigner transformation. Since the scaling of the Bravyi-Kitaev method is asymptotically better than the Jordan-Wigner method, this result for molecular hydrogen in a minimal basis demonstrates the superior efficiency of the Bravyi-Kitaev method for all quantum computations of electronic structure.

All-Particle Multiscale Computation of Hypersonic Rarefied Flow

NASA Astrophysics Data System (ADS)

Jun, E.; Burt, J. M.; Boyd, I. D.

2011-05-01

This study examines a new hybrid particle scheme used as an alternative means of multiscale flow simulation. The hybrid particle scheme employs the direct simulation Monte Carlo (DSMC) method in rarefied flow regions and the low diffusion (LD) particle method in continuum flow regions. The numerical procedures of the low diffusion particle method are implemented within an existing DSMC algorithm. The performance of the LD-DSMC approach is assessed by studying Mach 10 nitrogen flow over a sphere with a global Knudsen number of 0.002. The hybrid scheme results show good overall agreement with results from standard DSMC and CFD computation. Subcell procedures are utilized to improve computational efficiency and reduce sensitivity to DSMC cell size in the hybrid scheme. This makes it possible to perform the LD-DSMC simulation on a much coarser mesh that leads to a significant reduction in computation time.

Simulating Quantile Models with Applications to Economics and Management

NASA Astrophysics Data System (ADS)

Machado, José A. F.

2010-05-01

The massive increase in the speed of computers over the past forty years changed the way that social scientists, applied economists and statisticians approach their trades and also the very nature of the problems that they could feasibly tackle. The new methods that use intensively computer power go by the names of "computer-intensive" or "simulation". My lecture will start with bird's eye view of the uses of simulation in Economics and Statistics. Then I will turn out to my own research on uses of computer- intensive methods. From a methodological point of view the question I address is how to infer marginal distributions having estimated a conditional quantile process, (Counterfactual Decomposition of Changes in Wage Distributions using Quantile Regression," Journal of Applied Econometrics 20, 2005). Illustrations will be provided of the use of the method to perform counterfactual analysis in several different areas of knowledge.

Computation of the sound generated by isotropic turbulence

NASA Technical Reports Server (NTRS)

Sarkar, S.; Hussaini, M. Y.

1993-01-01

The acoustic radiation from isotropic turbulence is computed numerically. A hybrid direct numerical simulation approach which combines direct numerical simulation (DNS) of the turbulent flow with the Lighthill acoustic analogy is utilized. It is demonstrated that the hybrid DNS method is a feasible approach to the computation of sound generated by turbulent flows. The acoustic efficiency in the simulation of isotropic turbulence appears to be substantially less than that in subsonic jet experiments. The dominant frequency of the computed acoustic pressure is found to be somewhat larger than the dominant frequency of the energy-containing scales of motion. The acoustic power in the simulations is proportional to epsilon (M(sub t))(exp 5) where epsilon is the turbulent dissipation rate and M(sub t) is the turbulent Mach number. This is in agreement with the analytical result of Proudman (1952), but the constant of proportionality is smaller than the analytical result. Two different methods of computing the acoustic power from the DNS data bases yielded consistent results.

Method for Identification of Results of Dynamic Overloads in Assessment of Safety Use of the Mine Auxiliary Transportation System

NASA Astrophysics Data System (ADS)

Tokarczyk, Jarosław

2016-12-01

Method for identification the effects of dynamic overload affecting the people, which may occur in the emergency state of suspended monorail is presented in the paper. The braking curve using MBS (Multi-Body System) simulation was determined. For this purpose a computational model (MBS) of suspended monorail was developed and two different variants of numerical calculations were carried out. An algorithm of conducting numerical simulations to assess the effects of dynamic overload acting on the suspended monorails' users is also posted in the paper. An example of computational model FEM (Finite Element Method) composed of technical mean and the anthropometrical model ATB (Articulated Total Body) is shown. The simulation results are presented: graph of HIC (Head Injury Criterion) parameter and successive phases of dislocation of ATB model. Generator of computational models for safety criterion, which enables preparation of input data and remote starting the simulation, is proposed.

Computational methods for coupling microstructural and micromechanical materials response simulations

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

HOLM,ELIZABETH A.; BATTAILE,CORBETT C.; BUCHHEIT,THOMAS E.

2000-04-01

Computational materials simulations have traditionally focused on individual phenomena: grain growth, crack propagation, plastic flow, etc. However, real materials behavior results from a complex interplay between phenomena. In this project, the authors explored methods for coupling mesoscale simulations of microstructural evolution and micromechanical response. In one case, massively parallel (MP) simulations for grain evolution and microcracking in alumina stronglink materials were dynamically coupled. In the other, codes for domain coarsening and plastic deformation in CuSi braze alloys were iteratively linked. this program provided the first comparison of two promising ways to integrate mesoscale computer codes. Coupled microstructural/micromechanical codes were appliedmore » to experimentally observed microstructures for the first time. In addition to the coupled codes, this project developed a suite of new computational capabilities (PARGRAIN, GLAD, OOF, MPM, polycrystal plasticity, front tracking). The problem of plasticity length scale in continuum calculations was recognized and a solution strategy was developed. The simulations were experimentally validated on stockpile materials.« less

A hybrid method for the computation of quasi-3D seismograms.

NASA Astrophysics Data System (ADS)

Masson, Yder; Romanowicz, Barbara

2013-04-01

The development of powerful computer clusters and efficient numerical computation methods, such as the Spectral Element Method (SEM) made possible the computation of seismic wave propagation in a heterogeneous 3D earth. However, the cost of theses computations is still problematic for global scale tomography that requires hundreds of such simulations. Part of the ongoing research effort is dedicated to the development of faster modeling methods based on the spectral element method. Capdeville et al. (2002) proposed to couple SEM simulations with normal modes calculation (C-SEM). Nissen-Meyer et al. (2007) used 2D SEM simulations to compute 3D seismograms in a 1D earth model. Thanks to these developments, and for the first time, Lekic et al. (2011) developed a 3D global model of the upper mantle using SEM simulations. At the local and continental scale, adjoint tomography that is using a lot of SEM simulation can be implemented on current computers (Tape, Liu et al. 2009). Due to their smaller size, these models offer higher resolution. They provide us with images of the crust and the upper part of the mantle. In an attempt to teleport such local adjoint tomographic inversions into the deep earth, we are developing a hybrid method where SEM computation are limited to a region of interest within the earth. That region can have an arbitrary shape and size. Outside this region, the seismic wavefield is extrapolated to obtain synthetic data at the Earth's surface. A key feature of the method is the use of a time reversal mirror to inject the wavefield induced by distant seismic source into the region of interest (Robertsson and Chapman 2000). We compute synthetic seismograms as follow: Inside the region of interest, we are using regional spectral element software RegSEM to compute wave propagation in 3D. Outside this region, the wavefield is extrapolated to the surface by convolution with the Green's functions from the mirror to the seismic stations. For now, these Green's functions are computed using 2D SEM simulation in a 1D Earth model. Such seismograms account for the 3D structure inside the region of interest in a quasi-exact manner. Later we plan to extrapolate the misfit function computed from such seismograms at the stations back into the SEM region in order to compute local adjoint kernels. This opens a new path toward regional adjoint tomography into the deep Earth. Capdeville, Y., et al. (2002). "Coupling the spectral element method with a modal solution for elastic wave propagation in global Earth models." Geophysical Journal International 152(1): 34-67. Lekic, V. and B. Romanowicz (2011). "Inferring upper-mantle structure by full waveform tomography with the spectral element method." Geophysical Journal International 185(2): 799-831. Nissen-Meyer, T., et al. (2007). "A two-dimensional spectral-element method for computing spherical-earth seismograms-I. Moment-tensor source." Geophysical Journal International 168(3): 1067-1092. Robertsson, J. O. A. and C. H. Chapman (2000). "An efficient method for calculating finite-difference seismograms after model alterations." Geophysics 65(3): 907-918. Tape, C., et al. (2009). "Adjoint tomography of the southern California crust." Science 325(5943): 988-992.

MINIVER: Miniature version of real/ideal gas aero-heating and ablation computer program

NASA Technical Reports Server (NTRS)

Hendler, D. R.

1976-01-01

Computer code is used to determine heat transfer multiplication factors, special flow field simulation techniques, different heat transfer methods, different transition criteria, crossflow simulation, and more efficient thin skin thickness optimization procedure.

Computational simulation of composite structures with and without damage. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Wilt, Thomas F.

1994-01-01

A methodology is described which uses finite element analysis of various laminates to computationally simulate the effects of delamination damage initiation and growth on the structural behavior of laminated composite structures. The delamination area is expanded according to a set pattern. As the delamination area increases, how the structural response of the laminate changes with respect to buckling and strain energy release rate are investigated. Rules are presented for laminates of different configurations, materials and thickness. These results demonstrate that computational simulation methods can provide alternate methods to investigate the complex delamination damage mechanisms found in composite structures.

Prototype of a computer method for designing and analyzing heating, ventilating and air conditioning proportional, electronic control systems

NASA Astrophysics Data System (ADS)

Barlow, Steven J.

1986-09-01

The Air Force needs a better method of designing new and retrofit heating, ventilating and air conditioning (HVAC) control systems. Air Force engineers currently use manual design/predict/verify procedures taught at the Air Force Institute of Technology, School of Civil Engineering, HVAC Control Systems course. These existing manual procedures are iterative and time-consuming. The objectives of this research were to: (1) Locate and, if necessary, modify an existing computer-based method for designing and analyzing HVAC control systems that is compatible with the HVAC Control Systems manual procedures, or (2) Develop a new computer-based method of designing and analyzing HVAC control systems that is compatible with the existing manual procedures. Five existing computer packages were investigated in accordance with the first objective: MODSIM (for modular simulation), HVACSIM (for HVAC simulation), TRNSYS (for transient system simulation), BLAST (for building load and system thermodynamics) and Elite Building Energy Analysis Program. None were found to be compatible or adaptable to the existing manual procedures, and consequently, a prototype of a new computer method was developed in accordance with the second research objective.

A Kernel-Free Particle-Finite Element Method for Hypervelocity Impact Simulation. Chapter 4

NASA Technical Reports Server (NTRS)

Park, Young-Keun; Fahrenthold, Eric P.

2004-01-01

An improved hybrid particle-finite element method has been developed for the simulation of hypervelocity impact problems. Unlike alternative methods, the revised formulation computes the density without reference to any kernel or interpolation functions, for either the density or the rate of dilatation. This simplifies the state space model and leads to a significant reduction in computational cost. The improved method introduces internal energy variables as generalized coordinates in a new formulation of the thermomechanical Lagrange equations. Example problems show good agreement with exact solutions in one dimension and good agreement with experimental data in a three dimensional simulation.

Finite-Element Methods for Real-Time Simulation of Surgery

NASA Technical Reports Server (NTRS)

Basdogan, Cagatay

2003-01-01

Two finite-element methods have been developed for mathematical modeling of the time-dependent behaviors of deformable objects and, more specifically, the mechanical responses of soft tissues and organs in contact with surgical tools. These methods may afford the computational efficiency needed to satisfy the requirement to obtain computational results in real time for simulating surgical procedures as described in Simulation System for Training in Laparoscopic Surgery (NPO-21192) on page 31 in this issue of NASA Tech Briefs. Simulation of the behavior of soft tissue in real time is a challenging problem because of the complexity of soft-tissue mechanics. The responses of soft tissues are characterized by nonlinearities and by spatial inhomogeneities and rate and time dependences of material properties. Finite-element methods seem promising for integrating these characteristics of tissues into computational models of organs, but they demand much central-processing-unit (CPU) time and memory, and the demand increases with the number of nodes and degrees of freedom in a given finite-element model. Hence, as finite-element models become more realistic, it becomes more difficult to compute solutions in real time. In both of the present methods, one uses approximate mathematical models trading some accuracy for computational efficiency and thereby increasing the feasibility of attaining real-time up36 NASA Tech Briefs, October 2003 date rates. The first of these methods is based on modal analysis. In this method, one reduces the number of differential equations by selecting only the most significant vibration modes of an object (typically, a suitable number of the lowest-frequency modes) for computing deformations of the object in response to applied forces.

Gaming via Computer Simulation Techniques for Junior College Economics Education. Final Report.

ERIC Educational Resources Information Center

Thompson, Fred A.

A study designed to answer the need for more attractive and effective economics education involved the teaching of one junior college economics class by the conventional (lecture) method and an experimental class by computer simulation techniques. Econometric models approximating the "real world" were computer programed to enable the experimental…

Evaluation of a Computer Simulation in a Therapeutics Case Discussion.

ERIC Educational Resources Information Center

Kinkade, Raenel E.; And Others

1995-01-01

A computer program was used to simulate a case presentation in pharmacotherapeutics. Students (n=24) used their knowledge of the disease (glaucoma) and various topical agents on the computer program's formulary to "treat" the patient. Comparison of results with a control group found the method as effective as traditional case…

A class of hybrid finite element methods for electromagnetics: A review

NASA Technical Reports Server (NTRS)

Volakis, J. L.; Chatterjee, A.; Gong, J.

1993-01-01

Integral equation methods have generally been the workhorse for antenna and scattering computations. In the case of antennas, they continue to be the prominent computational approach, but for scattering applications the requirement for large-scale computations has turned researchers' attention to near neighbor methods such as the finite element method, which has low O(N) storage requirements and is readily adaptable in modeling complex geometrical features and material inhomogeneities. In this paper, we review three hybrid finite element methods for simulating composite scatterers, conformal microstrip antennas, and finite periodic arrays. Specifically, we discuss the finite element method and its application to electromagnetic problems when combined with the boundary integral, absorbing boundary conditions, and artificial absorbers for terminating the mesh. Particular attention is given to large-scale simulations, methods, and solvers for achieving low memory requirements and code performance on parallel computing architectures.

Computational Modeling and Numerical Methods for Spatiotemporal Calcium Cycling in Ventricular Myocytes

PubMed Central

Nivala, Michael; de Lange, Enno; Rovetti, Robert; Qu, Zhilin

2012-01-01

Intracellular calcium (Ca) cycling dynamics in cardiac myocytes is regulated by a complex network of spatially distributed organelles, such as sarcoplasmic reticulum (SR), mitochondria, and myofibrils. In this study, we present a mathematical model of intracellular Ca cycling and numerical and computational methods for computer simulations. The model consists of a coupled Ca release unit (CRU) network, which includes a SR domain and a myoplasm domain. Each CRU contains 10 L-type Ca channels and 100 ryanodine receptor channels, with individual channels simulated stochastically using a variant of Gillespie’s method, modified here to handle time-dependent transition rates. Both the SR domain and the myoplasm domain in each CRU are modeled by 5 × 5 × 5 voxels to maintain proper Ca diffusion. Advanced numerical algorithms implemented on graphical processing units were used for fast computational simulations. For a myocyte containing 100 × 20 × 10 CRUs, a 1-s heart time simulation takes about 10 min of machine time on a single NVIDIA Tesla C2050. Examples of simulated Ca cycling dynamics, such as Ca sparks, Ca waves, and Ca alternans, are shown. PMID:22586402

A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE

NASA Astrophysics Data System (ADS)

Fukushige, Toshiyuki; Taiji, Makoto; Makino, Junichiro; Ebisuzaki, Toshikazu; Sugimoto, Daiichiro

1996-09-01

We have developed a parallel, pipelined special-purpose computer for N-body simulations, MD-GRAPE (for "GRAvity PipE"). In gravitational N- body simulations, almost all computing time is spent on the calculation of interactions between particles. GRAPE is specialized hardware to calculate these interactions. It is used with a general-purpose front-end computer that performs all calculations other than the force calculation. MD-GRAPE is the first parallel GRAPE that can calculate an arbitrary central force. A force different from a pure 1/r potential is necessary for N-body simulations with periodic boundary conditions using the Ewald or particle-particle/particle-mesh (P^3^M) method. MD-GRAPE accelerates the calculation of particle-particle force for these algorithms. An MD- GRAPE board has four MD chips and its peak performance is 4.2 GFLOPS. On an MD-GRAPE board, a cosmological N-body simulation takes 6O0(N/10^6^)^3/2^ s per step for the Ewald method, where N is the number of particles, and would take 24O(N/10^6^) s per step for the P^3^M method, in a uniform distribution of particles.

Computer simulation of on-orbit manned maneuvering unit operations

NASA Technical Reports Server (NTRS)

Stuart, G. M.; Garcia, K. D.

1986-01-01

Simulation of spacecraft on-orbit operations is discussed in reference to Martin Marietta's Space Operations Simulation laboratory's use of computer software models to drive a six-degree-of-freedom moving base carriage and two target gimbal systems. In particular, key simulation issues and related computer software models associated with providing real-time, man-in-the-loop simulations of the Manned Maneuvering Unit (MMU) are addressed with special attention given to how effectively these models and motion systems simulate the MMU's actual on-orbit operations. The weightless effects of the space environment require the development of entirely new devices for locomotion. Since the access to space is very limited, it is necessary to design, build, and test these new devices within the physical constraints of earth using simulators. The simulation method that is discussed here is the technique of using computer software models to drive a Moving Base Carriage (MBC) that is capable of providing simultaneous six-degree-of-freedom motions. This method, utilized at Martin Marietta's Space Operations Simulation (SOS) laboratory, provides the ability to simulate the operation of manned spacecraft, provides the pilot with proper three-dimensional visual cues, and allows training of on-orbit operations. The purpose here is to discuss significant MMU simulation issues, the related models that were developed in response to these issues and how effectively these models simulate the MMU's actual on-orbiter operations.

A Parallel Sliding Region Algorithm to Make Agent-Based Modeling Possible for a Large-Scale Simulation: Modeling Hepatitis C Epidemics in Canada.

PubMed

Wong, William W L; Feng, Zeny Z; Thein, Hla-Hla

2016-11-01

Agent-based models (ABMs) are computer simulation models that define interactions among agents and simulate emergent behaviors that arise from the ensemble of local decisions. ABMs have been increasingly used to examine trends in infectious disease epidemiology. However, the main limitation of ABMs is the high computational cost for a large-scale simulation. To improve the computational efficiency for large-scale ABM simulations, we built a parallelizable sliding region algorithm (SRA) for ABM and compared it to a nonparallelizable ABM. We developed a complex agent network and performed two simulations to model hepatitis C epidemics based on the real demographic data from Saskatchewan, Canada. The first simulation used the SRA that processed on each postal code subregion subsequently. The second simulation processed the entire population simultaneously. It was concluded that the parallelizable SRA showed computational time saving with comparable results in a province-wide simulation. Using the same method, SRA can be generalized for performing a country-wide simulation. Thus, this parallel algorithm enables the possibility of using ABM for large-scale simulation with limited computational resources.

An Educational MONTE CARLO Simulation/Animation Program for the Cosmic Rays Muons and a Prototype Computer-Driven Hardware Display.

ERIC Educational Resources Information Center

Kalkanis, G.; Sarris, M. M.

1999-01-01

Describes an educational software program for the study of and detection methods for the cosmic ray muons passing through several light transparent materials (i.e., water, air, etc.). Simulates muons and Cherenkov photons' paths and interactions and visualizes/animates them on the computer screen using Monte Carlo methods/techniques which employ…

Computer technique for simulating the combustion of cellulose and other fuels

Treesearch

Andrew M. Stein; Brian W. Bauske

1971-01-01

A computer method has been developed for simulating the combustion of wood and other cellulosic fuels. The products of combustion are used as input for a convection model that slimulates real fires. The method allows the chemical process to proceed to equilibrium and then examines the effects of mass addition and repartitioning on the fluid mechanics of the convection...

Plans for wind energy system simulation

NASA Technical Reports Server (NTRS)

Dreier, M. E.

1978-01-01

A digital computer code and a special purpose hybrid computer, were introduced. The digital computer program, the Root Perturbation Method or RPM, is an implementation of the classic floquet procedure which circumvents numerical problems associated with the extraction of Floquet roots. The hybrid computer, the Wind Energy System Time domain simulator (WEST), yields real time loads and deformation information essential to design and system stability investigations.

Parallel discrete-event simulation of FCFS stochastic queueing networks

NASA Technical Reports Server (NTRS)

Nicol, David M.

1988-01-01

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

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Zonal methods for the parallel execution of range-limited N-body simulations

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

Bowers, Kevin J.; Dror, Ron O.; Shaw, David E.

2007-01-20

Particle simulations in fields ranging from biochemistry to astrophysics require the evaluation of interactions between all pairs of particles separated by less than some fixed interaction radius. The applicability of such simulations is often limited by the time required for calculation, but the use of massive parallelism to accelerate these computations is typically limited by inter-processor communication requirements. Recently, Snir [M. Snir, A note on N-body computations with cutoffs, Theor. Comput. Syst. 37 (2004) 295-318] and Shaw [D.E. Shaw, A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions, J. Comput. Chem. 26 (2005) 1318-1328] independently introducedmore » two distinct methods that offer asymptotic reductions in the amount of data transferred between processors. In the present paper, we show that these schemes represent special cases of a more general class of methods, and introduce several new algorithms in this class that offer practical advantages over all previously described methods for a wide range of problem parameters. We also show that several of these algorithms approach an approximate lower bound on inter-processor data transfer.« less

Higher-order methods for simulations on quantum computers

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

Sornborger, A.T.; Stewart, E.D.

1999-09-01

To implement many-qubit gates for use in quantum simulations on quantum computers efficiently, we develop and present methods reexpressing exp[[minus]i(H[sub 1]+H[sub 2]+[center dot][center dot][center dot])[Delta]t] as a product of factors exp[[minus]iH[sub 1][Delta]t], exp[[minus]iH[sub 2][Delta]t],[hor ellipsis], which is accurate to third or fourth order in [Delta]t. The methods we derive are an extended form of the symplectic method, and can also be used for an integration of classical Hamiltonians on classical computers. We derive both integral and irrational methods, and find the most efficient methods in both cases. [copyright] [ital 1999] [ital The American Physical Society

Physician Utilization of a Hospital Information System: A Computer Simulation Model

PubMed Central

Anderson, James G.; Jay, Stephen J.; Clevenger, Stephen J.; Kassing, David R.; Perry, Jane; Anderson, Marilyn M.

1988-01-01

The purpose of this research was to develop a computer simulation model that represents the process through which physicians enter orders into a hospital information system (HIS). Computer simulation experiments were performed to estimate the effects of two methods of order entry on outcome variables. The results of the computer simulation experiments were used to perform a cost-benefit analysis to compare the two different means of entering medical orders into the HIS. The results indicate that the use of personal order sets to enter orders into the HIS will result in a significant reduction in manpower, salaries and fringe benefits, and errors in order entry.

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

PubMed

Schwenke, Michael; Georgii, Joachim; Preusser, Tobias

2017-07-01

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

Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions.

PubMed

Salis, Howard; Kaznessis, Yiannis

2005-02-01

The dynamical solution of a well-mixed, nonlinear stochastic chemical kinetic system, described by the Master equation, may be exactly computed using the stochastic simulation algorithm. However, because the computational cost scales with the number of reaction occurrences, systems with one or more "fast" reactions become costly to simulate. This paper describes a hybrid stochastic method that partitions the system into subsets of fast and slow reactions, approximates the fast reactions as a continuous Markov process, using a chemical Langevin equation, and accurately describes the slow dynamics using the integral form of the "Next Reaction" variant of the stochastic simulation algorithm. The key innovation of this method is its mechanism of efficiently monitoring the occurrences of slow, discrete events while simultaneously simulating the dynamics of a continuous, stochastic or deterministic process. In addition, by introducing an approximation in which multiple slow reactions may occur within a time step of the numerical integration of the chemical Langevin equation, the hybrid stochastic method performs much faster with only a marginal decrease in accuracy. Multiple examples, including a biological pulse generator and a large-scale system benchmark, are simulated using the exact and proposed hybrid methods as well as, for comparison, a previous hybrid stochastic method. Probability distributions of the solutions are compared and the weak errors of the first two moments are computed. In general, these hybrid methods may be applied to the simulation of the dynamics of a system described by stochastic differential, ordinary differential, and Master equations.

Proceedings of the 14th International Conference on the Numerical Simulation of Plasmas

NASA Astrophysics Data System (ADS)

Partial Contents are as follows: Numerical Simulations of the Vlasov-Maxwell Equations by Coupled Particle-Finite Element Methods on Unstructured Meshes; Electromagnetic PIC Simulations Using Finite Elements on Unstructured Grids; Modelling Travelling Wave Output Structures with the Particle-in-Cell Code CONDOR; SST--A Single-Slice Particle Simulation Code; Graphical Display and Animation of Data Produced by Electromagnetic, Particle-in-Cell Codes; A Post-Processor for the PEST Code; Gray Scale Rendering of Beam Profile Data; A 2D Electromagnetic PIC Code for Distributed Memory Parallel Computers; 3-D Electromagnetic PIC Simulation on the NRL Connection Machine; Plasma PIC Simulations on MIMD Computers; Vlasov-Maxwell Algorithm for Electromagnetic Plasma Simulation on Distributed Architectures; MHD Boundary Layer Calculation Using the Vortex Method; and Eulerian Codes for Plasma Simulations.

Numerical Simulation of Rolling-Airframes Using a Multi-Level Cartesian Method

NASA Technical Reports Server (NTRS)

Murman, Scott M.; Aftosmis, Michael J.; Berger, Marsha J.; Kwak, Dochan (Technical Monitor)

2002-01-01

A supersonic rolling missile with two synchronous canard control surfaces is analyzed using an automated, inviscid, Cartesian method. Sequential-static and time-dependent dynamic simulations of the complete motion are computed for canard dither schedules for level flight, pitch, and yaw maneuver. The dynamic simulations are compared directly against both high-resolution viscous simulations and relevant experimental data, and are also utilized to compute dynamic stability derivatives. The results show that both the body roll rate and canard dither motion influence the roll-averaged forces and moments on the body. At the relatively, low roll rates analyzed in the current work these dynamic effects are modest, however the dynamic computations are effective in predicting the dynamic stability derivatives which can be significant for highly-maneuverable missiles.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

THC-MP: High performance numerical simulation of reactive transport and multiphase flow in porous media

NASA Astrophysics Data System (ADS)

Wei, Xiaohui; Li, Weishan; Tian, Hailong; Li, Hongliang; Xu, Haixiao; Xu, Tianfu

2015-07-01

The numerical simulation of multiphase flow and reactive transport in the porous media on complex subsurface problem is a computationally intensive application. To meet the increasingly computational requirements, this paper presents a parallel computing method and architecture. Derived from TOUGHREACT that is a well-established code for simulating subsurface multi-phase flow and reactive transport problems, we developed a high performance computing THC-MP based on massive parallel computer, which extends greatly on the computational capability for the original code. The domain decomposition method was applied to the coupled numerical computing procedure in the THC-MP. We designed the distributed data structure, implemented the data initialization and exchange between the computing nodes and the core solving module using the hybrid parallel iterative and direct solver. Numerical accuracy of the THC-MP was verified through a CO2 injection-induced reactive transport problem by comparing the results obtained from the parallel computing and sequential computing (original code). Execution efficiency and code scalability were examined through field scale carbon sequestration applications on the multicore cluster. The results demonstrate successfully the enhanced performance using the THC-MP on parallel computing facilities.

Computational plasticity algorithm for particle dynamics simulations

NASA Astrophysics Data System (ADS)

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

2018-01-01

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.

Comparison of Different Methods of Grading a Level Turn Task on a Flight Simulator

NASA Technical Reports Server (NTRS)

Heath, Bruce E.; Crier, tomyka

2003-01-01

With the advancements in the computing power of personal computers, pc-based flight simulators and trainers have opened new avenues in the training of airplane pilots. It may be desirable to have the flight simulator make a quantitative evaluation of the progress of a pilot's training thereby reducing the physical requirement of the flight instructor who must, in turn, watch every flight. In an experiment, University students conducted six different flights, each consisting of two level turns. The flights were three minutes in duration. By evaluating videotapes, two certified flight instructors provided separate letter grades for each turn. These level turns were also evaluated using two other computer based grading methods. One method determined automated grades based on prescribed tolerances in bank angle, airspeed and altitude. The other method used was deviations in altitude and bank angle for performance index and performance grades.

Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

PubMed

Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

2018-04-05

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

Predictive wind turbine simulation with an adaptive lattice Boltzmann method for moving boundaries

NASA Astrophysics Data System (ADS)

Deiterding, Ralf; Wood, Stephen L.

2016-09-01

Operating horizontal axis wind turbines create large-scale turbulent wake structures that affect the power output of downwind turbines considerably. The computational prediction of this phenomenon is challenging as efficient low dissipation schemes are necessary that represent the vorticity production by the moving structures accurately and that are able to transport wakes without significant artificial decay over distances of several rotor diameters. We have developed a parallel adaptive lattice Boltzmann method for large eddy simulation of turbulent weakly compressible flows with embedded moving structures that considers these requirements rather naturally and enables first principle simulations of wake-turbine interaction phenomena at reasonable computational costs. The paper describes the employed computational techniques and presents validation simulations for the Mexnext benchmark experiments as well as simulations of the wake propagation in the Scaled Wind Farm Technology (SWIFT) array consisting of three Vestas V27 turbines in triangular arrangement.

Multiple point statistical simulation using uncertain (soft) conditional data

NASA Astrophysics Data System (ADS)

Hansen, Thomas Mejer; Vu, Le Thanh; Mosegaard, Klaus; Cordua, Knud Skou

2018-05-01

Geostatistical simulation methods have been used to quantify spatial variability of reservoir models since the 80s. In the last two decades, state of the art simulation methods have changed from being based on covariance-based 2-point statistics to multiple-point statistics (MPS), that allow simulation of more realistic Earth-structures. In addition, increasing amounts of geo-information (geophysical, geological, etc.) from multiple sources are being collected. This pose the problem of integration of these different sources of information, such that decisions related to reservoir models can be taken on an as informed base as possible. In principle, though difficult in practice, this can be achieved using computationally expensive Monte Carlo methods. Here we investigate the use of sequential simulation based MPS simulation methods conditional to uncertain (soft) data, as a computational efficient alternative. First, it is demonstrated that current implementations of sequential simulation based on MPS (e.g. SNESIM, ENESIM and Direct Sampling) do not account properly for uncertain conditional information, due to a combination of using only co-located information, and a random simulation path. Then, we suggest two approaches that better account for the available uncertain information. The first make use of a preferential simulation path, where more informed model parameters are visited preferentially to less informed ones. The second approach involves using non co-located uncertain information. For different types of available data, these approaches are demonstrated to produce simulation results similar to those obtained by the general Monte Carlo based approach. These methods allow MPS simulation to condition properly to uncertain (soft) data, and hence provides a computationally attractive approach for integration of information about a reservoir model.

A Digital Simulation Program for Health Science Students to Follow Drug Levels in the Body

ERIC Educational Resources Information Center

Stavchansky, Salomon; And Others

1977-01-01

The Rayetheon Scientific Simulation Language (RSSL) program, an easily-used simulation on the CDC/6600 computer at the University of Texas at Austin, offers a simple method of solving differential equations on a digital computer. It is used by undergraduate biopharmaceutics-pharmacokinetics students and graduate students in all areas. (Author/LBH)

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

PubMed Central

Roux, Benoît; Weare, Jonathan

2013-01-01

An issue of general interest in computer simulations is to incorporate information from experiments into a structural model. An important caveat in pursuing this goal is to avoid corrupting the resulting model with spurious and arbitrary biases. While the problem of biasing thermodynamic ensembles can be formulated rigorously using the maximum entropy method introduced by Jaynes, the approach can be cumbersome in practical applications with the need to determine multiple unknown coefficients iteratively. A popular alternative strategy to incorporate the information from experiments is to rely on restrained-ensemble molecular dynamics simulations. However, the fundamental validity of this computational strategy remains in question. Here, it is demonstrated that the statistical distribution produced by restrained-ensemble simulations is formally consistent with the maximum entropy method of Jaynes. This clarifies the underlying conditions under which restrained-ensemble simulations will yield results that are consistent with the maximum entropy method. PMID:23464140

A vessel length-based method to compute coronary fractional flow reserve from optical coherence tomography images.

PubMed

Lee, Kyung Eun; Lee, Seo Ho; Shin, Eun-Seok; Shim, Eun Bo

2017-06-26

Hemodynamic simulation for quantifying fractional flow reserve (FFR) is often performed in a patient-specific geometry of coronary arteries reconstructed from the images from various imaging modalities. Because optical coherence tomography (OCT) images can provide more precise vascular lumen geometry, regardless of stenotic severity, hemodynamic simulation based on OCT images may be effective. The aim of this study is to perform OCT-FFR simulations by coupling a 3D CFD model from geometrically correct OCT images with a LPM based on vessel lengths extracted from CAG data with clinical validations for the present method. To simulate coronary hemodynamics, we developed a fast and accurate method that combined a computational fluid dynamics (CFD) model of an OCT-based region of interest (ROI) with a lumped parameter model (LPM) of the coronary microvasculature and veins. Here, the LPM was based on vessel lengths extracted from coronary X-ray angiography (CAG) images. Based on a vessel length-based approach, we describe a theoretical formulation for the total resistance of the LPM from a three-dimensional (3D) CFD model of the ROI. To show the utility of this method, we present calculated examples of FFR from OCT images. To validate the OCT-based FFR calculation (OCT-FFR) clinically, we compared the computed OCT-FFR values for 17 vessels of 13 patients with clinically measured FFR (M-FFR) values. A novel formulation for the total resistance of LPM is introduced to accurately simulate a 3D CFD model of the ROI. The simulated FFR values compared well with clinically measured ones, showing the accuracy of the method. Moreover, the present method is fast in terms of computational time, enabling clinicians to provide solutions handled within the hospital.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

PubMed Central

2014-01-01

Background Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulate solutions of bovine serum albumin and of hen egg white lysozyme. Results We found that the inclusion of the long-range electrostatic correction increased the accuracy of both the protein-protein interaction profiles and the protein diffusion coefficients at low ionic strength. Conclusions An advantage of this method is the low additional computational cost required to treat long-range electrostatic interactions in large biomacromolecular systems. Moreover, the implementation described here for BD simulations of protein solutions can also be applied in implicit solvent molecular dynamics simulations that make use of gridded interaction potentials. PMID:25045516

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

PubMed

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

2018-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

PubMed

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

2018-05-10

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

Accelerating sino-atrium computer simulations with graphic processing units.

PubMed

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

2015-01-01

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

Implementation and Testing of Turbulence Models for the F18-HARV Simulation

NASA Technical Reports Server (NTRS)

Yeager, Jessie C.

1998-01-01

This report presents three methods of implementing the Dryden power spectral density model for atmospheric turbulence. Included are the equations which define the three methods and computer source code written in Advanced Continuous Simulation Language to implement the equations. Time-history plots and sample statistics of simulated turbulence results from executing the code in a test program are also presented. Power spectral densities were computed for sample sequences of turbulence and are plotted for comparison with the Dryden spectra. The three model implementations were installed in a nonlinear six-degree-of-freedom simulation of the High Alpha Research Vehicle airplane. Aircraft simulation responses to turbulence generated with the three implementations are presented as plots.

Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

PubMed

Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

2014-12-18

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

PubMed Central

Doblack, Benjamin N.; Allis, Tim; Dávila, Lilian P.

2014-01-01

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced. PMID:25549300

Effect of Turbulence Modeling on an Excited Jet

NASA Technical Reports Server (NTRS)

Brown, Clifford A.; Hixon, Ray

2010-01-01

The flow dynamics in a high-speed jet are dominated by unsteady turbulent flow structures in the plume. Jet excitation seeks to control these flow structures through the natural instabilities present in the initial shear layer of the jet. Understanding and optimizing the excitation input, for jet noise reduction or plume mixing enhancement, requires many trials that may be done experimentally or computationally at a significant cost savings. Numerical simulations, which model various parts of the unsteady dynamics to reduce the computational expense of the simulation, must adequately capture the unsteady flow dynamics in the excited jet for the results are to be used. Four CFD methods are considered for use in an excited jet problem, including two turbulence models with an Unsteady Reynolds Averaged Navier-Stokes (URANS) solver, one Large Eddy Simulation (LES) solver, and one URANS/LES hybrid method. Each method is used to simulate a simplified excited jet and the results are evaluated based on the flow data, computation time, and numerical stability. The knowledge gained about the effect of turbulence modeling and CFD methods from these basic simulations will guide and assist future three-dimensional (3-D) simulations that will be used to understand and optimize a realistic excited jet for a particular application.

SEMICONDUCTOR INTEGRATED CIRCUITS: A quasi-3-dimensional simulation method for a high-voltage level-shifting circuit structure

NASA Astrophysics Data System (ADS)

Jizhi, Liu; Xingbi, Chen

2009-12-01

A new quasi-three-dimensional (quasi-3D) numeric simulation method for a high-voltage level-shifting circuit structure is proposed. The performances of the 3D structure are analyzed by combining some 2D device structures; the 2D devices are in two planes perpendicular to each other and to the surface of the semiconductor. In comparison with Davinci, the full 3D device simulation tool, the quasi-3D simulation method can give results for the potential and current distribution of the 3D high-voltage level-shifting circuit structure with appropriate accuracy and the total CPU time for simulation is significantly reduced. The quasi-3D simulation technique can be used in many cases with advantages such as saving computing time, making no demands on the high-end computer terminals, and being easy to operate.

Spatial adaptive sampling in multiscale simulation

NASA Astrophysics Data System (ADS)

Rouet-Leduc, Bertrand; Barros, Kipton; Cieren, Emmanuel; Elango, Venmugil; Junghans, Christoph; Lookman, Turab; Mohd-Yusof, Jamaludin; Pavel, Robert S.; Rivera, Axel Y.; Roehm, Dominic; McPherson, Allen L.; Germann, Timothy C.

2014-07-01

In a common approach to multiscale simulation, an incomplete set of macroscale equations must be supplemented with constitutive data provided by fine-scale simulation. Collecting statistics from these fine-scale simulations is typically the overwhelming computational cost. We reduce this cost by interpolating the results of fine-scale simulation over the spatial domain of the macro-solver. Unlike previous adaptive sampling strategies, we do not interpolate on the potentially very high dimensional space of inputs to the fine-scale simulation. Our approach is local in space and time, avoids the need for a central database, and is designed to parallelize well on large computer clusters. To demonstrate our method, we simulate one-dimensional elastodynamic shock propagation using the Heterogeneous Multiscale Method (HMM); we find that spatial adaptive sampling requires only ≈ 50 ×N0.14 fine-scale simulations to reconstruct the stress field at all N grid points. Related multiscale approaches, such as Equation Free methods, may also benefit from spatial adaptive sampling.

Improving the Aircraft Design Process Using Web-Based Modeling and Simulation

NASA Technical Reports Server (NTRS)

Reed, John A.; Follen, Gregory J.; Afjeh, Abdollah A.; Follen, Gregory J. (Technical Monitor)

2000-01-01

Designing and developing new aircraft systems is time-consuming and expensive. Computational simulation is a promising means for reducing design cycle times, but requires a flexible software environment capable of integrating advanced multidisciplinary and multifidelity analysis methods, dynamically managing data across heterogeneous computing platforms, and distributing computationally complex tasks. Web-based simulation, with its emphasis on collaborative composition of simulation models, distributed heterogeneous execution, and dynamic multimedia documentation, has the potential to meet these requirements. This paper outlines the current aircraft design process, highlighting its problems and complexities, and presents our vision of an aircraft design process using Web-based modeling and simulation.

Improving the Aircraft Design Process Using Web-based Modeling and Simulation

NASA Technical Reports Server (NTRS)

Reed, John A.; Follen, Gregory J.; Afjeh, Abdollah A.

2003-01-01

Designing and developing new aircraft systems is time-consuming and expensive. Computational simulation is a promising means for reducing design cycle times, but requires a flexible software environment capable of integrating advanced multidisciplinary and muitifidelity analysis methods, dynamically managing data across heterogeneous computing platforms, and distributing computationally complex tasks. Web-based simulation, with its emphasis on collaborative composition of simulation models, distributed heterogeneous execution, and dynamic multimedia documentation, has the potential to meet these requirements. This paper outlines the current aircraft design process, highlighting its problems and complexities, and presents our vision of an aircraft design process using Web-based modeling and simulation.

GATE Monte Carlo simulation of dose distribution using MapReduce in a cloud computing environment.

PubMed

Liu, Yangchuan; Tang, Yuguo; Gao, Xin

2017-12-01

The GATE Monte Carlo simulation platform has good application prospects of treatment planning and quality assurance. However, accurate dose calculation using GATE is time consuming. The purpose of this study is to implement a novel cloud computing method for accurate GATE Monte Carlo simulation of dose distribution using MapReduce. An Amazon Machine Image installed with Hadoop and GATE is created to set up Hadoop clusters on Amazon Elastic Compute Cloud (EC2). Macros, the input files for GATE, are split into a number of self-contained sub-macros. Through Hadoop Streaming, the sub-macros are executed by GATE in Map tasks and the sub-results are aggregated into final outputs in Reduce tasks. As an evaluation, GATE simulations were performed in a cubical water phantom for X-ray photons of 6 and 18 MeV. The parallel simulation on the cloud computing platform is as accurate as the single-threaded simulation on a local server and the simulation correctness is not affected by the failure of some worker nodes. The cloud-based simulation time is approximately inversely proportional to the number of worker nodes. For the simulation of 10 million photons on a cluster with 64 worker nodes, time decreases of 41× and 32× were achieved compared to the single worker node case and the single-threaded case, respectively. The test of Hadoop's fault tolerance showed that the simulation correctness was not affected by the failure of some worker nodes. The results verify that the proposed method provides a feasible cloud computing solution for GATE.

3D simulation of friction stir welding based on movable cellular automaton method

NASA Astrophysics Data System (ADS)

Eremina, Galina M.

2017-12-01

The paper is devoted to a 3D computer simulation of the peculiarities of material flow taking place in friction stir welding (FSW). The simulation was performed by the movable cellular automaton (MCA) method, which is a representative of particle methods in mechanics. Commonly, the flow of material in FSW is simulated based on computational fluid mechanics, assuming the material as continuum and ignoring its structure. The MCA method considers a material as an ensemble of bonded particles. The rupture of interparticle bonds and the formation of new bonds enable simulations of crack nucleation and healing as well as mas mixing and microwelding. The simulation results showed that using pins of simple shape (cylinder, cone, and pyramid) without a shoulder results in small displacements of plasticized material in workpiece thickness directions. Nevertheless, the optimal ratio of longitudinal velocity to rotational speed makes it possible to transport the welded material around the pin several times and to produce a joint of good quality.

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

Kaurov, Alexander A., E-mail: kaurov@uchicago.edu

The methods for studying the epoch of cosmic reionization vary from full radiative transfer simulations to purely analytical models. While numerical approaches are computationally expensive and are not suitable for generating many mock catalogs, analytical methods are based on assumptions and approximations. We explore the interconnection between both methods. First, we ask how the analytical framework of excursion set formalism can be used for statistical analysis of numerical simulations and visual representation of the morphology of ionization fronts. Second, we explore the methods of training the analytical model on a given numerical simulation. We present a new code which emergedmore » from this study. Its main application is to match the analytical model with a numerical simulation. Then, it allows one to generate mock reionization catalogs with volumes exceeding the original simulation quickly and computationally inexpensively, meanwhile reproducing large-scale statistical properties. These mock catalogs are particularly useful for cosmic microwave background polarization and 21 cm experiments, where large volumes are required to simulate the observed signal.« less

Particle-based simulation of charge transport in discrete-charge nano-scale systems: the electrostatic problem

PubMed Central

2012-01-01

The fast and accurate computation of the electric forces that drive the motion of charged particles at the nanometer scale represents a computational challenge. For this kind of system, where the discrete nature of the charges cannot be neglected, boundary element methods (BEM) represent a better approach than finite differences/finite elements methods. In this article, we compare two different BEM approaches to a canonical electrostatic problem in a three-dimensional space with inhomogeneous dielectrics, emphasizing their suitability for particle-based simulations: the iterative method proposed by Hoyles et al. and the Induced Charge Computation introduced by Boda et al. PMID:22338640

Particle-based simulation of charge transport in discrete-charge nano-scale systems: the electrostatic problem.

PubMed

Berti, Claudio; Gillespie, Dirk; Eisenberg, Robert S; Fiegna, Claudio

2012-02-16

The fast and accurate computation of the electric forces that drive the motion of charged particles at the nanometer scale represents a computational challenge. For this kind of system, where the discrete nature of the charges cannot be neglected, boundary element methods (BEM) represent a better approach than finite differences/finite elements methods. In this article, we compare two different BEM approaches to a canonical electrostatic problem in a three-dimensional space with inhomogeneous dielectrics, emphasizing their suitability for particle-based simulations: the iterative method proposed by Hoyles et al. and the Induced Charge Computation introduced by Boda et al.

Multi-level methods and approximating distribution functions

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

Wilson, D., E-mail: daniel.wilson@dtc.ox.ac.uk; Baker, R. E.

2016-07-15

Biochemical reaction networks are often modelled using discrete-state, continuous-time Markov chains. System statistics of these Markov chains usually cannot be calculated analytically and therefore estimates must be generated via simulation techniques. There is a well documented class of simulation techniques known as exact stochastic simulation algorithms, an example of which is Gillespie’s direct method. These algorithms often come with high computational costs, therefore approximate stochastic simulation algorithms such as the tau-leap method are used. However, in order to minimise the bias in the estimates generated using them, a relatively small value of tau is needed, rendering the computational costs comparablemore » to Gillespie’s direct method. The multi-level Monte Carlo method (Anderson and Higham, Multiscale Model. Simul. 10:146–179, 2012) provides a reduction in computational costs whilst minimising or even eliminating the bias in the estimates of system statistics. This is achieved by first crudely approximating required statistics with many sample paths of low accuracy. Then correction terms are added until a required level of accuracy is reached. Recent literature has primarily focussed on implementing the multi-level method efficiently to estimate a single system statistic. However, it is clearly also of interest to be able to approximate entire probability distributions of species counts. We present two novel methods that combine known techniques for distribution reconstruction with the multi-level method. We demonstrate the potential of our methods using a number of examples.« less

Asthma management simulation for children: translating theory, methods, and strategies to effect behavior change.

PubMed

Shegog, Ross; Bartholomew, L Kay; Gold, Robert S; Pierrel, Elaine; Parcel, Guy S; Sockrider, Marianna M; Czyzewski, Danita I; Fernandez, Maria E; Berlin, Nina J; Abramson, Stuart

2006-01-01

Translating behavioral theories, models, and strategies to guide the development and structure of computer-based health applications is well recognized, although a continued challenge for program developers. A stepped approach to translate behavioral theory in the design of simulations to teach chronic disease management to children is described. This includes the translation steps to: 1) define target behaviors and their determinants, 2) identify theoretical methods to optimize behavioral change, and 3) choose educational strategies to effectively apply these methods and combine these into a cohesive computer-based simulation for health education. Asthma is used to exemplify a chronic health management problem and a computer-based asthma management simulation (Watch, Discover, Think and Act) that has been evaluated and shown to effect asthma self-management in children is used to exemplify the application of theory to practice. Impact and outcome evaluation studies have indicated the effectiveness of these steps in providing increased rigor and accountability, suggesting their utility for educators and developers seeking to apply simulations to enhance self-management behaviors in patients.

Coniferous canopy BRF simulation based on 3-D realistic scene.

PubMed

Wang, Xin-Yun; Guo, Zhi-Feng; Qin, Wen-Han; Sun, Guo-Qing

2011-09-01

It is difficulties for the computer simulation method to study radiation regime at large-scale. Simplified coniferous model was investigated in the present study. It makes the computer simulation methods such as L-systems and radiosity-graphics combined method (RGM) more powerful in remote sensing of heterogeneous coniferous forests over a large-scale region. L-systems is applied to render 3-D coniferous forest scenarios, and RGM model was used to calculate BRF (bidirectional reflectance factor) in visible and near-infrared regions. Results in this study show that in most cases both agreed well. Meanwhile at a tree and forest level, the results are also good.

Coniferous Canopy BRF Simulation Based on 3-D Realistic Scene

NASA Technical Reports Server (NTRS)

Wang, Xin-yun; Guo, Zhi-feng; Qin, Wen-han; Sun, Guo-qing

2011-01-01

It is difficulties for the computer simulation method to study radiation regime at large-scale. Simplified coniferous model was investigate d in the present study. It makes the computer simulation methods such as L-systems and radiosity-graphics combined method (RGM) more powerf ul in remote sensing of heterogeneous coniferous forests over a large -scale region. L-systems is applied to render 3-D coniferous forest scenarios: and RGM model was used to calculate BRF (bidirectional refle ctance factor) in visible and near-infrared regions. Results in this study show that in most cases both agreed well. Meanwhiie at a tree and forest level. the results are also good.

3D Parallel Multigrid Methods for Real-Time Fluid Simulation

NASA Astrophysics Data System (ADS)

Wan, Feifei; Yin, Yong; Zhang, Suiyu

2018-03-01

The multigrid method is widely used in fluid simulation because of its strong convergence. In addition to operating accuracy, operational efficiency is also an important factor to consider in order to enable real-time fluid simulation in computer graphics. For this problem, we compared the performance of the Algebraic Multigrid and the Geometric Multigrid in the V-Cycle and Full-Cycle schemes respectively, and analyze the convergence and speed of different methods. All the calculations are done on the parallel computing of GPU in this paper. Finally, we experiment with the 3D-grid for each scale, and give the exact experimental results.

Intricacies of modern supercomputing illustrated with recent advances in simulations of strongly correlated electron systems

NASA Astrophysics Data System (ADS)

Schulthess, Thomas C.

2013-03-01

The continued thousand-fold improvement in sustained application performance per decade on modern supercomputers keeps opening new opportunities for scientific simulations. But supercomputers have become very complex machines, built with thousands or tens of thousands of complex nodes consisting of multiple CPU cores or, most recently, a combination of CPU and GPU processors. Efficient simulations on such high-end computing systems require tailored algorithms that optimally map numerical methods to particular architectures. These intricacies will be illustrated with simulations of strongly correlated electron systems, where the development of quantum cluster methods, Monte Carlo techniques, as well as their optimal implementation by means of algorithms with improved data locality and high arithmetic density have gone hand in hand with evolving computer architectures. The present work would not have been possible without continued access to computing resources at the National Center for Computational Science of Oak Ridge National Laboratory, which is funded by the Facilities Division of the Office of Advanced Scientific Computing Research, and the Swiss National Supercomputing Center (CSCS) that is funded by ETH Zurich.

Computational simulation of laser heat processing of materials

NASA Astrophysics Data System (ADS)

Shankar, Vijaya; Gnanamuthu, Daniel

1987-04-01

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

Basic study on a lower-energy defibrillation method using computer simulation and cultured myocardial cell models.

PubMed

Yaguchi, A; Nagase, K; Ishikawa, M; Iwasaka, T; Odagaki, M; Hosaka, H

2006-01-01

Computer simulation and myocardial cell models were used to evaluate a low-energy defibrillation technique. A generated spiral wave, considered to be a mechanism of fibrillation, and fibrillation were investigated using two myocardial sheet models: a two-dimensional computer simulation model and a two-dimensional experimental model. A new defibrillation technique that has few side effects, which are induced by the current passing into the patient's body, on cardiac muscle is desired. The purpose of the present study is to conduct a basic investigation into an efficient defibrillation method. In order to evaluate the defibrillation method, the propagation of excitation in the myocardial sheet is measured during the normal state and during fibrillation, respectively. The advantages of the low-energy defibrillation technique are then discussed based on the stimulation timing.

DNS of Flow in a Low-Pressure Turbine Cascade Using a Discontinuous-Galerkin Spectral-Element Method

NASA Technical Reports Server (NTRS)

Garai, Anirban; Diosady, Laslo Tibor; Murman, Scott; Madavan, Nateri

2015-01-01

A new computational capability under development for accurate and efficient high-fidelity direct numerical simulation (DNS) and large eddy simulation (LES) of turbomachinery is described. This capability is based on an entropy-stable Discontinuous-Galerkin spectral-element approach that extends to arbitrarily high orders of spatial and temporal accuracy and is implemented in a computationally efficient manner on a modern high performance computer architecture. A validation study using this method to perform DNS of flow in a low-pressure turbine airfoil cascade are presented. Preliminary results indicate that the method captures the main features of the flow. Discrepancies between the predicted results and the experiments are likely due to the effects of freestream turbulence not being included in the simulation and will be addressed in the final paper.

Application of multi-grid method on the simulation of incremental forging processes

NASA Astrophysics Data System (ADS)

Ramadan, Mohamad; Khaled, Mahmoud; Fourment, Lionel

2016-10-01

Numerical simulation becomes essential in manufacturing large part by incremental forging processes. It is a splendid tool allowing to show physical phenomena however behind the scenes, an expensive bill should be paid, that is the computational time. That is why many techniques are developed to decrease the computational time of numerical simulation. Multi-Grid method is a numerical procedure that permits to reduce computational time of numerical calculation by performing the resolution of the system of equations on several mesh of decreasing size which allows to smooth faster the low frequency of the solution as well as its high frequency. In this paper a Multi-Grid method is applied to cogging process in the software Forge 3. The study is carried out using increasing number of degrees of freedom. The results shows that calculation time is divide by two for a mesh of 39,000 nodes. The method is promising especially if coupled with Multi-Mesh method.

A novel patient-specific model to compute coronary fractional flow reserve.

PubMed

Kwon, Soon-Sung; Chung, Eui-Chul; Park, Jin-Seo; Kim, Gook-Tae; Kim, Jun-Woo; Kim, Keun-Hong; Shin, Eun-Seok; Shim, Eun Bo

2014-09-01

The fractional flow reserve (FFR) is a widely used clinical index to evaluate the functional severity of coronary stenosis. A computer simulation method based on patients' computed tomography (CT) data is a plausible non-invasive approach for computing the FFR. This method can provide a detailed solution for the stenosed coronary hemodynamics by coupling computational fluid dynamics (CFD) with the lumped parameter model (LPM) of the cardiovascular system. In this work, we have implemented a simple computational method to compute the FFR. As this method uses only coronary arteries for the CFD model and includes only the LPM of the coronary vascular system, it provides simpler boundary conditions for the coronary geometry and is computationally more efficient than existing approaches. To test the efficacy of this method, we simulated a three-dimensional straight vessel using CFD coupled with the LPM. The computed results were compared with those of the LPM. To validate this method in terms of clinically realistic geometry, a patient-specific model of stenosed coronary arteries was constructed from CT images, and the computed FFR was compared with clinically measured results. We evaluated the effect of a model aorta on the computed FFR and compared this with a model without the aorta. Computationally, the model without the aorta was more efficient than that with the aorta, reducing the CPU time required for computing a cardiac cycle to 43.4%. Copyright © 2014. Published by Elsevier Ltd.

Rotor dynamic simulation and system identification methods for application to vacuum whirl data

NASA Technical Reports Server (NTRS)

Berman, A.; Giansante, N.; Flannelly, W. G.

1980-01-01

Methods of using rotor vacuum whirl data to improve the ability to model helicopter rotors were developed. The work consisted of the formulation of the equations of motion of elastic blades on a hub using a Galerkin method; the development of a general computer program for simulation of these equations; the study and implementation of a procedure for determining physical parameters based on measured data; and the application of a method for computing the normal modes and natural frequencies based on test data.

Bringing global gyrokinetic turbulence simulations to the transport timescale using a multiscale approach

NASA Astrophysics Data System (ADS)

Parker, Jeffrey; Lodestro, Lynda; Told, Daniel; Merlo, Gabriele; Ricketson, Lee; Campos, Alejandro; Jenko, Frank; Hittinger, Jeffrey

2017-10-01

Predictive whole-device simulation models will play an increasingly important role in ensuring the success of fusion experiments and accelerating the development of fusion energy. In the core of tokamak plasmas, a separation of timescales between turbulence and transport makes a single direct simulation of both processes computationally expensive. We present the first demonstration of a multiple-timescale method coupling global gyrokinetic simulations with a transport solver to calculate the self-consistent, steady-state temperature profile. Initial results are highly encouraging, with the coupling method appearing robust to the difficult problem of turbulent fluctuations. The method holds potential for integrating first-principles turbulence simulations into whole-device models and advancing the understanding of global plasma behavior. Work supported by US DOE under Contract DE-AC52-07NA27344 and the Exascale Computing Project (17-SC-20-SC).

A Multi-domain Spectral Method for Supersonic Reactive Flows

NASA Technical Reports Server (NTRS)

Don, Wai-Sun; Gottlieb, David; Jung, Jae-Hun; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

This paper has a dual purpose: it presents a multidomain Chebyshev method for the solution of the two-dimensional reactive compressible Navier-Stokes equations, and it reports the results of the application of this code to the numerical simulations of high Mach number reactive flows in recessed cavity. The computational method utilizes newly derived interface boundary conditions as well as an adaptive filtering technique to stabilize the computations. The results of the simulations are relevant to recessed cavity flameholders.

[Design and study of parallel computing environment of Monte Carlo simulation for particle therapy planning using a public cloud-computing infrastructure].

PubMed

Yokohama, Noriya

2013-07-01

This report was aimed at structuring the design of architectures and studying performance measurement of a parallel computing environment using a Monte Carlo simulation for particle therapy using a high performance computing (HPC) instance within a public cloud-computing infrastructure. Performance measurements showed an approximately 28 times faster speed than seen with single-thread architecture, combined with improved stability. A study of methods of optimizing the system operations also indicated lower cost.

Case Study: The Use of a Hypercard Simulation to Aid in the Teaching of Laboratory Apparatus Operation.

ERIC Educational Resources Information Center

Waddick, John

1994-01-01

Compares the effect of a chemistry computer simulation, written by the author, with the effect of an instructor demonstration. The study indicates that in this particular situation the operation of a spectrophotometer can be effectively taught by computer simulation method. The program is written using HyperTalk, the HyperCard programming…

Monte Carlo Simulations and Generation of the SPI Response

NASA Technical Reports Server (NTRS)

Sturner, S. J.; Shrader, C. R.; Weidenspointner, G.; Teegarden, B. J.; Attie, D.; Diehl, R.; Ferguson, C.; Jean, P.; vonKienlin, A.

2003-01-01

In this paper we discuss the methods developed for the production of the INTEGRAL/SPI instrument response. The response files were produced using a suite of Monte Carlo simulation software developed at NASA/GSFC based on the GEANT-3 package available from CERN. The production of the INTEGRAL/SPI instrument response also required the development of a detailed computer mass model for SPI. We discuss our extensive investigations into methods to reduce both the computation time and storage requirements for the SPI response. We also discuss corrections to the simulated response based on our comparison of ground and inflight calibration data with MGEANT simulation.

Monte Carlo Simulations and Generation of the SPI Response

NASA Technical Reports Server (NTRS)

Sturner, S. J.; Shrader, C. R.; Weidenspointner, G.; Teegarden, B. J.; Attie, D.; Cordier, B.; Diehl, R.; Ferguson, C.; Jean, P.; vonKienlin, A.

2003-01-01

In this paper we discuss the methods developed for the production of the INTEGRAL/SPI instrument response. The response files were produced using a suite of Monte Carlo simulation software developed at NASA/GSFC based on the GEANT-3 package available from CERN. The production of the INTEGRAL/SPI instrument response also required the development of a detailed computer mass model for SPI. We discuss ow extensive investigations into methods to reduce both the computation time and storage requirements for the SPI response. We also discuss corrections to the simulated response based on our comparison of ground and infiight Calibration data with MGEANT simulations.

Improving operational plume forecasts

NASA Astrophysics Data System (ADS)

Balcerak, Ernie

2012-04-01

Forecasting how plumes of particles, such as radioactive particles from a nuclear disaster, will be transported and dispersed in the atmosphere is an important but computationally challenging task. During the Fukushima nuclear disaster in Japan, operational plume forecasts were produced each day, but as the emissions continued, previous emissions were not included in the simulations used for forecasts because it became impractical to rerun the simulations each day from the beginning of the accident. Draxler and Rolph examine whether it is possible to improve plume simulation speed and flexibility as conditions and input data change. The authors use a method known as a transfer coefficient matrix approach that allows them to simulate many radionuclides using only a few generic species for the computation. Their simulations work faster by dividing the computation into separate independent segments in such a way that the most computationally time consuming pieces of the calculation need to be done only once. This makes it possible to provide real-time operational plume forecasts by continuously updating the previous simulations as new data become available. They tested their method using data from the Fukushima incident to show that it performed well. (Journal of Geophysical Research-Atmospheres, doi:10.1029/2011JD017205, 2012)

A spectral approach for discrete dislocation dynamics simulations of nanoindentation

NASA Astrophysics Data System (ADS)

Bertin, Nicolas; Glavas, Vedran; Datta, Dibakar; Cai, Wei

2018-07-01

We present a spectral approach to perform nanoindentation simulations using three-dimensional nodal discrete dislocation dynamics. The method relies on a two step approach. First, the contact problem between an indenter of arbitrary shape and an isotropic elastic half-space is solved using a spectral iterative algorithm, and the contact pressure is fully determined on the half-space surface. The contact pressure is then used as a boundary condition of the spectral solver to determine the resulting stress field produced in the simulation volume. In both stages, the mechanical fields are decomposed into Fourier modes and are efficiently computed using fast Fourier transforms. To further improve the computational efficiency, the method is coupled with a subcycling integrator and a special approach is devised to approximate the displacement field associated with surface steps. As a benchmark, the method is used to compute the response of an elastic half-space using different types of indenter. An example of a dislocation dynamics nanoindentation simulation with complex initial microstructure is presented.

Efficient and Robust Optimization for Building Energy Simulation

PubMed Central

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-01-01

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell’s Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell’s method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell’s Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell’s Hybrid method presently used in HVACSIM+. PMID:27325907

Efficient and Robust Optimization for Building Energy Simulation.

PubMed

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-06-15

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell's Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell's method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell's Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell's Hybrid method presently used in HVACSIM+.

Micro-Energy Rates for Damage Tolerance and Durability of Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Minnetyan, Levon

2006-01-01

In this paper, the adhesive bond strength of lap-jointed graphite/aluminum composites is examined by computational simulation. Computed micro-stress level energy release rates are used to identify the damage mechanisms associated with the corresponding acoustic emission (AE) signals. Computed damage regions are similarly correlated with ultrasonically scanned damage regions. Results show that computational simulation can be used with suitable NDE methods for credible in-service monitoring of composites.

Recent advances in computational methodology for simulation of mechanical circulatory assist devices

PubMed Central

Marsden, Alison L.; Bazilevs, Yuri; Long, Christopher C.; Behr, Marek

2014-01-01

Ventricular assist devices (VADs) provide mechanical circulatory support to offload the work of one or both ventricles during heart failure. They are used in the clinical setting as destination therapy, as bridge to transplant, or more recently as bridge to recovery to allow for myocardial remodeling. Recent developments in computational simulation allow for detailed assessment of VAD hemodynamics for device design and optimization for both children and adults. Here, we provide a focused review of the recent literature on finite element methods and optimization for VAD simulations. As VAD designs typically fall into two categories, pulsatile and continuous flow devices, we separately address computational challenges of both types of designs, and the interaction with the circulatory system with three representative case studies. In particular, we focus on recent advancements in finite element methodology that has increased the fidelity of VAD simulations. We outline key challenges, which extend to the incorporation of biological response such as thrombosis and hemolysis, as well as shape optimization methods and challenges in computational methodology. PMID:24449607

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

PubMed Central

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

2016-01-01

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

Computational Aerodynamic Simulations of a 1215 ft/sec Tip Speed Transonic Fan System Model for Acoustic Methods Assessment and Development

NASA Technical Reports Server (NTRS)

Tweedt, Daniel L.

2014-01-01

Computational Aerodynamic simulations of a 1215 ft/sec tip speed transonic fan system were performed at five different operating points on the fan operating line, in order to provide detailed internal flow field information for use with fan acoustic prediction methods presently being developed, assessed and validated. The fan system is a sub-scale, low-noise research fan/nacelle model that has undergone extensive experimental testing in the 9- by 15-foot Low Speed Wind Tunnel at the NASA Glenn Research Center. Details of the fan geometry, the computational fluid dynamics methods, the computational grids, and various computational parameters relevant to the numerical simulations are discussed. Flow field results for three of the five operating points simulated are presented in order to provide a representative look at the computed solutions. Each of the five fan aerodynamic simulations involved the entire fan system, which for this model did not include a split flow path with core and bypass ducts. As a result, it was only necessary to adjust fan rotational speed in order to set the fan operating point, leading to operating points that lie on a fan operating line and making mass flow rate a fully dependent parameter. The resulting mass flow rates are in good agreement with measurement values. Computed blade row flow fields at all fan operating points are, in general, aerodynamically healthy. Rotor blade and fan exit guide vane flow characteristics are good, including incidence and deviation angles, chordwise static pressure distributions, blade surface boundary layers, secondary flow structures, and blade wakes. Examination of the flow fields at all operating conditions reveals no excessive boundary layer separations or related secondary-flow problems.

Visualizing ultrasound through computational modeling

NASA Technical Reports Server (NTRS)

Guo, Theresa W.

2004-01-01

The Doppler Ultrasound Hematocrit Project (DHP) hopes to find non-invasive methods of determining a person s blood characteristics. Because of the limits of microgravity and the space travel environment, it is important to find non-invasive methods of evaluating the health of persons in space. Presently, there is no well developed method of determining blood composition non-invasively. This projects hopes to use ultrasound and Doppler signals to evaluate the characteristic of hematocrit, the percentage by volume of red blood cells within whole blood. These non-invasive techniques may also be developed to be used on earth for trauma patients where invasive measure might be detrimental. Computational modeling is a useful tool for collecting preliminary information and predictions for the laboratory research. We hope to find and develop a computer program that will be able to simulate the ultrasound signals the project will work with. Simulated models of test conditions will more easily show what might be expected from laboratory results thus help the research group make informed decisions before and during experimentation. There are several existing Matlab based computer programs available, designed to interpret and simulate ultrasound signals. These programs will be evaluated to find which is best suited for the project needs. The criteria of evaluation that will be used are 1) the program must be able to specify transducer properties and specify transmitting and receiving signals, 2) the program must be able to simulate ultrasound signals through different attenuating mediums, 3) the program must be able to process moving targets in order to simulate the Doppler effects that are associated with blood flow, 4) the program should be user friendly and adaptable to various models. After a computer program is chosen, two simulation models will be constructed. These models will simulate and interpret an RF data signal and a Doppler signal.

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

NASA Technical Reports Server (NTRS)

Darmofal, David L.

2003-01-01

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

A new ChainMail approach for real-time soft tissue simulation.

PubMed

Zhang, Jinao; Zhong, Yongmin; Smith, Julian; Gu, Chengfan

2016-07-03

This paper presents a new ChainMail method for real-time soft tissue simulation. This method enables the use of different material properties for chain elements to accommodate various materials. Based on the ChainMail bounding region, a new time-saving scheme is developed to improve computational efficiency for isotropic materials. The proposed method also conserves volume and strain energy. Experimental results demonstrate that the proposed ChainMail method can not only accommodate isotropic, anisotropic and heterogeneous materials but also model incompressibility and relaxation behaviors of soft tissues. Further, the proposed method can achieve real-time computational performance.

OpenACC performance for simulating 2D radial dambreak using FVM HLLE flux

NASA Astrophysics Data System (ADS)

Gunawan, P. H.; Pahlevi, M. R.

2018-03-01

The aim of this paper is to investigate the performances of openACC platform for computing 2D radial dambreak. Here, the shallow water equation will be used to describe and simulate 2D radial dambreak with finite volume method (FVM) using HLLE flux. OpenACC is a parallel computing platform based on GPU cores. Indeed, from this research this platform is used to minimize computational time on the numerical scheme performance. The results show the using OpenACC, the computational time is reduced. For the dry and wet radial dambreak simulations using 2048 grids, the computational time of parallel is obtained 575.984 s and 584.830 s respectively for both simulations. These results show the successful of OpenACC when they are compared with the serial time of dry and wet radial dambreak simulations which are collected 28047.500 s and 29269.40 s respectively.

Computational time analysis of the numerical solution of 3D electrostatic Poisson's equation

NASA Astrophysics Data System (ADS)

Kamboh, Shakeel Ahmed; Labadin, Jane; Rigit, Andrew Ragai Henri; Ling, Tech Chaw; Amur, Khuda Bux; Chaudhary, Muhammad Tayyab

2015-05-01

3D Poisson's equation is solved numerically to simulate the electric potential in a prototype design of electrohydrodynamic (EHD) ion-drag micropump. Finite difference method (FDM) is employed to discretize the governing equation. The system of linear equations resulting from FDM is solved iteratively by using the sequential Jacobi (SJ) and sequential Gauss-Seidel (SGS) methods, simulation results are also compared to examine the difference between the results. The main objective was to analyze the computational time required by both the methods with respect to different grid sizes and parallelize the Jacobi method to reduce the computational time. In common, the SGS method is faster than the SJ method but the data parallelism of Jacobi method may produce good speedup over SGS method. In this study, the feasibility of using parallel Jacobi (PJ) method is attempted in relation to SGS method. MATLAB Parallel/Distributed computing environment is used and a parallel code for SJ method is implemented. It was found that for small grid size the SGS method remains dominant over SJ method and PJ method while for large grid size both the sequential methods may take nearly too much processing time to converge. Yet, the PJ method reduces computational time to some extent for large grid sizes.

Simulation of turbulent separated flows using a novel, evolution-based, eddy-viscosity formulation

NASA Astrophysics Data System (ADS)

Castellucci, Paul

Currently, there exists a lack of confidence in the computational simulation of turbulent separated flows at large Reynolds numbers. The most accurate methods available are too computationally costly to use in engineering applications. Thus, inexpensive models, developed using the Reynolds-averaged Navier-Stokes (RANS) equations, are often extended beyond their applicability. Although these methods will often reproduce integrated quantities within engineering tolerances, such metrics are often insensitive to details within a separated wake, and therefore, poor indicators of simulation fidelity. Using concepts borrowed from large-eddy simulation (LES), a two-equation RANS model is modified to simulate the turbulent wake behind a circular cylinder. This modification involves the computation of one additional scalar field, adding very little to the overall computational cost. When properly inserted into the baseline RANS model, this modification mimics LES in the separated wake, yet reverts to the unmodified form at the cylinder surface. In this manner, superior predictive capability may be achieved without the additional cost of fine spatial resolution associated with LES near solid boundaries. Simulations using modified and baseline RANS models are benchmarked against both LES and experimental data for a circular cylinder wake at Reynolds number 3900. In addition, the computational tool used in this investigation is subject to verification via the Method of Manufactured Solutions. Post-processing of the resultant flow fields includes both mean value and triple-decomposition analysis. These results reveal substantial improvements using the modified system and appear to drive the baseline wake solution toward that of LES, as intended.

Computational approach to integrate 3D X-ray microtomography and NMR data

NASA Astrophysics Data System (ADS)

Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G.; Trevizan, Willian A.; Fortulan, Carlos A.; Bonagamba, Tito J.

2018-07-01

Nowadays, most of the efforts in NMR applied to porous media are dedicated to studying the molecular fluid dynamics within and among the pores. These analyses have a higher complexity due to morphology and chemical composition of rocks, besides dynamic effects as restricted diffusion, diffusional coupling, and exchange processes. Since the translational nuclear spin diffusion in a confined geometry (e.g. pores and fractures) requires specific boundary conditions, the theoretical solutions are restricted to some special problems and, in many cases, computational methods are required. The Random Walk Method is a classic way to simulate self-diffusion along a Digital Porous Medium. Bergman model considers the magnetic relaxation process of the fluid molecules by including a probability rate of magnetization survival under surface interactions. Here we propose a statistical approach to correlate surface magnetic relaxivity with the computational method applied to the NMR relaxation in order to elucidate the relationship between simulated relaxation time and pore size of the Digital Porous Medium. The proposed computational method simulates one- and two-dimensional NMR techniques reproducing, for example, longitudinal and transverse relaxation times (T1 and T2, respectively), diffusion coefficients (D), as well as their correlations. For a good approximation between the numerical and experimental results, it is necessary to preserve the complexity of translational diffusion through the microstructures in the digital rocks. Therefore, we use Digital Porous Media obtained by 3D X-ray microtomography. To validate the method, relaxation times of ideal spherical pores were obtained and compared with the previous determinations by the Brownstein-Tarr model, as well as the computational approach proposed by Bergman. Furthermore, simulated and experimental results of synthetic porous media are compared. These results make evident the potential of computational physics in the analysis of the NMR data for complex porous materials.

Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods.

PubMed

Kawai, Ryoko; Araki, Mitsugu; Yoshimura, Masashi; Kamiya, Narutoshi; Ono, Masahiro; Saji, Hideo; Okuno, Yasushi

2018-05-16

Development of new diagnostic imaging probes for Alzheimer's disease, such as positron emission tomography (PET) and single photon emission computed tomography (SPECT) probes, has been strongly desired. In this study, we investigated the most accessible amyloid β (Aβ) binding site of [ 123 I]IMPY, a Thioflavin-T-derived SPECT probe, using experimental and computational methods. First, we performed a competitive inhibition assay with Orange-G, which recognizes the KLVFFA region in Aβ fibrils, suggesting that IMPY and Orange-G bind to different sites in Aβ fibrils. Next, we precisely predicted the IMPY binding site on a multiple-protofilament Aβ fibril model using computational approaches, consisting of molecular dynamics and docking simulations. We generated possible IMPY-binding structures using docking simulations to identify candidates for probe-binding sites. The binding free energy of IMPY with the Aβ fibril was calculated by a free energy simulation method, MP-CAFEE. These computational results suggest that IMPY preferentially binds to an interfacial pocket located between two protofilaments and is stabilized mainly through hydrophobic interactions. Finally, our computational approach was validated by comparing it with the experimental results. The present study demonstrates the possibility of computational approaches to screen new PET/SPECT probes for Aβ imaging.

Computational techniques for ECG analysis and interpretation in light of their contribution to medical advances

PubMed Central

Mincholé, Ana; Martínez, Juan Pablo; Laguna, Pablo; Rodriguez, Blanca

2018-01-01

Widely developed for clinical screening, electrocardiogram (ECG) recordings capture the cardiac electrical activity from the body surface. ECG analysis can therefore be a crucial first step to help diagnose, understand and predict cardiovascular disorders responsible for 30% of deaths worldwide. Computational techniques, and more specifically machine learning techniques and computational modelling are powerful tools for classification, clustering and simulation, and they have recently been applied to address the analysis of medical data, especially ECG data. This review describes the computational methods in use for ECG analysis, with a focus on machine learning and 3D computer simulations, as well as their accuracy, clinical implications and contributions to medical advances. The first section focuses on heartbeat classification and the techniques developed to extract and classify abnormal from regular beats. The second section focuses on patient diagnosis from whole recordings, applied to different diseases. The third section presents real-time diagnosis and applications to wearable devices. The fourth section highlights the recent field of personalized ECG computer simulations and their interpretation. Finally, the discussion section outlines the challenges of ECG analysis and provides a critical assessment of the methods presented. The computational methods reported in this review are a strong asset for medical discoveries and their translation to the clinical world may lead to promising advances. PMID:29321268

Application of CT-PSF-based computer-simulated lung nodules for evaluating the accuracy of computer-aided volumetry.

PubMed

Funaki, Ayumu; Ohkubo, Masaki; Wada, Shinichi; Murao, Kohei; Matsumoto, Toru; Niizuma, Shinji

2012-07-01

With the wide dissemination of computed tomography (CT) screening for lung cancer, measuring the nodule volume accurately with computer-aided volumetry software is increasingly important. Many studies for determining the accuracy of volumetry software have been performed using a phantom with artificial nodules. These phantom studies are limited, however, in their ability to reproduce the nodules both accurately and in the variety of sizes and densities required. Therefore, we propose a new approach of using computer-simulated nodules based on the point spread function measured in a CT system. The validity of the proposed method was confirmed by the excellent agreement obtained between computer-simulated nodules and phantom nodules regarding the volume measurements. A practical clinical evaluation of the accuracy of volumetry software was achieved by adding simulated nodules onto clinical lung images, including noise and artifacts. The tested volumetry software was revealed to be accurate within an error of 20 % for nodules >5 mm and with the difference between nodule density and background (lung) (CT value) being 400-600 HU. Such a detailed analysis can provide clinically useful information on the use of volumetry software in CT screening for lung cancer. We concluded that the proposed method is effective for evaluating the performance of computer-aided volumetry software.

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

NASA Astrophysics Data System (ADS)

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

2017-11-01

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

To simulate or not to simulate: what are the questions?

PubMed

Dudai, Yadin; Evers, Kathinka

2014-10-22

Simulation is a powerful method in science and engineering. However, simulation is an umbrella term, and its meaning and goals differ among disciplines. Rapid advances in neuroscience and computing draw increasing attention to large-scale brain simulations. What is the meaning of simulation, and what should the method expect to achieve? We discuss the concept of simulation from an integrated scientific and philosophical vantage point and pinpoint selected issues that are specific to brain simulation.

A Lattice-Boltzmann model to simulate diffractive nonlinear ultrasound beam propagation in a dissipative fluid medium

NASA Astrophysics Data System (ADS)

Abdi, Mohamad; Hajihasani, Mojtaba; Gharibzadeh, Shahriar; Tavakkoli, Jahan

2012-12-01

Ultrasound waves have been widely used in diagnostic and therapeutic medical applications. Accurate and effective simulation of ultrasound beam propagation and its interaction with tissue has been proved to be important. The nonlinear nature of the ultrasound beam propagation, especially in the therapeutic regime, plays an important role in the mechanisms of interaction with tissue. There are three main approaches in current computational fluid dynamics (CFD) methods to model and simulate nonlinear ultrasound beams: macroscopic, mesoscopic and microscopic approaches. In this work, a mesoscopic CFD method based on the Lattice-Boltzmann model (LBM) was investigated. In the developed method, the Boltzmann equation is evolved to simulate the flow of a Newtonian fluid with the collision model instead of solving the Navier-Stokes, continuity and state equations which are used in conventional CFD methods. The LBM has some prominent advantages over conventional CFD methods, including: (1) its parallel computational nature; (2) taking microscopic boundaries into account; and (3) capability of simulating in porous and inhomogeneous media. In our proposed method, the propagating medium is discretized with a square grid in 2 dimensions with 9 velocity vectors for each node. Using the developed model, the nonlinear distortion and shock front development of a finiteamplitude diffractive ultrasonic beam in a dissipative fluid medium was computed and validated against the published data. The results confirm that the LBM is an accurate and effective approach to model and simulate nonlinearity in finite-amplitude ultrasound beams with Mach numbers of up to 0.01 which, among others, falls within the range of therapeutic ultrasound regime such as high intensity focused ultrasound (HIFU) beams. A comparison between the HIFU nonlinear beam simulations using the proposed model and pseudospectral methods in a 2D geometry is presented.

Sawmill simulation: concepts and computer use

Treesearch

Hugh W. Reynolds; Charles J. Gatchell

1969-01-01

Product specifications were fed into a computer so that the yield of products from the same sample of logs could be determined for simulated sawing methods. Since different sawing patterns were tested on the same sample, variation among log samples was eliminated; hence, the statistical conclusions are very precise.

Practice Makes Perfect: Using a Computer-Based Business Simulation in Entrepreneurship Education

ERIC Educational Resources Information Center

Armer, Gina R. M.

2011-01-01

This article explains the use of a specific computer-based simulation program as a successful experiential learning model and as a way to increase student motivation while augmenting conventional methods of business instruction. This model is based on established adult learning principles.

Discontinuous Galerkin Methods and High-Speed Turbulent Flows

NASA Astrophysics Data System (ADS)

Atak, Muhammed; Larsson, Johan; Munz, Claus-Dieter

2014-11-01

Discontinuous Galerkin methods gain increasing importance within the CFD community as they combine arbitrary high order of accuracy in complex geometries with parallel efficiency. Particularly the discontinuous Galerkin spectral element method (DGSEM) is a promising candidate for both the direct numerical simulation (DNS) and large eddy simulation (LES) of turbulent flows due to its excellent scaling attributes. In this talk, we present a DNS of a compressible turbulent boundary layer along a flat plate at a free-stream Mach number of M = 2.67 and assess the computational efficiency of the DGSEM at performing high-fidelity simulations of both transitional and turbulent boundary layers. We compare the accuracy of the results as well as the computational performance to results using a high order finite difference method.

A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methods.

PubMed

Moore, Jason H; Shestov, Maksim; Schmitt, Peter; Olson, Randal S

2018-01-01

A central challenge of developing and evaluating artificial intelligence and machine learning methods for regression and classification is access to data that illuminates the strengths and weaknesses of different methods. Open data plays an important role in this process by making it easy for computational researchers to easily access real data for this purpose. Genomics has in some examples taken a leading role in the open data effort starting with DNA microarrays. While real data from experimental and observational studies is necessary for developing computational methods it is not sufficient. This is because it is not possible to know what the ground truth is in real data. This must be accompanied by simulated data where that balance between signal and noise is known and can be directly evaluated. Unfortunately, there is a lack of methods and software for simulating data with the kind of complexity found in real biological and biomedical systems. We present here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating complex biological and biomedical data. Further, we introduce new methods for developing simulation models that generate data that specifically allows discrimination between different machine learning methods.

Verifying a computational method for predicting extreme ground motion

USGS Publications Warehouse

Harris, R.A.; Barall, M.; Andrews, D.J.; Duan, B.; Ma, S.; Dunham, E.M.; Gabriel, A.-A.; Kaneko, Y.; Kase, Y.; Aagaard, Brad T.; Oglesby, D.D.; Ampuero, J.-P.; Hanks, T.C.; Abrahamson, N.

2011-01-01

In situations where seismological data is rare or nonexistent, computer simulations may be used to predict ground motions caused by future earthquakes. This is particularly practical in the case of extreme ground motions, where engineers of special buildings may need to design for an event that has not been historically observed but which may occur in the far-distant future. Once the simulations have been performed, however, they still need to be tested. The SCEC-USGS dynamic rupture code verification exercise provides a testing mechanism for simulations that involve spontaneous earthquake rupture. We have performed this examination for the specific computer code that was used to predict maximum possible ground motion near Yucca Mountain. Our SCEC-USGS group exercises have demonstrated that the specific computer code that was used for the Yucca Mountain simulations produces similar results to those produced by other computer codes when tackling the same science problem. We also found that the 3D ground motion simulations produced smaller ground motions than the 2D simulations.

Fast estimation of first-order scattering in a medical x-ray computed tomography scanner using a ray-tracing technique.

PubMed

Liu, Xin

2014-01-01

This study describes a deterministic method for simulating the first-order scattering in a medical computed tomography scanner. The method was developed based on a physics model of x-ray photon interactions with matter and a ray tracing technique. The results from simulated scattering were compared to the ones from an actual scattering measurement. Two phantoms with homogeneous and heterogeneous material distributions were used in the scattering simulation and measurement. It was found that the simulated scatter profile was in agreement with the measurement result, with an average difference of 25% or less. Finally, tomographic images with artifacts caused by scatter were corrected based on the simulated scatter profiles. The image quality improved significantly.

Intravenous catheter training system: computer-based education versus traditional learning methods.

PubMed

Engum, Scott A; Jeffries, Pamela; Fisher, Lisa

2003-07-01

Virtual reality simulators allow trainees to practice techniques without consequences, reduce potential risk associated with training, minimize animal use, and help to develop standards and optimize procedures. Current intravenous (IV) catheter placement training methods utilize plastic arms, however, the lack of variability can diminish the educational stimulus for the student. This study compares the effectiveness of an interactive, multimedia, virtual reality computer IV catheter simulator with a traditional laboratory experience of teaching IV venipuncture skills to both nursing and medical students. A randomized, pretest-posttest experimental design was employed. A total of 163 participants, 70 baccalaureate nursing students and 93 third-year medical students beginning their fundamental skills training were recruited. The students ranged in age from 20 to 55 years (mean 25). Fifty-eight percent were female and 68% percent perceived themselves as having average computer skills (25% declaring excellence). The methods of IV catheter education compared included a traditional method of instruction involving a scripted self-study module which involved a 10-minute videotape, instructor demonstration, and hands-on-experience using plastic mannequin arms. The second method involved an interactive multimedia, commercially made computer catheter simulator program utilizing virtual reality (CathSim). The pretest scores were similar between the computer and the traditional laboratory group. There was a significant improvement in cognitive gains, student satisfaction, and documentation of the procedure with the traditional laboratory group compared with the computer catheter simulator group. Both groups were similar in their ability to demonstrate the skill correctly. CONCLUSIONS; This evaluation and assessment was an initial effort to assess new teaching methodologies related to intravenous catheter placement and their effects on student learning outcomes and behaviors. Technology alone is not a solution for stand alone IV catheter placement education. A traditional learning method was preferred by students. The combination of these two methods of education may further enhance the trainee's satisfaction and skill acquisition level.

A Practical Cone-beam CT Scatter Correction Method with Optimized Monte Carlo Simulations for Image-Guided Radiation Therapy

PubMed Central

Xu, Yuan; Bai, Ti; Yan, Hao; Ouyang, Luo; Pompos, Arnold; Wang, Jing; Zhou, Linghong; Jiang, Steve B.; Jia, Xun

2015-01-01

Cone-beam CT (CBCT) has become the standard image guidance tool for patient setup in image-guided radiation therapy. However, due to its large illumination field, scattered photons severely degrade its image quality. While kernel-based scatter correction methods have been used routinely in the clinic, it is still desirable to develop Monte Carlo (MC) simulation-based methods due to their accuracy. However, the high computational burden of the MC method has prevented routine clinical application. This paper reports our recent development of a practical method of MC-based scatter estimation and removal for CBCT. In contrast with conventional MC approaches that estimate scatter signals using a scatter-contaminated CBCT image, our method used a planning CT image for MC simulation, which has the advantages of accurate image intensity and absence of image truncation. In our method, the planning CT was first rigidly registered with the CBCT. Scatter signals were then estimated via MC simulation. After scatter signals were removed from the raw CBCT projections, a corrected CBCT image was reconstructed. The entire workflow was implemented on a GPU platform for high computational efficiency. Strategies such as projection denoising, CT image downsampling, and interpolation along the angular direction were employed to further enhance the calculation speed. We studied the impact of key parameters in the workflow on the resulting accuracy and efficiency, based on which the optimal parameter values were determined. Our method was evaluated in numerical simulation, phantom, and real patient cases. In the simulation cases, our method reduced mean HU errors from 44 HU to 3 HU and from 78 HU to 9 HU in the full-fan and the half-fan cases, respectively. In both the phantom and the patient cases, image artifacts caused by scatter, such as ring artifacts around the bowtie area, were reduced. With all the techniques employed, we achieved computation time of less than 30 sec including the time for both the scatter estimation and CBCT reconstruction steps. The efficacy of our method and its high computational efficiency make our method attractive for clinical use. PMID:25860299

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

Simulation of Hypervelocity Impact on Aluminum-Nextel-Kevlar Orbital Debris Shields

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.

2000-01-01

An improved hybrid particle-finite element method has been developed for hypervelocity impact simulation. The method combines the general contact-impact capabilities of particle codes with the true Lagrangian kinematics of large strain finite element formulations. Unlike some alternative schemes which couple Lagrangian finite element models with smooth particle hydrodynamics, the present formulation makes no use of slidelines or penalty forces. The method has been implemented in a parallel, three dimensional computer code. Simulations of three dimensional orbital debris impact problems using this parallel hybrid particle-finite element code, show good agreement with experiment and good speedup in parallel computation. The simulations included single and multi-plate shields as well as aluminum and composite shielding materials. at an impact velocity of eleven kilometers per second.

First-principles simulations of heat transport

NASA Astrophysics Data System (ADS)

Puligheddu, Marcello; Gygi, Francois; Galli, Giulia

2017-11-01

Advances in understanding heat transport in solids were recently reported by both experiment and theory. However an efficient and predictive quantum simulation framework to investigate thermal properties of solids, with the same complexity as classical simulations, has not yet been developed. Here we present a method to compute the thermal conductivity of solids by performing ab initio molecular dynamics at close to equilibrium conditions, which only requires calculations of first-principles trajectories and atomic forces, thus avoiding direct computation of heat currents and energy densities. In addition the method requires much shorter sequential simulation times than ordinary molecular dynamics techniques, making it applicable within density functional theory. We discuss results for a representative oxide, MgO, at different temperatures and for ordered and nanostructured morphologies, showing the performance of the method in different conditions.

Perspectives on the Future of CFD

NASA Technical Reports Server (NTRS)

Kwak, Dochan

2000-01-01

This viewgraph presentation gives an overview of the future of computational fluid dynamics (CFD), which in the past has pioneered the field of flow simulation. Over time CFD has progressed as computing power. Numerical methods have been advanced as CPU and memory capacity increases. Complex configurations are routinely computed now and direct numerical simulations (DNS) and large eddy simulations (LES) are used to study turbulence. As the computing resources changed to parallel and distributed platforms, computer science aspects such as scalability (algorithmic and implementation) and portability and transparent codings have advanced. Examples of potential future (or current) challenges include risk assessment, limitations of the heuristic model, and the development of CFD and information technology (IT) tools.

Algorithms and architecture for multiprocessor based circuit simulation

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

Deutsch, J.T.

Accurate electrical simulation is critical to the design of high performance integrated circuits. Logic simulators can verify function and give first-order timing information. Switch level simulators are more effective at dealing with charge sharing than standard logic simulators, but cannot provide accurate timing information or discover DC problems. Delay estimation techniques and cell level simulation can be used in constrained design methods, but must be tuned for each application, and circuit simulation must still be used to generate the cell models. None of these methods has the guaranteed accuracy that many circuit designers desire, and none can provide detailed waveformmore » information. Detailed electrical-level simulation can predict circuit performance if devices and parasitics are modeled accurately. However, the computational requirements of conventional circuit simulators make it impractical to simulate current large circuits. In this dissertation, the implementation of Iterated Timing Analysis (ITA), a relaxation-based technique for accurate circuit simulation, on a special-purpose multiprocessor is presented. The ITA method is an SOR-Newton, relaxation-based method which uses event-driven analysis and selective trace to exploit the temporal sparsity of the electrical network. Because event-driven selective trace techniques are employed, this algorithm lends itself to implementation on a data-driven computer.« less

Probabilistic power flow using improved Monte Carlo simulation method with correlated wind sources

NASA Astrophysics Data System (ADS)

Bie, Pei; Zhang, Buhan; Li, Hang; Deng, Weisi; Wu, Jiasi

2017-01-01

Probabilistic Power Flow (PPF) is a very useful tool for power system steady-state analysis. However, the correlation among different random injection power (like wind power) brings great difficulties to calculate PPF. Monte Carlo simulation (MCS) and analytical methods are two commonly used methods to solve PPF. MCS has high accuracy but is very time consuming. Analytical method like cumulants method (CM) has high computing efficiency but the cumulants calculating is not convenient when wind power output does not obey any typical distribution, especially when correlated wind sources are considered. In this paper, an Improved Monte Carlo simulation method (IMCS) is proposed. The joint empirical distribution is applied to model different wind power output. This method combines the advantages of both MCS and analytical method. It not only has high computing efficiency, but also can provide solutions with enough accuracy, which is very suitable for on-line analysis.

VERAIn

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

Simunovic, Srdjan

2015-02-16

CASL's modeling and simulation technology, the Virtual Environment for Reactor Applications (VERA), incorporates coupled physics and science-based models, state-of-the-art numerical methods, modern computational science, integrated uncertainty quantification (UQ) and validation against data from operating pressurized water reactors (PWRs), single-effect experiments, and integral tests. The computational simulation component of VERA is the VERA Core Simulator (VERA-CS). The core simulator is the specific collection of multi-physics computer codes used to model and deplete a LWR core over multiple cycles. The core simulator has a single common input file that drives all of the different physics codes. The parser code, VERAIn, converts VERAmore » Input into an XML file that is used as input to different VERA codes.« less

Dynamic Deployment Simulations of Inflatable Space Structures

NASA Technical Reports Server (NTRS)

Wang, John T.

2005-01-01

The feasibility of using Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method in LSDYNA to simulate the dynamic deployment of inflatable space structures is investigated. The CV and ALE methods were used to predict the inflation deployments of three folded tube configurations. The CV method was found to be a simple and computationally efficient method that may be adequate for modeling slow inflation deployment sine the inertia of the inflation gas can be neglected. The ALE method was found to be very computationally intensive since it involves the solving of three conservative equations of fluid as well as dealing with complex fluid structure interactions.

Local-Area-Network Simulator

NASA Technical Reports Server (NTRS)

Gibson, Jim; Jordan, Joe; Grant, Terry

1990-01-01

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

Efficient Computation Of Manipulator Inertia Matrix

NASA Technical Reports Server (NTRS)

Fijany, Amir; Bejczy, Antal K.

1991-01-01

Improved method for computation of manipulator inertia matrix developed, based on concept of spatial inertia of composite rigid body. Required for implementation of advanced dynamic-control schemes as well as dynamic simulation of manipulator motion. Motivated by increasing demand for fast algorithms to provide real-time control and simulation capability and, particularly, need for faster-than-real-time simulation capability, required in many anticipated space teleoperation applications.

Multilevel Monte Carlo simulation of Coulomb collisions

DOE PAGES

Rosin, M. S.; Ricketson, L. F.; Dimits, A. M.; ...

2014-05-29

We present a new, for plasma physics, highly efficient multilevel Monte Carlo numerical method for simulating Coulomb collisions. The method separates and optimally minimizes the finite-timestep and finite-sampling errors inherent in the Langevin representation of the Landau–Fokker–Planck equation. It does so by combining multiple solutions to the underlying equations with varying numbers of timesteps. For a desired level of accuracy ε , the computational cost of the method is O(ε –2) or (ε –2(lnε) 2), depending on the underlying discretization, Milstein or Euler–Maruyama respectively. This is to be contrasted with a cost of O(ε –3) for direct simulation Monte Carlomore » or binary collision methods. We successfully demonstrate the method with a classic beam diffusion test case in 2D, making use of the Lévy area approximation for the correlated Milstein cross terms, and generating a computational saving of a factor of 100 for ε=10 –5. Lastly, we discuss the importance of the method for problems in which collisions constitute the computational rate limiting step, and its limitations.« less

Understanding Islamist political violence through computational social simulation

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

Watkins, Jennifer H; Mackerrow, Edward P; Patelli, Paolo G

Understanding the process that enables political violence is of great value in reducing the future demand for and support of violent opposition groups. Methods are needed that allow alternative scenarios and counterfactuals to be scientifically researched. Computational social simulation shows promise in developing 'computer experiments' that would be unfeasible or unethical in the real world. Additionally, the process of modeling and simulation reveals and challenges assumptions that may not be noted in theories, exposes areas where data is not available, and provides a rigorous, repeatable, and transparent framework for analyzing the complex dynamics of political violence. This paper demonstrates themore » computational modeling process using two simulation techniques: system dynamics and agent-based modeling. The benefits and drawbacks of both techniques are discussed. In developing these social simulations, we discovered that the social science concepts and theories needed to accurately simulate the associated psychological and social phenomena were lacking.« less

System and method for measuring residual stress

DOEpatents

Prime, Michael B.

2002-01-01

The present invention is a method and system for determining the residual stress within an elastic object. In the method, an elastic object is cut along a path having a known configuration. The cut creates a portion of the object having a new free surface. The free surface then deforms to a contour which is different from the path. Next, the contour is measured to determine how much deformation has occurred across the new free surface. Points defining the contour are collected in an empirical data set. The portion of the object is then modeled in a computer simulator. The points in the empirical data set are entered into the computer simulator. The computer simulator then calculates the residual stress along the path which caused the points within the object to move to the positions measured in the empirical data set. The calculated residual stress is then presented in a useful format to an analyst.

Radiative properties of flame-generated soot

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

Koeylue, U.O.; Faeth, G.M.

1993-05-01

Approximate methods for estimating the optical properties of flame-generated soot aggregates were evaluated using existing computer simulations and measurements in the visible and near-infrared portions of the spectrum. The following approximate methods were evaluated for both individual aggregates and polydisperse aggregate populations: the Rayleigh scattering approximation, Mie scattering for an equivalent sphere, and Rayleigh-Debye-Gans (R-D-G) scattering for both given and fractal aggregates. Results of computer simulations involved both prescribed aggregate geometry and numerically generated aggregates by cluster-cluster aggregation; multiple scattering was considered exactly using the mean-field approximation, and ignored using the R-D-G approximation. Measurements involved the angular scattering properties ofmore » soot in the postflame regions of both premixed and nonpremixed flames. The results show that available computer simulations and measurements of soot aggregate optical properties are not adequate to provide a definitive evaluation of the approximate prediction methods. 40 refs., 7 figs., 1 tab.« less

Numerical simulation using vorticity-vector potential formulation

NASA Technical Reports Server (NTRS)

Tokunaga, Hiroshi

1993-01-01

An accurate and efficient computational method is needed for three-dimensional incompressible viscous flows in engineering applications. On solving the turbulent shear flows directly or using the subgrid scale model, it is indispensable to resolve the small scale fluid motions as well as the large scale motions. From this point of view, the pseudo-spectral method is used so far as the computational method. However, the finite difference or the finite element methods are widely applied for computing the flow with practical importance since these methods are easily applied to the flows with complex geometric configurations. However, there exist several problems in applying the finite difference method to direct and large eddy simulations. Accuracy is one of most important problems. This point was already addressed by the present author on the direct simulations on the instability of the plane Poiseuille flow and also on the transition to turbulence. In order to obtain high efficiency, the multi-grid Poisson solver is combined with the higher-order, accurate finite difference method. The formulation method is also one of the most important problems in applying the finite difference method to the incompressible turbulent flows. The three-dimensional Navier-Stokes equations have been solved so far in the primitive variables formulation. One of the major difficulties of this method is the rigorous satisfaction of the equation of continuity. In general, the staggered grid is used for the satisfaction of the solenoidal condition for the velocity field at the wall boundary. However, the velocity field satisfies the equation of continuity automatically in the vorticity-vector potential formulation. From this point of view, the vorticity-vector potential method was extended to the generalized coordinate system. In the present article, we adopt the vorticity-vector potential formulation, the generalized coordinate system, and the 4th-order accurate difference method as the computational method. We present the computational method and apply the present method to computations of flows in a square cavity at large Reynolds number in order to investigate its effectiveness.

A multiscale approach to accelerate pore-scale simulation of porous electrodes

NASA Astrophysics Data System (ADS)

Zheng, Weibo; Kim, Seung Hyun

2017-04-01

A new method to accelerate pore-scale simulation of porous electrodes is presented. The method combines the macroscopic approach with pore-scale simulation by decomposing a physical quantity into macroscopic and local variations. The multiscale method is applied to the potential equation in pore-scale simulation of a Proton Exchange Membrane Fuel Cell (PEMFC) catalyst layer, and validated with the conventional approach for pore-scale simulation. Results show that the multiscale scheme substantially reduces the computational cost without sacrificing accuracy.

Damage progression in Composite Structures

NASA Technical Reports Server (NTRS)

Minnetyan, Levon

1996-01-01

A computational simulation tool is used to evaluate the various stages of damage progression in composite materials during Iosipescu sheat testing. Unidirectional composite specimens with either the major or minor material axis in the load direction are considered. Damage progression characteristics are described for each specimen using two types of boundary conditions. A procedure is outlined regarding the use of computational simulation in composites testing. Iosipescu shear testing using the V-notched beam specimen is a convenient method to measure both shear strength and shear stiffness simultaneously. The evaluation of composite test response can be made more productive and informative via computational simulation of progressive damage and fracture. Computational simulation performs a complete evaluation of laminated composite fracture via assessment of ply and subply level damage/fracture processes.

Computational Methods for HSCT-Inlet Controls/CFD Interdisciplinary Research

NASA Technical Reports Server (NTRS)

Cole, Gary L.; Melcher, Kevin J.; Chicatelli, Amy K.; Hartley, Tom T.; Chung, Joongkee

1994-01-01

A program aimed at facilitating the use of computational fluid dynamics (CFD) simulations by the controls discipline is presented. The objective is to reduce the development time and cost for propulsion system controls by using CFD simulations to obtain high-fidelity system models for control design and as numerical test beds for control system testing and validation. An interdisciplinary team has been formed to develop analytical and computational tools in three discipline areas: controls, CFD, and computational technology. The controls effort has focused on specifying requirements for an interface between the controls specialist and CFD simulations and a new method for extracting linear, reduced-order control models from CFD simulations. Existing CFD codes are being modified to permit time accurate execution and provide realistic boundary conditions for controls studies. Parallel processing and distributed computing techniques, along with existing system integration software, are being used to reduce CFD execution times and to support the development of an integrated analysis/design system. This paper describes: the initial application for the technology being developed, the high speed civil transport (HSCT) inlet control problem; activities being pursued in each discipline area; and a prototype analysis/design system in place for interactive operation and visualization of a time-accurate HSCT-inlet simulation.

Efficient Monte Carlo Estimation of the Expected Value of Sample Information Using Moment Matching.

PubMed

Heath, Anna; Manolopoulou, Ioanna; Baio, Gianluca

2018-02-01

The Expected Value of Sample Information (EVSI) is used to calculate the economic value of a new research strategy. Although this value would be important to both researchers and funders, there are very few practical applications of the EVSI. This is due to computational difficulties associated with calculating the EVSI in practical health economic models using nested simulations. We present an approximation method for the EVSI that is framed in a Bayesian setting and is based on estimating the distribution of the posterior mean of the incremental net benefit across all possible future samples, known as the distribution of the preposterior mean. Specifically, this distribution is estimated using moment matching coupled with simulations that are available for probabilistic sensitivity analysis, which is typically mandatory in health economic evaluations. This novel approximation method is applied to a health economic model that has previously been used to assess the performance of other EVSI estimators and accurately estimates the EVSI. The computational time for this method is competitive with other methods. We have developed a new calculation method for the EVSI which is computationally efficient and accurate. This novel method relies on some additional simulation so can be expensive in models with a large computational cost.

Modelling rollover behaviour of exacavator-based forest machines

Treesearch

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

2003-01-01

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

A Hybrid Computer Simulation to Generate the DNA Distribution of a Cell Population.

ERIC Educational Resources Information Center

Griebling, John L.; Adams, William S.

1981-01-01

Described is a method of simulating the formation of a DNA distribution, on which statistical results and experimentally measured parameters from DNA distribution and percent-labeled mitosis studies are combined. An EAI-680 and DECSystem-10 Hybrid Computer configuration are used. (Author/CS)

TEACHING ENGINEERING DESIGN, A STUDY OF JOBSHOP.

ERIC Educational Resources Information Center

ENTWISLE, DORIS R.; HUGGINS, W.H.

THE USE OF A COMPUTER PROGRAM BY ENGINEERING STUDENTS TO SIMULATE A JOB SHOP THAT MANUFACTURES ELECTRONIC DEVICES HAS INDICATED THAT SIMULATION METHODS OFFER REALISTIC ASSISTANCE IN TEACHING. EACH STUDENT IN THE STUDY SUBMITTED SPECIFICATIONS FOR A CIRCUIT DESIGN AND, FROM THE COMPUTER, RECEIVED PERFORMANCE ASSESSMENTS OF THE CIRCUIT WHICH…

An immersed boundary method for modeling a dirty geometry data

NASA Astrophysics Data System (ADS)

Onishi, Keiji; Tsubokura, Makoto

2017-11-01

We present a robust, fast, and low preparation cost immersed boundary method (IBM) for simulating an incompressible high Re flow around highly complex geometries. The method is achieved by the dispersion of the momentum by the axial linear projection and the approximate domain assumption satisfying the mass conservation around the wall including cells. This methodology has been verified against an analytical theory and wind tunnel experiment data. Next, we simulate the problem of flow around a rotating object and demonstrate the ability of this methodology to the moving geometry problem. This methodology provides the possibility as a method for obtaining a quick solution at a next large scale supercomputer. This research was supported by MEXT as ``Priority Issue on Post-K computer'' (Development of innovative design and production processes) and used computational resources of the K computer provided by the RIKEN Advanced Institute for Computational Science.

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

NASA Astrophysics Data System (ADS)

Czerepicki, A.; Koniak, M.

2017-06-01

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

Statistical Surrogate Modeling of Atmospheric Dispersion Events Using Bayesian Adaptive Splines

NASA Astrophysics Data System (ADS)

Francom, D.; Sansó, B.; Bulaevskaya, V.; Lucas, D. D.

2016-12-01

Uncertainty in the inputs of complex computer models, including atmospheric dispersion and transport codes, is often assessed via statistical surrogate models. Surrogate models are computationally efficient statistical approximations of expensive computer models that enable uncertainty analysis. We introduce Bayesian adaptive spline methods for producing surrogate models that capture the major spatiotemporal patterns of the parent model, while satisfying all the necessities of flexibility, accuracy and computational feasibility. We present novel methodological and computational approaches motivated by a controlled atmospheric tracer release experiment conducted at the Diablo Canyon nuclear power plant in California. Traditional methods for building statistical surrogate models often do not scale well to experiments with large amounts of data. Our approach is well suited to experiments involving large numbers of model inputs, large numbers of simulations, and functional output for each simulation. Our approach allows us to perform global sensitivity analysis with ease. We also present an approach to calibration of simulators using field data.

SIMULATION OF FLOOD HYDROGRAPHS FOR GEORGIA STREAMS.

USGS Publications Warehouse

Inman, E.J.; Armbruster, J.T.

1986-01-01

Flood hydrographs are needed for the design of many highway drainage structures and embankments. A method for simulating these flood hydrographs at urban and rural ungauged sites in Georgia is presented. The O'Donnell method was used to compute unit hydrographs from 355 flood events from 80 stations. An average unit hydrograph and an average lag time were computed for each station. These average unit hydrographs were transformed to unit hydrographs having durations of one-fourth, one-third, one-half, and three-fourths lag time and then reduced to dimensionless terms by dividing the time by lag time and the discharge by peak discharge. Hydrographs were simulated for these 355 flood events and their widths were compared with the widths of the observed hydrographs at 50 and 75 percent of peak flow. For simulating hydrographs at sites larger than 500 mi**2, the U. S. Geological Survey computer model CONROUT can be used.

Towards the simulation of molecular collisions with a superconducting quantum computer

NASA Astrophysics Data System (ADS)

Geller, Michael

2013-05-01

I will discuss the prospects for the use of large-scale, error-corrected quantum computers to simulate complex quantum dynamics such as molecular collisions. This will likely require millions qubits. I will also discuss an alternative approach [M. R. Geller et al., arXiv:1210.5260] that is ideally suited for today's superconducting circuits, which uses the single-excitation subspace (SES) of a system of n tunably coupled qubits. The SES method allows many operations in the unitary group SU(n) to be implemented in a single step, bypassing the need for elementary gates, thereby making large computations possible without error correction. The method enables universal quantum simulation, including simulation of the time-dependent Schrodinger equation, and we argue that a 1000-qubit SES processor should be capable of achieving quantum speedup relative to a petaflop supercomputer. We speculate on the utility and practicality of such a simulator for atomic and molecular collision physics. Work supported by the US National Science Foundation CDI program.

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

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

Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn

2015-03-28

The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much lessmore » computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.« less

Full Quantum Dynamics Simulation of a Realistic Molecular System Using the Adaptive Time-Dependent Density Matrix Renormalization Group Method.

PubMed

Yao, Yao; Sun, Ke-Wei; Luo, Zhen; Ma, Haibo

2018-01-18

The accurate theoretical interpretation of ultrafast time-resolved spectroscopy experiments relies on full quantum dynamics simulations for the investigated system, which is nevertheless computationally prohibitive for realistic molecular systems with a large number of electronic and/or vibrational degrees of freedom. In this work, we propose a unitary transformation approach for realistic vibronic Hamiltonians, which can be coped with using the adaptive time-dependent density matrix renormalization group (t-DMRG) method to efficiently evolve the nonadiabatic dynamics of a large molecular system. We demonstrate the accuracy and efficiency of this approach with an example of simulating the exciton dissociation process within an oligothiophene/fullerene heterojunction, indicating that t-DMRG can be a promising method for full quantum dynamics simulation in large chemical systems. Moreover, it is also shown that the proper vibronic features in the ultrafast electronic process can be obtained by simulating the two-dimensional (2D) electronic spectrum by virtue of the high computational efficiency of the t-DMRG method.

Influence of model order reduction methods on dynamical-optical simulations

NASA Astrophysics Data System (ADS)

Störkle, Johannes; Eberhard, Peter

2017-04-01

In this work, the influence of model order reduction (MOR) methods on optical aberrations is analyzed within a dynamical-optical simulation of a high precision optomechanical system. Therefore, an integrated modeling process and new methods have to be introduced for the computation and investigation of the overall dynamical-optical behavior. For instance, this optical system can be a telescope optic or a lithographic objective. In order to derive a simplified mechanical model for transient time simulations with low computational cost, the method of elastic multibody systems in combination with MOR methods can be used. For this, software tools and interfaces are defined and created. Furthermore, mechanical and optical simulation models are derived and implemented. With these, on the one hand, the mechanical sensitivity can be investigated for arbitrary external excitations and on the other hand, the related optical behavior can be predicted. In order to clarify these methods, academic examples are chosen and the influences of the MOR methods and simulation strategies are analyzed. Finally, the systems are investigated with respect to the mechanical-optical frequency responses, and in conclusion, some recommendations for the application of reduction methods are given.

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

DOE PAGES

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

2016-03-04

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

Aspects of numerical and representational methods related to the finite-difference simulation of advective and dispersive transport of freshwater in a thin brackish aquifer

USGS Publications Warehouse

Merritt, M.L.

1993-01-01

The simulation of the transport of injected freshwater in a thin brackish aquifer, overlain and underlain by confining layers containing more saline water, is shown to be influenced by the choice of the finite-difference approximation method, the algorithm for representing vertical advective and dispersive fluxes, and the values assigned to parametric coefficients that specify the degree of vertical dispersion and molecular diffusion that occurs. Computed potable water recovery efficiencies will differ depending upon the choice of algorithm and approximation method, as will dispersion coefficients estimated based on the calibration of simulations to match measured data. A comparison of centered and backward finite-difference approximation methods shows that substantially different transition zones between injected and native waters are depicted by the different methods, and computed recovery efficiencies vary greatly. Standard and experimental algorithms and a variety of values for molecular diffusivity, transverse dispersivity, and vertical scaling factor were compared in simulations of freshwater storage in a thin brackish aquifer. Computed recovery efficiencies vary considerably, and appreciable differences are observed in the distribution of injected freshwater in the various cases tested. The results demonstrate both a qualitatively different description of transport using the experimental algorithms and the interrelated influences of molecular diffusion and transverse dispersion on simulated recovery efficiency. When simulating natural aquifer flow in cross-section, flushing of the aquifer occurred for all tested coefficient choices using both standard and experimental algorithms. ?? 1993.

The ensemble switch method for computing interfacial tensions

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

Schmitz, Fabian; Virnau, Peter

2015-04-14

We present a systematic thermodynamic integration approach to compute interfacial tensions for solid-liquid interfaces, which is based on the ensemble switch method. Applying Monte Carlo simulations and finite-size scaling techniques, we obtain results for hard spheres, which are in agreement with previous computations. The case of solid-liquid interfaces in a variant of the effective Asakura-Oosawa model and of liquid-vapor interfaces in the Lennard-Jones model are discussed as well. We demonstrate that a thorough finite-size analysis of the simulation data is required to obtain precise results for the interfacial tension.

Applying Parallel Adaptive Methods with GeoFEST/PYRAMID to Simulate Earth Surface Crustal Dynamics

NASA Technical Reports Server (NTRS)

Norton, Charles D.; Lyzenga, Greg; Parker, Jay; Glasscoe, Margaret; Donnellan, Andrea; Li, Peggy

2006-01-01

This viewgraph presentation reviews the use Adaptive Mesh Refinement (AMR) in simulating the Crustal Dynamics of Earth's Surface. AMR simultaneously improves solution quality, time to solution, and computer memory requirements when compared to generating/running on a globally fine mesh. The use of AMR in simulating the dynamics of the Earth's Surface is spurred by future proposed NASA missions, such as InSAR for Earth surface deformation and other measurements. These missions will require support for large-scale adaptive numerical methods using AMR to model observations. AMR was chosen because it has been successful in computation fluid dynamics for predictive simulation of complex flows around complex structures.

A Comparative Study of High and Low Fidelity Fan Models for Turbofan Engine System Simulation

NASA Technical Reports Server (NTRS)

Reed, John A.; Afjeh, Abdollah A.

1991-01-01

In this paper, a heterogeneous propulsion system simulation method is presented. The method is based on the formulation of a cycle model of a gas turbine engine. The model includes the nonlinear characteristics of the engine components via use of empirical data. The potential to simulate the entire engine operation on a computer without the aid of data is demonstrated by numerically generating "performance maps" for a fan component using two flow models of varying fidelity. The suitability of the fan models were evaluated by comparing the computed performance with experimental data. A discussion of the potential benefits and/or difficulties in connecting simulations solutions of differing fidelity is given.

Adjoint-Based Aerodynamic Design of Complex Aerospace Configurations

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.

2016-01-01

An overview of twenty years of adjoint-based aerodynamic design research at NASA Langley Research Center is presented. Adjoint-based algorithms provide a powerful tool for efficient sensitivity analysis of complex large-scale computational fluid dynamics (CFD) simulations. Unlike alternative approaches for which computational expense generally scales with the number of design parameters, adjoint techniques yield sensitivity derivatives of a simulation output with respect to all input parameters at the cost of a single additional simulation. With modern large-scale CFD applications often requiring millions of compute hours for a single analysis, the efficiency afforded by adjoint methods is critical in realizing a computationally tractable design optimization capability for such applications.

GAP Noise Computation By The CE/SE Method

NASA Technical Reports Server (NTRS)

Loh, Ching Y.; Chang, Sin-Chung; Wang, Xiao Y.; Jorgenson, Philip C. E.

2001-01-01

A typical gap noise problem is considered in this paper using the new space-time conservation element and solution element (CE/SE) method. Implementation of the computation is straightforward. No turbulence model, LES (large eddy simulation) or a preset boundary layer profile is used, yet the computed frequency agrees well with the experimental one.

New method of processing heat treatment experiments with numerical simulation support

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

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

PubMed Central

2011-01-01

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

Computer Simulation in Tomorrow's Schools.

ERIC Educational Resources Information Center

Foster, David

1984-01-01

Suggests use of simulation as an educational strategy has promise for the school of the future; discusses specific advantages of simulations over alternative educational methods, role of microcomputers in educational simulation, and past obstacles and future promise of microcomputer simulations; and presents a literature review on effectiveness of…

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

A Simple Graphical Method for Quantification of Disaster Management Surge Capacity Using Computer Simulation and Process-control Tools.

PubMed

Franc, Jeffrey Michael; Ingrassia, Pier Luigi; Verde, Manuela; Colombo, Davide; Della Corte, Francesco

2015-02-01

Surge capacity, or the ability to manage an extraordinary volume of patients, is fundamental for hospital management of mass-casualty incidents. However, quantification of surge capacity is difficult and no universal standard for its measurement has emerged, nor has a standardized statistical method been advocated. As mass-casualty incidents are rare, simulation may represent a viable alternative to measure surge capacity. Hypothesis/Problem The objective of the current study was to develop a statistical method for the quantification of surge capacity using a combination of computer simulation and simple process-control statistical tools. Length-of-stay (LOS) and patient volume (PV) were used as metrics. The use of this method was then demonstrated on a subsequent computer simulation of an emergency department (ED) response to a mass-casualty incident. In the derivation phase, 357 participants in five countries performed 62 computer simulations of an ED response to a mass-casualty incident. Benchmarks for ED response were derived from these simulations, including LOS and PV metrics for triage, bed assignment, physician assessment, and disposition. In the application phase, 13 students of the European Master in Disaster Medicine (EMDM) program completed the same simulation scenario, and the results were compared to the standards obtained in the derivation phase. Patient-volume metrics included number of patients to be triaged, assigned to rooms, assessed by a physician, and disposed. Length-of-stay metrics included median time to triage, room assignment, physician assessment, and disposition. Simple graphical methods were used to compare the application phase group to the derived benchmarks using process-control statistical tools. The group in the application phase failed to meet the indicated standard for LOS from admission to disposition decision. This study demonstrates how simulation software can be used to derive values for objective benchmarks of ED surge capacity using PV and LOS metrics. These objective metrics can then be applied to other simulation groups using simple graphical process-control tools to provide a numeric measure of surge capacity. Repeated use in simulations of actual EDs may represent a potential means of objectively quantifying disaster management surge capacity. It is hoped that the described statistical method, which is simple and reusable, will be useful for investigators in this field to apply to their own research.

Numerical Simulation of Flow Through an Artificial Heart

NASA Technical Reports Server (NTRS)

Rogers, Stuart E.; Kutler, Paul; Kwak, Dochan; Kiris, Cetin

1989-01-01

A solution procedure was developed that solves the unsteady, incompressible Navier-Stokes equations, and was used to numerically simulate viscous incompressible flow through a model of the Pennsylvania State artificial heart. The solution algorithm is based on the artificial compressibility method, and uses flux-difference splitting to upwind the convective terms; a line-relaxation scheme is used to solve the equations. The time-accuracy of the method is obtained by iteratively solving the equations at each physical time step. The artificial heart geometry involves a piston-type action with a moving solid wall. A single H-grid is fit inside the heart chamber. The grid is continuously compressed and expanded with a constant number of grid points to accommodate the moving piston. The computational domain ends at the valve openings where nonreflective boundary conditions based on the method of characteristics are applied. Although a number of simplifing assumptions were made regarding the geometry, the computational results agreed reasonably well with an experimental picture. The computer time requirements for this flow simulation, however, are quite extensive. Computational study of this type of geometry would benefit greatly from improvements in computer hardware speed and algorithm efficiency enhancements.

Numerical simulation of biofilm growth in flow channels using a cellular automaton approach coupled with a macro flow computation.

PubMed

Yamamoto, Takehiro; Ueda, Shuya

2013-01-01

Biofilm is a slime-like complex aggregate of microorganisms and their products, extracellular polymer substances, that grows on a solid surface. The growth phenomenon of biofilm is relevant to the corrosion and clogging of water pipes, the chemical processes in a bioreactor, and bioremediation. In these phenomena, the behavior of the biofilm under flow has an important role. Therefore, controlling the biofilm behavior in each process is important. To provide a computational tool for analyzing biofilm growth, the present study proposes a computational model for the simulation of biofilm growth in flows. This model accounts for the growth, decay, detachment and adhesion of biofilms. The proposed model couples the computation of the surrounding fluid flow, using the finite volume method, with the simulation of biofilm growth, using the cellular automaton approach, a relatively low-computational-cost method. Furthermore, a stochastic approach for considering the adhesion process is proposed. Numerical simulations for the biofilm growth on a planar wall and that in an L-shaped rectangular channel were carried out. A variety of biofilm structures were observed depending on the strength of the flow. Moreover, the importance of the detachment and adhesion processes was confirmed.

DAKOTA Design Analysis Kit for Optimization and Terascale

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

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

2010-02-24

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

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

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

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

2015-01-15

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

Educational aspects of molecular simulation

NASA Astrophysics Data System (ADS)

Allen, Michael P.

This article addresses some aspects of teaching simulation methods to undergraduates and graduate students. Simulation is increasingly a cross-disciplinary activity, which means that the students who need to learn about simulation methods may have widely differing backgrounds. Also, they may have a wide range of views on what constitutes an interesting application of simulation methods. Almost always, a successful simulation course includes an element of practical, hands-on activity: a balance always needs to be struck between treating the simulation software as a 'black box', and becoming bogged down in programming issues. With notebook computers becoming widely available, students often wish to take away the programs to run themselves, and access to raw computer power is not the limiting factor that it once was; on the other hand, the software should be portable and, if possible, free. Examples will be drawn from the author's experience in three different contexts. (1) An annual simulation summer school for graduate students, run by the UK CCP5 organization, in which practical sessions are combined with an intensive programme of lectures describing the methodology. (2) A molecular modelling module, given as part of a doctoral training centre in the Life Sciences at Warwick, for students who might not have a first degree in the physical sciences. (3) An undergraduate module in Physics at Warwick, also taken by students from other disciplines, teaching high performance computing, visualization, and scripting in the context of a physical application such as Monte Carlo simulation.

FastMag: Fast micromagnetic simulator for complex magnetic structures (invited)

NASA Astrophysics Data System (ADS)

Chang, R.; Li, S.; Lubarda, M. V.; Livshitz, B.; Lomakin, V.

2011-04-01

A fast micromagnetic simulator (FastMag) for general problems is presented. FastMag solves the Landau-Lifshitz-Gilbert equation and can handle multiscale problems with a high computational efficiency. The simulator derives its high performance from efficient methods for evaluating the effective field and from implementations on massively parallel graphics processing unit (GPU) architectures. FastMag discretizes the computational domain into tetrahedral elements and therefore is highly flexible for general problems. The magnetostatic field is computed via the superposition principle for both volume and surface parts of the computational domain. This is accomplished by implementing efficient quadrature rules and analytical integration for overlapping elements in which the integral kernel is singular. Thus, discretized superposition integrals are computed using a nonuniform grid interpolation method, which evaluates the field from N sources at N collocated observers in O(N) operations. This approach allows handling objects of arbitrary shape, allows easily calculating of the field outside the magnetized domains, does not require solving a linear system of equations, and requires little memory. FastMag is implemented on GPUs with ?> GPU-central processing unit speed-ups of 2 orders of magnitude. Simulations are shown of a large array of magnetic dots and a recording head fully discretized down to the exchange length, with over a hundred million tetrahedral elements on an inexpensive desktop computer.

Winter Simulation Conference, Miami Beach, Fla., December 4-6, 1978, Proceedings. Volumes 1 & 2

NASA Technical Reports Server (NTRS)

Highland, H. J. (Editor); Nielsen, N. R.; Hull, L. G.

1978-01-01

The papers report on the various aspects of simulation such as random variate generation, simulation optimization, ranking and selection of alternatives, model management, documentation, data bases, and instructional methods. Simulation studies in a wide variety of fields are described, including system design and scheduling, government and social systems, agriculture, computer systems, the military, transportation, corporate planning, ecosystems, health care, manufacturing and industrial systems, computer networks, education, energy, production planning and control, financial models, behavioral models, information systems, and inventory control.

Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

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

Candel, A.; Kabel, A.; Lee, L.

In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

Fast multipurpose Monte Carlo simulation for proton therapy using multi- and many-core CPU architectures.

PubMed

Souris, Kevin; Lee, John Aldo; Sterpin, Edmond

2016-04-01

Accuracy in proton therapy treatment planning can be improved using Monte Carlo (MC) simulations. However the long computation time of such methods hinders their use in clinical routine. This work aims to develop a fast multipurpose Monte Carlo simulation tool for proton therapy using massively parallel central processing unit (CPU) architectures. A new Monte Carlo, called MCsquare (many-core Monte Carlo), has been designed and optimized for the last generation of Intel Xeon processors and Intel Xeon Phi coprocessors. These massively parallel architectures offer the flexibility and the computational power suitable to MC methods. The class-II condensed history algorithm of MCsquare provides a fast and yet accurate method of simulating heavy charged particles such as protons, deuterons, and alphas inside voxelized geometries. Hard ionizations, with energy losses above a user-specified threshold, are simulated individually while soft events are regrouped in a multiple scattering theory. Elastic and inelastic nuclear interactions are sampled from ICRU 63 differential cross sections, thereby allowing for the computation of prompt gamma emission profiles. MCsquare has been benchmarked with the gate/geant4 Monte Carlo application for homogeneous and heterogeneous geometries. Comparisons with gate/geant4 for various geometries show deviations within 2%-1 mm. In spite of the limited memory bandwidth of the coprocessor simulation time is below 25 s for 10(7) primary 200 MeV protons in average soft tissues using all Xeon Phi and CPU resources embedded in a single desktop unit. MCsquare exploits the flexibility of CPU architectures to provide a multipurpose MC simulation tool. Optimized code enables the use of accurate MC calculation within a reasonable computation time, adequate for clinical practice. MCsquare also simulates prompt gamma emission and can thus be used also for in vivo range verification.

QM/MM free energy simulations: recent progress and challenges

PubMed Central

Lu, Xiya; Fang, Dong; Ito, Shingo; Okamoto, Yuko; Ovchinnikov, Victor

2016-01-01

Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections. PMID:27563170

Simulator certification methods and the vertical motion simulator

NASA Technical Reports Server (NTRS)

Showalter, T. W.

1981-01-01

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

PARALLEL HOP: A SCALABLE HALO FINDER FOR MASSIVE COSMOLOGICAL DATA SETS

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

Skory, Stephen; Turk, Matthew J.; Norman, Michael L.

2010-11-15

Modern N-body cosmological simulations contain billions (10{sup 9}) of dark matter particles. These simulations require hundreds to thousands of gigabytes of memory and employ hundreds to tens of thousands of processing cores on many compute nodes. In order to study the distribution of dark matter in a cosmological simulation, the dark matter halos must be identified using a halo finder, which establishes the halo membership of every particle in the simulation. The resources required for halo finding are similar to the requirements for the simulation itself. In particular, simulations have become too extensive to use commonly employed halo finders, suchmore » that the computational requirements to identify halos must now be spread across multiple nodes and cores. Here, we present a scalable-parallel halo finding method called Parallel HOP for large-scale cosmological simulation data. Based on the halo finder HOP, it utilizes message passing interface and domain decomposition to distribute the halo finding workload across multiple compute nodes, enabling analysis of much larger data sets than is possible with the strictly serial or previous parallel implementations of HOP. We provide a reference implementation of this method as a part of the toolkit {sup yt}, an analysis toolkit for adaptive mesh refinement data that include complementary analysis modules. Additionally, we discuss a suite of benchmarks that demonstrate that this method scales well up to several hundred tasks and data sets in excess of 2000{sup 3} particles. The Parallel HOP method and our implementation can be readily applied to any kind of N-body simulation data and is therefore widely applicable.« less

Computational Fluid Dynamics of Whole-Body Aircraft

NASA Astrophysics Data System (ADS)

Agarwal, Ramesh

1999-01-01

The current state of the art in computational aerodynamics for whole-body aircraft flowfield simulations is described. Recent advances in geometry modeling, surface and volume grid generation, and flow simulation algorithms have led to accurate flowfield predictions for increasingly complex and realistic configurations. As a result, computational aerodynamics has emerged as a crucial enabling technology for the design and development of flight vehicles. Examples illustrating the current capability for the prediction of transport and fighter aircraft flowfields are presented. Unfortunately, accurate modeling of turbulence remains a major difficulty in the analysis of viscosity-dominated flows. In the future, inverse design methods, multidisciplinary design optimization methods, artificial intelligence technology, and massively parallel computer technology will be incorporated into computational aerodynamics, opening up greater opportunities for improved product design at substantially reduced costs.

2D Quantum Simulation of MOSFET Using the Non Equilibrium Green's Function Method

NASA Technical Reports Server (NTRS)

Svizhenko, Alexel; Anantram, M. P.; Govindan, T. R.; Yan, Jerry (Technical Monitor)

2000-01-01

The objectives this viewgraph presentation summarizes include: (1) the development of a quantum mechanical simulator for ultra short channel MOSFET simulation, including theory, physical approximations, and computer code; (2) explore physics that is not accessible by semiclassical methods; (3) benchmarking of semiclassical and classical methods; and (4) study other two-dimensional devices and molecular structure, from discretized Hamiltonian to tight-binding Hamiltonian.

Computational methods for diffusion-influenced biochemical reactions.

PubMed

Dobrzynski, Maciej; Rodríguez, Jordi Vidal; Kaandorp, Jaap A; Blom, Joke G

2007-08-01

We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli. In the regime where the number of molecules is small and reactions are diffusion-limited predicted fluctuations in the product number vary between the methods, while the average is the same. Computational approaches at the level of the reaction-diffusion master equation compute the same fluctuations as the reference result obtained from the particle-based method if the size of the sub-volumes is comparable to the diameter of reactants. Using numerical simulations of reversible binding of a pair of molecules we argue that the disagreement in predicted fluctuations is due to different modeling of inter-arrival times between reaction events. Simulations for a more complex biological study show that the different approaches lead to different results due to modeling issues. Finally, we present the physical assumptions behind the mesoscopic models for the reaction-diffusion systems. Input files for the simulations and the source code of GMP can be found under the following address: http://www.cwi.nl/projects/sic/bioinformatics2007/

Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations.

PubMed

Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume

2017-09-14

The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.

A Hybrid Method for Accelerated Simulation of Coulomb Collisions in a Plasma

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

Caflisch, R; Wang, C; Dimarco, G

2007-10-09

If the collisional time scale for Coulomb collisions is comparable to the characteristic time scales for a plasma, then simulation of Coulomb collisions may be important for computation of kinetic plasma dynamics. This can be a computational bottleneck because of the large number of simulated particles and collisions (or phase-space resolution requirements in continuum algorithms), as well as the wide range of collision rates over the velocity distribution function. This paper considers Monte Carlo simulation of Coulomb collisions using the binary collision models of Takizuka & Abe and Nanbu. It presents a hybrid method for accelerating the computation of Coulombmore » collisions. The hybrid method represents the velocity distribution function as a combination of a thermal component (a Maxwellian distribution) and a kinetic component (a set of discrete particles). Collisions between particles from the thermal component preserve the Maxwellian; collisions between particles from the kinetic component are performed using the method of or Nanbu. Collisions between the kinetic and thermal components are performed by sampling a particle from the thermal component and selecting a particle from the kinetic component. Particles are also transferred between the two components according to thermalization and dethermalization probabilities, which are functions of phase space.« less

Failure Bounding And Sensitivity Analysis Applied To Monte Carlo Entry, Descent, And Landing Simulations

NASA Technical Reports Server (NTRS)

Gaebler, John A.; Tolson, Robert H.

2010-01-01

In the study of entry, descent, and landing, Monte Carlo sampling methods are often employed to study the uncertainty in the designed trajectory. The large number of uncertain inputs and outputs, coupled with complicated non-linear models, can make interpretation of the results difficult. Three methods that provide statistical insights are applied to an entry, descent, and landing simulation. The advantages and disadvantages of each method are discussed in terms of the insights gained versus the computational cost. The first method investigated was failure domain bounding which aims to reduce the computational cost of assessing the failure probability. Next a variance-based sensitivity analysis was studied for the ability to identify which input variable uncertainty has the greatest impact on the uncertainty of an output. Finally, probabilistic sensitivity analysis is used to calculate certain sensitivities at a reduced computational cost. These methods produce valuable information that identifies critical mission parameters and needs for new technology, but generally at a significant computational cost.

Method and Apparatus for Encouraging Physiological Self-Regulation Through Modulation of an Operator's Control Input to a Video Game or Training Simulator

NASA Technical Reports Server (NTRS)

Palsson, Olafur S. (Inventor); Harris, Randall L., Sr. (Inventor); Pope, Alan T. (Inventor)

2002-01-01

Apparatus and methods for modulating the control authority (i.e., control function) of a computer simulation or game input device (e.g., joystick, button control) using physiological information so as to affect the user's ability to impact or control the simulation or game with the input device. One aspect is to use the present invention, along with a computer simulation or game, to affect physiological state or physiological self-regulation according to some programmed criterion (e.g., increase, decrease, or maintain) in order to perform better at the game task. When the affected physiological state or physiological self-regulation is the target of self-regulation or biofeedback training, the simulation or game play reinforces therapeutic changes in the physiological signal(s).

Tools for 3D scientific visualization in computational aerodynamics

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Fast multipurpose Monte Carlo simulation for proton therapy using multi- and many-core CPU architectures

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

Souris, Kevin, E-mail: kevin.souris@uclouvain.be; Lee, John Aldo; Sterpin, Edmond

2016-04-15

Purpose: Accuracy in proton therapy treatment planning can be improved using Monte Carlo (MC) simulations. However the long computation time of such methods hinders their use in clinical routine. This work aims to develop a fast multipurpose Monte Carlo simulation tool for proton therapy using massively parallel central processing unit (CPU) architectures. Methods: A new Monte Carlo, called MCsquare (many-core Monte Carlo), has been designed and optimized for the last generation of Intel Xeon processors and Intel Xeon Phi coprocessors. These massively parallel architectures offer the flexibility and the computational power suitable to MC methods. The class-II condensed history algorithmmore » of MCsquare provides a fast and yet accurate method of simulating heavy charged particles such as protons, deuterons, and alphas inside voxelized geometries. Hard ionizations, with energy losses above a user-specified threshold, are simulated individually while soft events are regrouped in a multiple scattering theory. Elastic and inelastic nuclear interactions are sampled from ICRU 63 differential cross sections, thereby allowing for the computation of prompt gamma emission profiles. MCsquare has been benchmarked with the GATE/GEANT4 Monte Carlo application for homogeneous and heterogeneous geometries. Results: Comparisons with GATE/GEANT4 for various geometries show deviations within 2%–1 mm. In spite of the limited memory bandwidth of the coprocessor simulation time is below 25 s for 10{sup 7} primary 200 MeV protons in average soft tissues using all Xeon Phi and CPU resources embedded in a single desktop unit. Conclusions: MCsquare exploits the flexibility of CPU architectures to provide a multipurpose MC simulation tool. Optimized code enables the use of accurate MC calculation within a reasonable computation time, adequate for clinical practice. MCsquare also simulates prompt gamma emission and can thus be used also for in vivo range verification.« less

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Solutions of the Taylor-Green Vortex Problem Using High-Resolution Explicit Finite Difference Methods

NASA Technical Reports Server (NTRS)

DeBonis, James R.

2013-01-01

A computational fluid dynamics code that solves the compressible Navier-Stokes equations was applied to the Taylor-Green vortex problem to examine the code s ability to accurately simulate the vortex decay and subsequent turbulence. The code, WRLES (Wave Resolving Large-Eddy Simulation), uses explicit central-differencing to compute the spatial derivatives and explicit Low Dispersion Runge-Kutta methods for the temporal discretization. The flow was first studied and characterized using Bogey & Bailley s 13-point dispersion relation preserving (DRP) scheme. The kinetic energy dissipation rate, computed both directly and from the enstrophy field, vorticity contours, and the energy spectra are examined. Results are in excellent agreement with a reference solution obtained using a spectral method and provide insight into computations of turbulent flows. In addition the following studies were performed: a comparison of 4th-, 8th-, 12th- and DRP spatial differencing schemes, the effect of the solution filtering on the results, the effect of large-eddy simulation sub-grid scale models, and the effect of high-order discretization of the viscous terms.

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation.

PubMed

Erban, Radek; Kevrekidis, Ioannis G; Adalsteinsson, David; Elston, Timothy C

2006-02-28

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately initialized short bursts of stochastic simulations; the results of these are processed to estimate coarse-grained quantities of interest, such as mesoscopic transport coefficients. In particular, using a simple model of a genetic toggle switch, we illustrate the computation of an effective free energy Phi and of a state-dependent effective diffusion coefficient D that characterize an unavailable effective Fokker-Planck equation. Additionally we illustrate the linking of equation-free techniques with continuation methods for performing a form of stochastic "bifurcation analysis"; estimation of mean switching times in the case of a bistable switch is also implemented in this equation-free context. The accuracy of our methods is tested by direct comparison with long-time stochastic simulations. This type of equation-free analysis appears to be a promising approach to computing features of the long-time, coarse-grained behavior of certain classes of complex stochastic models of gene regulatory networks, circumventing the need for long Monte Carlo simulations.

Investigation of optimal method for inducing harmonic motion in tissue using a linear ultrasound phased array--a simulation study.

PubMed

Heikkilä, Janne; Hynynen, Kullervo

2006-04-01

Many noninvasive ultrasound techniques have been developed to explore mechanical properties of soft tissues. One of these methods, Localized Harmonic Motion Imaging (LHMI), has been proposed to be used for ultrasound surgery monitoring. In LHMI, dynamic ultrasound radiation-force stimulation induces displacements in a target that can be measured using pulse-echo imaging and used to estimate the elastic properties of the target. In this initial, simulation study, the use of a one-dimensional phased array is explored for the induction of the tissue motion. The study compares three different dual-frequency and amplitude-modulated single-frequency methods for the inducing tissue motion. Simulations were computed in a homogeneous soft-tissue volume. The Rayleigh integral was used in the simulations of the ultrasound fields and the tissue displacements were computed using a finite-element method (FEM). The simulations showed that amplitude-modulated sonication using a single frequency produced the largest vibration amplitude of the target tissue. These simulations demonstrate that the properties of the tissue motion are highly dependent on the sonication method and that it is important to consider the full three-dimensional distribution of the ultrasound field for controlling the induction of tissue motion.

Two-step simulation of velocity and passive scalar mixing at high Schmidt number in turbulent jets

NASA Astrophysics Data System (ADS)

Rah, K. Jeff; Blanquart, Guillaume

2016-11-01

Simulation of passive scalar in the high Schmidt number turbulent mixing process requires higher computational cost than that of velocity fields, because the scalar is associated with smaller length scales than velocity. Thus, full simulation of both velocity and passive scalar with high Sc for a practical configuration is difficult to perform. In this work, a new approach to simulate velocity and passive scalar mixing at high Sc is suggested to reduce the computational cost. First, the velocity fields are resolved by Large Eddy Simulation (LES). Then, by extracting the velocity information from LES, the scalar inside a moving fluid blob is simulated by Direct Numerical Simulation (DNS). This two-step simulation method is applied to a turbulent jet and provides a new way to examine a scalar mixing process in a practical application with smaller computational cost. NSF, Samsung Scholarship.

Advances in Integrated Computational Materials Engineering "ICME"

NASA Astrophysics Data System (ADS)

Hirsch, Jürgen

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

Computer simulation of rapid crystal growth under microgravity

NASA Astrophysics Data System (ADS)

Hisada, Yasuhiro; Saito, Osami; Mitachi, Koshi; Nishinaga, Tatau

We are planning to grow a Ge single crystal under microgravity by the TR-IA rocket in 1992. The furnace temperature should be controlled so as to finish the crystal growth in a quite short time interval (about 6 min). This study deals with the computer simulation of rapid crystal growth in space to find the proper conditions for the experiment. The crystal growth process is influenced by various physical phenomena such as heat conduction, natural and Marangoni convections, phase change, and radiation from the furnace. In this study, a 2D simulation with axial symmetry is carried out, taking into account the radiation field with a specific temperature distribution of the furnace wall. The simulation program consists of four modules. The first module is applied for the calculation of the parabolic partial differential equation by using the control volume method. The second one evaluates implicitly the phase change by the enthalpy method. The third one is for computing the heat flux from surface by radiation. The last one is for calculating with the Monte Carlo method the view factors which are necessary to obtain the heat flux.

Adaptive hybrid simulations for multiscale stochastic reaction networks

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

Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa

2015-01-21

The probability distribution describing the state of a Stochastic Reaction Network (SRN) evolves according to the Chemical Master Equation (CME). It is common to estimate its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases, these simulations can take an impractical amount of computational time. Therefore, many methods have been developed that approximate sample paths of the underlying stochastic process and estimate the solution of the CME. A prominent class of these methods include hybrid methods that partition the set of species and the set of reactions into discrete and continuous subsets. Such amore » partition separates the dynamics into a discrete and a continuous part. Simulating such a stochastic process can be computationally much easier than simulating the exact discrete stochastic process with SSA. Moreover, the quasi-stationary assumption to approximate the dynamics of fast subnetworks can be applied for certain classes of networks. However, as the dynamics of a SRN evolves, these partitions may have to be adapted during the simulation. We develop a hybrid method that approximates the solution of a CME by automatically partitioning the reactions and species sets into discrete and continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require any user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy-numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from systems biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time. This is especially the case for systems with oscillatory dynamics, where the system dynamics change considerably throughout the time-period of interest.« less

Adaptive hybrid simulations for multiscale stochastic reaction networks.

PubMed

Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa

2015-01-21

The probability distribution describing the state of a Stochastic Reaction Network (SRN) evolves according to the Chemical Master Equation (CME). It is common to estimate its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases, these simulations can take an impractical amount of computational time. Therefore, many methods have been developed that approximate sample paths of the underlying stochastic process and estimate the solution of the CME. A prominent class of these methods include hybrid methods that partition the set of species and the set of reactions into discrete and continuous subsets. Such a partition separates the dynamics into a discrete and a continuous part. Simulating such a stochastic process can be computationally much easier than simulating the exact discrete stochastic process with SSA. Moreover, the quasi-stationary assumption to approximate the dynamics of fast subnetworks can be applied for certain classes of networks. However, as the dynamics of a SRN evolves, these partitions may have to be adapted during the simulation. We develop a hybrid method that approximates the solution of a CME by automatically partitioning the reactions and species sets into discrete and continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require any user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy-numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from systems biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time. This is especially the case for systems with oscillatory dynamics, where the system dynamics change considerably throughout the time-period of interest.

Computational Aerodynamic Simulations of an 840 ft/sec Tip Speed Advanced Ducted Propulsor Fan System Model for Acoustic Methods Assessment and Development

NASA Technical Reports Server (NTRS)

Tweedt, Daniel L.

2014-01-01

Computational Aerodynamic simulations of an 840 ft/sec tip speed, Advanced Ducted Propulsor fan system were performed at five different operating points on the fan operating line, in order to provide detailed internal flow field information for use with fan acoustic prediction methods presently being developed, assessed and validated. The fan system is a sub-scale, lownoise research fan/nacelle model that has undergone extensive experimental testing in the 9- by 15- foot Low Speed Wind Tunnel at the NASA Glenn Research Center, resulting in quality, detailed aerodynamic and acoustic measurement data. Details of the fan geometry, the computational fluid dynamics methods, the computational grids, and various computational parameters relevant to the numerical simulations are discussed. Flow field results for three of the five operating conditions simulated are presented in order to provide a representative look at the computed solutions. Each of the five fan aerodynamic simulations involved the entire fan system, excluding a long core duct section downstream of the core inlet guide vane. As a result, only fan rotational speed and system bypass ratio, set by specifying static pressure downstream of the core inlet guide vane row, were adjusted in order to set the fan operating point, leading to operating points that lie on a fan operating line and making mass flow rate a fully dependent parameter. The resulting mass flow rates are in good agreement with measurement values. The computed blade row flow fields for all five fan operating points are, in general, aerodynamically healthy. Rotor blade and fan exit guide vane flow characteristics are good, including incidence and deviation angles, chordwise static pressure distributions, blade surface boundary layers, secondary flow structures, and blade wakes. Examination of the computed flow fields reveals no excessive boundary layer separations or related secondary-flow problems. A few spanwise comparisons between computational and measurement data in the bypass duct show that they are in good agreement, thus providing a partial validation of the computational results.

Balancing Curricular and Pedagogical Needs in Computational Construction Kits: Lessons from the DeltaTick Project

ERIC Educational Resources Information Center

Wilkerson-Jerde, Michelle; Wagh, Aditi; Wilensky, Uri

2015-01-01

To successfully integrate simulation and computational methods into K-12 STEM education, learning environments should be designed to help educators maintain balance between (a) addressing curricular content and practices and (b) attending to student knowledge and interests. We describe DeltaTick, a graphical simulation construction interface for…

Turbocharged molecular discovery of OLED emitters: from high-throughput quantum simulation to highly efficient TADF devices

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Ha, Dong-Gwang; Einzinger, Markus; Wu, Tony; Baldo, Marc A.; Aspuru-Guzik, Alán.

2016-09-01

Discovering new OLED emitters requires many experiments to synthesize candidates and test performance in devices. Large scale computer simulation can greatly speed this search process but the problem remains challenging enough that brute force application of massive computing power is not enough to successfully identify novel structures. We report a successful High Throughput Virtual Screening study that leveraged a range of methods to optimize the search process. The generation of candidate structures was constrained to contain combinatorial explosion. Simulations were tuned to the specific problem and calibrated with experimental results. Experimentalists and theorists actively collaborated such that experimental feedback was regularly utilized to update and shape the computational search. Supervised machine learning methods prioritized candidate structures prior to quantum chemistry simulation to prevent wasting compute on likely poor performers. With this combination of techniques, each multiplying the strength of the search, this effort managed to navigate an area of molecular space and identify hundreds of promising OLED candidate structures. An experimentally validated selection of this set shows emitters with external quantum efficiencies as high as 22%.

Computer-assisted virtual preoperative planning in orthopedic surgery for acetabular fractures based on actual computed tomography data.

PubMed

Wang, Guang-Ye; Huang, Wen-Jun; Song, Qi; Qin, Yun-Tian; Liang, Jin-Feng

2016-12-01

Acetabular fractures have always been very challenging for orthopedic surgeons; therefore, appropriate preoperative evaluation and planning are particularly important. This study aimed to explore the application methods and clinical value of preoperative computer simulation (PCS) in treating pelvic and acetabular fractures. Spiral computed tomography (CT) was performed on 13 patients with pelvic and acetabular fractures, and Digital Imaging and Communications in Medicine (DICOM) data were then input into Mimics software to reconstruct three-dimensional (3D) models of actual pelvic and acetabular fractures for preoperative simulative reduction and fixation, and to simulate each surgical procedure. The times needed for virtual surgical modeling and reduction and fixation were also recorded. The average fracture-modeling time was 45 min (30-70 min), and the average time for bone reduction and fixation was 28 min (16-45 min). Among the surgical approaches planned for these 13 patients, 12 were finally adopted; 12 cases used the simulated surgical fixation, and only 1 case used a partial planned fixation method. PCS can provide accurate surgical plans and data support for actual surgeries.

PREFACE: New trends in Computer Simulations in Physics and not only in physics

NASA Astrophysics Data System (ADS)

Shchur, Lev N.; Krashakov, Serge A.

2016-02-01

In this volume we have collected papers based on the presentations given at the International Conference on Computer Simulations in Physics and beyond (CSP2015), held in Moscow, September 6-10, 2015. We hope that this volume will be helpful and scientifically interesting for readers. The Conference was organized for the first time with the common efforts of the Moscow Institute for Electronics and Mathematics (MIEM) of the National Research University Higher School of Economics, the Landau Institute for Theoretical Physics, and the Science Center in Chernogolovka. The name of the Conference emphasizes the multidisciplinary nature of computational physics. Its methods are applied to the broad range of current research in science and society. The choice of venue was motivated by the multidisciplinary character of the MIEM. It is a former independent university, which has recently become the part of the National Research University Higher School of Economics. The Conference Computer Simulations in Physics and beyond (CSP) is planned to be organized biannually. This year's Conference featured 99 presentations, including 21 plenary and invited talks ranging from the analysis of Irish myths with recent methods of statistical physics, to computing with novel quantum computers D-Wave and D-Wave2. This volume covers various areas of computational physics and emerging subjects within the computational physics community. Each section was preceded by invited talks presenting the latest algorithms and methods in computational physics, as well as new scientific results. Both parallel and poster sessions paid special attention to numerical methods, applications and results. For all the abstracts presented at the conference please follow the link http://csp2015.ac.ru/files/book5x.pdf

Large scale simulation of liquid water transport in a gas diffusion layer of polymer electrolyte membrane fuel cells using the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Sakaida, Satoshi; Tabe, Yutaka; Chikahisa, Takemi

2017-09-01

A method for the large-scale simulation with the lattice Boltzmann method (LBM) is proposed for liquid water movement in a gas diffusion layer (GDL) of polymer electrolyte membrane fuel cells. The LBM is able to analyze two-phase flows in complex structures, however the simulation domain is limited due to heavy computational loads. This study investigates a variety means to reduce computational loads and increase the simulation areas. One is applying an LBM treating two-phases as having the same density, together with keeping numerical stability with large time steps. The applicability of this approach is confirmed by comparing the results with rigorous simulations using actual density. The second is establishing the maximum limit of the Capillary number that maintains flow patterns similar to the precise simulation; this is attempted as the computational load is inversely proportional to the Capillary number. The results show that the Capillary number can be increased to 3.0 × 10-3, where the actual operation corresponds to Ca = 10-5∼10-8. The limit is also investigated experimentally using an enlarged scale model satisfying similarity conditions for the flow. Finally, a demonstration is made of the effects of pore uniformity in GDL as an example of a large-scale simulation covering a channel.

Toward real-time Monte Carlo simulation using a commercial cloud computing infrastructure.

PubMed

Wang, Henry; Ma, Yunzhi; Pratx, Guillem; Xing, Lei

2011-09-07

Monte Carlo (MC) methods are the gold standard for modeling photon and electron transport in a heterogeneous medium; however, their computational cost prohibits their routine use in the clinic. Cloud computing, wherein computing resources are allocated on-demand from a third party, is a new approach for high performance computing and is implemented to perform ultra-fast MC calculation in radiation therapy. We deployed the EGS5 MC package in a commercial cloud environment. Launched from a single local computer with Internet access, a Python script allocates a remote virtual cluster. A handshaking protocol designates master and worker nodes. The EGS5 binaries and the simulation data are initially loaded onto the master node. The simulation is then distributed among independent worker nodes via the message passing interface, and the results aggregated on the local computer for display and data analysis. The described approach is evaluated for pencil beams and broad beams of high-energy electrons and photons. The output of cloud-based MC simulation is identical to that produced by single-threaded implementation. For 1 million electrons, a simulation that takes 2.58 h on a local computer can be executed in 3.3 min on the cloud with 100 nodes, a 47× speed-up. Simulation time scales inversely with the number of parallel nodes. The parallelization overhead is also negligible for large simulations. Cloud computing represents one of the most important recent advances in supercomputing technology and provides a promising platform for substantially improved MC simulation. In addition to the significant speed up, cloud computing builds a layer of abstraction for high performance parallel computing, which may change the way dose calculations are performed and radiation treatment plans are completed.

10 CFR 431.173 - Requirements applicable to all manufacturers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... COMMERCIAL AND INDUSTRIAL EQUIPMENT Provisions for Commercial Heating, Ventilating, Air-Conditioning and... is based on engineering or statistical analysis, computer simulation or modeling, or other analytic... method or methods used; (B) The mathematical model, the engineering or statistical analysis, computer...

Confidence Intervals for Error Rates Observed in Coded Communications Systems

NASA Astrophysics Data System (ADS)

Hamkins, J.

2015-05-01

We present methods to compute confidence intervals for the codeword error rate (CWER) and bit error rate (BER) of a coded communications link. We review several methods to compute exact and approximate confidence intervals for the CWER, and specifically consider the situation in which the true CWER is so low that only a handful, if any, codeword errors are able to be simulated. In doing so, we answer the question of how long an error-free simulation must be run in order to certify that a given CWER requirement is met with a given level of confidence, and discuss the bias introduced by aborting a simulation after observing the first codeword error. Next, we turn to the lesser studied problem of determining confidence intervals for the BER of coded systems. Since bit errors in systems that use coding or higher-order modulation do not occur independently, blind application of a method that assumes independence leads to inappropriately narrow confidence intervals. We present a new method to compute the confidence interval properly, using the first and second sample moments of the number of bit errors per codeword. This is the first method we know of to compute a confidence interval for the BER of a coded or higher-order modulation system.

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

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

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scalingmore » laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.« less

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

DOE PAGES

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; ...

2017-11-27

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scalingmore » laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.« less

Marc Henry de Frahan | NREL

Science.gov Websites

Computing Project, Marc develops high-fidelity turbulence models to enhance simulation accuracy and efficient numerical algorithms for future high performance computing hardware architectures. Research Interests High performance computing High order numerical methods for computational fluid dynamics Fluid

Simulator for neural networks and action potentials.

PubMed

Baxter, Douglas A; Byrne, John H

2007-01-01

A key challenge for neuroinformatics is to devise methods for representing, accessing, and integrating vast amounts of diverse and complex data. A useful approach to represent and integrate complex data sets is to develop mathematical models [Arbib (The Handbook of Brain Theory and Neural Networks, pp. 741-745, 2003); Arbib and Grethe (Computing the Brain: A Guide to Neuroinformatics, 2001); Ascoli (Computational Neuroanatomy: Principles and Methods, 2002); Bower and Bolouri (Computational Modeling of Genetic and Biochemical Networks, 2001); Hines et al. (J. Comput. Neurosci. 17, 7-11, 2004); Shepherd et al. (Trends Neurosci. 21, 460-468, 1998); Sivakumaran et al. (Bioinformatics 19, 408-415, 2003); Smolen et al. (Neuron 26, 567-580, 2000); Vadigepalli et al. (OMICS 7, 235-252, 2003)]. Models of neural systems provide quantitative and modifiable frameworks for representing data and analyzing neural function. These models can be developed and solved using neurosimulators. One such neurosimulator is simulator for neural networks and action potentials (SNNAP) [Ziv (J. Neurophysiol. 71, 294-308, 1994)]. SNNAP is a versatile and user-friendly tool for developing and simulating models of neurons and neural networks. SNNAP simulates many features of neuronal function, including ionic currents and their modulation by intracellular ions and/or second messengers, and synaptic transmission and synaptic plasticity. SNNAP is written in Java and runs on most computers. Moreover, SNNAP provides a graphical user interface (GUI) and does not require programming skills. This chapter describes several capabilities of SNNAP and illustrates methods for simulating neurons and neural networks. SNNAP is available at http://snnap.uth.tmc.edu .

Moving Computational Domain Method and Its Application to Flow Around a High-Speed Car Passing Through a Hairpin Curve

NASA Astrophysics Data System (ADS)

Watanabe, Koji; Matsuno, Kenichi

This paper presents a new method for simulating flows driven by a body traveling with neither restriction on motion nor a limit of a region size. In the present method named 'Moving Computational Domain Method', the whole of the computational domain including bodies inside moves in the physical space without the limit of region size. Since the whole of the grid of the computational domain moves according to the movement of the body, a flow solver of the method has to be constructed on the moving grid system and it is important for the flow solver to satisfy physical and geometric conservation laws simultaneously on moving grid. For this issue, the Moving-Grid Finite-Volume Method is employed as the flow solver. The present Moving Computational Domain Method makes it possible to simulate flow driven by any kind of motion of the body in any size of the region with satisfying physical and geometric conservation laws simultaneously. In this paper, the method is applied to the flow around a high-speed car passing through a hairpin curve. The distinctive flow field driven by the car at the hairpin curve has been demonstrated in detail. The results show the promising feature of the method.

Method and apparatus for transfer function simulator for testing complex systems

NASA Technical Reports Server (NTRS)

Kavaya, M. J. (Inventor)

1985-01-01

A method and apparatus for testing the operation of a complex stabilization circuit in a closed loop system is presented. The method is comprised of a programmed analog or digital computing system for implementing the transfer function of a load thereby providing a predictable load. The digital computing system employs a table stored in a microprocessor in which precomputed values of the load transfer function are stored for values of input signal from the stabilization circuit over the range of interest. This technique may be used not only for isolating faults in the stabilization circuit, but also for analyzing a fault in a faulty load by so varying parameters of the computing system as to simulate operation of the actual load with the fault.

Simulation and visualization of face seal motion stability by means of computer generated movies

NASA Technical Reports Server (NTRS)

Etsion, I.; Auer, B. M.

1980-01-01

A computer aided design method for mechanical face seals is described. Based on computer simulation, the actual motion of the flexibly mounted element of the seal can be visualized. This is achieved by solving the equations of motion of this element, calculating the displacements in its various degrees of freedom vs. time, and displaying the transient behavior in the form of a motion picture. Incorporating such a method in the design phase allows one to detect instabilities and to correct undesirable behavior of the seal. A theoretical background is presented. Details of the motion display technique are described, and the usefulness of the method is demonstrated by an example of a noncontacting conical face seal.

Simulation and visualization of face seal motion stability by means of computer generated movies

NASA Technical Reports Server (NTRS)

Etsion, I.; Auer, B. M.

1981-01-01

A computer aided design method for mechanical face seals is described. Based on computer simulation, the actual motion of the flexibly mounted element of the seal can be visualized. This is achieved by solving the equations of motion of this element, calculating the displacements in its various degrees of freedom vs. time, and displaying the transient behavior in the form of a motion picture. Incorporating such a method in the design phase allows one to detect instabilities and to correct undesirable behavior of the seal. A theoretical background is presented. Details of the motion display technique are described, and the usefulness of the method is demonstrated by an example of a noncontacting conical face seal.

Modeling of carbon dioxide condensation in the high pressure flows using the statistical BGK approach

NASA Astrophysics Data System (ADS)

Kumar, Rakesh; Li, Zheng; Levin, Deborah A.

2011-05-01

In this work, we propose a new heat accommodation model to simulate freely expanding homogeneous condensation flows of gaseous carbon dioxide using a new approach, the statistical Bhatnagar-Gross-Krook method. The motivation for the present work comes from the earlier work of Li et al. [J. Phys. Chem. 114, 5276 (2010)] in which condensation models were proposed and used in the direct simulation Monte Carlo method to simulate the flow of carbon dioxide from supersonic expansions of small nozzles into near-vacuum conditions. Simulations conducted for stagnation pressures of one and three bar were compared with the measurements of gas and cluster number densities, cluster size, and carbon dioxide rotational temperature obtained by Ramos et al. [Phys. Rev. A 72, 3204 (2005)]. Due to the high computational cost of direct simulation Monte Carlo method, comparison between simulations and data could only be performed for these stagnation pressures, with good agreement obtained beyond the condensation onset point, in the farfield. As the stagnation pressure increases, the degree of condensation also increases; therefore, to improve the modeling of condensation onset, one must be able to simulate higher stagnation pressures. In simulations of an expanding flow of argon through a nozzle, Kumar et al. [AIAA J. 48, 1531 (2010)] found that the statistical Bhatnagar-Gross-Krook method provides the same accuracy as direct simulation Monte Carlo method, but, at one half of the computational cost. In this work, the statistical Bhatnagar-Gross-Krook method was modified to account for internal degrees of freedom for multi-species polyatomic gases. With the computational approach in hand, we developed and tested a new heat accommodation model for a polyatomic system to properly account for the heat release of condensation. We then developed condensation models in the framework of the statistical Bhatnagar-Gross-Krook method. Simulations were found to agree well with the experiment for all stagnation pressure cases (1-5 bar), validating the accuracy of the Bhatnagar-Gross-Krook based condensation model in capturing the physics of condensation.

Research in Computational Astrobiology

NASA Technical Reports Server (NTRS)

Chaban, Galina; Colombano, Silvano; Scargle, Jeff; New, Michael H.; Pohorille, Andrew; Wilson, Michael A.

2003-01-01

We report on several projects in the field of computational astrobiology, which is devoted to advancing our understanding of the origin, evolution and distribution of life in the Universe using theoretical and computational tools. Research projects included modifying existing computer simulation codes to use efficient, multiple time step algorithms, statistical methods for analysis of astrophysical data via optimal partitioning methods, electronic structure calculations on water-nuclei acid complexes, incorporation of structural information into genomic sequence analysis methods and calculations of shock-induced formation of polycylic aromatic hydrocarbon compounds.

Freud: a software suite for high-throughput simulation analysis

NASA Astrophysics Data System (ADS)

Harper, Eric; Spellings, Matthew; Anderson, Joshua; Glotzer, Sharon

Computer simulation is an indispensable tool for the study of a wide variety of systems. As simulations scale to fill petascale and exascale supercomputing clusters, so too does the size of the data produced, as well as the difficulty in analyzing these data. We present Freud, an analysis software suite for efficient analysis of simulation data. Freud makes no assumptions about the system being analyzed, allowing for general analysis methods to be applied to nearly any type of simulation. Freud includes standard analysis methods such as the radial distribution function, as well as new methods including the potential of mean force and torque and local crystal environment analysis. Freud combines a Python interface with fast, parallel C + + analysis routines to run efficiently on laptops, workstations, and supercomputing clusters. Data analysis on clusters reduces data transfer requirements, a prohibitive cost for petascale computing. Used in conjunction with simulation software, Freud allows for smart simulations that adapt to the current state of the system, enabling the study of phenomena such as nucleation and growth, intelligent investigation of phases and phase transitions, and determination of effective pair potentials.

Time Accurate Unsteady Pressure Loads Simulated for the Space Launch System at a Wind Tunnel Condition

NASA Technical Reports Server (NTRS)

Alter, Stephen J.; Brauckmann, Gregory J.; Kleb, Bil; Streett, Craig L; Glass, Christopher E.; Schuster, David M.

2015-01-01

Using the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics code, an unsteady, time-accurate flow field about a Space Launch System configuration was simulated at a transonic wind tunnel condition (Mach = 0.9). Delayed detached eddy simulation combined with Reynolds Averaged Naiver-Stokes and a Spallart-Almaras turbulence model were employed for the simulation. Second order accurate time evolution scheme was used to simulate the flow field, with a minimum of 0.2 seconds of simulated time to as much as 1.4 seconds. Data was collected at 480 pressure taps at locations, 139 of which matched a 3% wind tunnel model, tested in the Transonic Dynamic Tunnel (TDT) facility at NASA Langley Research Center. Comparisons between computation and experiment showed agreement within 5% in terms of location for peak RMS levels, and 20% for frequency and magnitude of power spectral densities. Grid resolution and time step sensitivity studies were performed to identify methods for improved accuracy comparisons to wind tunnel data. With limited computational resources, accurate trends for reduced vibratory loads on the vehicle were observed. Exploratory methods such as determining minimized computed errors based on CFL number and sub-iterations, as well as evaluating frequency content of the unsteady pressures and evaluation of oscillatory shock structures were used in this study to enhance computational efficiency and solution accuracy. These techniques enabled development of a set of best practices, for the evaluation of future flight vehicle designs in terms of vibratory loads.

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

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

A variational multiscale method for particle-cloud tracking in turbomachinery flows

NASA Astrophysics Data System (ADS)

Corsini, A.; Rispoli, F.; Sheard, A. G.; Takizawa, K.; Tezduyar, T. E.; Venturini, P.

2014-11-01

We present a computational method for simulation of particle-laden flows in turbomachinery. The method is based on a stabilized finite element fluid mechanics formulation and a finite element particle-cloud tracking method. We focus on induced-draft fans used in process industries to extract exhaust gases in the form of a two-phase fluid with a dispersed solid phase. The particle-laden flow causes material wear on the fan blades, degrading their aerodynamic performance, and therefore accurate simulation of the flow would be essential in reliable computational turbomachinery analysis and design. The turbulent-flow nature of the problem is dealt with a Reynolds-Averaged Navier-Stokes model and Streamline-Upwind/Petrov-Galerkin/Pressure-Stabilizing/Petrov-Galerkin stabilization, the particle-cloud trajectories are calculated based on the flow field and closure models for the turbulence-particle interaction, and one-way dependence is assumed between the flow field and particle dynamics. We propose a closure model utilizing the scale separation feature of the variational multiscale method, and compare that to the closure utilizing the eddy viscosity model. We present computations for axial- and centrifugal-fan configurations, and compare the computed data to those obtained from experiments, analytical approaches, and other computational methods.

Rapid high performance liquid chromatography method development with high prediction accuracy, using 5cm long narrow bore columns packed with sub-2microm particles and Design Space computer modeling.

PubMed

Fekete, Szabolcs; Fekete, Jeno; Molnár, Imre; Ganzler, Katalin

2009-11-06

Many different strategies of reversed phase high performance liquid chromatographic (RP-HPLC) method development are used today. This paper describes a strategy for the systematic development of ultrahigh-pressure liquid chromatographic (UHPLC or UPLC) methods using 5cmx2.1mm columns packed with sub-2microm particles and computer simulation (DryLab((R)) package). Data for the accuracy of computer modeling in the Design Space under ultrahigh-pressure conditions are reported. An acceptable accuracy for these predictions of the computer models is presented. This work illustrates a method development strategy, focusing on time reduction up to a factor 3-5, compared to the conventional HPLC method development and exhibits parts of the Design Space elaboration as requested by the FDA and ICH Q8R1. Furthermore this paper demonstrates the accuracy of retention time prediction at elevated pressure (enhanced flow-rate) and shows that the computer-assisted simulation can be applied with sufficient precision for UHPLC applications (p>400bar). Examples of fast and effective method development in pharmaceutical analysis, both for gradient and isocratic separations are presented.

Moose: An Open-Source Framework to Enable Rapid Development of Collaborative, Multi-Scale, Multi-Physics Simulation Tools

NASA Astrophysics Data System (ADS)

Slaughter, A. E.; Permann, C.; Peterson, J. W.; Gaston, D.; Andrs, D.; Miller, J.

2014-12-01

The Idaho National Laboratory (INL)-developed Multiphysics Object Oriented Simulation Environment (MOOSE; www.mooseframework.org), is an open-source, parallel computational framework for enabling the solution of complex, fully implicit multiphysics systems. MOOSE provides a set of computational tools that scientists and engineers can use to create sophisticated multiphysics simulations. Applications built using MOOSE have computed solutions for chemical reaction and transport equations, computational fluid dynamics, solid mechanics, heat conduction, mesoscale materials modeling, geomechanics, and others. To facilitate the coupling of diverse and highly-coupled physical systems, MOOSE employs the Jacobian-free Newton-Krylov (JFNK) method when solving the coupled nonlinear systems of equations arising in multiphysics applications. The MOOSE framework is written in C++, and leverages other high-quality, open-source scientific software packages such as LibMesh, Hypre, and PETSc. MOOSE uses a "hybrid parallel" model which combines both shared memory (thread-based) and distributed memory (MPI-based) parallelism to ensure efficient resource utilization on a wide range of computational hardware. MOOSE-based applications are inherently modular, which allows for simulation expansion (via coupling of additional physics modules) and the creation of multi-scale simulations. Any application developed with MOOSE supports running (in parallel) any other MOOSE-based application. Each application can be developed independently, yet easily communicate with other applications (e.g., conductivity in a slope-scale model could be a constant input, or a complete phase-field micro-structure simulation) without additional code being written. This method of development has proven effective at INL and expedites the development of sophisticated, sustainable, and collaborative simulation tools.

Explicit finite-difference simulation of optical integrated devices on massive parallel computers.

PubMed

Sterkenburgh, T; Michels, R M; Dress, P; Franke, H

1997-02-20

An explicit method for the numerical simulation of optical integrated circuits by means of the finite-difference time-domain (FDTD) method is presented. This method, based on an explicit solution of Maxwell's equations, is well established in microwave technology. Although the simulation areas are small, we verified the behavior of three interesting problems, especially nonparaxial problems, with typical aspects of integrated optical devices. Because numerical losses are within acceptable limits, we suggest the use of the FDTD method to achieve promising quantitative simulation results.

Simulation Methods for Optics and Electromagnetics in Complex Geometries and Extreme Nonlinear Regimes with Disparate Scales

DTIC Science & Technology

2014-09-30

software devel- oped with this project support. S1 Cork School 2013: I. UPPEcore Simulator design and usage, Simulation examples II. Nonlinear pulse...pulse propagation 08/28/13 — 08/02/13, University College Cork , Ireland S2 ACMS MURI School 2012: Computational Methods for Nonlinear PDEs describing

A cis-regulatory logic simulator.

PubMed

Zeigler, Robert D; Gertz, Jason; Cohen, Barak A

2007-07-27

A major goal of computational studies of gene regulation is to accurately predict the expression of genes based on the cis-regulatory content of their promoters. The development of computational methods to decode the interactions among cis-regulatory elements has been slow, in part, because it is difficult to know, without extensive experimental validation, whether a particular method identifies the correct cis-regulatory interactions that underlie a given set of expression data. There is an urgent need for test expression data in which the interactions among cis-regulatory sites that produce the data are known. The ability to rapidly generate such data sets would facilitate the development and comparison of computational methods that predict gene expression patterns from promoter sequence. We developed a gene expression simulator which generates expression data using user-defined interactions between cis-regulatory sites. The simulator can incorporate additive, cooperative, competitive, and synergistic interactions between regulatory elements. Constraints on the spacing, distance, and orientation of regulatory elements and their interactions may also be defined and Gaussian noise can be added to the expression values. The simulator allows for a data transformation that simulates the sigmoid shape of expression levels from real promoters. We found good agreement between sets of simulated promoters and predicted regulatory modules from real expression data. We present several data sets that may be useful for testing new methodologies for predicting gene expression from promoter sequence. We developed a flexible gene expression simulator that rapidly generates large numbers of simulated promoters and their corresponding transcriptional output based on specified interactions between cis-regulatory sites. When appropriate rule sets are used, the data generated by our simulator faithfully reproduces experimentally derived data sets. We anticipate that using simulated gene expression data sets will facilitate the direct comparison of computational strategies to predict gene expression from promoter sequence. The source code is available online and as additional material. The test sets are available as additional material.

High performance computing in biology: multimillion atom simulations of nanoscale systems

PubMed Central

Sanbonmatsu, K. Y.; Tung, C.-S.

2007-01-01

Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nanoscale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

Space-Time Conservation Element and Solution Element Method Being Developed

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung; Himansu, Ananda; Jorgenson, Philip C. E.; Loh, Ching-Yuen; Wang, Xiao-Yen; Yu, Sheng-Tao

1999-01-01

The engineering research and design requirements of today pose great computer-simulation challenges to engineers and scientists who are called on to analyze phenomena in continuum mechanics. The future will bring even more daunting challenges, when increasingly complex phenomena must be analyzed with increased accuracy. Traditionally used numerical simulation methods have evolved to their present state by repeated incremental extensions to broaden their scope. They are reaching the limits of their applicability and will need to be radically revised, at the very least, to meet future simulation challenges. At the NASA Lewis Research Center, researchers have been developing a new numerical framework for solving conservation laws in continuum mechanics, namely, the Space-Time Conservation Element and Solution Element Method, or the CE/SE method. This method has been built from fundamentals and is not a modification of any previously existing method. It has been designed with generality, simplicity, robustness, and accuracy as cornerstones. The CE/SE method has thus far been applied in the fields of computational fluid dynamics, computational aeroacoustics, and computational electromagnetics. Computer programs based on the CE/SE method have been developed for calculating flows in one, two, and three spatial dimensions. Results have been obtained for numerous problems and phenomena, including various shock-tube problems, ZND detonation waves, an implosion and explosion problem, shocks over a forward-facing step, a blast wave discharging from a nozzle, various acoustic waves, and shock/acoustic-wave interactions. The method can clearly resolve shock/acoustic-wave interactions, wherein the difference of the magnitude between the acoustic wave and shock could be up to six orders. In two-dimensional flows, the reflected shock is as crisp as the leading shock. CE/SE schemes are currently being used for advanced applications to jet and fan noise prediction and to chemically reacting flows.

A PDE Sensitivity Equation Method for Optimal Aerodynamic Design

NASA Technical Reports Server (NTRS)

Borggaard, Jeff; Burns, John

1996-01-01

The use of gradient based optimization algorithms in inverse design is well established as a practical approach to aerodynamic design. A typical procedure uses a simulation scheme to evaluate the objective function (from the approximate states) and its gradient, then passes this information to an optimization algorithm. Once the simulation scheme (CFD flow solver) has been selected and used to provide approximate function evaluations, there are several possible approaches to the problem of computing gradients. One popular method is to differentiate the simulation scheme and compute design sensitivities that are then used to obtain gradients. Although this black-box approach has many advantages in shape optimization problems, one must compute mesh sensitivities in order to compute the design sensitivity. In this paper, we present an alternative approach using the PDE sensitivity equation to develop algorithms for computing gradients. This approach has the advantage that mesh sensitivities need not be computed. Moreover, when it is possible to use the CFD scheme for both the forward problem and the sensitivity equation, then there are computational advantages. An apparent disadvantage of this approach is that it does not always produce consistent derivatives. However, for a proper combination of discretization schemes, one can show asymptotic consistency under mesh refinement, which is often sufficient to guarantee convergence of the optimal design algorithm. In particular, we show that when asymptotically consistent schemes are combined with a trust-region optimization algorithm, the resulting optimal design method converges. We denote this approach as the sensitivity equation method. The sensitivity equation method is presented, convergence results are given and the approach is illustrated on two optimal design problems involving shocks.

Robust and High Order Computational Method for Parachute and Air Delivery and MAV System

DTIC Science & Technology

2017-11-01

Report: Robust and High Order Computational Method for Parachute and Air Delivery and MAV System The views, opinions and/or findings contained in this...University Title: Robust and High Order Computational Method for Parachute and Air Delivery and MAV System Report Term: 0-Other Email: xiaolin.li...model coupled with an incompressible fluid solver through the impulse method . Our approach to simulating the parachute system is based on the front

A Fourier-based total-field/scattered-field technique for three-dimensional broadband simulations of elastic targets near a water-sand interface.

PubMed

Shao, Yu; Wang, Shumin

2016-12-01

The numerical simulation of acoustic scattering from elastic objects near a water-sand interface is critical to underwater target identification. Frequency-domain methods are computationally expensive, especially for large-scale broadband problems. A numerical technique is proposed to enable the efficient use of finite-difference time-domain method for broadband simulations. By incorporating a total-field/scattered-field boundary, the simulation domain is restricted inside a tightly bounded region. The incident field is further synthesized by the Fourier transform for both subcritical and supercritical incidences. Finally, the scattered far field is computed using a half-space Green's function. Numerical examples are further provided to demonstrate the accuracy and efficiency of the proposed technique.

Implementation of the force decomposition machine for molecular dynamics simulations.

PubMed

Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka

2012-09-01

We present the design and implementation of the force decomposition machine (FDM), a cluster of personal computers (PCs) that is tailored to running molecular dynamics (MD) simulations using the distributed diagonal force decomposition (DDFD) parallelization method. The cluster interconnect architecture is optimized for the communication pattern of the DDFD method. Our implementation of the FDM relies on standard commodity components even for networking. Although the cluster is meant for DDFD MD simulations, it remains general enough for other parallel computations. An analysis of several MD simulation runs on both the FDM and a standard PC cluster demonstrates that the FDM's interconnect architecture provides a greater performance compared to a more general cluster interconnect. Copyright © 2012 Elsevier Inc. All rights reserved.

Aeroelastic analysis of bridge girder section using computer modeling

DOT National Transportation Integrated Search

2001-05-01

This report describes the numerical simulation of wind flow around bridges using the Finite Element Method (FEM) and the principles of Computational Fluid Dynamics (CFD) and Computational Structural Dynamics (CSD). Since, the suspension bridges are p...

Computer Simulation of the Elastic Properties of Titanium Alloys for Medical Applications

NASA Astrophysics Data System (ADS)

Estevez, Elsa Paz; Burganova, R. M.; Lysogorskii, Yu. V.

2016-09-01

Results of a computer simulation of the elastic properties of α+β- and β-titanium alloys, used for medical purposes, within the framework of the molecular-dynamics method are presented. It is shown that β-titanium alloys are best suited for the use as bone implants because of their small moduli of elasticity. The advisability of the use of the molecular-dynamics method for the study of the elastic properties of titanium alloys, serving as bone implants, is demonstrated.

Metrics for comparing dynamic earthquake rupture simulations

USGS Publications Warehouse

Barall, Michael; Harris, Ruth A.

2014-01-01

Earthquakes are complex events that involve a myriad of interactions among multiple geologic features and processes. One of the tools that is available to assist with their study is computer simulation, particularly dynamic rupture simulation. A dynamic rupture simulation is a numerical model of the physical processes that occur during an earthquake. Starting with the fault geometry, friction constitutive law, initial stress conditions, and assumptions about the condition and response of the near‐fault rocks, a dynamic earthquake rupture simulation calculates the evolution of fault slip and stress over time as part of the elastodynamic numerical solution (Ⓔ see the simulation description in the electronic supplement to this article). The complexity of the computations in a dynamic rupture simulation make it challenging to verify that the computer code is operating as intended, because there are no exact analytic solutions against which these codes’ results can be directly compared. One approach for checking if dynamic rupture computer codes are working satisfactorily is to compare each code’s results with the results of other dynamic rupture codes running the same earthquake simulation benchmark. To perform such a comparison consistently, it is necessary to have quantitative metrics. In this paper, we present a new method for quantitatively comparing the results of dynamic earthquake rupture computer simulation codes.

Signal-to-noise ratio estimation in digital computer simulation of lowpass and bandpass systems with applications to analog and digital communications, volume 3

NASA Technical Reports Server (NTRS)

Tranter, W. H.; Turner, M. D.

1977-01-01

Techniques are developed to estimate power gain, delay, signal-to-noise ratio, and mean square error in digital computer simulations of lowpass and bandpass systems. The techniques are applied to analog and digital communications. The signal-to-noise ratio estimates are shown to be maximum likelihood estimates in additive white Gaussian noise. The methods are seen to be especially useful for digital communication systems where the mapping from the signal-to-noise ratio to the error probability can be obtained. Simulation results show the techniques developed to be accurate and quite versatile in evaluating the performance of many systems through digital computer simulation.

Teaching Materials and Methods.

ERIC Educational Resources Information Center

Physiologist, 1982

1982-01-01

Twelve abstracts of papers presented at the 33rd Annual Fall Meeting of the American Physiological Society are listed, focusing on teaching materials/methods. Topics, among others, include trends in physiology laboratory programs, cardiovascular system model, cardiovascular computer simulation with didactic feedback, and computer generated figures…

PyFly: A fast, portable aerodynamics simulator

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

Garcia, Daniel; Ghommem, M.; Collier, Nathaniel O.

Here, we present a fast, user-friendly implementation of a potential flow solver based on the unsteady vortex lattice method (UVLM), namely PyFly. UVLM computes the aerodynamic loads applied on lifting surfaces while capturing the unsteady effects such as the added mass forces, the growth of bound circulation, and the wake while assuming that the flow separation location is known a priori. This method is based on discretizing the body surface into a lattice of vortex rings and relies on the Biot–Savart law to construct the velocity field at every point in the simulated domain. We introduce the pointwise approximation approachmore » to simulate the interactions of the far-field vortices to overcome the computational burden associated with the classical implementation of UVLM. The computational framework uses the Python programming language to provide an easy to handle user interface while the computational kernels are written in Fortran. The mixed language approach enables high performance regarding solution time and great flexibility concerning easiness of code adaptation to different system configurations and applications. The computational tool predicts the unsteady aerodynamic behavior of multiple moving bodies (e.g., flapping wings, rotating blades, suspension bridges) subject to incoming air. The aerodynamic simulator can also deal with enclosure effects, multi-body interactions, and B-spline representation of body shapes. Finally, we simulate different aerodynamic problems to illustrate the usefulness and effectiveness of PyFly.« less

PyFly: A fast, portable aerodynamics simulator

DOE PAGES

Garcia, Daniel; Ghommem, M.; Collier, Nathaniel O.; ...

2018-03-14

Here, we present a fast, user-friendly implementation of a potential flow solver based on the unsteady vortex lattice method (UVLM), namely PyFly. UVLM computes the aerodynamic loads applied on lifting surfaces while capturing the unsteady effects such as the added mass forces, the growth of bound circulation, and the wake while assuming that the flow separation location is known a priori. This method is based on discretizing the body surface into a lattice of vortex rings and relies on the Biot–Savart law to construct the velocity field at every point in the simulated domain. We introduce the pointwise approximation approachmore » to simulate the interactions of the far-field vortices to overcome the computational burden associated with the classical implementation of UVLM. The computational framework uses the Python programming language to provide an easy to handle user interface while the computational kernels are written in Fortran. The mixed language approach enables high performance regarding solution time and great flexibility concerning easiness of code adaptation to different system configurations and applications. The computational tool predicts the unsteady aerodynamic behavior of multiple moving bodies (e.g., flapping wings, rotating blades, suspension bridges) subject to incoming air. The aerodynamic simulator can also deal with enclosure effects, multi-body interactions, and B-spline representation of body shapes. Finally, we simulate different aerodynamic problems to illustrate the usefulness and effectiveness of PyFly.« less

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

PubMed

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

2011-06-20

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

Using spatial principles to optimize distributed computing for enabling the physical science discoveries

PubMed Central

Yang, Chaowei; Wu, Huayi; Huang, Qunying; Li, Zhenlong; Li, Jing

2011-01-01

Contemporary physical science studies rely on the effective analyses of geographically dispersed spatial data and simulations of physical phenomena. Single computers and generic high-end computing are not sufficient to process the data for complex physical science analysis and simulations, which can be successfully supported only through distributed computing, best optimized through the application of spatial principles. Spatial computing, the computing aspect of a spatial cyberinfrastructure, refers to a computing paradigm that utilizes spatial principles to optimize distributed computers to catalyze advancements in the physical sciences. Spatial principles govern the interactions between scientific parameters across space and time by providing the spatial connections and constraints to drive the progression of the phenomena. Therefore, spatial computing studies could better position us to leverage spatial principles in simulating physical phenomena and, by extension, advance the physical sciences. Using geospatial science as an example, this paper illustrates through three research examples how spatial computing could (i) enable data intensive science with efficient data/services search, access, and utilization, (ii) facilitate physical science studies with enabling high-performance computing capabilities, and (iii) empower scientists with multidimensional visualization tools to understand observations and simulations. The research examples demonstrate that spatial computing is of critical importance to design computing methods to catalyze physical science studies with better data access, phenomena simulation, and analytical visualization. We envision that spatial computing will become a core technology that drives fundamental physical science advancements in the 21st century. PMID:21444779

Using spatial principles to optimize distributed computing for enabling the physical science discoveries.

PubMed

Yang, Chaowei; Wu, Huayi; Huang, Qunying; Li, Zhenlong; Li, Jing

2011-04-05

Contemporary physical science studies rely on the effective analyses of geographically dispersed spatial data and simulations of physical phenomena. Single computers and generic high-end computing are not sufficient to process the data for complex physical science analysis and simulations, which can be successfully supported only through distributed computing, best optimized through the application of spatial principles. Spatial computing, the computing aspect of a spatial cyberinfrastructure, refers to a computing paradigm that utilizes spatial principles to optimize distributed computers to catalyze advancements in the physical sciences. Spatial principles govern the interactions between scientific parameters across space and time by providing the spatial connections and constraints to drive the progression of the phenomena. Therefore, spatial computing studies could better position us to leverage spatial principles in simulating physical phenomena and, by extension, advance the physical sciences. Using geospatial science as an example, this paper illustrates through three research examples how spatial computing could (i) enable data intensive science with efficient data/services search, access, and utilization, (ii) facilitate physical science studies with enabling high-performance computing capabilities, and (iii) empower scientists with multidimensional visualization tools to understand observations and simulations. The research examples demonstrate that spatial computing is of critical importance to design computing methods to catalyze physical science studies with better data access, phenomena simulation, and analytical visualization. We envision that spatial computing will become a core technology that drives fundamental physical science advancements in the 21st century.

Simulation of Structural Transformations in Heating of Alloy Steel

NASA Astrophysics Data System (ADS)

Kurkin, A. S.; Makarov, E. L.; Kurkin, A. B.; Rubtsov, D. E.; Rubtsov, M. E.

2017-07-01

Amathematical model for computer simulation of structural transformations in an alloy steel under the conditions of the thermal cycle of multipass welding is presented. The austenitic transformation under the heating and the processes of decomposition of bainite and martensite under repeated heating are considered. Amethod for determining the necessary temperature-time parameters of the model from the chemical composition of the steel is described. Published data are processed and the results used to derive regression models of the temperature ranges and parameters of transformation kinetics of alloy steels. The method developed is used in computer simulation of the process of multipass welding of pipes by the finite-element method.

n-body simulations using message passing parallel computers.

NASA Astrophysics Data System (ADS)

Grama, A. Y.; Kumar, V.; Sameh, A.

The authors present new parallel formulations of the Barnes-Hut method for n-body simulations on message passing computers. These parallel formulations partition the domain efficiently incurring minimal communication overhead. This is in contrast to existing schemes that are based on sorting a large number of keys or on the use of global data structures. The new formulations are augmented by alternate communication strategies which serve to minimize communication overhead. The impact of these communication strategies is experimentally studied. The authors report on experimental results obtained from an astrophysical simulation on an nCUBE2 parallel computer.

A review of recent advances in the spherical harmonics expansion method for semiconductor device simulation.

PubMed

Rupp, K; Jungemann, C; Hong, S-M; Bina, M; Grasser, T; Jüngel, A

The Boltzmann transport equation is commonly considered to be the best semi-classical description of carrier transport in semiconductors, providing precise information about the distribution of carriers with respect to time (one dimension), location (three dimensions), and momentum (three dimensions). However, numerical solutions for the seven-dimensional carrier distribution functions are very demanding. The most common solution approach is the stochastic Monte Carlo method, because the gigabytes of memory requirements of deterministic direct solution approaches has not been available until recently. As a remedy, the higher accuracy provided by solutions of the Boltzmann transport equation is often exchanged for lower computational expense by using simpler models based on macroscopic quantities such as carrier density and mean carrier velocity. Recent developments for the deterministic spherical harmonics expansion method have reduced the computational cost for solving the Boltzmann transport equation, enabling the computation of carrier distribution functions even for spatially three-dimensional device simulations within minutes to hours. We summarize recent progress for the spherical harmonics expansion method and show that small currents, reasonable execution times, and rare events such as low-frequency noise, which are all hard or even impossible to simulate with the established Monte Carlo method, can be handled in a straight-forward manner. The applicability of the method for important practical applications is demonstrated for noise simulation, small-signal analysis, hot-carrier degradation, and avalanche breakdown.

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

PubMed Central

Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

2013-01-01

Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules. As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.g., in cells. Stokesian dynamics (SD) is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. This algorithm traditionally involves an O(N3) operation to compute Brownian forces at each time step, although asymptotically faster but more complex SD methods are now available. Motivated by the idea of hydrodynamic screening, the far-field part of the hydrodynamic matrix in SD may be approximated by a diagonal matrix, which is equivalent to assuming that long range hydrodynamic interactions are completely screened. This approximation allows sparse matrix methods to be used, which can reduce the apparent computational scaling to O(N). Previously there were several simulation studies using this approximation for monodisperse suspensions. Here, we employ newly designed preconditioned iterative methods for both the computation of Brownian forces and the solution of linear systems, and consider the validity of this approximation in polydisperse suspensions. We evaluate the accuracy of the diagonal approximation method using an intracellular-like suspension. The diffusivities of particles obtained with this approximation are close to those with the original method. However, this approximation underestimates intermolecular correlated motions, which is a trade-off between accuracy and computing efficiency. The new method makes it possible to perform large-scale and long-time simulation with an approximate accounting of hydrodynamic interactions. PMID:24089734

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

DTIC Science & Technology

2011-12-01

REMD while reproducing the energy landscape of explicit solvent simulations . ’ INTRODUCTION Molecular dynamics (MD) simulations of proteins can pro...Mongan, J.; McCammon, J. A. Accelerated molecular dynamics : a promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120 (24...Chemical Theory and Computation ARTICLE (8) Abraham,M. J.; Gready, J. E. Ensuringmixing efficiency of replica- exchange molecular dynamics simulations . J

Predicting knee replacement damage in a simulator machine using a computational model with a consistent wear factor.

PubMed

Zhao, Dong; Sakoda, Hideyuki; Sawyer, W Gregory; Banks, Scott A; Fregly, Benjamin J

2008-02-01

Wear of ultrahigh molecular weight polyethylene remains a primary factor limiting the longevity of total knee replacements (TKRs). However, wear testing on a simulator machine is time consuming and expensive, making it impractical for iterative design purposes. The objectives of this paper were first, to evaluate whether a computational model using a wear factor consistent with the TKR material pair can predict accurate TKR damage measured in a simulator machine, and second, to investigate how choice of surface evolution method (fixed or variable step) and material model (linear or nonlinear) affect the prediction. An iterative computational damage model was constructed for a commercial knee implant in an AMTI simulator machine. The damage model combined a dynamic contact model with a surface evolution model to predict how wear plus creep progressively alter tibial insert geometry over multiple simulations. The computational framework was validated by predicting wear in a cylinder-on-plate system for which an analytical solution was derived. The implant damage model was evaluated for 5 million cycles of simulated gait using damage measurements made on the same implant in an AMTI machine. Using a pin-on-plate wear factor for the same material pair as the implant, the model predicted tibial insert wear volume to within 2% error and damage depths and areas to within 18% and 10% error, respectively. Choice of material model had little influence, while inclusion of surface evolution affected damage depth and area but not wear volume predictions. Surface evolution method was important only during the initial cycles, where variable step was needed to capture rapid geometry changes due to the creep. Overall, our results indicate that accurate TKR damage predictions can be made with a computational model using a constant wear factor obtained from pin-on-plate tests for the same material pair, and furthermore, that surface evolution method matters only during the initial "break in" period of the simulation.

ISCFD Nagoya 1989 - International Symposium on Computational Fluid Dynamics, 3rd, Nagoya, Japan, Aug. 28-31, 1989, Technical Papers

NASA Astrophysics Data System (ADS)

Recent advances in computational fluid dynamics are discussed in reviews and reports. Topics addressed include large-scale LESs for turbulent pipe and channel flows, numerical solutions of the Euler and Navier-Stokes equations on parallel computers, multigrid methods for steady high-Reynolds-number flow past sudden expansions, finite-volume methods on unstructured grids, supersonic wake flow on a blunt body, a grid-characteristic method for multidimensional gas dynamics, and CIC numerical simulation of a wave boundary layer. Consideration is given to vortex simulations of confined two-dimensional jets, supersonic viscous shear layers, spectral methods for compressible flows, shock-wave refraction at air/water interfaces, oscillatory flow in a two-dimensional collapsible channel, the growth of randomness in a spatially developing wake, and an efficient simplex algorithm for the finite-difference and dynamic linear-programming method in optimal potential control.

Linear solver performance in elastoplastic problem solution on GPU cluster

NASA Astrophysics Data System (ADS)

Khalevitsky, Yu. V.; Konovalov, A. V.; Burmasheva, N. V.; Partin, A. S.

2017-12-01

Applying the finite element method to severe plastic deformation problems involves solving linear equation systems. While the solution procedure is relatively hard to parallelize and computationally intensive by itself, a long series of large scale systems need to be solved for each problem. When dealing with fine computational meshes, such as in the simulations of three-dimensional metal matrix composite microvolume deformation, tens and hundreds of hours may be needed to complete the whole solution procedure, even using modern supercomputers. In general, one of the preconditioned Krylov subspace methods is used in a linear solver for such problems. The method convergence highly depends on the operator spectrum of a problem stiffness matrix. In order to choose the appropriate method, a series of computational experiments is used. Different methods may be preferable for different computational systems for the same problem. In this paper we present experimental data obtained by solving linear equation systems from an elastoplastic problem on a GPU cluster. The data can be used to substantiate the choice of the appropriate method for a linear solver to use in severe plastic deformation simulations.

Large-Eddy/Lattice Boltzmann Simulations of Micro-blowing Strategies for Subsonic and Supersonic Drag Control

NASA Technical Reports Server (NTRS)

Menon, Suresh

2003-01-01

This report summarizes the progress made in the first 8 to 9 months of this research. The Lattice Boltzmann Equation (LBE) methodology for Large-eddy Simulations (LES) of microblowing has been validated using a jet-in-crossflow test configuration. In this study, the flow intake is also simulated to allow the interaction to occur naturally. The Lattice Boltzmann Equation Large-eddy Simulations (LBELES) approach is capable of capturing not only the flow features associated with the flow, such as hairpin vortices and recirculation behind the jet, but also is able to show better agreement with experiments when compared to previous RANS predictions. The LBELES is shown to be computationally very efficient and therefore, a viable method for simulating the injection process. Two strategies have been developed to simulate multi-hole injection process as in the experiment. In order to allow natural interaction between the injected fluid and the primary stream, the flow intakes for all the holes have to be simulated. The LBE method is computationally efficient but is still 3D in nature and therefore, there may be some computational penalty. In order to study a large number or holes, a new 1D subgrid model has been developed that will simulate a reduced form of the Navier-Stokes equation in these holes.

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

PubMed Central

Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

2013-01-01

This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. PMID:23913979

Image-based computer-assisted diagnosis system for benign paroxysmal positional vertigo

NASA Astrophysics Data System (ADS)

Kohigashi, Satoru; Nakamae, Koji; Fujioka, Hiromu

2005-04-01

We develop the image based computer assisted diagnosis system for benign paroxysmal positional vertigo (BPPV) that consists of the balance control system simulator, the 3D eye movement simulator, and the extraction method of nystagmus response directly from an eye movement image sequence. In the system, the causes and conditions of BPPV are estimated by searching the database for record matching with the nystagmus response for the observed eye image sequence of the patient with BPPV. The database includes the nystagmus responses for simulated eye movement sequences. The eye movement velocity is obtained by using the balance control system simulator that allows us to simulate BPPV under various conditions such as canalithiasis, cupulolithiasis, number of otoconia, otoconium size, and so on. Then the eye movement image sequence is displayed on the CRT by the 3D eye movement simulator. The nystagmus responses are extracted from the image sequence by the proposed method and are stored in the database. In order to enhance the diagnosis accuracy, the nystagmus response for a newly simulated sequence is matched with that for the observed sequence. From the matched simulation conditions, the causes and conditions of BPPV are estimated. We apply our image based computer assisted diagnosis system to two real eye movement image sequences for patients with BPPV to show its validity.

New Challenges in Computational Thermal Hydraulics

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

Yadigaroglu, George; Lakehal, Djamel

New needs and opportunities drive the development of novel computational methods for the design and safety analysis of light water reactors (LWRs). Some new methods are likely to be three dimensional. Coupling is expected between system codes, computational fluid dynamics (CFD) modules, and cascades of computations at scales ranging from the macro- or system scale to the micro- or turbulence scales, with the various levels continuously exchanging information back and forth. The ISP-42/PANDA and the international SETH project provide opportunities for testing applications of single-phase CFD methods to LWR safety problems. Although industrial single-phase CFD applications are commonplace, computational multifluidmore » dynamics is still under development. However, first applications are appearing; the state of the art and its potential uses are discussed. The case study of condensation of steam/air mixtures injected from a downward-facing vent into a pool of water is a perfect illustration of a simulation cascade: At the top of the hierarchy of scales, system behavior can be modeled with a system code; at the central level, the volume-of-fluid method can be applied to predict large-scale bubbling behavior; at the bottom of the cascade, direct-contact condensation can be treated with direct numerical simulation, in which turbulent flow (in both the gas and the liquid), interfacial dynamics, and heat/mass transfer are directly simulated without resorting to models.« less

Response Matrix Monte Carlo for electron transport

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

Ballinger, C.T.; Nielsen, D.E. Jr.; Rathkopf, J.A.

1990-11-01

A Response Matrix Monte Carol (RMMC) method has been developed for solving electron transport problems. This method was born of the need to have a reliable, computationally efficient transport method for low energy electrons (below a few hundred keV) in all materials. Today, condensed history methods are used which reduce the computation time by modeling the combined effect of many collisions but fail at low energy because of the assumptions required to characterize the electron scattering. Analog Monte Carlo simulations are prohibitively expensive since electrons undergo coulombic scattering with little state change after a collision. The RMMC method attempts tomore » combine the accuracy of an analog Monte Carlo simulation with the speed of the condensed history methods. The combined effect of many collisions is modeled, like condensed history, except it is precalculated via an analog Monte Carol simulation. This avoids the scattering kernel assumptions associated with condensed history methods. Results show good agreement between the RMMC method and analog Monte Carlo. 11 refs., 7 figs., 1 tabs.« less

On the simulation and mitigation of anisoplanatic optical turbulence for long range imaging

NASA Astrophysics Data System (ADS)

Hardie, Russell C.; LeMaster, Daniel A.

2017-05-01

We describe a numerical wave propagation method for simulating long range imaging of an extended scene under anisoplanatic conditions. Our approach computes an array of point spread functions (PSFs) for a 2D grid on the object plane. The PSFs are then used in a spatially varying weighted sum operation, with an ideal image, to produce a simulated image with realistic optical turbulence degradation. To validate the simulation we compare simulated outputs with the theoretical anisoplanatic tilt correlation and differential tilt variance. This is in addition to comparing the long- and short-exposure PSFs, and isoplanatic angle. Our validation analysis shows an excellent match between the simulation statistics and the theoretical predictions. The simulation tool is also used here to quantitatively evaluate a recently proposed block- matching and Wiener filtering (BMWF) method for turbulence mitigation. In this method block-matching registration algorithm is used to provide geometric correction for each of the individual input frames. The registered frames are then averaged and processed with a Wiener filter for restoration. A novel aspect of the proposed BMWF method is that the PSF model used for restoration takes into account the level of geometric correction achieved during image registration. This way, the Wiener filter is able fully exploit the reduced blurring achieved by registration. The BMWF method is relatively simple computationally, and yet, has excellent performance in comparison to state-of-the-art benchmark methods.

Computational Aerodynamic Simulations of a 1484 ft/sec Tip Speed Quiet High-Speed Fan System Model for Acoustic Methods Assessment and Development

NASA Technical Reports Server (NTRS)

Tweedt, Daniel L.

2014-01-01

Computational Aerodynamic simulations of a 1484 ft/sec tip speed quiet high-speed fan system were performed at five different operating points on the fan operating line, in order to provide detailed internal flow field information for use with fan acoustic prediction methods presently being developed, assessed and validated. The fan system is a sub-scale, low-noise research fan/nacelle model that has undergone experimental testing in the 9- by 15-foot Low Speed Wind Tunnel at the NASA Glenn Research Center. Details of the fan geometry, the computational fluid dynamics methods, the computational grids, and various computational parameters relevant to the numerical simulations are discussed. Flow field results for three of the five operating points simulated are presented in order to provide a representative look at the computed solutions. Each of the five fan aerodynamic simulations involved the entire fan system, which includes a core duct and a bypass duct that merge upstream of the fan system nozzle. As a result, only fan rotational speed and the system bypass ratio, set by means of a translating nozzle plug, were adjusted in order to set the fan operating point, leading to operating points that lie on a fan operating line and making mass flow rate a fully dependent parameter. The resulting mass flow rates are in good agreement with measurement values. Computed blade row flow fields at all fan operating points are, in general, aerodynamically healthy. Rotor blade and fan exit guide vane flow characteristics are good, including incidence and deviation angles, chordwise static pressure distributions, blade surface boundary layers, secondary flow structures, and blade wakes. Examination of the computed flow fields reveals no excessive or critical boundary layer separations or related secondary-flow problems, with the exception of the hub boundary layer at the core duct entrance. At that location a significant flow separation is present. The region of local flow recirculation extends through a mixing plane, however, which for the particular mixing-plane model used is now known to exaggerate the recirculation. In any case, the flow separation has relatively little impact on the computed rotor and FEGV flow fields.

Computational Fluid Dynamics (CFD) Simulation of Hypersonic Turbine-Based Combined-Cycle (TBCC) Inlet Mode Transition

NASA Technical Reports Server (NTRS)

Slater, John W.; Saunders, John D.

2010-01-01

Methods of computational fluid dynamics were applied to simulate the aerodynamics within the turbine flowpath of a turbine-based combined-cycle propulsion system during inlet mode transition at Mach 4. Inlet mode transition involved the rotation of a splitter cowl to close the turbine flowpath to allow the full operation of a parallel dual-mode ramjet/scramjet flowpath. Steady-state simulations were performed at splitter cowl positions of 0deg, -2deg, -4deg, and -5.7deg, at which the turbine flowpath was closed half way. The simulations satisfied one objective of providing a greater understanding of the flow during inlet mode transition. Comparisons of the simulation results with wind-tunnel test data addressed another objective of assessing the applicability of the simulation methods for simulating inlet mode transition. The simulations showed that inlet mode transition could occur in a stable manner and that accurate modeling of the interactions among the shock waves, boundary layers, and porous bleed regions was critical for evaluating the inlet static and total pressures, bleed flow rates, and bleed plenum pressures. The simulations compared well with some of the wind-tunnel data, but uncertainties in both the windtunnel data and simulations prevented a formal evaluation of the accuracy of the simulation methods.

Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

NASA Astrophysics Data System (ADS)

Dednam, W.; Botha, A. E.

2015-01-01

Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution function method.

Direct simulation of high-vorticity gas flows

NASA Technical Reports Server (NTRS)

Bird, G. A.

1987-01-01

The computational limitations associated with the molecular dynamics (MD) method and the direct simulation Monte Carlo (DSMC) method are reviewed in the context of the computation of dilute gas flows with high vorticity. It is concluded that the MD method is generally limited to the dense gas case in which the molecular diameter is one-tenth or more of the mean free path. It is shown that the cell size in DSMC calculations should be small in comparison with the mean free path, and that this may be facilitated by a new subcell procedure for the selection of collision partners.

Parallel scalability and efficiency of vortex particle method for aeroelasticity analysis of bluff bodies

NASA Astrophysics Data System (ADS)

Tolba, Khaled Ibrahim; Morgenthal, Guido

2018-01-01

This paper presents an analysis of the scalability and efficiency of a simulation framework based on the vortex particle method. The code is applied for the numerical aerodynamic analysis of line-like structures. The numerical code runs on multicore CPU and GPU architectures using OpenCL framework. The focus of this paper is the analysis of the parallel efficiency and scalability of the method being applied to an engineering test case, specifically the aeroelastic response of a long-span bridge girder at the construction stage. The target is to assess the optimal configuration and the required computer architecture, such that it becomes feasible to efficiently utilise the method within the computational resources available for a regular engineering office. The simulations and the scalability analysis are performed on a regular gaming type computer.

Systems Biology in Immunology – A Computational Modeling Perspective

PubMed Central

Germain, Ronald N.; Meier-Schellersheim, Martin; Nita-Lazar, Aleksandra; Fraser, Iain D. C.

2011-01-01

Systems biology is an emerging discipline that combines high-content, multiplexed measurements with informatic and computational modeling methods to better understand biological function at various scales. Here we present a detailed review of the methods used to create computational models and conduct simulations of immune function, We provide descriptions of the key data gathering techniques employed to generate the quantitative and qualitative data required for such modeling and simulation and summarize the progress to date in applying these tools and techniques to questions of immunological interest, including infectious disease. We include comments on what insights modeling can provide that complement information obtained from the more familiar experimental discovery methods used by most investigators and why quantitative methods are needed to eventually produce a better understanding of immune system operation in health and disease. PMID:21219182

Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

PubMed

Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao

2013-09-10

Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.

Composite mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1987-01-01

Recent research activities and accomplishments at Lewis Research Center on composite mechanics for engine structures are summarized. The activities focused mainly on developing procedures for the computational simulation of composite intrinsic and structural behavior. The computational simulation encompasses all aspects of composite mechanics, advanced three-dimensional finite-element methods, damage tolerance, composite structural and dynamic response, and structural tailoring and optimization.

Composite mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1989-01-01

Recent research activities and accomplishments at Lewis Research Center on composite mechanics for engine structures are summarized. The activities focused mainly on developing procedures for the computational simulation of composite intrinsic and structural behavior. The computational simulation encompasses all aspects of composite mechanics, advanced three-dimensional finite-element methods, damage tolerance, composite structural and dynamic response, and structural tailoring and optimization.

A Comparative Analysis of Student Learning with a Collaborative Computer Simulation of the Cardiopulmonary System

ERIC Educational Resources Information Center

Keyser, Diane

2010-01-01

To design a series of assessments that could be used to compare the learning gains of high school students studying the cardiopulmonary system using traditional methods to those who used a collaborative computer simulation, called "Mr. Vetro". Five teachers and 264 HS biology students participated in the study. The students were in…

Computational approach to integrate 3D X-ray microtomography and NMR data.

PubMed

Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G; Trevizan, Willian A; Fortulan, Carlos A; Bonagamba, Tito J

2018-05-04

Nowadays, most of the efforts in NMR applied to porous media are dedicated to studying the molecular fluid dynamics within and among the pores. These analyses have a higher complexity due to morphology and chemical composition of rocks, besides dynamic effects as restricted diffusion, diffusional coupling, and exchange processes. Since the translational nuclear spin diffusion in a confined geometry (e.g. pores and fractures) requires specific boundary conditions, the theoretical solutions are restricted to some special problems and, in many cases, computational methods are required. The Random Walk Method is a classic way to simulate self-diffusion along a Digital Porous Medium. Bergman model considers the magnetic relaxation process of the fluid molecules by including a probability rate of magnetization survival under surface interactions. Here we propose a statistical approach to correlate surface magnetic relaxivity with the computational method applied to the NMR relaxation in order to elucidate the relationship between simulated relaxation time and pore size of the Digital Porous Medium. The proposed computational method simulates one- and two-dimensional NMR techniques reproducing, for example, longitudinal and transverse relaxation times (T 1 and T 2 , respectively), diffusion coefficients (D), as well as their correlations. For a good approximation between the numerical and experimental results, it is necessary to preserve the complexity of translational diffusion through the microstructures in the digital rocks. Therefore, we use Digital Porous Media obtained by 3D X-ray microtomography. To validate the method, relaxation times of ideal spherical pores were obtained and compared with the previous determinations by the Brownstein-Tarr model, as well as the computational approach proposed by Bergman. Furthermore, simulated and experimental results of synthetic porous media are compared. These results make evident the potential of computational physics in the analysis of the NMR data for complex porous materials. Copyright © 2018 Elsevier Inc. All rights reserved.

Multiscale Modeling of UHTC: Thermal Conductivity

NASA Technical Reports Server (NTRS)

Lawson, John W.; Murry, Daw; Squire, Thomas; Bauschlicher, Charles W.

2012-01-01

We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.

Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores.

PubMed

Wells, David B; Bhattacharya, Swati; Carr, Rogan; Maffeo, Christopher; Ho, Anthony; Comer, Jeffrey; Aksimentiev, Aleksei

2012-01-01

Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.

Evaluating variability with atomistic simulations: the effect of potential and calculation methodology on the modeling of lattice and elastic constants

NASA Astrophysics Data System (ADS)

Hale, Lucas M.; Trautt, Zachary T.; Becker, Chandler A.

2018-07-01

Atomistic simulations using classical interatomic potentials are powerful investigative tools linking atomic structures to dynamic properties and behaviors. It is well known that different interatomic potentials produce different results, thus making it necessary to characterize potentials based on how they predict basic properties. Doing so makes it possible to compare existing interatomic models in order to select those best suited for specific use cases, and to identify any limitations of the models that may lead to unrealistic responses. While the methods for obtaining many of these properties are often thought of as simple calculations, there are many underlying aspects that can lead to variability in the reported property values. For instance, multiple methods may exist for computing the same property and values may be sensitive to certain simulation parameters. Here, we introduce a new high-throughput computational framework that encodes various simulation methodologies as Python calculation scripts. Three distinct methods for evaluating the lattice and elastic constants of bulk crystal structures are implemented and used to evaluate the properties across 120 interatomic potentials, 18 crystal prototypes, and all possible combinations of unique lattice site and elemental model pairings. Analysis of the results reveals which potentials and crystal prototypes are sensitive to the calculation methods and parameters, and it assists with the verification of potentials, methods, and molecular dynamics software. The results, calculation scripts, and computational infrastructure are self-contained and openly available to support researchers in performing meaningful simulations.

An adaptive multi-level simulation algorithm for stochastic biological systems

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

Lester, C., E-mail: lesterc@maths.ox.ac.uk; 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 Montemore » 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 efficiency of our method using a number of examples.« less

Electric Power Distribution System Model Simplification Using Segment Substitution

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

Reiman, Andrew P.; McDermott, Thomas E.; Akcakaya, Murat

Quasi-static time-series (QSTS) simulation is used to simulate the behavior of distribution systems over long periods of time (typically hours to years). The technique involves repeatedly solving the load-flow problem for a distribution system model and is useful for distributed energy resource (DER) planning. When a QSTS simulation has a small time step and a long duration, the computational burden of the simulation can be a barrier to integration into utility workflows. One way to relieve the computational burden is to simplify the system model. The segment substitution method of simplifying distribution system models introduced in this paper offers modelmore » bus reduction of up to 98% with a simplification error as low as 0.2% (0.002 pu voltage). In contrast to existing methods of distribution system model simplification, which rely on topological inspection and linearization, the segment substitution method uses black-box segment data and an assumed simplified topology.« less

Simulation of spacecraft attitude dynamics using TREETOPS and model-specific computer Codes

NASA Technical Reports Server (NTRS)

Cochran, John E.; No, T. S.; Fitz-Coy, Norman G.

1989-01-01

The simulation of spacecraft attitude dynamics and control using the generic, multi-body code called TREETOPS and other codes written especially to simulate particular systems is discussed. Differences in the methods used to derive equations of motion--Kane's method for TREETOPS and the Lagrangian and Newton-Euler methods, respectively, for the other two codes--are considered. Simulation results from the TREETOPS code are compared with those from the other two codes for two example systems. One system is a chain of rigid bodies; the other consists of two rigid bodies attached to a flexible base body. Since the computer codes were developed independently, consistent results serve as a verification of the correctness of all the programs. Differences in the results are discussed. Results for the two-rigid-body, one-flexible-body system are useful also as information on multi-body, flexible, pointing payload dynamics.

Simulation of dilute polymeric fluids in a three-dimensional contraction using a multiscale FENE model

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

Griebel, M., E-mail: griebel@ins.uni-bonn.de, E-mail: ruettgers@ins.uni-bonn.de; Rüttgers, A., E-mail: griebel@ins.uni-bonn.de, E-mail: ruettgers@ins.uni-bonn.de

The multiscale FENE model is applied to a 3D square-square contraction flow problem. For this purpose, the stochastic Brownian configuration field method (BCF) has been coupled with our fully parallelized three-dimensional Navier-Stokes solver NaSt3DGPF. The robustness of the BCF method enables the numerical simulation of high Deborah number flows for which most macroscopic methods suffer from stability issues. The results of our simulations are compared with that of experimental measurements from literature and show a very good agreement. In particular, flow phenomena such as a strong vortex enhancement, streamline divergence and a flow inversion for highly elastic flows are reproduced.more » Due to their computational complexity, our simulations require massively parallel computations. Using a domain decomposition approach with MPI, the implementation achieves excellent scale-up results for up to 128 processors.« less

An efficient formulation of robot arm dynamics for control and computer simulation

NASA Astrophysics Data System (ADS)

Lee, C. S. G.; Nigam, R.

This paper describes an efficient formulation of the dynamic equations of motion of industrial robots based on the Lagrange formulation of d'Alembert's principle. This formulation, as applied to a PUMA robot arm, results in a set of closed form second order differential equations with cross product terms. They are not as efficient in computation as those formulated by the Newton-Euler method, but provide a better analytical model for control analysis and computer simulation. Computational complexities of this dynamic model together with other models are tabulated for discussion.

Effective Energy Simulation and Optimal Design of Side-lit Buildings with Venetian Blinds

NASA Astrophysics Data System (ADS)

Cheng, Tian

Venetian blinds are popularly used in buildings to control the amount of incoming daylight for improving visual comfort and reducing heat gains in air-conditioning systems. Studies have shown that the proper design and operation of window systems could result in significant energy savings in both lighting and cooling. However, there is no convenient computer tool that allows effective and efficient optimization of the envelope of side-lit buildings with blinds now. Three computer tools, Adeline, DOE2 and EnergyPlus widely used for the above-mentioned purpose have been experimentally examined in this study. Results indicate that the two former tools give unacceptable accuracy due to unrealistic assumptions adopted while the last one may generate large errors in certain conditions. Moreover, current computer tools have to conduct hourly energy simulations, which are not necessary for life-cycle energy analysis and optimal design, to provide annual cooling loads. This is not computationally efficient, particularly not suitable for optimal designing a building at initial stage because the impacts of many design variations and optional features have to be evaluated. A methodology is therefore developed for efficient and effective thermal and daylighting simulations and optimal design of buildings with blinds. Based on geometric optics and radiosity method, a mathematical model is developed to reasonably simulate the daylighting behaviors of venetian blinds. Indoor illuminance at any reference point can be directly and efficiently computed. They have been validated with both experiments and simulations with Radiance. Validation results show that indoor illuminances computed by the new models agree well with the measured data, and the accuracy provided by them is equivalent to that of Radiance. The computational efficiency of the new models is much higher than that of Radiance as well as EnergyPlus. Two new methods are developed for the thermal simulation of buildings. A fast Fourier transform (FFT) method is presented to avoid the root-searching process in the inverse Laplace transform of multilayered walls. Generalized explicit FFT formulae for calculating the discrete Fourier transform (DFT) are developed for the first time. They can largely facilitate the implementation of FFT. The new method also provides a basis for generating the symbolic response factors. Validation simulations show that it can generate the response factors as accurate as the analytical solutions. The second method is for direct estimation of annual or seasonal cooling loads without the need for tedious hourly energy simulations. It is validated by hourly simulation results with DOE2. Then symbolic long-term cooling load can be created by combining the two methods with thermal network analysis. The symbolic long-term cooling load can keep the design parameters of interest as symbols, which is particularly useful for the optimal design and sensitivity analysis. The methodology is applied to an office building in Hong Kong for the optimal design of building envelope. Design variables such as window-to-wall ratio, building orientation, and glazing optical and thermal properties are included in the study. Results show that the selected design values could significantly impact the energy performance of windows, and the optimal design of side-lit buildings could greatly enhance energy savings. The application example also demonstrates that the developed methodology significantly facilitates the optimal building design and sensitivity analysis, and leads to high computational efficiency.

Monte Carlo Methodology Serves Up a Software Success

NASA Technical Reports Server (NTRS)

2003-01-01

Widely used for the modeling of gas flows through the computation of the motion and collisions of representative molecules, the Direct Simulation Monte Carlo method has become the gold standard for producing research and engineering predictions in the field of rarefied gas dynamics. Direct Simulation Monte Carlo was first introduced in the early 1960s by Dr. Graeme Bird, a professor at the University of Sydney, Australia. It has since proved to be a valuable tool to the aerospace and defense industries in providing design and operational support data, as well as flight data analysis. In 2002, NASA brought to the forefront a software product that maintains the same basic physics formulation of Dr. Bird's method, but provides effective modeling of complex, three-dimensional, real vehicle simulations and parallel processing capabilities to handle additional computational requirements, especially in areas where computational fluid dynamics (CFD) is not applicable. NASA's Direct Simulation Monte Carlo Analysis Code (DAC) software package is now considered the Agency s premier high-fidelity simulation tool for predicting vehicle aerodynamics and aerothermodynamic environments in rarified, or low-density, gas flows.

Assessment of Different Discrete Particle Methods Ability To Predict Gas-Particle Flow in a Small-Scale Fluidized Bed

DOE PAGES

Lu, Liqiang; Gopalan, Balaji; Benyahia, Sofiane

2017-06-21

Several discrete particle methods exist in the open literature to simulate fluidized bed systems, such as discrete element method (DEM), time driven hard sphere (TDHS), coarse-grained particle method (CGPM), coarse grained hard sphere (CGHS), and multi-phase particle-in-cell (MP-PIC). These different approaches usually solve the fluid phase in a Eulerian fixed frame of reference and the particle phase using the Lagrangian method. The first difference between these models lies in tracking either real particles or lumped parcels. The second difference is in the treatment of particle-particle interactions: by calculating collision forces (DEM and CGPM), using momentum conservation laws (TDHS and CGHS),more » or based on particle stress model (MP-PIC). These major model differences lead to a wide range of results accuracy and computation speed. However, these models have never been compared directly using the same experimental dataset. In this research, a small-scale fluidized bed is simulated with these methods using the same open-source code MFIX. The results indicate that modeling the particle-particle collision by TDHS increases the computation speed while maintaining good accuracy. Also, lumping few particles in a parcel increases the computation speed with little loss in accuracy. However, modeling particle-particle interactions with solids stress leads to a big loss in accuracy with a little increase in computation speed. The MP-PIC method predicts an unphysical particle-particle overlap, which results in incorrect voidage distribution and incorrect overall bed hydrodynamics. Based on this study, we recommend using the CGHS method for fluidized bed simulations due to its computational speed that rivals that of MPPIC while maintaining a much better accuracy.« less

Assessment of Different Discrete Particle Methods Ability To Predict Gas-Particle Flow in a Small-Scale Fluidized Bed

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

Lu, Liqiang; Gopalan, Balaji; Benyahia, Sofiane

Several discrete particle methods exist in the open literature to simulate fluidized bed systems, such as discrete element method (DEM), time driven hard sphere (TDHS), coarse-grained particle method (CGPM), coarse grained hard sphere (CGHS), and multi-phase particle-in-cell (MP-PIC). These different approaches usually solve the fluid phase in a Eulerian fixed frame of reference and the particle phase using the Lagrangian method. The first difference between these models lies in tracking either real particles or lumped parcels. The second difference is in the treatment of particle-particle interactions: by calculating collision forces (DEM and CGPM), using momentum conservation laws (TDHS and CGHS),more » or based on particle stress model (MP-PIC). These major model differences lead to a wide range of results accuracy and computation speed. However, these models have never been compared directly using the same experimental dataset. In this research, a small-scale fluidized bed is simulated with these methods using the same open-source code MFIX. The results indicate that modeling the particle-particle collision by TDHS increases the computation speed while maintaining good accuracy. Also, lumping few particles in a parcel increases the computation speed with little loss in accuracy. However, modeling particle-particle interactions with solids stress leads to a big loss in accuracy with a little increase in computation speed. The MP-PIC method predicts an unphysical particle-particle overlap, which results in incorrect voidage distribution and incorrect overall bed hydrodynamics. Based on this study, we recommend using the CGHS method for fluidized bed simulations due to its computational speed that rivals that of MPPIC while maintaining a much better accuracy.« less

PREFACE: Proceedings of the 2nd International Conference on Quantum Simulators and Design (Tokyo, Japan, 31 May-3 June 2008) Proceedings of the 2nd International Conference on Quantum Simulators and Design (Tokyo, Japan, 31 May-3 June 2008)

NASA Astrophysics Data System (ADS)

Akai, Hisazumi; Tsuneyuki, Shinji

2009-02-01

This special issue of Journal of Physics: Condensed Matter comprises selected papers from the proceedings of the 2nd International Conference on Quantum Simulators and Design (QSD2008) held in Tokyo, Japan, between 31 May and 3 June 2008. This conference was organized under the auspices of the Development of New Quantum Simulators and Quantum Design Grant-in-Aid for Scientific Research on Priority Areas, Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). The conference focused on the development of first principles electronic structure calculations and their applications. The aim was to provide an opportunity for discussion on the progress in computational materials design and, in particular, the development of quantum simulators and quantum design. Computational materials design is a computational approach to the development of new materials. The essential ingredient is the use of quantum simulators to design a material that meets a given specification of properties and functionalities. For this to be successful, the quantum simulator should be very reliable and be applicable to systems of realistic size. During the conference, new methods of quantum simulation and quantum design were discussed including methods beyond the local density approximation of density functional theory, order-N methods, methods dealing with excitations and reactions, and the application of these methods to the design of novel materials, devices and systems. The conference provided an international forum for experimental and theoretical researchers to exchange ideas. A total of 220 delegates from eight countries participated in the conference. There were 13 invited talks, ten oral presentations and 120 posters. The 3rd International Conference on Quantum Simulators and Design will be held in Germany in the autumn of 2011.

Gravitational waveforms for neutron star binaries from binary black hole simulations

NASA Astrophysics Data System (ADS)

Barkett, Kevin; Scheel, Mark; Haas, Roland; Ott, Christian; Bernuzzi, Sebastiano; Brown, Duncan; Szilagyi, Bela; Kaplan, Jeffrey; Lippuner, Jonas; Muhlberger, Curran; Foucart, Francois; Duez, Matthew

2016-03-01

Gravitational waves from binary neutron star (BNS) and black-hole/neutron star (BHNS) inspirals are primary sources for detection by the Advanced Laser Interferometer Gravitational-Wave Observatory. The tidal forces acting on the neutron stars induce changes in the phase evolution of the gravitational waveform, and these changes can be used to constrain the nuclear equation of state. Current methods of generating BNS and BHNS waveforms rely on either computationally challenging full 3D hydrodynamical simulations or approximate analytic solutions. We introduce a new method for computing inspiral waveforms for BNS/BHNS systems by adding the post-Newtonian (PN) tidal effects to full numerical simulations of binary black holes (BBHs), effectively replacing the non-tidal terms in the PN expansion with BBH results. Comparing a waveform generated with this method against a full hydrodynamical simulation of a BNS inspiral yields a phase difference of < 1 radian over ~ 15 orbits. The numerical phase accuracy required of BNS simulations to measure the accuracy of the method we present here is estimated as a function of the tidal deformability parameter λ.

Gravitational waveforms for neutron star binaries from binary black hole simulations

NASA Astrophysics Data System (ADS)

Barkett, Kevin; Scheel, Mark A.; Haas, Roland; Ott, Christian D.; Bernuzzi, Sebastiano; Brown, Duncan A.; Szilágyi, Béla; Kaplan, Jeffrey D.; Lippuner, Jonas; Muhlberger, Curran D.; Foucart, Francois; Duez, Matthew D.

2016-02-01

Gravitational waves from binary neutron star (BNS) and black hole/neutron star (BHNS) inspirals are primary sources for detection by the Advanced Laser Interferometer Gravitational-Wave Observatory. The tidal forces acting on the neutron stars induce changes in the phase evolution of the gravitational waveform, and these changes can be used to constrain the nuclear equation of state. Current methods of generating BNS and BHNS waveforms rely on either computationally challenging full 3D hydrodynamical simulations or approximate analytic solutions. We introduce a new method for computing inspiral waveforms for BNS/BHNS systems by adding the post-Newtonian (PN) tidal effects to full numerical simulations of binary black holes (BBHs), effectively replacing the nontidal terms in the PN expansion with BBH results. Comparing a waveform generated with this method against a full hydrodynamical simulation of a BNS inspiral yields a phase difference of <1 radian over ˜15 orbits. The numerical phase accuracy required of BNS simulations to measure the accuracy of the method we present here is estimated as a function of the tidal deformability parameter λ .

Kirchhoff and Ohm in action: solving electric currents in continuous extended media

NASA Astrophysics Data System (ADS)

Dolinko, A. E.

2018-03-01

In this paper we show a simple and versatile computational simulation method for determining electric currents and electric potential in 2D and 3D media with arbitrary distribution of resistivity. One of the highlights of the proposed method is that the simulation space containing the distribution of resistivity and the points of external applied voltage are introduced by means of digital images or bitmaps, which easily allows simulating any phenomena involving distributions of resistivity. The simulation is based on the Kirchhoff’s laws of electric currents and it is solved by means of an iterative procedure. The method is also generalised to account for media with distributions of reactive impedance. At the end of this work, we show an example of application of the simulation, consisting in reproducing the response obtained with the geophysical method of electric resistivity tomography in presence of soil cracks. This paper is aimed at undergraduate or graduated students interested in computational physics and electricity and also researchers involved in the area of continuous electric media, which could find a simple and powerful tool for investigation.

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

NASA Technical Reports Server (NTRS)

Balaban, Mariusz A.; Hester, Patrick T.

2012-01-01

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

Radio Frequency Mass Gauging of Propellants

NASA Technical Reports Server (NTRS)

Zimmerli, Gregory A.; Vaden, Karl R.; Herlacher, Michael D.; Buchanan, David A.; VanDresar, Neil T.

2007-01-01

A combined experimental and computer simulation effort was conducted to measure radio frequency (RF) tank resonance modes in a dewar partially filled with liquid oxygen, and compare the measurements with numerical simulations. The goal of the effort was to demonstrate that computer simulations of a tank's electromagnetic eigenmodes can be used to accurately predict ground-based measurements, thereby providing a computational tool for predicting tank modes in a low-gravity environment. Matching the measured resonant frequencies of several tank modes with computer simulations can be used to gauge the amount of liquid in a tank, thus providing a possible method to gauge cryogenic propellant tanks in low-gravity. Using a handheld RF spectrum analyzer and a small antenna in a 46 liter capacity dewar for experimental measurements, we have verified that the four lowest transverse magnetic eigenmodes can be accurately predicted as a function of liquid oxygen fill level using computer simulations. The input to the computer simulations consisted of tank dimensions, and the dielectric constant of the fluid. Without using any adjustable parameters, the calculated and measured frequencies agree such that the liquid oxygen fill level was gauged to within 2 percent full scale uncertainty. These results demonstrate the utility of using electromagnetic simulations to form the basis of an RF mass gauging technology with the power to simulate tank resonance frequencies from arbitrary fluid configurations.

A Simple Method for Automated Equilibration Detection in Molecular Simulations.

PubMed

Chodera, John D

2016-04-12

Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure and demonstrate its utility on typical molecular simulation data.

A simple method for automated equilibration detection in molecular simulations

PubMed Central

Chodera, John D.

2016-01-01

Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest, in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure, and demonstrate its utility on typical molecular simulation data. PMID:26771390

Computational Evaluation of the Traceback Method

ERIC Educational Resources Information Center

Kol, Sheli; Nir, Bracha; Wintner, Shuly

2014-01-01

Several models of language acquisition have emerged in recent years that rely on computational algorithms for simulation and evaluation. Computational models are formal and precise, and can thus provide mathematically well-motivated insights into the process of language acquisition. Such models are amenable to robust computational evaluation,…

Investigation on the forced response of a radial turbine under aerodynamic excitations

NASA Astrophysics Data System (ADS)

Ma, Chaochen; Huang, Zhi; Qi, Mingxu

2016-04-01

Rotor blades in a radial turbine with nozzle guide vanes typically experience harmonic aerodynamic excitations due to the rotor stator interaction. Dynamic stresses induced by the harmonic excitations can result in high cycle fatigue (HCF) of the blades. A reliable prediction method for forced response issue is essential to avoid the HCF problem. In this work, the forced response mechanisms were investigated based on a fluid structure interaction (FSI) method. Aerodynamic excitations were obtained by three-dimensional unsteady computational fluid dynamics (CFD) simulation with phase shifted periodic boundary conditions. The first two harmonic pressures were determined as the primary components of the excitation and applied to finite element (FE) model to conduct the computational structural dynamics (CSD) simulation. The computed results from the harmonic forced response analysis show good agreement with the predictions of Singh's advanced frequency evaluation (SAFE) diagram. Moreover, the mode superposition method used in FE simulation offers an efficient way to provide quantitative assessments of mode response levels and resonant strength.

Computational Methods for Structural Mechanics and Dynamics

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

1989-01-01

Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.

An Overview of Computational Aeroacoustic Modeling at NASA Langley

NASA Technical Reports Server (NTRS)

Lockard, David P.

2001-01-01

The use of computational techniques in the area of acoustics is known as computational aeroacoustics and has shown great promise in recent years. Although an ultimate goal is to use computational simulations as a virtual wind tunnel, the problem is so complex that blind applications of traditional algorithms are typically unable to produce acceptable results. The phenomena of interest are inherently unsteady and cover a wide range of frequencies and amplitudes. Nonetheless, with appropriate simplifications and special care to resolve specific phenomena, currently available methods can be used to solve important acoustic problems. These simulations can be used to complement experiments, and often give much more detailed information than can be obtained in a wind tunnel. The use of acoustic analogy methods to inexpensively determine far-field acoustics from near-field unsteadiness has greatly reduced the computational requirements. A few examples of current applications of computational aeroacoustics at NASA Langley are given. There remains a large class of problems that require more accurate and efficient methods. Research to develop more advanced methods that are able to handle the geometric complexity of realistic problems using block-structured and unstructured grids are highlighted.

[Automobile versus pedestrian accidents analysis by fixed-parameters computer simulation].

PubMed

Mao, Ming-Yuan; Chen, Yi-Jiu; Liu, Ning-Guo; Zou, Dong-Hua; Liu, Jun-Yong; Jin, Xian-Long

2008-04-01

Using computer simulation to analyze the effects of speed, type of automobile and impacted position on crash-course and injuries of pedestrians in automobile vs. pedestrian accidents. Automobiles (bus, minibus, car and truck) and pedestrian models were constructed with multi-body dynamics computing method. The crashes were simulated at different impact speeds (20, 30, 40, 50 and 60 km/h) and different positions (front, lateral and rear of pedestrians). Crash-courses and their biomechanical responses were studied. If the type of automobile and impact position were the same, the crash-courses were similar (impact speed < or = 60 km/h). There were some characteristics in the head acceleration, upper neck axial force and leg axial force. Multi-body dynamics computer simulation of crash can be applied to analyze crash-course and injuries (head, neck and leg) of pedestrians.

Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

NASA Astrophysics Data System (ADS)

Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

2016-07-01

Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

Design of a dynamic optical tissue phantom to model extravasation pharmacokinetics

NASA Astrophysics Data System (ADS)

Zhang, Jane Y.; Ergin, Aysegul; Andken, Kerry Lee; Sheng, Chao; Bigio, Irving J.

2010-02-01

We describe an optical tissue phantom that enables the simulation of drug extravasation from microvessels and validates computational compartmental models of drug delivery. The phantom consists of a microdialysis tubing bundle to simulate the permeable blood vessels, immersed in either an aqueous suspension of titanium dioxide (TiO2) or a TiO2 mixed agarose scattering medium. Drug administration is represented by a dye circulated through this porous microdialysis tubing bundle. Optical pharmacokinetic (OP) methods are used to measure changes in the absorption coefficient of the scattering medium due to the arrival and diffusion of the dye. We have established particle sizedependent concentration profiles over time of phantom drug delivery by intravenous (IV) and intra-arterial (IA) routes. Additionally, pharmacokinetic compartmental models are implemented in computer simulations for the conditions studied within the phantom. The simulated concentration-time profiles agree well with measurements from the phantom. The results are encouraging for future optical pharmacokinetic method development, both physical and computational, to understand drug extravasation under various physiological conditions.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations.

PubMed

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-07

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

NASA Astrophysics Data System (ADS)

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-01

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.

Assessing the convergence of LHS Monte Carlo simulations of wastewater treatment models.

PubMed

Benedetti, Lorenzo; Claeys, Filip; Nopens, Ingmar; Vanrolleghem, Peter A

2011-01-01

Monte Carlo (MC) simulation appears to be the only currently adopted tool to estimate global sensitivities and uncertainties in wastewater treatment modelling. Such models are highly complex, dynamic and non-linear, requiring long computation times, especially in the scope of MC simulation, due to the large number of simulations usually required. However, no stopping rule to decide on the number of simulations required to achieve a given confidence in the MC simulation results has been adopted so far in the field. In this work, a pragmatic method is proposed to minimize the computation time by using a combination of several criteria. It makes no use of prior knowledge about the model, is very simple, intuitive and can be automated: all convenient features in engineering applications. A case study is used to show an application of the method, and the results indicate that the required number of simulations strongly depends on the model output(s) selected, and on the type and desired accuracy of the analysis conducted. Hence, no prior indication is available regarding the necessary number of MC simulations, but the proposed method is capable of dealing with these variations and stopping the calculations after convergence is reached.

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

Biyikli, Emre; To, Albert C., E-mail: albertto@pitt.edu

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with themore » associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3–8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.« less

Multiresolution molecular mechanics: Implementation and efficiency

NASA Astrophysics Data System (ADS)

Biyikli, Emre; To, Albert C.

2017-01-01

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3-8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

Using a computer simulation for teaching communication skills: A blinded multisite mixed methods randomized controlled trial

PubMed Central

Kron, Frederick W.; Fetters, Michael D.; Scerbo, Mark W.; White, Casey B.; Lypson, Monica L.; Padilla, Miguel A.; Gliva-McConvey, Gayle A.; Belfore, Lee A.; West, Temple; Wallace, Amelia M.; Guetterman, Timothy C.; Schleicher, Lauren S.; Kennedy, Rebecca A.; Mangrulkar, Rajesh S.; Cleary, James F.; Marsella, Stacy C.; Becker, Daniel M.

2016-01-01

Objectives To assess advanced communication skills among second-year medical students exposed either to a computer simulation (MPathic-VR) featuring virtual humans, or to a multimedia computer-based learning module, and to understand each group’s experiences and learning preferences. Methods A single-blinded, mixed methods, randomized, multisite trial compared MPathic-VR (N=210) to computer-based learning (N=211). Primary outcomes: communication scores during repeat interactions with MPathic-VR’s intercultural and interprofessional communication scenarios and scores on a subsequent advanced communication skills objective structured clinical examination (OSCE). Multivariate analysis of variance was used to compare outcomes. Secondary outcomes: student attitude surveys and qualitative assessments of their experiences with MPathic-VR or computer-based learning. Results MPathic-VR-trained students improved their intercultural and interprofessional communication performance between their first and second interactions with each scenario. They also achieved significantly higher composite scores on the OSCE than computer-based learning-trained students. Attitudes and experiences were more positive among students trained with MPathic-VR, who valued its providing immediate feedback, teaching nonverbal communication skills, and preparing them for emotion-charged patient encounters. Conclusions MPathic-VR was effective in training advanced communication skills and in enabling knowledge transfer into a more realistic clinical situation. Practice Implications MPathic-VR’s virtual human simulation offers an effective and engaging means of advanced communication training. PMID:27939846

Lumber values from computerized simulation of hardwood log sawing

Treesearch

D.B. Richards; W.K. Adkins; H. Hallock; E.H. Bulgrin

1980-01-01

Computer simulation sawing programs were used to study the sawing of mathematical models of hardwood logs by me live sawing and three 4-sided sawing methods. One of the 4-sided methods simulated "grade sawing" by sawing each successive board from the log face with the highest potential grade. Logs from 10 through 28 inches in diameter were sawn. In addition,...

A hybrid method combining the surface integral equation method and ray tracing for the numerical simulation of high frequency diffraction involved in ultrasonic NDT

NASA Astrophysics Data System (ADS)

Bonnet, M.; Collino, F.; Demaldent, E.; Imperiale, A.; Pesudo, L.

2018-05-01

Ultrasonic Non-Destructive Testing (US NDT) has become widely used in various fields of applications to probe media. Exploiting the surface measurements of the ultrasonic incident waves echoes after their propagation through the medium, it allows to detect potential defects (cracks and inhomogeneities) and characterize the medium. The understanding and interpretation of those experimental measurements is performed with the help of numerical modeling and simulations. However, classical numerical methods can become computationally very expensive for the simulation of wave propagation in the high frequency regime. On the other hand, asymptotic techniques are better suited to model high frequency scattering over large distances but nevertheless do not allow accurate simulation of complex diffraction phenomena. Thus, neither numerical nor asymptotic methods can individually solve high frequency diffraction problems in large media, as those involved in UNDT controls, both quickly and accurately, but their advantages and limitations are complementary. Here we propose a hybrid strategy coupling the surface integral equation method and the ray tracing method to simulate high frequency diffraction under speed and accuracy constraints. This strategy is general and applicable to simulate diffraction phenomena in acoustic or elastodynamic media. We provide its implementation and investigate its performances for the 2D acoustic diffraction problem. The main features of this hybrid method are described and results of 2D computational experiments discussed.

Parallel Fokker–Planck-DSMC algorithm for rarefied gas flow simulation in complex domains at all Knudsen numbers

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

Küchlin, Stephan, E-mail: kuechlin@ifd.mavt.ethz.ch; Jenny, Patrick

2017-01-01

A major challenge for the conventional Direct Simulation Monte Carlo (DSMC) technique lies in the fact that its computational cost becomes prohibitive in the near continuum regime, where the Knudsen number (Kn)—characterizing the degree of rarefaction—becomes small. In contrast, the Fokker–Planck (FP) based particle Monte Carlo scheme allows for computationally efficient simulations of rarefied gas flows in the low and intermediate Kn regime. The Fokker–Planck collision operator—instead of performing binary collisions employed by the DSMC method—integrates continuous stochastic processes for the phase space evolution in time. This allows for time step and grid cell sizes larger than the respective collisionalmore » scales required by DSMC. Dynamically switching between the FP and the DSMC collision operators in each computational cell is the basis of the combined FP-DSMC method, which has been proven successful in simulating flows covering the whole Kn range. Until recently, this algorithm had only been applied to two-dimensional test cases. In this contribution, we present the first general purpose implementation of the combined FP-DSMC method. Utilizing both shared- and distributed-memory parallelization, this implementation provides the capability for simulations involving many particles and complex geometries by exploiting state of the art computer cluster technologies.« less

Numerical experiment for ultrasonic-measurement-integrated simulation of three-dimensional unsteady blood flow.

PubMed

Funamoto, Kenichi; Hayase, Toshiyuki; Saijo, Yoshifumi; Yambe, Tomoyuki

2008-08-01

Integration of ultrasonic measurement and numerical simulation is a possible way to break through limitations of existing methods for obtaining complete information on hemodynamics. We herein propose Ultrasonic-Measurement-Integrated (UMI) simulation, in which feedback signals based on the optimal estimation of errors in the velocity vector determined by measured and computed Doppler velocities at feedback points are added to the governing equations. With an eye towards practical implementation of UMI simulation with real measurement data, its efficiency for three-dimensional unsteady blood flow analysis and a method for treating low time resolution of ultrasonic measurement were investigated by a numerical experiment dealing with complicated blood flow in an aneurysm. Even when simplified boundary conditions were applied, the UMI simulation reduced the errors of velocity and pressure to 31% and 53% in the feedback domain which covered the aneurysm, respectively. Local maximum wall shear stress was estimated, showing both the proper position and the value with 1% deviance. A properly designed intermittent feedback applied only at the time when measurement data were obtained had the same computational accuracy as feedback applied at every computational time step. Hence, this feedback method is a possible solution to overcome the insufficient time resolution of ultrasonic measurement.

Application of the finite-element method and the eigenmode expansion method to investigate the periodic and spectral characteristic of discrete phase-shift fiber Bragg grating

NASA Astrophysics Data System (ADS)

He, Yue-Jing; Hung, Wei-Chih; Syu, Cheng-Jyun

2017-12-01

The finite-element method (FEM) and eigenmode expansion method (EEM) were adopted to analyze the guided modes and spectrum of phase-shift fiber Bragg grating at five phase-shift degrees (including zero, 1/4π, 1/2π, 3/4π, and π). In previous studies on optical fiber grating, conventional coupled-mode theory was crucial. This theory contains abstruse knowledge about physics and complex computational processes, and thus is challenging for users. Therefore, a numerical simulation method was coupled with a simple and rigorous design procedure to help beginners and users to overcome difficulty in entering the field; in addition, graphical simulation results were presented. To reduce the difference between the simulated context and the actual context, a perfectly matched layer and perfectly reflecting boundary were added to the FEM and the EEM. When the FEM was used for grid cutting, the object meshing method and the boundary meshing method proposed in this study were used to effectively enhance computational accuracy and substantially reduce the time required for simulation. In summary, users can use the simulation results in this study to easily and rapidly design an optical fiber communication system and optical sensors with spectral characteristics.

A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules

PubMed Central

Elcock, Adrian H.

2013-01-01

Inclusion of hydrodynamic interactions (HIs) is essential in simulations of biological macromolecules that treat the solvent implicitly if the macromolecules are to exhibit correct translational and rotational diffusion. The present work describes the development and testing of a simple approach aimed at allowing more rapid computation of HIs in coarse-grained Brownian dynamics simulations of systems that contain large numbers of flexible macromolecules. The method combines a complete treatment of intramolecular HIs with an approximate treatment of the intermolecular HIs which assumes that the molecules are effectively spherical; all of the HIs are calculated at the Rotne-Prager-Yamakawa level of theory. When combined with Fixman’s Chebyshev polynomial method for calculating correlated random displacements, the proposed method provides an approach that is simple to program but sufficiently fast that it makes it computationally viable to include HIs in large-scale simulations. Test calculations performed on very coarse-grained models of the pyruvate dehydrogenase (PDH) E2 complex and on oligomers of ParM (ranging in size from 1 to 20 monomers) indicate that the method reproduces the translational diffusion behavior seen in more complete HI simulations surprisingly well; the method performs less well at capturing rotational diffusion but its discrepancies diminish with increasing size of the simulated assembly. Simulations of residue-level models of two tetrameric protein models demonstrate that the method also works well when more structurally detailed models are used in the simulations. Finally, test simulations of systems containing up to 1024 coarse-grained PDH molecules indicate that the proposed method rapidly becomes more efficient than the conventional BD approach in which correlated random displacements are obtained via a Cholesky decomposition of the complete diffusion tensor. PMID:23914146

Modeling nonlinear ultrasound propagation in heterogeneous media with power law absorption using a k-space pseudospectral method.

PubMed

Treeby, Bradley E; Jaros, Jiri; Rendell, Alistair P; Cox, B T

2012-06-01

The simulation of nonlinear ultrasound propagation through tissue realistic media has a wide range of practical applications. However, this is a computationally difficult problem due to the large size of the computational domain compared to the acoustic wavelength. Here, the k-space pseudospectral method is used to reduce the number of grid points required per wavelength for accurate simulations. The model is based on coupled first-order acoustic equations valid for nonlinear wave propagation in heterogeneous media with power law absorption. These are derived from the equations of fluid mechanics and include a pressure-density relation that incorporates the effects of nonlinearity, power law absorption, and medium heterogeneities. The additional terms accounting for convective nonlinearity and power law absorption are expressed as spatial gradients making them efficient to numerically encode. The governing equations are then discretized using a k-space pseudospectral technique in which the spatial gradients are computed using the Fourier-collocation method. This increases the accuracy of the gradient calculation and thus relaxes the requirement for dense computational grids compared to conventional finite difference methods. The accuracy and utility of the developed model is demonstrated via several numerical experiments, including the 3D simulation of the beam pattern from a clinical ultrasound probe.

Reducing statistical uncertainties in simulated organ doses of phantoms immersed in water

DOE PAGES

Hiller, Mauritius M.; Veinot, Kenneth G.; Easterly, Clay E.; ...

2016-08-13

In this study, methods are addressed to reduce the computational time to compute organ-dose rate coefficients using Monte Carlo techniques. Several variance reduction techniques are compared including the reciprocity method, importance sampling, weight windows and the use of the ADVANTG software package. For low-energy photons, the runtime was reduced by a factor of 10 5 when using the reciprocity method for kerma computation for immersion of a phantom in contaminated water. This is particularly significant since impractically long simulation times are required to achieve reasonable statistical uncertainties in organ dose for low-energy photons in this source medium and geometry. Althoughmore » the MCNP Monte Carlo code is used in this paper, the reciprocity technique can be used equally well with other Monte Carlo codes.« less

Nonlinear relaxation algorithms for circuit simulation

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

Saleh, R.A.

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

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

PubMed

Curuksu, Jeremy; Zacharias, Martin

2009-03-14

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

A parallelization method for time periodic steady state in simulation of radio frequency sheath dynamics

NASA Astrophysics Data System (ADS)

Kwon, Deuk-Chul; Shin, Sung-Sik; Yu, Dong-Hun

2017-10-01

In order to reduce the computing time in simulation of radio frequency (rf) plasma sources, various numerical schemes were developed. It is well known that the upwind, exponential, and power-law schemes can efficiently overcome the limitation on the grid size for fluid transport simulations of high density plasma discharges. Also, the semi-implicit method is a well-known numerical scheme to overcome on the simulation time step. However, despite remarkable advances in numerical techniques and computing power over the last few decades, efficient multi-dimensional modeling of low temperature plasma discharges has remained a considerable challenge. In particular, there was a difficulty on parallelization in time for the time periodic steady state problems such as capacitively coupled plasma discharges and rf sheath dynamics because values of plasma parameters in previous time step are used to calculate new values each time step. Therefore, we present a parallelization method for the time periodic steady state problems by using period-slices. In order to evaluate the efficiency of the developed method, one-dimensional fluid simulations are conducted for describing rf sheath dynamics. The result shows that speedup can be achieved by using a multithreading method.

Vectorization of a particle simulation method for hypersonic rarefied flow

NASA Technical Reports Server (NTRS)

Mcdonald, Jeffrey D.; Baganoff, Donald

1988-01-01

An efficient particle simulation technique for hypersonic rarefied flows is presented at an algorithmic and implementation level. The implementation is for a vector computer architecture, specifically the Cray-2. The method models an ideal diatomic Maxwell molecule with three translational and two rotational degrees of freedom. Algorithms are designed specifically for compatibility with fine grain parallelism by reducing the number of data dependencies in the computation. By insisting on this compatibility, the method is capable of performing simulation on a much larger scale than previously possible. A two-dimensional simulation of supersonic flow over a wedge is carried out for the near-continuum limit where the gas is in equilibrium and the ideal solution can be used as a check on the accuracy of the gas model employed in the method. Also, a three-dimensional, Mach 8, rarefied flow about a finite-span flat plate at a 45 degree angle of attack was simulated. It utilized over 10 to the 7th particles carried through 400 discrete time steps in less than one hour of Cray-2 CPU time. This problem was chosen to exhibit the capability of the method in handling a large number of particles and a true three-dimensional geometry.

Analysis of vibrational-translational energy transfer using the direct simulation Monte Carlo method

NASA Technical Reports Server (NTRS)

Boyd, Iain D.

1991-01-01

A new model is proposed for energy transfer between the vibrational and translational modes for use in the direct simulation Monte Carlo method (DSMC). The model modifies the Landau-Teller theory for a harmonic oscillator and the rate transition is related to an experimental correlation for the vibrational relaxation time. Assessment of the model is made with respect to three different computations: relaxation in a heat bath, a one-dimensional shock wave, and hypersonic flow over a two-dimensional wedge. These studies verify that the model achieves detailed balance, and excellent agreement with experimental data is obtained in the shock wave calculation. The wedge flow computation reveals that the usual phenomenological method for simulating vibrational nonequilibrium in the DSMC technique predicts much higher vibrational temperatures in the wake region.

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

NASA Astrophysics Data System (ADS)

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

2011-07-01

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

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

NASA Astrophysics Data System (ADS)

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

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

Need for speed: An optimized gridding approach for spatially explicit disease simulations.

PubMed

Sellman, Stefan; Tsao, Kimberly; Tildesley, Michael J; Brommesson, Peter; Webb, Colleen T; Wennergren, Uno; Keeling, Matt J; Lindström, Tom

2018-04-01

Numerical models for simulating outbreaks of infectious diseases are powerful tools for informing surveillance and control strategy decisions. However, large-scale spatially explicit models can be limited by the amount of computational resources they require, which poses a problem when multiple scenarios need to be explored to provide policy recommendations. We introduce an easily implemented method that can reduce computation time in a standard Susceptible-Exposed-Infectious-Removed (SEIR) model without introducing any further approximations or truncations. It is based on a hierarchical infection process that operates on entire groups of spatially related nodes (cells in a grid) in order to efficiently filter out large volumes of susceptible nodes that would otherwise have required expensive calculations. After the filtering of the cells, only a subset of the nodes that were originally at risk are then evaluated for actual infection. The increase in efficiency is sensitive to the exact configuration of the grid, and we describe a simple method to find an estimate of the optimal configuration of a given landscape as well as a method to partition the landscape into a grid configuration. To investigate its efficiency, we compare the introduced methods to other algorithms and evaluate computation time, focusing on simulated outbreaks of foot-and-mouth disease (FMD) on the farm population of the USA, the UK and Sweden, as well as on three randomly generated populations with varying degree of clustering. The introduced method provided up to 500 times faster calculations than pairwise computation, and consistently performed as well or better than other available methods. This enables large scale, spatially explicit simulations such as for the entire continental USA without sacrificing realism or predictive power.

Need for speed: An optimized gridding approach for spatially explicit disease simulations

PubMed Central

Tildesley, Michael J.; Brommesson, Peter; Webb, Colleen T.; Wennergren, Uno; Lindström, Tom

2018-01-01

Numerical models for simulating outbreaks of infectious diseases are powerful tools for informing surveillance and control strategy decisions. However, large-scale spatially explicit models can be limited by the amount of computational resources they require, which poses a problem when multiple scenarios need to be explored to provide policy recommendations. We introduce an easily implemented method that can reduce computation time in a standard Susceptible-Exposed-Infectious-Removed (SEIR) model without introducing any further approximations or truncations. It is based on a hierarchical infection process that operates on entire groups of spatially related nodes (cells in a grid) in order to efficiently filter out large volumes of susceptible nodes that would otherwise have required expensive calculations. After the filtering of the cells, only a subset of the nodes that were originally at risk are then evaluated for actual infection. The increase in efficiency is sensitive to the exact configuration of the grid, and we describe a simple method to find an estimate of the optimal configuration of a given landscape as well as a method to partition the landscape into a grid configuration. To investigate its efficiency, we compare the introduced methods to other algorithms and evaluate computation time, focusing on simulated outbreaks of foot-and-mouth disease (FMD) on the farm population of the USA, the UK and Sweden, as well as on three randomly generated populations with varying degree of clustering. The introduced method provided up to 500 times faster calculations than pairwise computation, and consistently performed as well or better than other available methods. This enables large scale, spatially explicit simulations such as for the entire continental USA without sacrificing realism or predictive power. PMID:29624574

Validation of GPU-accelerated superposition-convolution dose computations for the Small Animal Radiation Research Platform.

PubMed

Cho, Nathan; Tsiamas, Panagiotis; Velarde, Esteban; Tryggestad, Erik; Jacques, Robert; Berbeco, Ross; McNutt, Todd; Kazanzides, Peter; Wong, John

2018-05-01

The Small Animal Radiation Research Platform (SARRP) has been developed for conformal microirradiation with on-board cone beam CT (CBCT) guidance. The graphics processing unit (GPU)-accelerated Superposition-Convolution (SC) method for dose computation has been integrated into the treatment planning system (TPS) for SARRP. This paper describes the validation of the SC method for the kilovoltage energy by comparing with EBT2 film measurements and Monte Carlo (MC) simulations. MC data were simulated by EGSnrc code with 3 × 10 8 -1.5 × 10 9 histories, while 21 photon energy bins were used to model the 220 kVp x-rays in the SC method. Various types of phantoms including plastic water, cork, graphite, and aluminum were used to encompass the range of densities of mouse organs. For the comparison, percentage depth dose (PDD) of SC, MC, and film measurements were analyzed. Cross beam (x,y) dosimetric profiles of SC and film measurements are also presented. Correction factors (CFz) to convert SC to MC dose-to-medium are derived from the SC and MC simulations in homogeneous phantoms of aluminum and graphite to improve the estimation. The SC method produces dose values that are within 5% of film measurements and MC simulations in the flat regions of the profile. The dose is less accurate at the edges, due to factors such as geometric uncertainties of film placement and difference in dose calculation grids. The GPU-accelerated Superposition-Convolution dose computation method was successfully validated with EBT2 film measurements and MC calculations. The SC method offers much faster computation speed than MC and provides calculations of both dose-to-water in medium and dose-to-medium in medium. © 2018 American Association of Physicists in Medicine.

An Improved Computing Method for 3D Mechanical Connectivity Rates Based on a Polyhedral Simulation Model of Discrete Fracture Network in Rock Masses

NASA Astrophysics Data System (ADS)

Li, Mingchao; Han, Shuai; Zhou, Sibao; Zhang, Ye

2018-06-01

Based on a 3D model of a discrete fracture network (DFN) in a rock mass, an improved projective method for computing the 3D mechanical connectivity rate was proposed. The Monte Carlo simulation method, 2D Poisson process and 3D geological modeling technique were integrated into a polyhedral DFN modeling approach, and the simulation results were verified by numerical tests and graphical inspection. Next, the traditional projective approach for calculating the rock mass connectivity rate was improved using the 3D DFN models by (1) using the polyhedral model to replace the Baecher disk model; (2) taking the real cross section of the rock mass, rather than a part of the cross section, as the test plane; and (3) dynamically searching the joint connectivity rates using different dip directions and dip angles at different elevations to calculate the maximum, minimum and average values of the joint connectivity at each elevation. In a case study, the improved method and traditional method were used to compute the mechanical connectivity rate of the slope of a dam abutment. The results of the two methods were further used to compute the cohesive force of the rock masses. Finally, a comparison showed that the cohesive force derived from the traditional method had a higher error, whereas the cohesive force derived from the improved method was consistent with the suggested values. According to the comparison, the effectivity and validity of the improved method were verified indirectly.

Reliability computation using fault tree analysis

NASA Technical Reports Server (NTRS)

Chelson, P. O.

1971-01-01

A method is presented for calculating event probabilities from an arbitrary fault tree. The method includes an analytical derivation of the system equation and is not a simulation program. The method can handle systems that incorporate standby redundancy and it uses conditional probabilities for computing fault trees where the same basic failure appears in more than one fault path.

2HOT: An Improved Parallel Hashed Oct-Tree N-Body Algorithm for Cosmological Simulation

DOE PAGES

Warren, Michael S.

2014-01-01

We report on improvements made over the past two decades to our adaptive treecode N-body method (HOT). A mathematical and computational approach to the cosmological N-body problem is described, with performance and scalability measured up to 256k (2 18 ) processors. We present error analysis and scientific application results from a series of more than ten 69 billion (4096 3 ) particle cosmological simulations, accounting for 4×10 20 floating point operations. These results include the first simulations using the new constraints on the standard model of cosmology from the Planck satellite. Our simulations set a new standard for accuracy andmore » scientific throughput, while meeting or exceeding the computational efficiency of the latest generation of hybrid TreePM N-body methods.« less

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.

Numerical Simulation of a Seaway with Breaking

NASA Astrophysics Data System (ADS)

Dommermuth, Douglas; O'Shea, Thomas; Brucker, Kyle; Wyatt, Donald

2012-11-01

The focus of this presentation is to describe the recent efforts to simulate a fully non-linear seaway with breaking by using a high-order spectral (HOS) solution of the free-surface boundary value problem to drive a three-dimensional Volume of Fluid (VOF) solution. Historically, the two main types of simulations to simulate free-surface flows are the boundary integral equations method (BIEM) and high-order spectral (HOS) methods. BIEM calculations fail at the point at which the surface impacts upon itself, if not sooner, and HOS methods can only simulate a single valued free-surface. Both also employ a single-phase approximation in which the effects of the air on the water are neglected. Due to these limitations they are unable to simulate breaking waves and air entrainment. The Volume of Fluid (VOF) method on the other hand is suitable for modeling breaking waves and air entrainment. However it is computationally intractable to generate a realistic non-linear sea-state. Here, we use the HOS solution to quickly drive, or nudge, the VOF solution into a non-linear state. The computational strategies, mathematical formulation, and numerical implementation will be discussed. The results of the VOF simulation of a seaway with breaking will also be presented, and compared to the single phase, single valued HOS results.

Computing Radiative Transfer in a 3D Medium

NASA Technical Reports Server (NTRS)

Von Allmen, Paul; Lee, Seungwon

2012-01-01

A package of software computes the time-dependent propagation of a narrow laser beam in an arbitrary three- dimensional (3D) medium with absorption and scattering, using the transient-discrete-ordinates method and a direct integration method. Unlike prior software that utilizes a Monte Carlo method, this software enables simulation at very small signal-to-noise ratios. The ability to simulate propagation of a narrow laser beam in a 3D medium is an improvement over other discrete-ordinate software. Unlike other direct-integration software, this software is not limited to simulation of propagation of thermal radiation with broad angular spread in three dimensions or of a laser pulse with narrow angular spread in two dimensions. Uses for this software include (1) computing scattering of a pulsed laser beam on a material having given elastic scattering and absorption profiles, and (2) evaluating concepts for laser-based instruments for sensing oceanic turbulence and related measurements of oceanic mixed-layer depths. With suitable augmentation, this software could be used to compute radiative transfer in ultrasound imaging in biological tissues, radiative transfer in the upper Earth crust for oil exploration, and propagation of laser pulses in telecommunication applications.

Supervised learning from human performance at the computationally hard problem of optimal traffic signal control on a network of junctions

PubMed Central

Box, Simon

2014-01-01

Optimal switching of traffic lights on a network of junctions is a computationally intractable problem. In this research, road traffic networks containing signallized junctions are simulated. A computer game interface is used to enable a human ‘player’ to control the traffic light settings on the junctions within the simulation. A supervised learning approach, based on simple neural network classifiers can be used to capture human player's strategies in the game and thus develop a human-trained machine control (HuTMaC) system that approaches human levels of performance. Experiments conducted within the simulation compare the performance of HuTMaC to two well-established traffic-responsive control systems that are widely deployed in the developed world and also to a temporal difference learning-based control method. In all experiments, HuTMaC outperforms the other control methods in terms of average delay and variance over delay. The conclusion is that these results add weight to the suggestion that HuTMaC may be a viable alternative, or supplemental method, to approximate optimization for some practical engineering control problems where the optimal strategy is computationally intractable. PMID:26064570

Supervised learning from human performance at the computationally hard problem of optimal traffic signal control on a network of junctions.

PubMed

Box, Simon

2014-12-01

Optimal switching of traffic lights on a network of junctions is a computationally intractable problem. In this research, road traffic networks containing signallized junctions are simulated. A computer game interface is used to enable a human 'player' to control the traffic light settings on the junctions within the simulation. A supervised learning approach, based on simple neural network classifiers can be used to capture human player's strategies in the game and thus develop a human-trained machine control (HuTMaC) system that approaches human levels of performance. Experiments conducted within the simulation compare the performance of HuTMaC to two well-established traffic-responsive control systems that are widely deployed in the developed world and also to a temporal difference learning-based control method. In all experiments, HuTMaC outperforms the other control methods in terms of average delay and variance over delay. The conclusion is that these results add weight to the suggestion that HuTMaC may be a viable alternative, or supplemental method, to approximate optimization for some practical engineering control problems where the optimal strategy is computationally intractable.

Editorial

NASA Astrophysics Data System (ADS)

Wang, Tianmin; Gao, Fei; Hu, Wangyu; Lai, Wensheng; Lu, Guang-Hong; Zu, Xiaotao

2009-09-01

The Ninth International Conference on Computer Simulation of Radiation Effects in Solids (COSIRES 2008) was hosted by Beihang University in Beijing, China from 12 to 17 October 2008. Started in 1992 in Berlin, Germany, this conference series has been held biennially in Santa Barbara, CA, USA (1994); Guildford, UK (1996); Okayama, Japan (1998); State College, PA, USA (2000); Dresden, Germany (2002); Helsinki Finland (2004); and Richland, WA USA (2006). The COSIRES conferences are the foremost international forum on the theory, development and application of advanced computer simulation methods and algorithms to achieve fundamental understanding and predictive modeling of the interaction of energetic particles and clusters with solids. As can be noticed in the proceedings of the COSIRES conferences, these computer simulation methods and algorithms have been proven to be very useful for the study of fundamental radiation effect processes, which are not easily accessible by experimental methods owing to small time and length scales. Moreover, with advance in computing power, they have remarkably been developed in the different scales ranging from meso to atomistic, and even down to electronic levels, as well as coupling of the different scales. They are now becoming increasingly applicable for materials processing and performance prediction in advance engineering and energy-production technologies.

Numerical simulation of a powered-lift landing, tracking flow features using overset grids, and simulation of high lift devices on a fighter-lift-and-control wing

NASA Technical Reports Server (NTRS)

Chawla, Kalpana

1993-01-01

Attached as appendices to this report are documents describing work performed on the simulation of a landing powered-lift delta wing, the tracking of flow features using overset grids, and the simulation of flaps on the Wright Patterson Lab's fighter-lift-and-control (FLAC) wing. Numerical simulation of a powered-lift landing includes the computation of flow about a delta wing at four fixed heights as well as a simulated landing, in which the delta wing descends toward the ground. Comparison of computed and experimental lift coefficients indicates that the simulations capture the qualitative trends in lift-loss encountered by thrust-vectoring aircraft operating in ground effect. Power spectra of temporal variations of pressure indicate computed vortex shedding frequencies close to the jet exit are in the experimentally observed frequency range; the power spectra of pressure also provide insights into the mechanisms of lift oscillations. Also, a method for using overset grids to track dynamic flow features is described and the method is validated by tracking a moving shock and vortices shed behind a circular cylinder. Finally, Chimera gridding strategies were used to develop pressure coefficient contours for the FLAC wing for a Mach no. of 0.18 and Reynolds no. of 2.5 million.

Optimal simulations of ultrasonic fields produced by large thermal therapy arrays using the angular spectrum approach

PubMed Central

Zeng, Xiaozheng; McGough, Robert J.

2009-01-01

The angular spectrum approach is evaluated for the simulation of focused ultrasound fields produced by large thermal therapy arrays. For an input pressure or normal particle velocity distribution in a plane, the angular spectrum approach rapidly computes the output pressure field in a three dimensional volume. To determine the optimal combination of simulation parameters for angular spectrum calculations, the effect of the size, location, and the numerical accuracy of the input plane on the computed output pressure is evaluated. Simulation results demonstrate that angular spectrum calculations performed with an input pressure plane are more accurate than calculations with an input velocity plane. Results also indicate that when the input pressure plane is slightly larger than the array aperture and is located approximately one wavelength from the array, angular spectrum simulations have very small numerical errors for two dimensional planar arrays. Furthermore, the root mean squared error from angular spectrum simulations asymptotically approaches a nonzero lower limit as the error in the input plane decreases. Overall, the angular spectrum approach is an accurate and robust method for thermal therapy simulations of large ultrasound phased arrays when the input pressure plane is computed with the fast nearfield method and an optimal combination of input parameters. PMID:19425640

Physically-Based Modelling and Real-Time Simulation of Fluids.

NASA Astrophysics Data System (ADS)

Chen, Jim Xiong

1995-01-01

Simulating physically realistic complex fluid behaviors presents an extremely challenging problem for computer graphics researchers. Such behaviors include the effects of driving boats through water, blending differently colored fluids, rain falling and flowing on a terrain, fluids interacting in a Distributed Interactive Simulation (DIS), etc. Such capabilities are useful in computer art, advertising, education, entertainment, and training. We present a new method for physically-based modeling and real-time simulation of fluids in computer graphics and dynamic virtual environments. By solving the 2D Navier -Stokes equations using a CFD method, we map the surface into 3D using the corresponding pressures in the fluid flow field. This achieves realistic real-time fluid surface behaviors by employing the physical governing laws of fluids but avoiding extensive 3D fluid dynamics computations. To complement the surface behaviors, we calculate fluid volume and external boundary changes separately to achieve full 3D general fluid flow. To simulate physical activities in a DIS, we introduce a mechanism which uses a uniform time scale proportional to the clock-time and variable time-slicing to synchronize physical models such as fluids in the networked environment. Our approach can simulate many different fluid behaviors by changing the internal or external boundary conditions. It can model different kinds of fluids by varying the Reynolds number. It can simulate objects moving or floating in fluids. It can also produce synchronized general fluid flows in a DIS. Our model can serve as a testbed to simulate many other fluid phenomena which have never been successfully modeled previously.

Grid connected integrated community energy system. Phase II: final state 2 report. Cost benefit analysis, operating costs and computer simulation

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

Not Available

1978-03-22

A grid-connected Integrated Community Energy System (ICES) with a coal-burning power plant located on the University of Minnesota campus is planned. The cost benefit analysis performed for this ICES, the cost accounting methods used, and a computer simulation of the operation of the power plant are described. (LCL)

Consistent data-driven computational mechanics

NASA Astrophysics Data System (ADS)

González, D.; Chinesta, F.; Cueto, E.

2018-05-01

We present a novel method, within the realm of data-driven computational mechanics, to obtain reliable and thermodynamically sound simulation from experimental data. We thus avoid the need to fit any phenomenological model in the construction of the simulation model. This kind of techniques opens unprecedented possibilities in the framework of data-driven application systems and, particularly, in the paradigm of industry 4.0.

Development of an Efficient Binaural Simulation for the Analysis of Structural Acoustic Data

NASA Technical Reports Server (NTRS)

Johnson, Marty E.; Lalime, Aimee L.; Grosveld, Ferdinand W.; Rizzi, Stephen A.; Sullivan, Brenda M.

2003-01-01

Applying binaural simulation techniques to structural acoustic data can be very computationally intensive as the number of discrete noise sources can be very large. Typically, Head Related Transfer Functions (HRTFs) are used to individually filter the signals from each of the sources in the acoustic field. Therefore, creating a binaural simulation implies the use of potentially hundreds of real time filters. This paper details two methods of reducing the number of real-time computations required by: (i) using the singular value decomposition (SVD) to reduce the complexity of the HRTFs by breaking them into dominant singular values and vectors and (ii) by using equivalent source reduction (ESR) to reduce the number of sources to be analyzed in real-time by replacing sources on the scale of a structural wavelength with sources on the scale of an acoustic wavelength. The ESR and SVD reduction methods can be combined to provide an estimated computation time reduction of 99.4% for the structural acoustic data tested. In addition, preliminary tests have shown that there is a 97% correlation between the results of the combined reduction methods and the results found with the current binaural simulation techniques

Deformation of Soft Tissue and Force Feedback Using the Smoothed Particle Hydrodynamics

PubMed Central

Liu, Xuemei; Wang, Ruiyi; Li, Yunhua; Song, Dongdong

2015-01-01

We study the deformation and haptic feedback of soft tissue in virtual surgery based on a liver model by using a force feedback device named PHANTOM OMNI developed by SensAble Company in USA. Although a significant amount of research efforts have been dedicated to simulating the behaviors of soft tissue and implementing force feedback, it is still a challenging problem. This paper introduces a kind of meshfree method for deformation simulation of soft tissue and force computation based on viscoelastic mechanical model and smoothed particle hydrodynamics (SPH). Firstly, viscoelastic model can present the mechanical characteristics of soft tissue which greatly promotes the realism. Secondly, SPH has features of meshless technique and self-adaption, which supply higher precision than methods based on meshes for force feedback computation. Finally, a SPH method based on dynamic interaction area is proposed to improve the real time performance of simulation. The results reveal that SPH methodology is suitable for simulating soft tissue deformation and force feedback calculation, and SPH based on dynamic local interaction area has a higher computational efficiency significantly compared with usual SPH. Our algorithm has a bright prospect in the area of virtual surgery. PMID:26417380

A method for spectral DNS of low Rm channel flows based on the least dissipative modes

NASA Astrophysics Data System (ADS)

Kornet, Kacper; Pothérat, Alban

2015-10-01

We put forward a new type of spectral method for the direct numerical simulation of flows where anisotropy or very fine boundary layers are present. The main idea is to take advantage of the fact that such structures are dissipative and that their presence should reduce the number of degrees of freedom of the flow, when paradoxically, their fine resolution incurs extra computational cost in most current methods. The principle of this method is to use a functional basis with elements that already include these fine structures so as to avoid these extra costs. This leads us to develop an algorithm to implement a spectral method for arbitrary functional bases, and in particular, non-orthogonal ones. We construct a basic implementation of this algorithm to simulate magnetohydrodynamic (MHD) channel flows with an externally imposed, transverse magnetic field, where very thin boundary layers are known to develop along the channel walls. In this case, the sought functional basis can be built out of the eigenfunctions of the dissipation operator, which incorporate these boundary layers, and it turns out to be non-orthogonal. We validate this new scheme against numerical simulations of freely decaying MHD turbulence based on a finite volume code and it is found to provide accurate results. Its ability to fully resolve wall-bounded turbulence with a number of modes close to that required by the dynamics is demonstrated on a simple example. This opens the way to full-blown simulations of MHD turbulence under very high magnetic fields. Until now such simulations were too computationally expensive. In contrast to traditional methods the computational cost of the proposed method, does not depend on the intensity of the magnetic field.

Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

NASA Astrophysics Data System (ADS)

Stalter, S.; Yelash, L.; Emamy, N.; Statt, A.; Hanke, M.; Lukáčová-Medvid'ová, M.; Virnau, P.

2018-03-01

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations typically pose a computational bottleneck, which we investigate in detail in this study. We find that it is preferable to simulate many small systems as opposed to a few large systems, and that a choice of a simple isokinetic thermostat is typically sufficient while thermostats such as Lowe-Andersen allow for simulations at elevated viscosity. We discuss suitable choices for time steps and finite-size effects which arise in the limit of very small simulation boxes. We also argue that if colloidal systems are considered as opposed to atomistic systems, the gap between microscopic and macroscopic simulations regarding time and length scales is significantly smaller. We propose a novel reduced-order technique for the coupling to the macroscopic solver, which allows us to approximate a non-linear stress-strain relation efficiently and thus further reduce computational effort of microscopic simulations.

Virtual reality simulation in neurosurgery: technologies and evolution.

PubMed

Chan, Sonny; Conti, François; Salisbury, Kenneth; Blevins, Nikolas H

2013-01-01

Neurosurgeons are faced with the challenge of learning, planning, and performing increasingly complex surgical procedures in which there is little room for error. With improvements in computational power and advances in visual and haptic display technologies, virtual surgical environments can now offer potential benefits for surgical training, planning, and rehearsal in a safe, simulated setting. This article introduces the various classes of surgical simulators and their respective purposes through a brief survey of representative simulation systems in the context of neurosurgery. Many technical challenges currently limit the application of virtual surgical environments. Although we cannot yet expect a digital patient to be indistinguishable from reality, new developments in computational methods and related technology bring us closer every day. We recognize that the design and implementation of an immersive virtual reality surgical simulator require expert knowledge from many disciplines. This article highlights a selection of recent developments in research areas related to virtual reality simulation, including anatomic modeling, computer graphics and visualization, haptics, and physics simulation, and discusses their implication for the simulation of neurosurgery.

Curvilinear immersed-boundary method for simulating unsteady flows in shallow natural streams with arbitrarily complex obstacles

NASA Astrophysics Data System (ADS)

Kang, Seokkoo; Borazjani, Iman; Sotiropoulos, Fotis

2008-11-01

Unsteady 3D simulations of flows in natural streams is a challenging task due to the complexity of the bathymetry, the shallowness of the flow, and the presence of multiple nature- and man-made obstacles. This work is motivated by the need to develop a powerful numerical method for simulating such flows using coherent-structure-resolving turbulence models. We employ the curvilinear immersed boundary method of Ge and Sotiropoulos (Journal of Computational Physics, 2007) and address the critical issue of numerical efficiency in large aspect ratio computational domains and grids such as those encountered in long and shallow open channels. We show that the matrix-free Newton-Krylov method for solving the momentum equations coupled with an algebraic multigrid method with incomplete LU preconditioner for solving the Poisson equation yield a robust and efficient procedure for obtaining time-accurate solutions in such problems. We demonstrate the potential of the numerical approach by carrying out a direct numerical simulation of flow in a long and shallow meandering stream with multiple hydraulic structures.

Soft tissue deformation estimation by spatio-temporal Kalman filter finite element method.

PubMed

Yarahmadian, Mehran; Zhong, Yongmin; Gu, Chengfan; Shin, Jaehyun

2018-01-01

Soft tissue modeling plays an important role in the development of surgical training simulators as well as in robot-assisted minimally invasive surgeries. It has been known that while the traditional Finite Element Method (FEM) promises the accurate modeling of soft tissue deformation, it still suffers from a slow computational process. This paper presents a Kalman filter finite element method to model soft tissue deformation in real time without sacrificing the traditional FEM accuracy. The proposed method employs the FEM equilibrium equation and formulates it as a filtering process to estimate soft tissue behavior using real-time measurement data. The model is temporally discretized using the Newmark method and further formulated as the system state equation. Simulation results demonstrate that the computational time of KF-FEM is approximately 10 times shorter than the traditional FEM and it is still as accurate as the traditional FEM. The normalized root-mean-square error of the proposed KF-FEM in reference to the traditional FEM is computed as 0.0116. It is concluded that the proposed method significantly improves the computational performance of the traditional FEM without sacrificing FEM accuracy. The proposed method also filters noises involved in system state and measurement data.

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

PubMed

Marquez-Lago, Tatiana T; Burrage, Kevin

2007-09-14

In cell biology, cell signaling pathway problems are often tackled with deterministic temporal models, well mixed stochastic simulators, and/or hybrid methods. But, in fact, three dimensional stochastic spatial modeling of reactions happening inside the cell is needed in order to fully understand these cell signaling pathways. This is because noise effects, low molecular concentrations, and spatial heterogeneity can all affect the cellular dynamics. However, there are ways in which important effects can be accounted without going to the extent of using highly resolved spatial simulators (such as single-particle software), hence reducing the overall computation time significantly. We present a new coarse grained modified version of the next subvolume method that allows the user to consider both diffusion and reaction events in relatively long simulation time spans as compared with the original method and other commonly used fully stochastic computational methods. Benchmarking of the simulation algorithm was performed through comparison with the next subvolume method and well mixed models (MATLAB), as well as stochastic particle reaction and transport simulations (CHEMCELL, Sandia National Laboratories). Additionally, we construct a model based on a set of chemical reactions in the epidermal growth factor receptor pathway. For this particular application and a bistable chemical system example, we analyze and outline the advantages of our presented binomial tau-leap spatial stochastic simulation algorithm, in terms of efficiency and accuracy, in scenarios of both molecular homogeneity and heterogeneity.

Automating approximate Bayesian computation by local linear regression.

PubMed

Thornton, Kevin R

2009-07-07

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

Numerical characteristics of quantum computer simulation

NASA Astrophysics Data System (ADS)

Chernyavskiy, A.; Khamitov, K.; Teplov, A.; Voevodin, V.; Voevodin, Vl.

2016-12-01

The simulation of quantum circuits is significantly important for the implementation of quantum information technologies. The main difficulty of such modeling is the exponential growth of dimensionality, thus the usage of modern high-performance parallel computations is relevant. As it is well known, arbitrary quantum computation in circuit model can be done by only single- and two-qubit gates, and we analyze the computational structure and properties of the simulation of such gates. We investigate the fact that the unique properties of quantum nature lead to the computational properties of the considered algorithms: the quantum parallelism make the simulation of quantum gates highly parallel, and on the other hand, quantum entanglement leads to the problem of computational locality during simulation. We use the methodology of the AlgoWiki project (algowiki-project.org) to analyze the algorithm. This methodology consists of theoretical (sequential and parallel complexity, macro structure, and visual informational graph) and experimental (locality and memory access, scalability and more specific dynamic characteristics) parts. Experimental part was made by using the petascale Lomonosov supercomputer (Moscow State University, Russia). We show that the simulation of quantum gates is a good base for the research and testing of the development methods for data intense parallel software, and considered methodology of the analysis can be successfully used for the improvement of the algorithms in quantum information science.

Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

PubMed

Harris, Robert C; Deng, Nanjie; Levy, Ronald M; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2017-06-05

Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Software for Brain Network Simulations: A Comparative Study

PubMed Central

Tikidji-Hamburyan, Ruben A.; Narayana, Vikram; Bozkus, Zeki; El-Ghazawi, Tarek A.

2017-01-01

Numerical simulations of brain networks are a critical part of our efforts in understanding brain functions under pathological and normal conditions. For several decades, the community has developed many software packages and simulators to accelerate research in computational neuroscience. In this article, we select the three most popular simulators, as determined by the number of models in the ModelDB database, such as NEURON, GENESIS, and BRIAN, and perform an independent evaluation of these simulators. In addition, we study NEST, one of the lead simulators of the Human Brain Project. First, we study them based on one of the most important characteristics, the range of supported models. Our investigation reveals that brain network simulators may be biased toward supporting a specific set of models. However, all simulators tend to expand the supported range of models by providing a universal environment for the computational study of individual neurons and brain networks. Next, our investigations on the characteristics of computational architecture and efficiency indicate that all simulators compile the most computationally intensive procedures into binary code, with the aim of maximizing their computational performance. However, not all simulators provide the simplest method for module development and/or guarantee efficient binary code. Third, a study of their amenability for high-performance computing reveals that NEST can almost transparently map an existing model on a cluster or multicore computer, while NEURON requires code modification if the model developed for a single computer has to be mapped on a computational cluster. Interestingly, parallelization is the weakest characteristic of BRIAN, which provides no support for cluster computations and limited support for multicore computers. Fourth, we identify the level of user support and frequency of usage for all simulators. Finally, we carry out an evaluation using two case studies: a large network with simplified neural and synaptic models and a small network with detailed models. These two case studies allow us to avoid any bias toward a particular software package. The results indicate that BRIAN provides the most concise language for both cases considered. Furthermore, as expected, NEST mostly favors large network models, while NEURON is better suited for detailed models. Overall, the case studies reinforce our general observation that simulators have a bias in the computational performance toward specific types of the brain network models. PMID:28775687

An immersed boundary-simplified sphere function-based gas kinetic scheme for simulation of 3D incompressible flows

NASA Astrophysics Data System (ADS)

Yang, L. M.; Shu, C.; Yang, W. M.; Wang, Y.; Wu, J.

2017-08-01

In this work, an immersed boundary-simplified sphere function-based gas kinetic scheme (SGKS) is presented for the simulation of 3D incompressible flows with curved and moving boundaries. At first, the SGKS [Yang et al., "A three-dimensional explicit sphere function-based gas-kinetic flux solver for simulation of inviscid compressible flows," J. Comput. Phys. 295, 322 (2015) and Yang et al., "Development of discrete gas kinetic scheme for simulation of 3D viscous incompressible and compressible flows," J. Comput. Phys. 319, 129 (2016)], which is often applied for the simulation of compressible flows, is simplified to improve the computational efficiency for the simulation of incompressible flows. In the original SGKS, the integral domain along the spherical surface for computing conservative variables and numerical fluxes is usually not symmetric at the cell interface. This leads the expression of numerical fluxes at the cell interface to be relatively complicated. For incompressible flows, the sphere at the cell interface can be approximately considered to be symmetric as shown in this work. Besides that, the energy equation is usually not needed for the simulation of incompressible isothermal flows. With all these simplifications, the simple and explicit formulations for the conservative variables and numerical fluxes at the cell interface can be obtained. Second, to effectively implement the no-slip boundary condition for fluid flow problems with complex geometry as well as moving boundary, the implicit boundary condition-enforced immersed boundary method [Wu and Shu, "Implicit velocity correction-based immersed boundary-lattice Boltzmann method and its applications," J. Comput. Phys. 228, 1963 (2009)] is introduced into the simplified SGKS. That is, the flow field is solved by the simplified SGKS without considering the presence of an immersed body and the no-slip boundary condition is implemented by the immersed boundary method. The accuracy and efficiency of the present scheme are validated by simulating the decaying vortex flow, flow past a stationary and rotating sphere, flow past a stationary torus, and flows over dragonfly flight.

Numerical experiments in homogeneous turbulence

NASA Technical Reports Server (NTRS)

Rogallo, R. S.

1981-01-01

The direct simulation methods developed by Orszag and Patternson (1972) for isotropic turbulence were extended to homogeneous turbulence in an incompressible fluid subjected to uniform deformation or rotation. The results of simulations for irrotational strain (plane and axisymmetric), shear, rotation, and relaxation toward isotropy following axisymmetric strain are compared with linear theory and experimental data. Emphasis is placed on the shear flow because of its importance and because of the availability of accurate and detailed experimental data. The computed results are used to assess the accuracy of two popular models used in the closure of the Reynolds-stress equations. Data from a variety of the computed fields and the details of the numerical methods used in the simulation are also presented.

The viability of ADVANTG deterministic method for synthetic radiography generation

NASA Astrophysics Data System (ADS)

Bingham, Andrew; Lee, Hyoung K.

2018-07-01

Fast simulation techniques to generate synthetic radiographic images of high resolution are helpful when new radiation imaging systems are designed. However, the standard stochastic approach requires lengthy run time with poorer statistics at higher resolution. The investigation of the viability of a deterministic approach to synthetic radiography image generation was explored. The aim was to analyze a computational time decrease over the stochastic method. ADVANTG was compared to MCNP in multiple scenarios including a small radiography system prototype, to simulate high resolution radiography images. By using ADVANTG deterministic code to simulate radiography images the computational time was found to decrease 10 to 13 times compared to the MCNP stochastic approach while retaining image quality.

Computer simulation of schlieren images of rotationally symmetric plasma systems: a simple method.

PubMed

Noll, R; Haas, C R; Weikl, B; Herziger, G

1986-03-01

Schlieren techniques are commonly used methods for quantitative analysis of cylindrical or spherical index of refraction profiles. Many schlieren objects, however, are characterized by more complex geometries, so we have investigated the more general case of noncylindrical, rotationally symmetric distributions of index of refraction n(r,z). Assuming straight ray paths in the schlieren object we have calculated 2-D beam deviation profiles. It is shown that experimental schlieren images of the noncylindrical plasma generated by a plasma focus device can be simulated with these deviation profiles. The computer simulation allows a quantitative analysis of these schlieren images, which yields, for example, the plasma parameters, electron density, and electron density gradients.

Method for simulating paint mixing on computer monitors

NASA Astrophysics Data System (ADS)

Carabott, Ferdinand; Lewis, Garth; Piehl, Simon

2002-06-01

Computer programs like Adobe Photoshop can generate a mixture of two 'computer' colors by using the Gradient control. However, the resulting colors diverge from the equivalent paint mixtures in both hue and value. This study examines why programs like Photoshop are unable to simulate paint or pigment mixtures, and offers a solution using Photoshops existing tools. The article discusses how a library of colors, simulating paint mixtures, is created from 13 artists' colors. The mixtures can be imported into Photoshop as a color swatch palette of 1248 colors and as 78 continuous or stepped gradient files, all accessed in a new software package, Chromafile.

Efficient Voronoi volume estimation for DEM simulations of granular materials under confined conditions

PubMed Central

Frenning, Göran

2015-01-01

When the discrete element method (DEM) is used to simulate confined compression of granular materials, the need arises to estimate the void space surrounding each particle with Voronoi polyhedra. This entails recurring Voronoi tessellation with small changes in the geometry, resulting in a considerable computational overhead. To overcome this limitation, we propose a method with the following features:•A local determination of the polyhedron volume is used, which considerably simplifies implementation of the method.•A linear approximation of the polyhedron volume is utilised, with intermittent exact volume calculations when needed.•The method allows highly accurate volume estimates to be obtained at a considerably reduced computational cost. PMID:26150975

New Flutter Analysis Technique for Time-Domain Computational Aeroelasticity

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Lung, Shun-Fat

2017-01-01

A new time-domain approach for computing flutter speed is presented. Based on the time-history result of aeroelastic simulation, the unknown unsteady aerodynamics model is estimated using a system identification technique. The full aeroelastic model is generated via coupling the estimated unsteady aerodynamic model with the known linear structure model. The critical dynamic pressure is computed and used in the subsequent simulation until the convergence of the critical dynamic pressure is achieved. The proposed method is applied to a benchmark cantilevered rectangular wing.

Flow in curved ducts of varying cross-section

NASA Astrophysics Data System (ADS)

Sotiropoulos, F.; Patel, V. C.

1992-07-01

Two numerical methods for solving the incompressible Navier-Stokes equations are compared with each other by applying them to calculate laminar and turbulent flows through curved ducts of regular cross-section. Detailed comparisons, between the computed solutions and experimental data, are carried out in order to validate the two methods and to identify their relative merits and disadvantages. Based on the conclusions of this comparative study a numerical method is developed for simulating viscous flows through curved ducts of varying cross-sections. The proposed method is capable of simulating the near-wall turbulence using fine computational meshes across the sublayer in conjunction with a two-layer k-epsilon model. Numerical solutions are obtained for: (1) a straight transition duct geometry, and (2) a hydroturbine draft-tube configuration at model scale Reynolds number for various inlet swirl intensities. The report also provides a detailed literature survey that summarizes all the experimental and computational work in the area of duct flows.

Simulation and study of small numbers of random events

NASA Technical Reports Server (NTRS)

Shelton, R. D.

1986-01-01

Random events were simulated by computer and subjected to various statistical methods to extract important parameters. Various forms of curve fitting were explored, such as least squares, least distance from a line, maximum likelihood. Problems considered were dead time, exponential decay, and spectrum extraction from cosmic ray data using binned data and data from individual events. Computer programs, mostly of an iterative nature, were developed to do these simulations and extractions and are partially listed as appendices. The mathematical basis for the compuer programs is given.

NASA Advanced Supercomputing Facility Expansion

NASA Technical Reports Server (NTRS)

Thigpen, William W.

2017-01-01

The NASA Advanced Supercomputing (NAS) Division enables advances in high-end computing technologies and in modeling and simulation methods to tackle some of the toughest science and engineering challenges facing NASA today. The name "NAS" has long been associated with leadership and innovation throughout the high-end computing (HEC) community. We play a significant role in shaping HEC standards and paradigms, and provide leadership in the areas of large-scale InfiniBand fabrics, Lustre open-source filesystems, and hyperwall technologies. We provide an integrated high-end computing environment to accelerate NASA missions and make revolutionary advances in science. Pleiades, a petaflop-scale supercomputer, is used by scientists throughout the U.S. to support NASA missions, and is ranked among the most powerful systems in the world. One of our key focus areas is in modeling and simulation to support NASA's real-world engineering applications and make fundamental advances in modeling and simulation methods.

Achieving a high mode count in the exact electromagnetic simulation of diffractive optical elements.

PubMed

Junker, André; Brenner, Karl-Heinz

2018-03-01

The application of rigorous optical simulation algorithms, both in the modal as well as in the time domain, is known to be limited to the nano-optical scale due to severe computing time and memory constraints. This is true even for today's high-performance computers. To address this problem, we develop the fast rigorous iterative method (FRIM), an algorithm based on an iterative approach, which, under certain conditions, allows solving also large-size problems approximation free. We achieve this in the case of a modal representation by avoiding the computationally complex eigenmode decomposition. Thereby, the numerical cost is reduced from O(N 3 ) to O(N log N), enabling a simulation of structures like certain diffractive optical elements with a significantly higher mode count than presently possible. Apart from speed, another major advantage of the iterative FRIM over standard modal methods is the possibility to trade runtime against accuracy.

High-Performance Computation of Distributed-Memory Parallel 3D Voronoi and Delaunay Tessellation

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

Peterka, Tom; Morozov, Dmitriy; Phillips, Carolyn

2014-11-14

Computing a Voronoi or Delaunay tessellation from a set of points is a core part of the analysis of many simulated and measured datasets: N-body simulations, molecular dynamics codes, and LIDAR point clouds are just a few examples. Such computational geometry methods are common in data analysis and visualization; but as the scale of simulations and observations surpasses billions of particles, the existing serial and shared-memory algorithms no longer suffice. A distributed-memory scalable parallel algorithm is the only feasible approach. The primary contribution of this paper is a new parallel Delaunay and Voronoi tessellation algorithm that automatically determines which neighbormore » points need to be exchanged among the subdomains of a spatial decomposition. Other contributions include periodic and wall boundary conditions, comparison of our method using two popular serial libraries, and application to numerous science datasets.« less

Hybrid Monte Carlo/Deterministic Methods for Accelerating Active Interrogation Modeling

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

Peplow, Douglas E.; Miller, Thomas Martin; Patton, Bruce W

2013-01-01

The potential for smuggling special nuclear material (SNM) into the United States is a major concern to homeland security, so federal agencies are investigating a variety of preventive measures, including detection and interdiction of SNM during transport. One approach for SNM detection, called active interrogation, uses a radiation source, such as a beam of neutrons or photons, to scan cargo containers and detect the products of induced fissions. In realistic cargo transport scenarios, the process of inducing and detecting fissions in SNM is difficult due to the presence of various and potentially thick materials between the radiation source and themore » SNM, and the practical limitations on radiation source strength and detection capabilities. Therefore, computer simulations are being used, along with experimental measurements, in efforts to design effective active interrogation detection systems. The computer simulations mostly consist of simulating radiation transport from the source to the detector region(s). Although the Monte Carlo method is predominantly used for these simulations, difficulties persist related to calculating statistically meaningful detector responses in practical computing times, thereby limiting their usefulness for design and evaluation of practical active interrogation systems. In previous work, the benefits of hybrid methods that use the results of approximate deterministic transport calculations to accelerate high-fidelity Monte Carlo simulations have been demonstrated for source-detector type problems. In this work, the hybrid methods are applied and evaluated for three example active interrogation problems. Additionally, a new approach is presented that uses multiple goal-based importance functions depending on a particle s relevance to the ultimate goal of the simulation. Results from the examples demonstrate that the application of hybrid methods to active interrogation problems dramatically increases their calculational efficiency.« less

Simulation Studies as Designed Experiments: The Comparison of Penalized Regression Models in the “Large p, Small n” Setting

PubMed Central

Chaibub Neto, Elias; Bare, J. Christopher; Margolin, Adam A.

2014-01-01

New algorithms are continuously proposed in computational biology. Performance evaluation of novel methods is important in practice. Nonetheless, the field experiences a lack of rigorous methodology aimed to systematically and objectively evaluate competing approaches. Simulation studies are frequently used to show that a particular method outperforms another. Often times, however, simulation studies are not well designed, and it is hard to characterize the particular conditions under which different methods perform better. In this paper we propose the adoption of well established techniques in the design of computer and physical experiments for developing effective simulation studies. By following best practices in planning of experiments we are better able to understand the strengths and weaknesses of competing algorithms leading to more informed decisions about which method to use for a particular task. We illustrate the application of our proposed simulation framework with a detailed comparison of the ridge-regression, lasso and elastic-net algorithms in a large scale study investigating the effects on predictive performance of sample size, number of features, true model sparsity, signal-to-noise ratio, and feature correlation, in situations where the number of covariates is usually much larger than sample size. Analysis of data sets containing tens of thousands of features but only a few hundred samples is nowadays routine in computational biology, where “omics” features such as gene expression, copy number variation and sequence data are frequently used in the predictive modeling of complex phenotypes such as anticancer drug response. The penalized regression approaches investigated in this study are popular choices in this setting and our simulations corroborate well established results concerning the conditions under which each one of these methods is expected to perform best while providing several novel insights. PMID:25289666

The Role of Multiphysics Simulation in Multidisciplinary Analysis

NASA Technical Reports Server (NTRS)

Rifai, Steven M.; Ferencz, Robert M.; Wang, Wen-Ping; Spyropoulos, Evangelos T.; Lawrence, Charles; Melis, Matthew E.

1998-01-01

This article describes the applications of the Spectrum(Tm) Solver in Multidisciplinary Analysis (MDA). Spectrum, a multiphysics simulation software based on the finite element method, addresses compressible and incompressible fluid flow, structural, and thermal modeling as well as the interaction between these disciplines. Multiphysics simulation is based on a single computational framework for the modeling of multiple interacting physical phenomena. Interaction constraints are enforced in a fully-coupled manner using the augmented-Lagrangian method. Within the multiphysics framework, the finite element treatment of fluids is based on Galerkin-Least-Squares (GLS) method with discontinuity capturing operators. The arbitrary-Lagrangian-Eulerian method is utilized to account for deformable fluid domains. The finite element treatment of solids and structures is based on the Hu-Washizu variational principle. The multiphysics architecture lends itself naturally to high-performance parallel computing. Aeroelastic, propulsion, thermal management and manufacturing applications are presented.

A Control Variate Method for Probabilistic Performance Assessment. Improved Estimates for Mean Performance Quantities of Interest

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

MacKinnon, Robert J.; Kuhlman, Kristopher L

2016-05-01

We present a method of control variates for calculating improved estimates for mean performance quantities of interest, E(PQI) , computed from Monte Carlo probabilistic simulations. An example of a PQI is the concentration of a contaminant at a particular location in a problem domain computed from simulations of transport in porous media. To simplify the presentation, the method is described in the setting of a one- dimensional elliptical model problem involving a single uncertain parameter represented by a probability distribution. The approach can be easily implemented for more complex problems involving multiple uncertain parameters and in particular for application tomore » probabilistic performance assessment of deep geologic nuclear waste repository systems. Numerical results indicate the method can produce estimates of E(PQI)having superior accuracy on coarser meshes and reduce the required number of simulations needed to achieve an acceptable estimate.« less

Using a computer-based simulation with an artificial intelligence component and discovery learning to formulate training needs for a new technology

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

Hillis, D.R.

A computer-based simulation with an artificial intelligence component and discovery learning was investigated as a method to formulate training needs for new or unfamiliar technologies. Specifically, the study examined if this simulation method would provide for the recognition of applications and knowledge/skills which would be the basis for establishing training needs. The study also examined the effect of field-dependence/independence on recognition of applications and knowledge/skills. A pretest-posttest control group experimental design involving fifty-eight college students from an industrial technology program was used. The study concluded that the simulation was effective in developing recognition of applications and the knowledge/skills for amore » new or unfamiliar technology. And, the simulation's effectiveness for providing this recognition was not limited by an individual's field-dependence/independence.« less

Modified Monte Carlo method for study of electron transport in degenerate electron gas in the presence of electron-electron interactions, application to graphene

NASA Astrophysics Data System (ADS)

Borowik, Piotr; Thobel, Jean-Luc; Adamowicz, Leszek

2017-07-01

Standard computational methods used to take account of the Pauli Exclusion Principle into Monte Carlo (MC) simulations of electron transport in semiconductors may give unphysical results in low field regime, where obtained electron distribution function takes values exceeding unity. Modified algorithms were already proposed and allow to correctly account for electron scattering on phonons or impurities. Present paper extends this approach and proposes improved simulation scheme allowing including Pauli exclusion principle for electron-electron (e-e) scattering into MC simulations. Simulations with significantly reduced computational cost recreate correct values of the electron distribution function. Proposed algorithm is applied to study transport properties of degenerate electrons in graphene with e-e interactions. This required adapting the treatment of e-e scattering in the case of linear band dispersion relation. Hence, this part of the simulation algorithm is described in details.

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

PubMed

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

2011-01-01

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

Simulation Analysis of Computer-Controlled pressurization for Mixture Ratio Control

NASA Technical Reports Server (NTRS)

Alexander, Leslie A.; Bishop-Behel, Karen; Benfield, Michael P. J.; Kelley, Anthony; Woodcock, Gordon R.

2005-01-01

A procedural code (C++) simulation was developed to investigate potentials for mixture ratio control of pressure-fed spacecraft rocket propulsion systems by measuring propellant flows, tank liquid quantities, or both, and using feedback from these measurements to adjust propellant tank pressures to set the correct operating mixture ratio for minimum propellant residuals. The pressurization system eliminated mechanical regulators in favor of a computer-controlled, servo- driven throttling valve. We found that a quasi-steady state simulation (pressure and flow transients in the pressurization systems resulting from changes in flow control valve position are ignored) is adequate for this purpose. Monte-Carlo methods are used to obtain simulated statistics on propellant depletion. Mixture ratio control algorithms based on proportional-integral-differential (PID) controller methods were developed. These algorithms actually set target tank pressures; the tank pressures are controlled by another PID controller. Simulation indicates this approach can provide reductions in residual propellants.

Cosmic reionization on computers. I. Design and calibration of simulations

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

Gnedin, Nickolay Y., E-mail: gnedin@fnal.gov

Cosmic Reionization On Computers is a long-term program of numerical simulations of cosmic reionization. Its goal is to model fully self-consistently (albeit not necessarily from the first principles) all relevant physics, from radiative transfer to gas dynamics and star formation, in simulation volumes of up to 100 comoving Mpc, and with spatial resolution approaching 100 pc in physical units. In this method paper, we describe our numerical method, the design of simulations, and the calibration of numerical parameters. Using several sets (ensembles) of simulations in 20 h {sup –1} Mpc and 40 h {sup –1} Mpc boxes with spatial resolutionmore » reaching 125 pc at z = 6, we are able to match the observed galaxy UV luminosity functions at all redshifts between 6 and 10, as well as obtain reasonable agreement with the observational measurements of the Gunn-Peterson optical depth at z < 6.« less

AESS: Accelerated Exact Stochastic Simulation

NASA Astrophysics Data System (ADS)

Jenkins, David D.; Peterson, Gregory D.

2011-12-01

The Stochastic Simulation Algorithm (SSA) developed by Gillespie provides a powerful mechanism for exploring the behavior of chemical systems with small species populations or with important noise contributions. Gene circuit simulations for systems biology commonly employ the SSA method, as do ecological applications. This algorithm tends to be computationally expensive, so researchers seek an efficient implementation of SSA. In this program package, the Accelerated Exact Stochastic Simulation Algorithm (AESS) contains optimized implementations of Gillespie's SSA that improve the performance of individual simulation runs or ensembles of simulations used for sweeping parameters or to provide statistically significant results. Program summaryProgram title: AESS Catalogue identifier: AEJW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: University of Tennessee copyright agreement No. of lines in distributed program, including test data, etc.: 10 861 No. of bytes in distributed program, including test data, etc.: 394 631 Distribution format: tar.gz Programming language: C for processors, CUDA for NVIDIA GPUs Computer: Developed and tested on various x86 computers and NVIDIA C1060 Tesla and GTX 480 Fermi GPUs. The system targets x86 workstations, optionally with multicore processors or NVIDIA GPUs as accelerators. Operating system: Tested under Ubuntu Linux OS and CentOS 5.5 Linux OS Classification: 3, 16.12 Nature of problem: Simulation of chemical systems, particularly with low species populations, can be accurately performed using Gillespie's method of stochastic simulation. Numerous variations on the original stochastic simulation algorithm have been developed, including approaches that produce results with statistics that exactly match the chemical master equation (CME) as well as other approaches that approximate the CME. Solution method: The Accelerated Exact Stochastic Simulation (AESS) tool provides implementations of a wide variety of popular variations on the Gillespie method. Users can select the specific algorithm considered most appropriate. Comparisons between the methods and with other available implementations indicate that AESS provides the fastest known implementation of Gillespie's method for a variety of test models. Users may wish to execute ensembles of simulations to sweep parameters or to obtain better statistical results, so AESS supports acceleration of ensembles of simulation using parallel processing with MPI, SSE vector units on x86 processors, and/or using NVIDIA GPUs with CUDA.

Computational Methods for Predictive Simulation of Stochastic Turbulence Systems

DTIC Science & Technology

2015-11-05

Science and Engineering, Venice , Italy, May 18-20, 2015, pp. 1261-1272. [21] Yong Li and P.D. Williams Analysis of the RAW Filter in Composite-Tendency...leapfrog scheme, Proceedings of the VI Conference on Computational Methods for Coupled Problems in Science and Engineering, Venice , Italy, May 18-20

Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

Computational Challenges of Viscous Incompressible Flows

NASA Technical Reports Server (NTRS)

Kwak, Dochan; Kiris, Cetin; Kim, Chang Sung

2004-01-01

Over the past thirty years, numerical methods and simulation tools for incompressible flows have been advanced as a subset of the computational fluid dynamics (CFD) discipline. Although incompressible flows are encountered in many areas of engineering, simulation of compressible flow has been the major driver for developing computational algorithms and tools. This is probably due to the rather stringent requirements for predicting aerodynamic performance characteristics of flight vehicles, while flow devices involving low-speed or incompressible flow could be reasonably well designed without resorting to accurate numerical simulations. As flow devices are required to be more sophisticated and highly efficient CFD took become increasingly important in fluid engineering for incompressible and low-speed flow. This paper reviews some of the successes made possible by advances in computational technologies during the same period, and discusses some of the current challenges faced in computing incompressible flows.

Toward real-time Monte Carlo simulation using a commercial cloud computing infrastructure

NASA Astrophysics Data System (ADS)

Wang, Henry; Ma, Yunzhi; Pratx, Guillem; Xing, Lei

2011-09-01

Monte Carlo (MC) methods are the gold standard for modeling photon and electron transport in a heterogeneous medium; however, their computational cost prohibits their routine use in the clinic. Cloud computing, wherein computing resources are allocated on-demand from a third party, is a new approach for high performance computing and is implemented to perform ultra-fast MC calculation in radiation therapy. We deployed the EGS5 MC package in a commercial cloud environment. Launched from a single local computer with Internet access, a Python script allocates a remote virtual cluster. A handshaking protocol designates master and worker nodes. The EGS5 binaries and the simulation data are initially loaded onto the master node. The simulation is then distributed among independent worker nodes via the message passing interface, and the results aggregated on the local computer for display and data analysis. The described approach is evaluated for pencil beams and broad beams of high-energy electrons and photons. The output of cloud-based MC simulation is identical to that produced by single-threaded implementation. For 1 million electrons, a simulation that takes 2.58 h on a local computer can be executed in 3.3 min on the cloud with 100 nodes, a 47× speed-up. Simulation time scales inversely with the number of parallel nodes. The parallelization overhead is also negligible for large simulations. Cloud computing represents one of the most important recent advances in supercomputing technology and provides a promising platform for substantially improved MC simulation. In addition to the significant speed up, cloud computing builds a layer of abstraction for high performance parallel computing, which may change the way dose calculations are performed and radiation treatment plans are completed. This work was presented in part at the 2010 Annual Meeting of the American Association of Physicists in Medicine (AAPM), Philadelphia, PA.

Multilevel Monte Carlo and improved timestepping methods in atmospheric dispersion modelling

NASA Astrophysics Data System (ADS)

Katsiolides, Grigoris; Müller, Eike H.; Scheichl, Robert; Shardlow, Tony; Giles, Michael B.; Thomson, David J.

2018-02-01

A common way to simulate the transport and spread of pollutants in the atmosphere is via stochastic Lagrangian dispersion models. Mathematically, these models describe turbulent transport processes with stochastic differential equations (SDEs). The computational bottleneck is the Monte Carlo algorithm, which simulates the motion of a large number of model particles in a turbulent velocity field; for each particle, a trajectory is calculated with a numerical timestepping method. Choosing an efficient numerical method is particularly important in operational emergency-response applications, such as tracking radioactive clouds from nuclear accidents or predicting the impact of volcanic ash clouds on international aviation, where accurate and timely predictions are essential. In this paper, we investigate the application of the Multilevel Monte Carlo (MLMC) method to simulate the propagation of particles in a representative one-dimensional dispersion scenario in the atmospheric boundary layer. MLMC can be shown to result in asymptotically superior computational complexity and reduced computational cost when compared to the Standard Monte Carlo (StMC) method, which is currently used in atmospheric dispersion modelling. To reduce the absolute cost of the method also in the non-asymptotic regime, it is equally important to choose the best possible numerical timestepping method on each level. To investigate this, we also compare the standard symplectic Euler method, which is used in many operational models, with two improved timestepping algorithms based on SDE splitting methods.

Models and Methods for Adaptive Management of Individual and Team-Based Training Using a Simulator

NASA Astrophysics Data System (ADS)

Lisitsyna, L. S.; Smetyuh, N. P.; Golikov, S. P.

2017-05-01

Research of adaptive individual and team-based training has been analyzed and helped find out that both in Russia and abroad, individual and team-based training and retraining of AASTM operators usually includes: production training, training of general computer and office equipment skills, simulator training including virtual simulators which use computers to simulate real-world manufacturing situation, and, as a rule, the evaluation of AASTM operators’ knowledge determined by completeness and adequacy of their actions under the simulated conditions. Such approach to training and re-training of AASTM operators stipulates only technical training of operators and testing their knowledge based on assessing their actions in a simulated environment.