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

NASA Technical Reports Server (NTRS)

1979-01-01

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

HRSSA - Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

NASA Astrophysics Data System (ADS)

Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong

2016-07-01

This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

Strategy and gaps for modeling, simulation, and control of hybrid systems

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

Rabiti, Cristian; Garcia, Humberto E.; Hovsapian, Rob

2015-04-01

The purpose of this report is to establish a strategy for modeling and simulation of candidate hybrid energy systems. Modeling and simulation is necessary to design, evaluate, and optimize the system technical and economic performance. Accordingly, this report first establishes the simulation requirements to analysis candidate hybrid systems. Simulation fidelity levels are established based on the temporal scale, real and synthetic data availability or needs, solution accuracy, and output parameters needed to evaluate case-specific figures of merit. Accordingly, the associated computational and co-simulation resources needed are established; including physical models when needed, code assembly and integrated solutions platforms, mathematical solvers,more » and data processing. This report first attempts to describe the figures of merit, systems requirements, and constraints that are necessary and sufficient to characterize the grid and hybrid systems behavior and market interactions. Loss of Load Probability (LOLP) and effective cost of Effective Cost of Energy (ECE), as opposed to the standard Levelized Cost of Electricty (LCOE), are introduced as technical and economical indices for integrated energy system evaluations. Financial assessment methods are subsequently introduced for evaluation of non-traditional, hybrid energy systems. Algorithms for coupled and iterative evaluation of the technical and economic performance are subsequently discussed. This report further defines modeling objectives, computational tools, solution approaches, and real-time data collection and processing (in some cases using real test units) that will be required to model, co-simulate, and optimize; (a) an energy system components (e.g., power generation unit, chemical process, electricity management unit), (b) system domains (e.g., thermal, electrical or chemical energy generation, conversion, and transport), and (c) systems control modules. Co-simulation of complex, tightly coupled, dynamic energy systems requires multiple simulation tools, potentially developed in several programming languages and resolved on separate time scales. Whereas further investigation and development of hybrid concepts will provide a more complete understanding of the joint computational and physical modeling needs, this report highlights areas in which co-simulation capabilities are warranted. The current development status, quality assurance, availability and maintainability of simulation tools that are currently available for hybrid systems modeling is presented. Existing gaps in the modeling and simulation toolsets and development needs are subsequently discussed. This effort will feed into a broader Roadmap activity for designing, developing, and demonstrating hybrid energy systems.« less

HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

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

Marchetti, Luca, E-mail: marchetti@cosbi.eu; Priami, Corrado, E-mail: priami@cosbi.eu; University of Trento, Department of Mathematics

This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance andmore » accuracy of HRSSA against other state of the art algorithms.« less

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

USGS Publications Warehouse

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

2004-01-01

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

Performance of hybrid programming models for multiscale cardiac simulations: preparing for petascale computation.

PubMed

Pope, Bernard J; Fitch, Blake G; Pitman, Michael C; Rice, John J; Reumann, Matthias

2011-10-01

Future multiscale and multiphysics models that support research into human disease, translational medical science, and treatment can utilize the power of high-performance computing (HPC) systems. We anticipate that computationally efficient multiscale models will require the use of sophisticated hybrid programming models, mixing distributed message-passing processes [e.g., the message-passing interface (MPI)] with multithreading (e.g., OpenMP, Pthreads). The objective of this study is to compare the performance of such hybrid programming models when applied to the simulation of a realistic physiological multiscale model of the heart. Our results show that the hybrid models perform favorably when compared to an implementation using only the MPI and, furthermore, that OpenMP in combination with the MPI provides a satisfactory compromise between performance and code complexity. Having the ability to use threads within MPI processes enables the sophisticated use of all processor cores for both computation and communication phases. Considering that HPC systems in 2012 will have two orders of magnitude more cores than what was used in this study, we believe that faster than real-time multiscale cardiac simulations can be achieved on these systems.

Hybrid computer optimization of systems with random parameters

NASA Technical Reports Server (NTRS)

White, R. C., Jr.

1972-01-01

A hybrid computer Monte Carlo technique for the simulation and optimization of systems with random parameters is presented. The method is applied to the simultaneous optimization of the means and variances of two parameters in the radar-homing missile problem treated by McGhee and Levine.

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.

Computational study of nonlinear plasma waves. [plasma simulation model applied to electrostatic waves in collisionless plasma

NASA Technical Reports Server (NTRS)

Matsuda, Y.

1974-01-01

A low-noise plasma simulation model is developed and applied to a series of linear and nonlinear problems associated with electrostatic wave propagation in a one-dimensional, collisionless, Maxwellian plasma, in the absence of magnetic field. It is demonstrated that use of the hybrid simulation model allows economical studies to be carried out in both the linear and nonlinear regimes with better quantitative results, for comparable computing time, than can be obtained by conventional particle simulation models, or direct solution of the Vlasov equation. The characteristics of the hybrid simulation model itself are first investigated, and it is shown to be capable of verifying the theoretical linear dispersion relation at wave energy levels as low as .000001 of the plasma thermal energy. Having established the validity of the hybrid simulation model, it is then used to study the nonlinear dynamics of monochromatic wave, sideband instability due to trapped particles, and satellite growth.

Development of Hybrid Computer Programs for AAFSS/COBRA/COIN Weapons Effectiveness Studies. Volume I. Simulating Aircraft Maneuvers and Weapon Firing Runs.

DTIC Science & Technology

for the game. Subsequent duels , flown with single armed escorts, calculated reduction in losses and damage states. For the study, hybrid computer...6) a duel between a ground weapon, armed escort, and formation of lift aircraft. (Author)

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.

Mountain bicycle frame testing as an example of practical implementation of hybrid simulation using RTFEM

NASA Astrophysics Data System (ADS)

Mucha, Waldemar; Kuś, Wacław

2018-01-01

The paper presents a practical implementation of hybrid simulation using Real Time Finite Element Method (RTFEM). Hybrid simulation is a technique for investigating dynamic material and structural properties of mechanical systems by performing numerical analysis and experiment at the same time. It applies to mechanical systems with elements too difficult or impossible to model numerically. These elements are tested experimentally, while the rest of the system is simulated numerically. Data between the experiment and numerical simulation are exchanged in real time. Authors use Finite Element Method to perform the numerical simulation. The following paper presents the general algorithm for hybrid simulation using RTFEM and possible improvements of the algorithm for computation time reduction developed by the authors. The paper focuses on practical implementation of presented methods, which involves testing of a mountain bicycle frame, where the shock absorber is tested experimentally while the rest of the frame is simulated numerically.

Numerical characterization of landing gear aeroacoustics using advanced simulation and analysis techniques

NASA Astrophysics Data System (ADS)

Redonnet, S.; Ben Khelil, S.; Bulté, J.; Cunha, G.

2017-09-01

With the objective of aircraft noise mitigation, we here address the numerical characterization of the aeroacoustics by a simplified nose landing gear (NLG), through the use of advanced simulation and signal processing techniques. To this end, the NLG noise physics is first simulated through an advanced hybrid approach, which relies on Computational Fluid Dynamics (CFD) and Computational AeroAcoustics (CAA) calculations. Compared to more traditional hybrid methods (e.g. those relying on the use of an Acoustic Analogy), and although it is used here with some approximations made (e.g. design of the CFD-CAA interface), the present approach does not rely on restrictive assumptions (e.g. equivalent noise source, homogeneous propagation medium), which allows to incorporate more realism into the prediction. In a second step, the outputs coming from such CFD-CAA hybrid calculations are processed through both traditional and advanced post-processing techniques, thus offering to further investigate the NLG's noise source mechanisms. Among other things, this work highlights how advanced computational methodologies are now mature enough to not only simulate realistic problems of airframe noise emission, but also to investigate their underlying physics.

Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models.

PubMed

Pope, Bernard J; Fitch, Blake G; Pitman, Michael C; Rice, John J; Reumann, Matthias

2011-01-01

Future multiscale and multiphysics models must use the power of high performance computing (HPC) systems to enable research into human disease, translational medical science, and treatment. Previously we showed that computationally efficient multiscale models will require the use of sophisticated hybrid programming models, mixing distributed message passing processes (e.g. the message passing interface (MPI)) with multithreading (e.g. OpenMP, POSIX pthreads). The objective of this work is to compare the performance of such hybrid programming models when applied to the simulation of a lightweight multiscale cardiac model. Our results show that the hybrid models do not perform favourably when compared to an implementation using only MPI which is in contrast to our results using complex physiological models. Thus, with regards to lightweight multiscale cardiac models, the user may not need to increase programming complexity by using a hybrid programming approach. However, considering that model complexity will increase as well as the HPC system size in both node count and number of cores per node, it is still foreseeable that we will achieve faster than real time multiscale cardiac simulations on these systems using hybrid programming models.

Hybrid Method for Power Control Simulation of a Single Fluid Plasma Thruster

NASA Astrophysics Data System (ADS)

Jaisankar, S.; Sheshadri, T. S.

2018-05-01

Propulsive plasma flow through a cylindrical-conical diverging thruster is simulated by a power controlled hybrid method to obtain the basic flow, thermodynamic and electromagnetic variables. Simulation is based on a single fluid model with electromagnetics being described by the equations of potential Poisson, Maxwell and the Ohm's law while the compressible fluid dynamics by the Navier Stokes in cylindrical form. The proposed method solved the electromagnetics and fluid dynamics separately, both to segregate the two prominent scales for an efficient computation and for the delivery of voltage controlled rated power. The magnetic transport is solved for steady state while fluid dynamics is allowed to evolve in time along with an electromagnetic source using schemes based on generalized finite difference discretization. The multistep methodology with power control is employed for simulating fully ionized propulsive flow of argon plasma through the thruster. Numerical solution shows convergence of every part of the solver including grid stability causing the multistep hybrid method to converge for a rated power delivery. Simulation results are reasonably in agreement with the reported physics of plasma flow in the thruster thus indicating the potential utility of this hybrid computational framework, especially when single fluid approximation of plasma is relevant.

Hybrid RANS-LES using high order numerical methods

NASA Astrophysics Data System (ADS)

Henry de Frahan, Marc; Yellapantula, Shashank; Vijayakumar, Ganesh; Knaus, Robert; Sprague, Michael

2017-11-01

Understanding the impact of wind turbine wake dynamics on downstream turbines is particularly important for the design of efficient wind farms. Due to their tractable computational cost, hybrid RANS/LES models are an attractive framework for simulating separation flows such as the wake dynamics behind a wind turbine. High-order numerical methods can be computationally efficient and provide increased accuracy in simulating complex flows. In the context of LES, high-order numerical methods have shown some success in predictions of turbulent flows. However, the specifics of hybrid RANS-LES models, including the transition region between both modeling frameworks, pose unique challenges for high-order numerical methods. In this work, we study the effect of increasing the order of accuracy of the numerical scheme in simulations of canonical turbulent flows using RANS, LES, and hybrid RANS-LES models. We describe the interactions between filtering, model transition, and order of accuracy and their effect on turbulence quantities such as kinetic energy spectra, boundary layer evolution, and dissipation rate. This work was funded by the U.S. Department of Energy, Exascale Computing Project, under Contract No. DE-AC36-08-GO28308 with the National Renewable Energy Laboratory.

Mathematical and computational model for the analysis of micro hybrid rocket motor

NASA Astrophysics Data System (ADS)

Stoia-Djeska, Marius; Mingireanu, Florin

2012-11-01

The hybrid rockets use a two-phase propellant system. In the present work we first develop a simplified model of the coupling of the hybrid combustion process with the complete unsteady flow, starting from the combustion port and ending with the nozzle. The physical and mathematical model are adapted to the simulations of micro hybrid rocket motors. The flow model is based on the one-dimensional Euler equations with source terms. The flow equations and the fuel regression rate law are solved in a coupled manner. The platform of the numerical simulations is an implicit fourth-order Runge-Kutta second order cell-centred finite volume method. The numerical results obtained with this model show a good agreement with published experimental and numerical results. The computational model developed in this work is simple, computationally efficient and offers the advantage of taking into account a large number of functional and constructive parameters that are used by the engineers.

Advanced EMT and Phasor-Domain Hybrid Simulation with Simulation Mode Switching Capability for Transmission and Distribution Systems

DOE PAGES

Huang, Qiuhua; Vittal, Vijay

2018-05-09

Conventional electromagnetic transient (EMT) and phasor-domain hybrid simulation approaches presently exist for trans-mission system level studies. Their simulation efficiency is generally constrained by the EMT simulation. With an increasing number of distributed energy resources and non-conventional loads being installed in distribution systems, it is imperative to extend the hybrid simulation application to include distribution systems and integrated transmission and distribution systems. Meanwhile, it is equally important to improve the simulation efficiency as the modeling scope and complexity of the detailed system in the EMT simulation increases. To meet both requirements, this paper introduces an advanced EMT and phasor-domain hybrid simulationmore » approach. This approach has two main features: 1) a comprehensive phasor-domain modeling framework which supports positive-sequence, three-sequence, three-phase and mixed three-sequence/three-phase representations and 2) a robust and flexible simulation mode switching scheme. The developed scheme enables simulation switching from hybrid simulation mode back to pure phasor-domain dynamic simulation mode to achieve significantly improved simulation efficiency. The proposed method has been tested on integrated transmission and distribution systems. In conclusion, the results show that with the developed simulation switching feature, the total computational time is significantly reduced compared to running the hybrid simulation for the whole simulation period, while maintaining good simulation accuracy.« less

Advanced EMT and Phasor-Domain Hybrid Simulation with Simulation Mode Switching Capability for Transmission and Distribution Systems

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

Huang, Qiuhua; Vittal, Vijay

Conventional electromagnetic transient (EMT) and phasor-domain hybrid simulation approaches presently exist for trans-mission system level studies. Their simulation efficiency is generally constrained by the EMT simulation. With an increasing number of distributed energy resources and non-conventional loads being installed in distribution systems, it is imperative to extend the hybrid simulation application to include distribution systems and integrated transmission and distribution systems. Meanwhile, it is equally important to improve the simulation efficiency as the modeling scope and complexity of the detailed system in the EMT simulation increases. To meet both requirements, this paper introduces an advanced EMT and phasor-domain hybrid simulationmore » approach. This approach has two main features: 1) a comprehensive phasor-domain modeling framework which supports positive-sequence, three-sequence, three-phase and mixed three-sequence/three-phase representations and 2) a robust and flexible simulation mode switching scheme. The developed scheme enables simulation switching from hybrid simulation mode back to pure phasor-domain dynamic simulation mode to achieve significantly improved simulation efficiency. The proposed method has been tested on integrated transmission and distribution systems. In conclusion, the results show that with the developed simulation switching feature, the total computational time is significantly reduced compared to running the hybrid simulation for the whole simulation period, while maintaining good simulation accuracy.« less

Hybrid and Electric Advanced Vehicle Systems Simulation

NASA Technical Reports Server (NTRS)

Beach, R. F.; Hammond, R. A.; Mcgehee, R. K.

1985-01-01

Predefined components connected to represent wide variety of propulsion systems. Hybrid and Electric Advanced Vehicle System (HEAVY) computer program is flexible tool for evaluating performance and cost of electric and hybrid vehicle propulsion systems. Allows designer to quickly, conveniently, and economically predict performance of proposed drive train.

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics.

PubMed

Strehl, Robert; Ilie, Silvana

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

Digital quantum simulators in a scalable architecture of hybrid spin-photon qubits

PubMed Central

Chiesa, Alessandro; Santini, Paolo; Gerace, Dario; Raftery, James; Houck, Andrew A.; Carretta, Stefano

2015-01-01

Resolving quantum many-body problems represents one of the greatest challenges in physics and physical chemistry, due to the prohibitively large computational resources that would be required by using classical computers. A solution has been foreseen by directly simulating the time evolution through sequences of quantum gates applied to arrays of qubits, i.e. by implementing a digital quantum simulator. Superconducting circuits and resonators are emerging as an extremely promising platform for quantum computation architectures, but a digital quantum simulator proposal that is straightforwardly scalable, universal, and realizable with state-of-the-art technology is presently lacking. Here we propose a viable scheme to implement a universal quantum simulator with hybrid spin-photon qubits in an array of superconducting resonators, which is intrinsically scalable and allows for local control. As representative examples we consider the transverse-field Ising model, a spin-1 Hamiltonian, and the two-dimensional Hubbard model and we numerically simulate the scheme by including the main sources of decoherence. PMID:26563516

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

PubMed

Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

2015-09-15

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

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

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Hardware simulation of fuel cell/gas turbine hybrids

NASA Astrophysics Data System (ADS)

Smith, Thomas Paul

Hybrid solid oxide fuel cell/gas turbine (SOFC/GT) systems offer high efficiency power generation, but face numerous integration and operability challenges. This dissertation addresses the application of hardware-in-the-loop simulation (HILS) to explore the performance of a solid oxide fuel cell stack and gas turbine when combined into a hybrid system. Specifically, this project entailed developing and demonstrating a methodology for coupling a numerical SOFC subsystem model with a gas turbine that has been modified with supplemental process flow and control paths to mimic a hybrid system. This HILS approach was implemented with the U.S. Department of Energy Hybrid Performance Project (HyPer) located at the National Energy Technology Laboratory. By utilizing HILS the facility provides a cost effective and capable platform for characterizing the response of hybrid systems to dynamic variations in operating conditions. HILS of a hybrid system was accomplished by first interfacing a numerical model with operating gas turbine hardware. The real-time SOFC stack model responds to operating turbine flow conditions in order to predict the level of thermal effluent from the SOFC stack. This simulated level of heating then dynamically sets the turbine's "firing" rate to reflect the stack output heat rate. Second, a high-speed computer system with data acquisition capabilities was integrated with the existing controls and sensors of the turbine facility. In the future, this will allow for the utilization of high-fidelity fuel cell models that infer cell performance parameters while still computing the simulation in real-time. Once the integration of the numeric and the hardware simulation components was completed, HILS experiments were conducted to evaluate hybrid system performance. The testing identified non-intuitive transient responses arising from the large thermal capacitance of the stack that are inherent to hybrid systems. Furthermore, the tests demonstrated the capabilities of HILS as a research tool for investigating the dynamic behavior of SOFC/GT hybrid power generation systems.

Hybrid Quantum-Classical Approach to Quantum Optimal Control.

PubMed

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

2017-04-14

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

Computing all hybridization networks for multiple binary phylogenetic input trees.

PubMed

Albrecht, Benjamin

2015-07-30

The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events is the computation of hybridization networks. This work presents the first algorithm computing the hybridization number as well as a set of representative hybridization networks for multiple binary phylogenetic input trees on the same set of taxa. To improve its practical runtime, we show how this algorithm can be parallelized. Moreover, we demonstrate the efficiency of the software Hybroscale, containing an implementation of our algorithm, by comparing it to PIRNv2.0, which is so far the best available software computing the exact hybridization number for multiple binary phylogenetic trees on the same set of taxa. The algorithm is part of the software Hybroscale, which was developed specifically for the investigation of hybridization networks including their computation and visualization. Hybroscale is freely available(1) and runs on all three major operating systems. Our simulation study indicates that our approach is on average 100 times faster than PIRNv2.0. Moreover, we show how Hybroscale improves the interpretation of the reported hybridization networks by adding certain features to its graphical representation.

Hybrid General Pattern Search and Simulated Annealing for Industrail Production Planning Problems

NASA Astrophysics Data System (ADS)

Vasant, P.; Barsoum, N.

2010-06-01

In this paper, the hybridization of GPS (General Pattern Search) method and SA (Simulated Annealing) incorporated in the optimization process in order to look for the global optimal solution for the fitness function and decision variables as well as minimum computational CPU time. The real strength of SA approach been tested in this case study problem of industrial production planning. This is due to the great advantage of SA for being easily escaping from trapped in local minima by accepting up-hill move through a probabilistic procedure in the final stages of optimization process. Vasant [1] in his Ph. D thesis has provided 16 different techniques of heuristic and meta-heuristic in solving industrial production problems with non-linear cubic objective functions, eight decision variables and 29 constraints. In this paper, fuzzy technological problems have been solved using hybrid techniques of general pattern search and simulated annealing. The simulated and computational results are compared to other various evolutionary techniques.

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

A design framework for teleoperators with kinesthetic feedback

NASA Technical Reports Server (NTRS)

Hannaford, Blake

1989-01-01

The application of a hybrid two-port model to teleoperators with force and velocity sensing at the master and slave is presented. The interfaces between human operator and master, and between environment and slave, are ports through which the teleoperator is designed to exchange energy between the operator and the environment. By computing or measuring the input-output properties of this two-port network, the hybrid two-port model of an actual or simulated teleoperator system can be obtained. It is shown that the hybrid model (as opposed to other two-port forms) leads to an intuitive representation of ideal teleoperator performace and applies to several teleoperator architectures. Thus measured values of the h matrix or values computed from a simulation can be used to compare performance with th ideal. The frequency-dependent h matrix is computed from a detailed SPICE model of an actual system, and the method is applied to a proposed architecture.

Hybrid Multiscale Simulation of Hydrologic and Biogeochemical Processes in the River-Groundwater Interaction Zone

NASA Astrophysics Data System (ADS)

Yang, X.; Scheibe, T. D.; Chen, X.; Hammond, G. E.; Song, X.

2015-12-01

The zone in which river water and groundwater mix plays an important role in natural ecosystems as it regulates the mixing of nutrients that control biogeochemical transformations. Subsurface heterogeneity leads to local hotspots of microbial activity that are important to system function yet difficult to resolve computationally. To address this challenge, we are testing a hybrid multiscale approach that couples models at two distinct scales, based on field research at the U. S. Department of Energy's Hanford Site. The region of interest is a 400 x 400 x 20 m macroscale domain that intersects the aquifer and the river and contains a contaminant plume. However, biogeochemical activity is high in a thin zone (mud layer, <1 m thick) immediately adjacent to the river. This microscale domain is highly heterogeneous and requires fine spatial resolution to adequately represent the effects of local mixing on reactions. It is not computationally feasible to resolve the full macroscale domain at the fine resolution needed in the mud layer, and the reaction network needed in the mud layer is much more complex than that needed in the rest of the macroscale domain. Hence, a hybrid multiscale approach is used to efficiently and accurately predict flow and reactive transport at both scales. In our simulations, models at both scales are simulated using the PFLOTRAN code. Multiple microscale simulations in dynamically defined sub-domains (fine resolution, complex reaction network) are executed and coupled with a macroscale simulation over the entire domain (coarse resolution, simpler reaction network). The objectives of the research include: 1) comparing accuracy and computing cost of the hybrid multiscale simulation with a single-scale simulation; 2) identifying hot spots of microbial activity; and 3) defining macroscopic quantities such as fluxes, residence times and effective reaction rates.

Implementing Molecular Dynamics on Hybrid High Performance Computers - Three-Body Potentials

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

Brown, W Michael; Yamada, Masako

The use of coprocessors or accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power re- quirements. Hybrid high-performance computers, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. Although there has been extensive research into methods to efficiently use accelerators to improve the performance of molecular dynamics (MD) employing pairwise potential energy models, little is reported in the literature for models that includemore » many-body effects. 3-body terms are required for many popular potentials such as MEAM, Tersoff, REBO, AIREBO, Stillinger-Weber, Bond-Order Potentials, and others. Because the per-atom simulation times are much higher for models incorporating 3-body terms, there is a clear need for efficient algo- rithms usable on hybrid high performance computers. Here, we report a shared-memory force-decomposition for 3-body potentials that avoids memory conflicts to allow for a deterministic code with substantial performance improvements on hybrid machines. We describe modifications necessary for use in distributed memory MD codes and show results for the simulation of water with Stillinger-Weber on the hybrid Titan supercomputer. We compare performance of the 3-body model to the SPC/E water model when using accelerators. Finally, we demonstrate that our approach can attain a speedup of 5.1 with acceleration on Titan for production simulations to study water droplet freezing on a surface.« less

Hybrid water immersion simulation of manual IVA performance in weightlessness

NASA Technical Reports Server (NTRS)

Loats, H. L., Jr.; Mattingly, G. S.

1971-01-01

A description is given of the development, tests, and analysis of a manual simulator. The simulator was developed to test mass handling and translation under weightlessness conditions by a test subject. The system is composed of a hybrid simulator with a combination of water immersion and mechanical, Peter Pan, simulation. The concept operates on the equivalence principle, with the subject and the cargo remaining quasi-stationary. Movement is effected through a moving device controlled through force by the subject. Motion response is determined through computations of the inertial movement under such conditions.

Hybrid classical/quantum simulation for infrared spectroscopy of water

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

2018-05-01

We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

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

Strehl, Robert; Ilie, Silvana, E-mail: silvana@ryerson.ca

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated onmore » three benchmarking systems, with special focus on approximation accuracy and efficiency.« less

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

DOE PAGES

Radak, Brian K.; Chipot, Christophe; Suh, Donghyuk; ...

2017-11-07

We report that an increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementationmore » of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Finally, illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.« less

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+.

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

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

Radak, Brian K.; Chipot, Christophe; Suh, Donghyuk

We report that an increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementationmore » of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Finally, illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.« less

Robotics, Artificial Intelligence, Computer Simulation: Future Applications in Special Education.

ERIC Educational Resources Information Center

Moore, Gwendolyn B.; And Others

The report describes three advanced technologies--robotics, artificial intelligence, and computer simulation--and identifies the ways in which they might contribute to special education. A hybrid methodology was employed to identify existing technology and forecast future needs. Following this framework, each of the technologies is defined,…

Quantum Accelerators for High-performance Computing Systems

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

Humble, Travis S.; Britt, Keith A.; Mohiyaddin, Fahd A.

We define some of the programming and system-level challenges facing the application of quantum processing to high-performance computing. Alongside barriers to physical integration, prominent differences in the execution of quantum and conventional programs challenges the intersection of these computational models. Following a brief overview of the state of the art, we discuss recent advances in programming and execution models for hybrid quantum-classical computing. We discuss a novel quantum-accelerator framework that uses specialized kernels to offload select workloads while integrating with existing computing infrastructure. We elaborate on the role of the host operating system to manage these unique accelerator resources, themore » prospects for deploying quantum modules, and the requirements placed on the language hierarchy connecting these different system components. We draw on recent advances in the modeling and simulation of quantum computing systems with the development of architectures for hybrid high-performance computing systems and the realization of software stacks for controlling quantum devices. Finally, we present simulation results that describe the expected system-level behavior of high-performance computing systems composed from compute nodes with quantum processing units. We describe performance for these hybrid systems in terms of time-to-solution, accuracy, and energy consumption, and we use simple application examples to estimate the performance advantage of quantum acceleration.« less

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.

Hybrid annealing: Coupling a quantum simulator to a classical computer

NASA Astrophysics Data System (ADS)

Graß, Tobias; Lewenstein, Maciej

2017-05-01

Finding the global minimum in a rugged potential landscape is a computationally hard task, often equivalent to relevant optimization problems. Annealing strategies, either classical or quantum, explore the configuration space by evolving the system under the influence of thermal or quantum fluctuations. The thermal annealing dynamics can rapidly freeze the system into a low-energy configuration, and it can be simulated well on a classical computer, but it easily gets stuck in local minima. Quantum annealing, on the other hand, can be guaranteed to find the true ground state and can be implemented in modern quantum simulators; however, quantum adiabatic schemes become prohibitively slow in the presence of quasidegeneracies. Here, we propose a strategy which combines ideas from simulated annealing and quantum annealing. In such a hybrid algorithm, the outcome of a quantum simulator is processed on a classical device. While the quantum simulator explores the configuration space by repeatedly applying quantum fluctuations and performing projective measurements, the classical computer evaluates each configuration and enforces a lowering of the energy. We have simulated this algorithm for small instances of the random energy model, showing that it potentially outperforms both simulated thermal annealing and adiabatic quantum annealing. It becomes most efficient for problems involving many quasidegenerate ground states.

Power and energy computational models for the design and simulation of hybrid-electric combat vehicles

NASA Astrophysics Data System (ADS)

Smith, Wilford; Nunez, Patrick

2005-05-01

This paper describes the work being performed under the RDECOM Power and Energy (P&E) program (formerly the Combat Hybrid Power System (CHPS) program) developing hybrid power system models and integrating them into larger simulations, such as OneSAF, that can be used to find duty cycles to feed designers of hybrid power systems. This paper also describes efforts underway to link the TARDEC P&E System Integration Lab (SIL) in San Jose CA to the TARDEC Ground Vehicle Simulation Lab (GVSL) in Warren, MI. This linkage is being performed to provide a methodology for generating detailed driver profiles for use in the development of vignettes and mission profiles for system design excursions.

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.

A numerical code for the simulation of non-equilibrium chemically reacting flows on hybrid CPU-GPU clusters

NASA Astrophysics Data System (ADS)

Kudryavtsev, Alexey N.; Kashkovsky, Alexander V.; Borisov, Semyon P.; Shershnev, Anton A.

2017-10-01

In the present work a computer code RCFS for numerical simulation of chemically reacting compressible flows on hybrid CPU/GPU supercomputers is developed. It solves 3D unsteady Euler equations for multispecies chemically reacting flows in general curvilinear coordinates using shock-capturing TVD schemes. Time advancement is carried out using the explicit Runge-Kutta TVD schemes. Program implementation uses CUDA application programming interface to perform GPU computations. Data between GPUs is distributed via domain decomposition technique. The developed code is verified on the number of test cases including supersonic flow over a cylinder.

An automated procedure for calculating system matrices from perturbation data generated by an EAI Pacer and 100 hybrid computer system

NASA Technical Reports Server (NTRS)

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

1977-01-01

Techniques are presented for determining the elements of the A, B, C, and D state variable matrices for systems simulated on an EAI Pacer 100 hybrid computer. An automated procedure systematically generates disturbance data necessary to linearize the simulation model and stores these data on a floppy disk. A separate digital program verifies this data, calculates the elements of the system matrices, and prints these matrices appropriately labeled. The partial derivatives forming the elements of the state variable matrices are approximated by finite difference calculations.

Accelerating Climate and Weather Simulations through Hybrid Computing

NASA Technical Reports Server (NTRS)

Zhou, Shujia; Cruz, Carlos; Duffy, Daniel; Tucker, Robert; Purcell, Mark

2011-01-01

Unconventional multi- and many-core processors (e.g. IBM (R) Cell B.E.(TM) and NVIDIA (R) GPU) have emerged as effective accelerators in trial climate and weather simulations. Yet these climate and weather models typically run on parallel computers with conventional processors (e.g. Intel, AMD, and IBM) using Message Passing Interface. To address challenges involved in efficiently and easily connecting accelerators to parallel computers, we investigated using IBM's Dynamic Application Virtualization (TM) (IBM DAV) software in a prototype hybrid computing system with representative climate and weather model components. The hybrid system comprises two Intel blades and two IBM QS22 Cell B.E. blades, connected with both InfiniBand(R) (IB) and 1-Gigabit Ethernet. The system significantly accelerates a solar radiation model component by offloading compute-intensive calculations to the Cell blades. Systematic tests show that IBM DAV can seamlessly offload compute-intensive calculations from Intel blades to Cell B.E. blades in a scalable, load-balanced manner. However, noticeable communication overhead was observed, mainly due to IP over the IB protocol. Full utilization of IB Sockets Direct Protocol and the lower latency production version of IBM DAV will reduce this overhead.

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

Brief Survey of TSC Computing Facilities

DOT National Transportation Integrated Search

1972-05-01

The Transportation Systems Center (TSC) has four, essentially separate, in-house computing facilities. We shall call them Honeywell Facility, the Hybrid Facility, the Multimode Simulation Facility, and the Central Facility. In addition to these four,...

On the use of reverse Brownian motion to accelerate hybrid simulations

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

Bakarji, Joseph; Tartakovsky, Daniel M., E-mail: tartakovsky@stanford.edu

Multiscale and multiphysics simulations are two rapidly developing fields of scientific computing. Efficient coupling of continuum (deterministic or stochastic) constitutive solvers with their discrete (stochastic, particle-based) counterparts is a common challenge in both kinds of simulations. We focus on interfacial, tightly coupled simulations of diffusion that combine continuum and particle-based solvers. The latter employs the reverse Brownian motion (rBm), a Monte Carlo approach that allows one to enforce inhomogeneous Dirichlet, Neumann, or Robin boundary conditions and is trivially parallelizable. We discuss numerical approaches for improving the accuracy of rBm in the presence of inhomogeneous Neumann boundary conditions and alternative strategiesmore » for coupling the rBm solver with its continuum counterpart. Numerical experiments are used to investigate the convergence, stability, and computational efficiency of the proposed hybrid algorithm.« less

Comparison of optimization algorithms in intensity-modulated radiation therapy planning

NASA Astrophysics Data System (ADS)

Kendrick, Rachel

Intensity-modulated radiation therapy is used to better conform the radiation dose to the target, which includes avoiding healthy tissue. Planning programs employ optimization methods to search for the best fluence of each photon beam, and therefore to create the best treatment plan. The Computational Environment for Radiotherapy Research (CERR), a program written in MATLAB, was used to examine some commonly-used algorithms for one 5-beam plan. Algorithms include the genetic algorithm, quadratic programming, pattern search, constrained nonlinear optimization, simulated annealing, the optimization method used in Varian EclipseTM, and some hybrids of these. Quadratic programing, simulated annealing, and a quadratic/simulated annealing hybrid were also separately compared using different prescription doses. The results of each dose-volume histogram as well as the visual dose color wash were used to compare the plans. CERR's built-in quadratic programming provided the best overall plan, but avoidance of the organ-at-risk was rivaled by other programs. Hybrids of quadratic programming with some of these algorithms seems to suggest the possibility of better planning programs, as shown by the improved quadratic/simulated annealing plan when compared to the simulated annealing algorithm alone. Further experimentation will be done to improve cost functions and computational time.

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance

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

Dong, Han; Sharma, Diksha; Badano, Aldo, E-mail: aldo.badano@fda.hhs.gov

2014-12-15

Purpose: Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridMANTIS, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webMANTIS and visualMANTIS to facilitate the setup of computational experiments via hybridMANTIS. Methods: Themore » visualization tools visualMANTIS and webMANTIS enable the user to control simulation properties through a user interface. In the case of webMANTIS, control via a web browser allows access through mobile devices such as smartphones or tablets. webMANTIS acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. Results: The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridMANTIS. The users can download the output images and statistics through a zip file for future reference. In addition, webMANTIS provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. Conclusions: The visualization tools visualMANTIS and webMANTIS provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.« less

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

PubMed

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

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator-which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics.

SU-E-T-13: A Feasibility Study of the Use of Hybrid Computational Phantoms for Improved Historical Dose Reconstruction in the Study of Late Radiation Effects for Hodgkin's Lymphoma

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

Petroccia, H; O'Reilly, S; Bolch, W

Purpose: Radiation-induced cancer effects are well-documented following radiotherapy. Further investigation is needed to more accurately determine a dose-response relationship for late radiation effects. Recent dosimetry studies tend to use representative patients (Taylor 2009) or anthropomorphic phantoms (Wirth 2008) for estimating organ mean doses. In this study, we compare hybrid computational phantoms to patient-specific voxel phantoms to test the accuracy of University of Florida Hybrid Phantom Library (UFHP Library) for historical dose reconstructions. Methods: A cohort of 10 patients with CT images was used to reproduce the data that was collected historically for Hodgkin's lymphoma patients (i.e. caliper measurements and photographs).more » Four types of phantoms were generated to show a range of refinement from reference hybrid-computational phantom to patient-specific phantoms. Each patient is matched to a reference phantom from the UFHP Library based on height and weight. The reference phantom is refined in the anterior/posterior direction to create a ‘caliper-scaled phantom’. A photograph is simulated using a surface rendering from segmented CT images. Further refinement in the lateral direction is performed using ratios from a simulated-photograph to create a ‘photograph and caliper-scaled phantom’; breast size and position is visually adjusted. Patient-specific hybrid phantoms, with matched organ volumes, are generated and show the capabilities of the UF Hybrid Phantom Library. Reference, caliper-scaled, photograph and caliper-scaled, and patient-specific hybrid phantoms are compared with patient-specific voxel phantoms to determine the accuracy of the study. Results: Progression from reference phantom to patient specific hybrid shows good agreement with the patient specific voxel phantoms. Each stage of refinement shows an overall trend of improvement in dose accuracy within the study, which suggests that computational phantoms can show improved accuracy in historical dose estimates. Conclusion: Computational hybrid phantoms show promise for improved accuracy within retrospective studies when CTs and other x-ray images are not available.« less

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.

PubMed

Pahle, Jürgen

2009-01-01

Computer simulations have become an invaluable tool to study the sometimes counterintuitive temporal dynamics of (bio-)chemical systems. In particular, stochastic simulation methods have attracted increasing interest recently. In contrast to the well-known deterministic approach based on ordinary differential equations, they can capture effects that occur due to the underlying discreteness of the systems and random fluctuations in molecular numbers. Numerous stochastic, approximate stochastic and hybrid simulation methods have been proposed in the literature. In this article, they are systematically reviewed in order to guide the researcher and help her find the appropriate method for a specific problem.

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches

PubMed Central

2009-01-01

Computer simulations have become an invaluable tool to study the sometimes counterintuitive temporal dynamics of (bio-)chemical systems. In particular, stochastic simulation methods have attracted increasing interest recently. In contrast to the well-known deterministic approach based on ordinary differential equations, they can capture effects that occur due to the underlying discreteness of the systems and random fluctuations in molecular numbers. Numerous stochastic, approximate stochastic and hybrid simulation methods have been proposed in the literature. In this article, they are systematically reviewed in order to guide the researcher and help her find the appropriate method for a specific problem. PMID:19151097

A hybrid hydrostatic and non-hydrostatic numerical model for shallow flow simulations

NASA Astrophysics Data System (ADS)

Zhang, Jingxin; Liang, Dongfang; Liu, Hua

2018-05-01

Hydrodynamics of geophysical flows in oceanic shelves, estuaries, and rivers, are often studied by solving shallow water model equations. Although hydrostatic models are accurate and cost efficient for many natural flows, there are situations where the hydrostatic assumption is invalid, whereby a fully hydrodynamic model is necessary to increase simulation accuracy. There is a growing concern about the decrease of the computational cost of non-hydrostatic pressure models to improve the range of their applications in large-scale flows with complex geometries. This study describes a hybrid hydrostatic and non-hydrostatic model to increase the efficiency of simulating shallow water flows. The basic numerical model is a three-dimensional hydrostatic model solved by the finite volume method (FVM) applied to unstructured grids. Herein, a second-order total variation diminishing (TVD) scheme is adopted. Using a predictor-corrector method to calculate the non-hydrostatic pressure, we extended the hydrostatic model to a fully hydrodynamic model. By localising the computational domain in the corrector step for non-hydrostatic pressure calculations, a hybrid model was developed. There was no prior special treatment on mode switching, and the developed numerical codes were highly efficient and robust. The hybrid model is applicable to the simulation of shallow flows when non-hydrostatic pressure is predominant only in the local domain. Beyond the non-hydrostatic domain, the hydrostatic model is still accurate. The applicability of the hybrid method was validated using several study cases.

Testing trivializing maps in the Hybrid Monte Carlo algorithm

PubMed Central

Engel, Georg P.; Schaefer, Stefan

2011-01-01

We test a recent proposal to use approximate trivializing maps in a field theory to speed up Hybrid Monte Carlo simulations. Simulating the CPN−1 model, we find a small improvement with the leading order transformation, which is however compensated by the additional computational overhead. The scaling of the algorithm towards the continuum is not changed. In particular, the effect of the topological modes on the autocorrelation times is studied. PMID:21969733

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

PubMed Central

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

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator—which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics. PMID:25120463

Modeling and Controls Development of 48V Mild Hybrid Electric Vehicles

EPA Science Inventory

The Advanced Light-Duty Powertrain and Hybrid Analysis tool (ALPHA) was created by EPA to evaluate the Greenhouse Gas (GHG) emissions of Light-Duty (LD) vehicles. It is a physics-based, forward-looking, full vehicle computer simulator capable of analyzing various vehicle types c...

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.

Hybrid and electric advanced vehicle systems (heavy) simulation

NASA Technical Reports Server (NTRS)

Hammond, R. A.; Mcgehee, R. K.

1981-01-01

A computer program to simulate hybrid and electric advanced vehicle systems (HEAVY) is described. It is intended for use early in the design process: concept evaluation, alternative comparison, preliminary design, control and management strategy development, component sizing, and sensitivity studies. It allows the designer to quickly, conveniently, and economically predict the performance of a proposed drive train. The user defines the system to be simulated using a library of predefined component models that may be connected to represent a wide variety of propulsion systems. The development of three models are discussed as examples.

Generalized dynamic engine simulation techniques for the digital computer

NASA Technical Reports Server (NTRS)

Sellers, J.; Teren, F.

1974-01-01

Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program, DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design-point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar all-digital programs on future engine simulation philosophy is also discussed.

Generalized dynamic engine simulation techniques for the digital computer

NASA Technical Reports Server (NTRS)

Sellers, J.; Teren, F.

1974-01-01

Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design-point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar all-digital programs on future engine simulation philosophy is also discussed.

Generalized dynamic engine simulation techniques for the digital computers

NASA Technical Reports Server (NTRS)

Sellers, J.; Teren, F.

1975-01-01

Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program, DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar digital programs on future engine simulation philosophy is also discussed.

Accelerating Climate Simulations Through Hybrid Computing

NASA Technical Reports Server (NTRS)

Zhou, Shujia; Sinno, Scott; Cruz, Carlos; Purcell, Mark

2009-01-01

Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.

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.

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.

Development of Advanced Light-Duty Powertrain and Hybrid Analysis Tool (SAE 2013-01-0808)

EPA Science Inventory

The Advanced Light-Duty Powertrain and Hybrid Analysis tool was created by Environmental Protection Agency to evaluate the Greenhouse gas emissions and fuel efficiency from light-duty vehicles. It is a physics-based, forward-looking, full vehicle computer simulator, which is cap...

Benchmark of multi-phase method for the computation of fast ion distributions in a tokamak plasma in the presence of low-amplitude resonant MHD activity

NASA Astrophysics Data System (ADS)

Bierwage, A.; Todo, Y.

2017-11-01

The transport of fast ions in a beam-driven JT-60U tokamak plasma subject to resonant magnetohydrodynamic (MHD) mode activity is simulated using the so-called multi-phase method, where 4 ms intervals of classical Monte-Carlo simulations (without MHD) are interlaced with 1 ms intervals of hybrid simulations (with MHD). The multi-phase simulation results are compared to results obtained with continuous hybrid simulations, which were recently validated against experimental data (Bierwage et al., 2017). It is shown that the multi-phase method, in spite of causing significant overshoots in the MHD fluctuation amplitudes, accurately reproduces the frequencies and positions of the dominant resonant modes, as well as the spatial profile and velocity distribution of the fast ions, while consuming only a fraction of the computation time required by the continuous hybrid simulation. The present paper is limited to low-amplitude fluctuations consisting of a few long-wavelength modes that interact only weakly with each other. The success of this benchmark study paves the way for applying the multi-phase method to the simulation of Abrupt Large-amplitude Events (ALE), which were seen in the same JT-60U experiments but at larger time intervals. Possible implications for the construction of reduced models for fast ion transport are discussed.

Recourse-based facility-location problems in hybrid uncertain environment.

PubMed

Wang, Shuming; Watada, Junzo; Pedrycz, Witold

2010-08-01

The objective of this paper is to study facility-location problems in the presence of a hybrid uncertain environment involving both randomness and fuzziness. A two-stage fuzzy-random facility-location model with recourse (FR-FLMR) is developed in which both the demands and costs are assumed to be fuzzy-random variables. The bounds of the optimal objective value of the two-stage FR-FLMR are derived. As, in general, the fuzzy-random parameters of the FR-FLMR can be regarded as continuous fuzzy-random variables with an infinite number of realizations, the computation of the recourse requires solving infinite second-stage programming problems. Owing to this requirement, the recourse function cannot be determined analytically, and, hence, the model cannot benefit from the use of techniques of classical mathematical programming. In order to solve the location problems of this nature, we first develop a technique of fuzzy-random simulation to compute the recourse function. The convergence of such simulation scenarios is discussed. In the sequel, we propose a hybrid mutation-based binary ant-colony optimization (MBACO) approach to the two-stage FR-FLMR, which comprises the fuzzy-random simulation and the simplex algorithm. A numerical experiment illustrates the application of the hybrid MBACO algorithm. The comparison shows that the hybrid MBACO finds better solutions than the one using other discrete metaheuristic algorithms, such as binary particle-swarm optimization, genetic algorithm, and tabu search.

Hybrid Parallelization of Adaptive MHD-Kinetic Module in Multi-Scale Fluid-Kinetic Simulation Suite

DOE PAGES

Borovikov, Sergey; Heerikhuisen, Jacob; Pogorelov, Nikolai

2013-04-01

The Multi-Scale Fluid-Kinetic Simulation Suite has a computational tool set for solving partially ionized flows. In this paper we focus on recent developments of the kinetic module which solves the Boltzmann equation using the Monte-Carlo method. The module has been recently redesigned to utilize intra-node hybrid parallelization. We describe in detail the redesign process, implementation issues, and modifications made to the code. Finally, we conduct a performance analysis.

A hybrid optical switch architecture to integrate IP into optical networks to provide flexible and intelligent bandwidth on demand for cloud computing

NASA Astrophysics Data System (ADS)

Yang, Wei; Hall, Trevor J.

2013-12-01

The Internet is entering an era of cloud computing to provide more cost effective, eco-friendly and reliable services to consumer and business users. As a consequence, the nature of the Internet traffic has been fundamentally transformed from a pure packet-based pattern to today's predominantly flow-based pattern. Cloud computing has also brought about an unprecedented growth in the Internet traffic. In this paper, a hybrid optical switch architecture is presented to deal with the flow-based Internet traffic, aiming to offer flexible and intelligent bandwidth on demand to improve fiber capacity utilization. The hybrid optical switch is capable of integrating IP into optical networks for cloud-based traffic with predictable performance, for which the delay performance of the electronic module in the hybrid optical switch architecture is evaluated through simulation.

Effectiveness of Simulation in a Hybrid and Online Networking Course.

ERIC Educational Resources Information Center

Cameron, Brian H.

2003-01-01

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

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

PubMed

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

2017-09-30

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

Flow Simulation of N3-X Hybrid Wing-Body Configuration

NASA Technical Reports Server (NTRS)

Kim, Hyoungjin; Liou, Meng-Sing

2013-01-01

System studies show that a N3-X hybrid wing-body aircraft with a turboelectric distributed propulsion system using a mail-slot inlet/nozzle nacelle can meet the environmental and performance goals for N+3 generation transports (three generations beyond the current air transport technology level) set by NASA s Subsonic Fixed Wing Project. In this study, a Navier-Stokes flow simulation of N3-X on hybrid unstructured meshes was conducted, including the mail-slot propulsor. The geometry of the mail-slot propulsor was generated by a CAD (Computer-Aided Design)-free shape parameterization. A body force approach was used for a more realistic and efficient simulation of the turning and loss effects of the fan blades and the inlet-fan interactions. Flow simulation results of the N3-X demonstrates the validity of the present approach.

Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

PubMed Central

Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

2015-01-01

Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

Design and Implementation of Hybrid CORDIC Algorithm Based on Phase Rotation Estimation for NCO

PubMed Central

Zhang, Chaozhu; Han, Jinan; Li, Ke

2014-01-01

The numerical controlled oscillator has wide application in radar, digital receiver, and software radio system. Firstly, this paper introduces the traditional CORDIC algorithm. Then in order to improve computing speed and save resources, this paper proposes a kind of hybrid CORDIC algorithm based on phase rotation estimation applied in numerical controlled oscillator (NCO). Through estimating the direction of part phase rotation, the algorithm reduces part phase rotation and add-subtract unit, so that it decreases delay. Furthermore, the paper simulates and implements the numerical controlled oscillator by Quartus II software and Modelsim software. Finally, simulation results indicate that the improvement over traditional CORDIC algorithm is achieved in terms of ease of computation, resource utilization, and computing speed/delay while maintaining the precision. It is suitable for high speed and precision digital modulation and demodulation. PMID:25110750

Compact Method for Modeling and Simulation of Memristor Devices

DTIC Science & Technology

2011-08-01

single-valued equations. 15. SUBJECT TERMS Memristor, Neuromorphic , Cognitive, Computing, Memory, Emerging Technology, Computational Intelligence 16...resistance state depends on its previous state and present electrical biasing conditions, and when combined with transistors in a hybrid chip ...computers, reconfigurable electronics and neuromorphic computing [3,4]. According to Chua [4], the memristor behaves like a linear resistor with

Evaluation of an F100 multivariable control using a real-time engine simulation

NASA Technical Reports Server (NTRS)

Szuch, J. R.; Skira, C.; Soeder, J. F.

1977-01-01

A multivariable control design for the F100 turbofan engine was evaluated, as part of the F100 multivariable control synthesis (MVCS) program. The evaluation utilized a real-time, hybrid computer simulation of the engine and a digital computer implementation of the control. Significant results of the evaluation are presented and recommendations concerning future engine testing of the control are made.

A comparison between implicit and hybrid methods for the calculation of steady and unsteady inlet flows

NASA Technical Reports Server (NTRS)

Coakley, T. J.; Hsieh, T.

1985-01-01

Numerical simulation of steady and unsteady transonic diffuser flows using two different computer codes are discussed and compared with experimental data. The codes solve the Reynolds-averaged, compressible, Navier-Stokes equations using various turbulence models. One of the codes has been applied extensively to diffuser flows and uses the hybrid method of MacCormack. This code is relatively inefficient numerically. The second code, which was developed more recently, is fully implicit and is relatively efficient numerically. Simulations of steady flows using the implicit code are shown to be in good agreement with simulations using the hybrid code. Both simulations are in good agreement with experimental results. Simulations of unsteady flows using the two codes are in good qualitative agreement with each other, although the quantitative agreement is not as good as in the steady flow cases. The implicit code is shown to be eight times faster than the hybrid code for unsteady flow calculations and up to 32 times faster for steady flow calculations. Results of calculations using alternative turbulence models are also discussed.

Influence of technological factors on characteristics of hybrid fluid-film bearings

NASA Astrophysics Data System (ADS)

Koltsov, A.; Prosekova, A.; Rodichev, A.; Savin, L.

2017-08-01

The influence of the parameters of micro- and macrounevenness on the characteristics of a hybrid bearing with slotted throttling is considered in the present paper. The quantitative assumptions of calculation of pressure distribution, load capacity, lubricant flow rate and power loss due to friction in a radial hybrid bearing with slotted throttling are taken into account, considering the shape, dimensions and roughness of the support surfaces inaccuracies. Numerical simulation of processes in the lubricating layer is based on the finite-difference solution of the Reynolds equation using an uneven orthogonal computational grid with adaptive condensation. The results of computational and physical experiments are presented.

North Atlantic (NAT) aided inertial navigation system simulation volume I. : technical results

DOT National Transportation Integrated Search

1973-07-01

Current air traffic operations over the North ATlantic (NAT) and the application of hybrid navigation systems to obtain more accurate performance on these NAT routes are reviewed. A digital computer simulation program (NATNAV - North ATlantic NAVigat...

A unified RANS–LES model: Computational development, accuracy and cost

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

Gopalan, Harish, E-mail: hgopalan@uwyo.edu; Heinz, Stefan, E-mail: heinz@uwyo.edu; Stöllinger, Michael K., E-mail: MStoell@uwyo.edu

2013-09-15

Large eddy simulation (LES) is computationally extremely expensive for the investigation of wall-bounded turbulent flows at high Reynolds numbers. A way to reduce the computational cost of LES by orders of magnitude is to combine LES equations with Reynolds-averaged Navier–Stokes (RANS) equations used in the near-wall region. A large variety of such hybrid RANS–LES methods are currently in use such that there is the question of which hybrid RANS-LES method represents the optimal approach. The properties of an optimal hybrid RANS–LES model are formulated here by taking reference to fundamental properties of fluid flow equations. It is shown that unifiedmore » RANS–LES models derived from an underlying stochastic turbulence model have the properties of optimal hybrid RANS–LES models. The rest of the paper is organized in two parts. First, a priori and a posteriori analyses of channel flow data are used to find the optimal computational formulation of the theoretically derived unified RANS–LES model and to show that this computational model, which is referred to as linear unified model (LUM), does also have all the properties of an optimal hybrid RANS–LES model. Second, a posteriori analyses of channel flow data are used to study the accuracy and cost features of the LUM. The following conclusions are obtained. (i) Compared to RANS, which require evidence for their predictions, the LUM has the significant advantage that the quality of predictions is relatively independent of the RANS model applied. (ii) Compared to LES, the significant advantage of the LUM is a cost reduction of high-Reynolds number simulations by a factor of 0.07Re{sup 0.46}. For coarse grids, the LUM has a significant accuracy advantage over corresponding LES. (iii) Compared to other usually applied hybrid RANS–LES models, it is shown that the LUM provides significantly improved predictions.« less

hybrid\\scriptsize{{MANTIS}}: a CPU-GPU Monte Carlo method for modeling indirect x-ray detectors with columnar scintillators

NASA Astrophysics Data System (ADS)

Sharma, Diksha; Badal, Andreu; Badano, Aldo

2012-04-01

The computational modeling of medical imaging systems often requires obtaining a large number of simulated images with low statistical uncertainty which translates into prohibitive computing times. We describe a novel hybrid approach for Monte Carlo simulations that maximizes utilization of CPUs and GPUs in modern workstations. We apply the method to the modeling of indirect x-ray detectors using a new and improved version of the code \\scriptsize{{MANTIS}}, an open source software tool used for the Monte Carlo simulations of indirect x-ray imagers. We first describe a GPU implementation of the physics and geometry models in fast\\scriptsize{{DETECT}}2 (the optical transport model) and a serial CPU version of the same code. We discuss its new features like on-the-fly column geometry and columnar crosstalk in relation to the \\scriptsize{{MANTIS}} code, and point out areas where our model provides more flexibility for the modeling of realistic columnar structures in large area detectors. Second, we modify \\scriptsize{{PENELOPE}} (the open source software package that handles the x-ray and electron transport in \\scriptsize{{MANTIS}}) to allow direct output of location and energy deposited during x-ray and electron interactions occurring within the scintillator. This information is then handled by optical transport routines in fast\\scriptsize{{DETECT}}2. A load balancer dynamically allocates optical transport showers to the GPU and CPU computing cores. Our hybrid\\scriptsize{{MANTIS}} approach achieves a significant speed-up factor of 627 when compared to \\scriptsize{{MANTIS}} and of 35 when compared to the same code running only in a CPU instead of a GPU. Using hybrid\\scriptsize{{MANTIS}}, we successfully hide hours of optical transport time by running it in parallel with the x-ray and electron transport, thus shifting the computational bottleneck from optical to x-ray transport. The new code requires much less memory than \\scriptsize{{MANTIS}} and, as a result, allows us to efficiently simulate large area detectors.

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.

Modeling and Validation of Power-split and P2 Parallel Hybrid Electric Vehicles SAE 2013-01-1470)

EPA Science Inventory

The Advanced Light-Duty Powertrain and Hybrid Analysis tool was created by EPA to evaluate the Greenhouse Gas (GHG) emissions of Light-Duty (LD) vehicles. It is a physics-based, forward-looking, full vehicle computer simulator capable of analyzing various vehicle types combined ...

Acquisition of a High Performance Computer Cluster for Materials Research and Education

DTIC Science & Technology

2015-04-17

separation in all-organic and hybrid organic- inorganic solar cells. The outcome of the project 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13...diffusion and interfacial charge separation in all-organic and hybrid organic- inorganic solar cells. The outcome of the project is the development...simulations to predict charge carrier mobilities, exciton diffusion and interfacial charge separation in all- organic and hybrid organic- inorganic solar

Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water.

PubMed

Lin, Zhixiong; Riniker, Sereina; van Gunsteren, Wilfred F

2013-03-12

Atomistic molecular dynamics simulations of peptides or proteins in aqueous solution are still limited to the multi-nanosecond time scale and multi-nanometer range by computational cost. Combining atomic solutes with a supramolecular solvent model in hybrid fine-grained/coarse-grained (FG/CG) simulations allows atomic detail in the region of interest while being computationally more efficient. We used enveloping distribution sampling (EDS) to calculate the free enthalpy differences between different helical conformations, i.e., α-, π-, and 310-helices, of an atomic level FG alanine deca-peptide solvated in a supramolecular CG water solvent. The free enthalpy differences obtained show that by replacing the FG solvent by the CG solvent, the π-helix is destabilized with respect to the α-helix by about 2.5 kJ mol(-1), and the 310-helix is stabilized with respect to the α-helix by about 9 kJ mol(-1). In addition, the dynamics of the peptide becomes faster. By introducing a FG water layer of 0.8 nm around the peptide, both thermodynamic and dynamic properties are recovered, while the hybrid FG/CG simulations are still four times more efficient than the atomistic simulations, even when the cutoff radius for the nonbonded interactions is increased from 1.4 to 2.0 nm. Hence, the hybrid FG/CG model, which yields an appropriate balance between reduced accuracy and enhanced computational speed, is very suitable for molecular dynamics simulation investigations of biomolecules.

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.

A PSO-Based Hybrid Metaheuristic for Permutation Flowshop Scheduling Problems

PubMed Central

Zhang, Le; Wu, Jinnan

2014-01-01

This paper investigates the permutation flowshop scheduling problem (PFSP) with the objectives of minimizing the makespan and the total flowtime and proposes a hybrid metaheuristic based on the particle swarm optimization (PSO). To enhance the exploration ability of the hybrid metaheuristic, a simulated annealing hybrid with a stochastic variable neighborhood search is incorporated. To improve the search diversification of the hybrid metaheuristic, a solution replacement strategy based on the pathrelinking is presented to replace the particles that have been trapped in local optimum. Computational results on benchmark instances show that the proposed PSO-based hybrid metaheuristic is competitive with other powerful metaheuristics in the literature. PMID:24672389

A PSO-based hybrid metaheuristic for permutation flowshop scheduling problems.

PubMed

Zhang, Le; Wu, Jinnan

2014-01-01

This paper investigates the permutation flowshop scheduling problem (PFSP) with the objectives of minimizing the makespan and the total flowtime and proposes a hybrid metaheuristic based on the particle swarm optimization (PSO). To enhance the exploration ability of the hybrid metaheuristic, a simulated annealing hybrid with a stochastic variable neighborhood search is incorporated. To improve the search diversification of the hybrid metaheuristic, a solution replacement strategy based on the pathrelinking is presented to replace the particles that have been trapped in local optimum. Computational results on benchmark instances show that the proposed PSO-based hybrid metaheuristic is competitive with other powerful metaheuristics in the literature.

Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

2015-03-01

Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

A gas kinetic scheme for hybrid simulation of partially rarefied flows

NASA Astrophysics Data System (ADS)

Colonia, S.; Steijl, R.; Barakos, G.

2017-06-01

Approaches to predict flow fields that display rarefaction effects incur a cost in computational time and memory considerably higher than methods commonly employed for continuum flows. For this reason, to simulate flow fields where continuum and rarefied regimes coexist, hybrid techniques have been introduced. In the present work, analytically defined gas-kinetic schemes based on the Shakhov and Rykov models for monoatomic and diatomic gas flows, respectively, are proposed and evaluated with the aim to be used in the context of hybrid simulations. This should reduce the region where more expensive methods are needed by extending the validity of the continuum formulation. Moreover, since for high-speed rare¦ed gas flows it is necessary to take into account the nonequilibrium among the internal degrees of freedom, the extension of the approach to employ diatomic gas models including rotational relaxation process is a mandatory first step towards realistic simulations. Compared to previous works of Xu and coworkers, the presented scheme is de¦ned directly on the basis of kinetic models which involve a Prandtl number correction. Moreover, the methods are defined fully analytically instead of making use of Taylor expansion for the evaluation of the required derivatives. The scheme has been tested for various test cases and Mach numbers proving to produce reliable predictions in agreement with other approaches for near-continuum flows. Finally, the performance of the scheme, in terms of memory and computational time, compared to discrete velocity methods makes it a compelling alternative in place of more complex methods for hybrid simulations of weakly rarefied flows.

Intercomparison of Multiscale Modeling Approaches in Simulating Subsurface Flow and Transport

NASA Astrophysics Data System (ADS)

Yang, X.; Mehmani, Y.; Barajas-Solano, D. A.; Song, H. S.; Balhoff, M.; Tartakovsky, A. M.; Scheibe, T. D.

2016-12-01

Hybrid multiscale simulations that couple models across scales are critical to advance predictions of the larger system behavior using understanding of fundamental processes. In the current study, three hybrid multiscale methods are intercompared: multiscale loose-coupling method, multiscale finite volume (MsFV) method and multiscale mortar method. The loose-coupling method enables a parallel workflow structure based on the Swift scripting environment that manages the complex process of executing coupled micro- and macro-scale models without being intrusive to the at-scale simulators. The MsFV method applies microscale and macroscale models over overlapping subdomains of the modeling domain and enforces continuity of concentration and transport fluxes between models via restriction and prolongation operators. The mortar method is a non-overlapping domain decomposition approach capable of coupling all permutations of pore- and continuum-scale models with each other. In doing so, Lagrange multipliers are used at interfaces shared between the subdomains so as to establish continuity of species/fluid mass flux. Subdomain computations can be performed either concurrently or non-concurrently depending on the algorithm used. All the above methods have been proven to be accurate and efficient in studying flow and transport in porous media. However, there has not been any field-scale applications and benchmarking among various hybrid multiscale approaches. To address this challenge, we apply all three hybrid multiscale methods to simulate water flow and transport in a conceptualized 2D modeling domain of the hyporheic zone, where strong interactions between groundwater and surface water exist across multiple scales. In all three multiscale methods, fine-scale simulations are applied to a thin layer of riverbed alluvial sediments while the macroscopic simulations are used for the larger subsurface aquifer domain. Different numerical coupling methods are then applied between scales and inter-compared. Comparisons are drawn in terms of velocity distributions, solute transport behavior, algorithm-induced numerical error and computing cost. The intercomparison work provides support for confidence in a variety of hybrid multiscale methods and motivates further development and applications.

Hybrid model for simulation of plasma jet injection in tokamak

NASA Astrophysics Data System (ADS)

Galkin, Sergei A.; Bogatu, I. N.

2016-10-01

Hybrid kinetic model of plasma treats the ions as kinetic particles and the electrons as charge neutralizing massless fluid. The model is essentially applicable when most of the energy is concentrated in the ions rather than in the electrons, i.e. it is well suited for the high-density hyper-velocity C60 plasma jet. The hybrid model separates the slower ion time scale from the faster electron time scale, which becomes disregardable. That is why hybrid codes consistently outperform the traditional PIC codes in computational efficiency, still resolving kinetic ions effects. We discuss 2D hybrid model and code with exact energy conservation numerical algorithm and present some results of its application to simulation of C60 plasma jet penetration through tokamak-like magnetic barrier. We also examine the 3D model/code extension and its possible applications to tokamak and ionospheric plasmas. The work is supported in part by US DOE DE-SC0015776 Grant.

Development of hybrid computer plasma models for different pressure regimes

NASA Astrophysics Data System (ADS)

Hromadka, Jakub; Ibehej, Tomas; Hrach, Rudolf

2016-09-01

With increased performance of contemporary computers during last decades numerical simulations became a very powerful tool applicable also in plasma physics research. Plasma is generally an ensemble of mutually interacting particles that is out of the thermodynamic equilibrium and for this reason fluid computer plasma models give results with only limited accuracy. On the other hand, much more precise particle models are often limited only on 2D problems because of their huge demands on the computer resources. Our contribution is devoted to hybrid modelling techniques that combine advantages of both modelling techniques mentioned above, particularly to their so-called iterative version. The study is focused on mutual relations between fluid and particle models that are demonstrated on the calculations of sheath structures of low temperature argon plasma near a cylindrical Langmuir probe for medium and higher pressures. Results of a simple iterative hybrid plasma computer model are also given. The authors acknowledge the support of the Grant Agency of Charles University in Prague (project 220215).

A hybrid method for flood simulation in small catchments combining hydrodynamic and hydrological techniques

NASA Astrophysics Data System (ADS)

Bellos, Vasilis; Tsakiris, George

2016-09-01

The study presents a new hybrid method for the simulation of flood events in small catchments. It combines a physically-based two-dimensional hydrodynamic model and the hydrological unit hydrograph theory. Unit hydrographs are derived using the FLOW-R2D model which is based on the full form of two-dimensional Shallow Water Equations, solved by a modified McCormack numerical scheme. The method is tested at a small catchment in a suburb of Athens-Greece for a storm event which occurred in February 2013. The catchment is divided into three friction zones and unit hydrographs of 15 and 30 min are produced. The infiltration process is simulated by the empirical Kostiakov equation and the Green-Ampt model. The results from the implementation of the proposed hybrid method are compared with recorded data at the hydrometric station at the outlet of the catchment and the results derived from the fully hydrodynamic model FLOW-R2D. It is concluded that for the case studied, the proposed hybrid method produces results close to those of the fully hydrodynamic simulation at substantially shorter computational time. This finding, if further verified in a variety of case studies, can be useful in devising effective hybrid tools for the two-dimensional flood simulations, which are lead to accurate and considerably faster results than those achieved by the fully hydrodynamic simulations.

COMPARISON OF PARALLEL AND SERIES HYBRID POWERTRAINS FOR TRANSIT BUS APPLICATION

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

Gao, Zhiming; Daw, C Stuart; Smith, David E

2016-01-01

The fuel economy and emissions of both conventional and hybrid buses equipped with emissions aftertreatment were evaluated via computational simulation for six representative city bus drive cycles. Both series and parallel configurations for the hybrid case were studied. The simulation results indicate that series hybrid buses have the greatest overall advantage in fuel economy. The series and parallel hybrid buses were predicted to produce similar CO and HC tailpipe emissions but were also predicted to have reduced NOx tailpipe emissions compared to the conventional bus in higher speed cycles. For the New York bus cycle (NYBC), which has the lowestmore » average speed among the cycles evaluated, the series bus tailpipe emissions were somewhat higher than they were for the conventional bus, while the parallel hybrid bus had significantly lower tailpipe emissions. All three bus powertrains were found to require periodic active DPF regeneration to maintain PM control. Plug-in operation of series hybrid buses appears to offer significant fuel economy benefits and is easily employed due to the relatively large battery capacity that is typical of the series hybrid configuration.« less

N-S/DSMC hybrid simulation of hypersonic flow over blunt body including wakes

NASA Astrophysics Data System (ADS)

Li, Zhonghua; Li, Zhihui; Li, Haiyan; Yang, Yanguang; Jiang, Xinyu

2014-12-01

A hybrid N-S/DSMC method is presented and applied to solve the three-dimensional hypersonic transitional flows by employing the MPC (modular Particle-Continuum) technique based on the N-S and the DSMC method. A sub-relax technique is adopted to deal with information transfer between the N-S and the DSMC. The hypersonic flows over a 70-deg spherically blunted cone under different Kn numbers are simulated using the CFD, DSMC and hybrid N-S/DSMC method. The present computations are found in good agreement with DSMC and experimental results. The present method provides an efficient way to predict the hypersonic aerodynamics in near-continuum transitional flow regime.

Fracture resistance of implant- supported monolithic crowns cemented to zirconia hybrid-abutments: zirconia-based crowns vs. lithium disilicate crowns

PubMed Central

Nawafleh, Noor; Öchsner, Andreas; George, Roy

2018-01-01

PURPOSE The aim of this in vitro study was to investigate the fracture resistance under chewing simulation of implant-supported posterior restorations (crowns cemented to hybrid-abutments) made of different all-ceramic materials. MATERIALS AND METHODS Monolithic zirconia (MZr) and monolithic lithium disilicate (MLD) crowns for mandibular first molar were fabricated using computer-aided design/computer-aided manufacturing technology and then cemented to zirconia hybrid-abutments (Ti-based). Each group was divided into two subgroups (n=10): (A) control group, crowns were subjected to single load to fracture; (B) test group, crowns underwent chewing simulation using multiple loads for 1.2 million cycles at 1.2 Hz with simultaneous thermocycling between 5℃ and 55℃. Data was statistically analyzed with one-way ANOVA and a Post-Hoc test. RESULTS All tested crowns survived chewing simulation resulting in 100% survival rate. However, wear facets were observed on all the crowns at the occlusal contact point. Fracture load of monolithic lithium disilicate crowns was statistically significantly lower than that of monolithic zirconia crowns. Also, fracture load was significantly reduced in both of the all-ceramic materials after exposure to chewing simulation and thermocycling. Crowns of all test groups exhibited cohesive fracture within the monolithic crown structure only, and no abutment fractures or screw loosening were observed. CONCLUSION When supported by implants, monolithic zirconia restorations cemented to hybrid abutments withstand masticatory forces. Also, fatigue loading accompanied by simultaneous thermocycling significantly reduces the strength of both of the all-ceramic materials. Moreover, further research is needed to define potentials, limits, and long-term serviceability of the materials and hybrid abutments. PMID:29503716

Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network.

PubMed

Griffith, Mark; Courtney, Tod; Peccoud, Jean; Sanders, William H

2006-11-15

The stochastic kinetics of a well-mixed chemical system, governed by the chemical Master equation, can be simulated using the exact methods of Gillespie. However, these methods do not scale well as systems become more complex and larger models are built to include reactions with widely varying rates, since the computational burden of simulation increases with the number of reaction events. Continuous models may provide an approximate solution and are computationally less costly, but they fail to capture the stochastic behavior of small populations of macromolecules. In this article we present a hybrid simulation algorithm that dynamically partitions the system into subsets of continuous and discrete reactions, approximates the continuous reactions deterministically as a system of ordinary differential equations (ODE) and uses a Monte Carlo method for generating discrete reaction events according to a time-dependent propensity. Our approach to partitioning is improved such that we dynamically partition the system of reactions, based on a threshold relative to the distribution of propensities in the discrete subset. We have implemented the hybrid algorithm in an extensible framework, utilizing two rigorous ODE solvers to approximate the continuous reactions, and use an example model to illustrate the accuracy and potential speedup of the algorithm when compared with exact stochastic simulation. Software and benchmark models used for this publication can be made available upon request from the authors.

Organ doses for reference adult male and female undergoing computed tomography estimated by Monte Carlo simulations

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

Lee, Choonsik; Kim, Kwang Pyo; Long, Daniel

2011-03-15

Purpose: To develop a computed tomography (CT) organ dose estimation method designed to readily provide organ doses in a reference adult male and female for different scan ranges to investigate the degree to which existing commercial programs can reasonably match organ doses defined in these more anatomically realistic adult hybrid phantomsMethods: The x-ray fan beam in the SOMATOM Sensation 16 multidetector CT scanner was simulated within the Monte Carlo radiation transport code MCNPX2.6. The simulated CT scanner model was validated through comparison with experimentally measured lateral free-in-air dose profiles and computed tomography dose index (CTDI) values. The reference adult malemore » and female hybrid phantoms were coupled with the established CT scanner model following arm removal to simulate clinical head and other body region scans. A set of organ dose matrices were calculated for a series of consecutive axial scans ranging from the top of the head to the bottom of the phantoms with a beam thickness of 10 mm and the tube potentials of 80, 100, and 120 kVp. The organ doses for head, chest, and abdomen/pelvis examinations were calculated based on the organ dose matrices and compared to those obtained from two commercial programs, CT-EXPO and CTDOSIMETRY. Organ dose calculations were repeated for an adult stylized phantom by using the same simulation method used for the adult hybrid phantom. Results: Comparisons of both lateral free-in-air dose profiles and CTDI values through experimental measurement with the Monte Carlo simulations showed good agreement to within 9%. Organ doses for head, chest, and abdomen/pelvis scans reported in the commercial programs exceeded those from the Monte Carlo calculations in both the hybrid and stylized phantoms in this study, sometimes by orders of magnitude. Conclusions: The organ dose estimation method and dose matrices established in this study readily provides organ doses for a reference adult male and female for different CT scan ranges and technical parameters. Organ doses from existing commercial programs do not reasonably match organ doses calculated for the hybrid phantoms due to differences in phantom anatomy, as well as differences in organ dose scaling parameters. The organ dose matrices developed in this study will be extended to cover different technical parameters, CT scanner models, and various age groups.« less

Large-Scale Hybrid Density Functional Theory Calculations in the Condensed-Phase: Ab Initio Molecular Dynamics in the Isobaric-Isothermal Ensemble

NASA Astrophysics Data System (ADS)

Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto

Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

An efficient hybrid method for stochastic reaction-diffusion biochemical systems with delay

NASA Astrophysics Data System (ADS)

Sayyidmousavi, Alireza; Ilie, Silvana

2017-12-01

Many chemical reactions, such as gene transcription and translation in living cells, need a certain time to finish once they are initiated. Simulating stochastic models of reaction-diffusion systems with delay can be computationally expensive. In the present paper, a novel hybrid algorithm is proposed to accelerate the stochastic simulation of delayed reaction-diffusion systems. The delayed reactions may be of consuming or non-consuming delay type. The algorithm is designed for moderately stiff systems in which the events can be partitioned into slow and fast subsets according to their propensities. The proposed algorithm is applied to three benchmark problems and the results are compared with those of the delayed Inhomogeneous Stochastic Simulation Algorithm. The numerical results show that the new hybrid algorithm achieves considerable speed-up in the run time and very good accuracy.

Application of real-time engine simulations to the development of propulsion system controls

NASA Technical Reports Server (NTRS)

Szuch, J. R.

1975-01-01

The development of digital controls for turbojet and turbofan engines is presented by the use of real-time computer simulations of the engines. The engine simulation provides a test-bed for evaluating new control laws and for checking and debugging control software and hardware prior to engine testing. The development and use of real-time, hybrid computer simulations of the Pratt and Whitney TF30-P-3 and F100-PW-100 augmented turbofans are described in support of a number of controls research programs at the Lewis Research Center. The role of engine simulations in solving the propulsion systems integration problem is also discussed.

Automating NEURON Simulation Deployment in Cloud Resources.

PubMed

Stockton, David B; Santamaria, Fidel

2017-01-01

Simulations in neuroscience are performed on local servers or High Performance Computing (HPC) facilities. Recently, cloud computing has emerged as a potential computational platform for neuroscience simulation. In this paper we compare and contrast HPC and cloud resources for scientific computation, then report how we deployed NEURON, a widely used simulator of neuronal activity, in three clouds: Chameleon Cloud, a hybrid private academic cloud for cloud technology research based on the OpenStack software; Rackspace, a public commercial cloud, also based on OpenStack; and Amazon Elastic Cloud Computing, based on Amazon's proprietary software. We describe the manual procedures and how to automate cloud operations. We describe extending our simulation automation software called NeuroManager (Stockton and Santamaria, Frontiers in Neuroinformatics, 2015), so that the user is capable of recruiting private cloud, public cloud, HPC, and local servers simultaneously with a simple common interface. We conclude by performing several studies in which we examine speedup, efficiency, total session time, and cost for sets of simulations of a published NEURON model.

Automating NEURON Simulation Deployment in Cloud Resources

PubMed Central

Santamaria, Fidel

2016-01-01

Simulations in neuroscience are performed on local servers or High Performance Computing (HPC) facilities. Recently, cloud computing has emerged as a potential computational platform for neuroscience simulation. In this paper we compare and contrast HPC and cloud resources for scientific computation, then report how we deployed NEURON, a widely used simulator of neuronal activity, in three clouds: Chameleon Cloud, a hybrid private academic cloud for cloud technology research based on the Open-Stack software; Rackspace, a public commercial cloud, also based on OpenStack; and Amazon Elastic Cloud Computing, based on Amazon’s proprietary software. We describe the manual procedures and how to automate cloud operations. We describe extending our simulation automation software called NeuroManager (Stockton and Santamaria, Frontiers in Neuroinformatics, 2015), so that the user is capable of recruiting private cloud, public cloud, HPC, and local servers simultaneously with a simple common interface. We conclude by performing several studies in which we examine speedup, efficiency, total session time, and cost for sets of simulations of a published NEURON model. PMID:27655341

Hybrid time-frequency domain equalization based on sign-sign joint decision multimodulus algorithm for 6 × 6 mode division multiplexing system

NASA Astrophysics Data System (ADS)

Li, Jiao; Hu, Guijun; Gong, Caili; Li, Li

2018-02-01

In this paper, we propose a hybrid time-frequency domain sign-sign joint decision multimodulus algorithm (Hybrid-SJDMMA) for mode-demultiplexing in a 6 × 6 mode division multiplexing (MDM) system with high-order QAM modulation. The equalization performance of Hybrid-SJDMMA was evaluated and compared with the frequency domain multimodulus algorithm (FD-MMA) and the hybrid time-frequency domain sign-sign multimodulus algorithm (Hybrid-SMMA). Simulation results revealed that Hybrid-SJDMMA exhibits a significantly lower computational complexity than FD-MMA, and its convergence speed is similar to that of FD-MMA. Additionally, the bit-error-rate performance of Hybrid-SJDMMA was obviously better than FD-MMA and Hybrid-SMMA for 16 QAM and 64 QAM.

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.

Hybrid stochastic simplifications for multiscale gene networks.

PubMed

Crudu, Alina; Debussche, Arnaud; Radulescu, Ovidiu

2009-09-07

Stochastic simulation of gene networks by Markov processes has important applications in molecular biology. The complexity of exact simulation algorithms scales with the number of discrete jumps to be performed. Approximate schemes reduce the computational time by reducing the number of simulated discrete events. Also, answering important questions about the relation between network topology and intrinsic noise generation and propagation should be based on general mathematical results. These general results are difficult to obtain for exact models. We propose a unified framework for hybrid simplifications of Markov models of multiscale stochastic gene networks dynamics. We discuss several possible hybrid simplifications, and provide algorithms to obtain them from pure jump processes. In hybrid simplifications, some components are discrete and evolve by jumps, while other components are continuous. Hybrid simplifications are obtained by partial Kramers-Moyal expansion [1-3] which is equivalent to the application of the central limit theorem to a sub-model. By averaging and variable aggregation we drastically reduce simulation time and eliminate non-critical reactions. Hybrid and averaged simplifications can be used for more effective simulation algorithms and for obtaining general design principles relating noise to topology and time scales. The simplified models reproduce with good accuracy the stochastic properties of the gene networks, including waiting times in intermittence phenomena, fluctuation amplitudes and stationary distributions. The methods are illustrated on several gene network examples. Hybrid simplifications can be used for onion-like (multi-layered) approaches to multi-scale biochemical systems, in which various descriptions are used at various scales. Sets of discrete and continuous variables are treated with different methods and are coupled together in a physically justified approach.

Electric and hybrid electric vehicle study utilizing a time-stepping simulation

NASA Technical Reports Server (NTRS)

Schreiber, Jeffrey G.; Shaltens, Richard K.; Beremand, Donald G.

1992-01-01

The applicability of NASA's advanced power technologies to electric and hybrid vehicles was assessed using a time-stepping computer simulation to model electric and hybrid vehicles operating over the Federal Urban Driving Schedule (FUDS). Both the energy and power demands of the FUDS were taken into account and vehicle economy, range, and performance were addressed simultaneously. Results indicate that a hybrid electric vehicle (HEV) configured with a flywheel buffer energy storage device and a free-piston Stirling convertor fulfills the emissions, fuel economy, range, and performance requirements that would make it acceptable to the consumer. It is noted that an assessment to determine which of the candidate technologies are suited for the HEV application has yet to be made. A proper assessment should take into account the fuel economy and range, along with the driveability and total emissions produced.

Development of a Solid-Oxide Fuel Cell/Gas Turbine Hybrid System Model for Aerospace Applications

NASA Technical Reports Server (NTRS)

Freeh, Joshua E.; Pratt, Joseph W.; Brouwer, Jacob

2004-01-01

Recent interest in fuel cell-gas turbine hybrid applications for the aerospace industry has led to the need for accurate computer simulation models to aid in system design and performance evaluation. To meet this requirement, solid oxide fuel cell (SOFC) and fuel processor models have been developed and incorporated into the Numerical Propulsion Systems Simulation (NPSS) software package. The SOFC and reformer models solve systems of equations governing steady-state performance using common theoretical and semi-empirical terms. An example hybrid configuration is presented that demonstrates the new capability as well as the interaction with pre-existing gas turbine and heat exchanger models. Finally, a comparison of calculated SOFC performance with experimental data is presented to demonstrate model validity. Keywords: Solid Oxide Fuel Cell, Reformer, System Model, Aerospace, Hybrid System, NPSS

Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics.

PubMed

Sevink, G J A; Schmid, F; Kawakatsu, T; Milano, G

2017-02-22

We have extended an existing hybrid MD-SCF simulation technique that employs a coarsening step to enhance the computational efficiency of evaluating non-bonded particle interactions. This technique is conceptually equivalent to the single chain in mean-field (SCMF) method in polymer physics, in the sense that non-bonded interactions are derived from the non-ideal chemical potential in self-consistent field (SCF) theory, after a particle-to-field projection. In contrast to SCMF, however, MD-SCF evolves particle coordinates by the usual Newton's equation of motion. Since collisions are seriously affected by the softening of non-bonded interactions that originates from their evaluation at the coarser continuum level, we have devised a way to reinsert the effect of collisions on the structural evolution. Merging MD-SCF with multi-particle collision dynamics (MPCD), we mimic particle collisions at the level of computational cells and at the same time properly account for the momentum transfer that is important for a realistic system evolution. The resulting hybrid MD-SCF/MPCD method was validated for a particular coarse-grained model of phospholipids in aqueous solution, against reference full-particle simulations and the original MD-SCF model. We additionally implemented and tested an alternative and more isotropic finite difference gradient. Our results show that efficiency is improved by merging MD-SCF with MPCD, as properly accounting for hydrodynamic interactions considerably speeds up the phase separation dynamics, with negligible additional computational costs compared to efficient MD-SCF. This new method enables realistic simulations of large-scale systems that are needed to investigate the applications of self-assembled structures of lipids in nanotechnologies.

A hybrid framework for coupling arbitrary summation-by-parts schemes on general meshes

NASA Astrophysics Data System (ADS)

Lundquist, Tomas; Malan, Arnaud; Nordström, Jan

2018-06-01

We develop a general interface procedure to couple both structured and unstructured parts of a hybrid mesh in a non-collocated, multi-block fashion. The target is to gain optimal computational efficiency in fluid dynamics simulations involving complex geometries. While guaranteeing stability, the proposed procedure is optimized for accuracy and requires minimal algorithmic modifications to already existing schemes. Initial numerical investigations confirm considerable efficiency gains compared to non-hybrid calculations of up to an order of magnitude.

Near-term hybrid vehicle program, phase 1

NASA Technical Reports Server (NTRS)

1979-01-01

The preliminary design of a hybrid vehicle which fully meets or exceeds the requirements set forth in the Near Term Hybrid Vehicle Program is documented. Topics addressed include the general layout and styling, the power train specifications with discussion of each major component, vehicle weight and weight breakdown, vehicle performance, measures of energy consumption, and initial cost and ownership cost. Alternative design options considered and their relationship to the design adopted, computer simulation used, and maintenance and reliability considerations are also discussed.

Emulation of complex open quantum systems using superconducting qubits

NASA Astrophysics Data System (ADS)

Mostame, Sarah; Huh, Joonsuk; Kreisbeck, Christoph; Kerman, Andrew J.; Fujita, Takatoshi; Eisfeld, Alexander; Aspuru-Guzik, Alán

2017-02-01

With quantum computers being out of reach for now, quantum simulators are alternative devices for efficient and accurate simulation of problems that are challenging to tackle using conventional computers. Quantum simulators are classified into analog and digital, with the possibility of constructing "hybrid" simulators by combining both techniques. Here we focus on analog quantum simulators of open quantum systems and address the limit that they can beat classical computers. In particular, as an example, we discuss simulation of the chlorosome light-harvesting antenna from green sulfur bacteria with over 250 phonon modes coupled to each electronic state. Furthermore, we propose physical setups that can be used to reproduce the quantum dynamics of a standard and multiple-mode Holstein model. The proposed scheme is based on currently available technology of superconducting circuits consist of flux qubits and quantum oscillators.

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

Extension of a hybrid particle-continuum method for a mixture of chemical species

NASA Astrophysics Data System (ADS)

Verhoff, Ashley M.; Boyd, Iain D.

2012-11-01

Due to the physical accuracy and numerical efficiency achieved by analyzing transitional, hypersonic flow fields with hybrid particle-continuum methods, this paper describes a Modular Particle-Continuum (MPC) method and its extension to include multiple chemical species. Considerations that are specific to a hybrid approach for simulating gas mixtures are addressed, including a discussion of the Chapman-Enskog velocity distribution function (VDF) for near-equilibrium flows, and consistent viscosity models for the individual CFD and DSMC modules of the MPC method. Representative results for a hypersonic blunt-body flow are then presented, where the flow field properties, surface properties, and computational performance are compared for simulations employing full CFD, full DSMC, and the MPC method.

Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations.

PubMed

Fiévet, Julie B; Nidelet, Thibault; Dillmann, Christine; de Vienne, Dominique

2018-01-01

Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding as well as evolutionary biology. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels. We chose the enzyme-flux relationship as a model of the concave genotype-phenotype (GP) relationship, and showed that heterosis can be easily created in the laboratory. First, we reconstituted in vitro the upper part of glycolysis. We simulated genetic variability of enzyme activity by varying enzyme concentrations in test tubes. Mixing the content of "parental" tubes resulted in "hybrids," whose fluxes were compared to the parental fluxes. Frequent heterotic fluxes were observed, under conditions that were determined analytically and confirmed by computer simulation. Second, to test this model in a more realistic situation, we modeled the glycolysis/fermentation network in yeast by considering one input flux, glucose, and two output fluxes, glycerol and acetaldehyde. We simulated genetic variability by randomly drawing parental enzyme concentrations under various conditions, and computed the parental and hybrid fluxes using a system of differential equations. Again we found that a majority of hybrids exhibited positive heterosis for metabolic fluxes. Cases of negative heterosis were due to local convexity between certain enzyme concentrations and fluxes. In both approaches, heterosis was maximized when the parents were phenotypically close and when the distributions of parental enzyme concentrations were contrasted and constrained. These conclusions are not restricted to metabolic systems: they only depend on the concavity of the GP relationship, which is commonly observed at various levels of the phenotypic hierarchy, and could account for the pervasiveness of heterosis.

Predictive simulation of bidirectional Glenn shunt using a hybrid blood vessel model.

PubMed

Li, Hao; Leow, Wee Kheng; Chiu, Ing-Sh

2009-01-01

This paper proposes a method for performing predictive simulation of cardiac surgery. It applies a hybrid approach to model the deformation of blood vessels. The hybrid blood vessel model consists of a reference Cosserat rod and a surface mesh. The reference Cosserat rod models the blood vessel's global bending, stretching, twisting and shearing in a physically correct manner, and the surface mesh models the surface details of the blood vessel. In this way, the deformation of blood vessels can be computed efficiently and accurately. Our predictive simulation system can produce complex surgical results given a small amount of user inputs. It allows the surgeon to easily explore various surgical options and evaluate them. Tests of the system using bidirectional Glenn shunt (BDG) as an application example show that the results produc by the system are similar to real surgical results.

Energy efficient hybrid computing systems using spin devices

NASA Astrophysics Data System (ADS)

Sharad, Mrigank

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

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

Bakosi, Jozsef; Christon, Mark A.; Francois, Marianne M.

Progress is reported on computational capabilities for the grid-to-rod-fretting (GTRF) problem of pressurized water reactors. Numeca's Hexpress/Hybrid mesh generator is demonstrated as an excellent alternative to generating computational meshes for complex flow geometries, such as in GTRF. Mesh assessment is carried out using standard industrial computational fluid dynamics practices. Hydra-TH, a simulation code developed at LANL for reactor thermal-hydraulics, is demonstrated on hybrid meshes, containing different element types. A series of new Hydra-TH calculations has been carried out collecting turbulence statistics. Preliminary results on the newly generated meshes are discussed; full analysis will be documented in the L3 milestone, THM.CFD.P5.05,more » Sept. 2012.« less

Comparison of Parallel and Series Hybrid Power Trains for Transit Bus Applications

DOE PAGES

Gao, Zhiming; Daw, C. Stuart; Smith, David E.; ...

2016-08-01

The fuel economy and emissions of conventional and hybrid buses equipped with emissions after treatment were evaluated via computational simulation for six representative city bus drive cycles. Both series and parallel configurations for the hybrid case were studied. The simulation results indicated that series hybrid buses have the greatest overall advantage in fuel economy. The series and parallel hybrid buses were predicted to produce similar carbon monoxide and hydrocarbon tailpipe emissions but were also predicted to have reduced tailpipe emissions of nitrogen oxides compared with the conventional bus in higher speed cycles. For the New York bus cycle, which hasmore » the lowest average speed among the cycles evaluated, the series bus tailpipe emissions were somewhat higher than they were for the conventional bus; the parallel hybrid bus had significantly lower tailpipe emissions. All three bus power trains were found to require periodic active diesel particulate filter regeneration to maintain control of particulate matter. Finally, plug-in operation of series hybrid buses appears to offer significant fuel economy benefits and is easily employed because of the relatively large battery capacity that is typical of the series hybrid configuration.« less

Comparison of Parallel and Series Hybrid Power Trains for Transit Bus Applications

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

Gao, Zhiming; Daw, C. Stuart; Smith, David E.

The fuel economy and emissions of conventional and hybrid buses equipped with emissions after treatment were evaluated via computational simulation for six representative city bus drive cycles. Both series and parallel configurations for the hybrid case were studied. The simulation results indicated that series hybrid buses have the greatest overall advantage in fuel economy. The series and parallel hybrid buses were predicted to produce similar carbon monoxide and hydrocarbon tailpipe emissions but were also predicted to have reduced tailpipe emissions of nitrogen oxides compared with the conventional bus in higher speed cycles. For the New York bus cycle, which hasmore » the lowest average speed among the cycles evaluated, the series bus tailpipe emissions were somewhat higher than they were for the conventional bus; the parallel hybrid bus had significantly lower tailpipe emissions. All three bus power trains were found to require periodic active diesel particulate filter regeneration to maintain control of particulate matter. Finally, plug-in operation of series hybrid buses appears to offer significant fuel economy benefits and is easily employed because of the relatively large battery capacity that is typical of the series hybrid configuration.« less

Improved signal processing approaches in an offline simulation of a hybrid brain–computer interface

PubMed Central

Brunner, Clemens; Allison, Brendan Z.; Krusienski, Dean J.; Kaiser, Vera; Müller-Putz, Gernot R.; Pfurtscheller, Gert; Neuper, Christa

2012-01-01

In a conventional brain–computer interface (BCI) system, users perform mental tasks that yield specific patterns of brain activity. A pattern recognition system determines which brain activity pattern a user is producing and thereby infers the user’s mental task, allowing users to send messages or commands through brain activity alone. Unfortunately, despite extensive research to improve classification accuracy, BCIs almost always exhibit errors, which are sometimes so severe that effective communication is impossible. We recently introduced a new idea to improve accuracy, especially for users with poor performance. In an offline simulation of a “hybrid” BCI, subjects performed two mental tasks independently and then simultaneously. This hybrid BCI could use two different types of brain signals common in BCIs – event-related desynchronization (ERD) and steady-state evoked potentials (SSEPs). This study suggested that such a hybrid BCI is feasible. Here, we re-analyzed the data from our initial study. We explored eight different signal processing methods that aimed to improve classification and further assess both the causes and the extent of the benefits of the hybrid condition. Most analyses showed that the improved methods described here yielded a statistically significant improvement over our initial study. Some of these improvements could be relevant to conventional BCIs as well. Moreover, the number of illiterates could be reduced with the hybrid condition. Results are also discussed in terms of dual task interference and relevance to protocol design in hybrid BCIs. PMID:20153371

Computer Aided Design of Ka-Band Waveguide Power Combining Architectures for Interplanetary Spacecraft

NASA Technical Reports Server (NTRS)

Vaden, Karl R.

2006-01-01

Communication systems for future NASA interplanetary spacecraft require transmitter power ranging from several hundred watts to kilowatts. Several hybrid junctions are considered as elements within a corporate combining architecture for high power Ka-band space traveling-wave tube amplifiers (TWTAs). This report presents the simulated transmission characteristics of several hybrid junctions designed for a low loss, high power waveguide based power combiner.

Hybrid Reynolds-Averaged/Large-Eddy Simulations of a Co-Axial Supersonic Free-Jet Experiment

NASA Technical Reports Server (NTRS)

Baurle, R. A.; Edwards, J. R.

2009-01-01

Reynolds-averaged and hybrid Reynolds-averaged/large-eddy simulations have been applied to a supersonic coaxial jet flow experiment. The experiment utilized either helium or argon as the inner jet nozzle fluid, and the outer jet nozzle fluid consisted of laboratory air. The inner and outer nozzles were designed and operated to produce nearly pressure-matched Mach 1.8 flow conditions at the jet exit. The purpose of the computational effort was to assess the state-of-the-art for each modeling approach, and to use the hybrid Reynolds-averaged/large-eddy simulations to gather insight into the deficiencies of the Reynolds-averaged closure models. The Reynolds-averaged simulations displayed a strong sensitivity to choice of turbulent Schmidt number. The baseline value chosen for this parameter resulted in an over-prediction of the mixing layer spreading rate for the helium case, but the opposite trend was noted when argon was used as the injectant. A larger turbulent Schmidt number greatly improved the comparison of the results with measurements for the helium simulations, but variations in the Schmidt number did not improve the argon comparisons. The hybrid simulation results showed the same trends as the baseline Reynolds-averaged predictions. The primary reason conjectured for the discrepancy between the hybrid simulation results and the measurements centered around issues related to the transition from a Reynolds-averaged state to one with resolved turbulent content. Improvements to the inflow conditions are suggested as a remedy to this dilemma. Comparisons between resolved second-order turbulence statistics and their modeled Reynolds-averaged counterparts were also performed.

Hybrid LES/RANS simulation of a turbulent boundary layer over a rectangular cavity

NASA Astrophysics Data System (ADS)

Zhang, Qi; Haering, Sigfried; Oliver, Todd; Moser, Robert

2016-11-01

We report numerical investigations of a turbulent boundary layer over a rectangular cavity using a new hybrid RANS/LES model and the traditional Detached Eddy Simulation (DES). Our new hybrid method aims to address many of the shortcomings from the traditional DES. In the new method, RANS/LES blending controlled by a parameter that measures the ratio of the modeled subgrid kinetic energy to an estimate of the subgrid energy based on the resolved scales. The result is a hybrid method automatically resolves as much turbulence as can be supported by the grid and transitions appropriately from RANS to LES without the need for ad hoc delaying functions that are often required for DES. Further, the new model is designed to improve upon DES by accounting for the effects of grid anisotropy and inhomogeneity in the LES region. We present comparisons of the flow features inside the cavity and the pressure time history and spectra as computed using the new hybrid model and DES.

Development and Testing of an Automatic Transmission Shift Schedule Algorithm for Vehicle Simulation (SAE Paper 2015-01-1142)

EPA Science Inventory

The Advanced Light-Duty Powertrain and Hybrid Analysis (ALPHA) modeling tool was created by EPA to estimate greenhouse gas (GHG) emissions of light-duty vehicles. ALPHA is a physics-based, forward-looking, full vehicle computer simulation capable of analyzing various vehicle type...

Analysis of spatial thermal field in a magnetic bearing

NASA Astrophysics Data System (ADS)

Wajnert, Dawid; Tomczuk, Bronisław

2018-03-01

This paper presents two mathematical models for temperature field analysis in a new hybrid magnetic bearing. Temperature distributions have been calculated using a three dimensional simulation and a two dimensional one. A physical model for temperature testing in the magnetic bearing has been developed. Some results obtained from computer simulations were compared with measurements.

Hybrid stochastic simulations of intracellular reaction-diffusion systems.

PubMed

Kalantzis, Georgios

2009-06-01

With the observation that stochasticity is important in biological systems, chemical kinetics have begun to receive wider interest. While the use of Monte Carlo discrete event simulations most accurately capture the variability of molecular species, they become computationally costly for complex reaction-diffusion systems with large populations of molecules. On the other hand, continuous time models are computationally efficient but they fail to capture any variability in the molecular species. In this study a hybrid stochastic approach is introduced for simulating reaction-diffusion systems. We developed an adaptive partitioning strategy in which processes with high frequency are simulated with deterministic rate-based equations, and those with low frequency using the exact stochastic algorithm of Gillespie. Therefore the stochastic behavior of cellular pathways is preserved while being able to apply it to large populations of molecules. We describe our method and demonstrate its accuracy and efficiency compared with the Gillespie algorithm for two different systems. First, a model of intracellular viral kinetics with two steady states and second, a compartmental model of the postsynaptic spine head for studying the dynamics of Ca+2 and NMDA receptors.

Hybrid stochastic simplifications for multiscale gene networks

PubMed Central

Crudu, Alina; Debussche, Arnaud; Radulescu, Ovidiu

2009-01-01

Background Stochastic simulation of gene networks by Markov processes has important applications in molecular biology. The complexity of exact simulation algorithms scales with the number of discrete jumps to be performed. Approximate schemes reduce the computational time by reducing the number of simulated discrete events. Also, answering important questions about the relation between network topology and intrinsic noise generation and propagation should be based on general mathematical results. These general results are difficult to obtain for exact models. Results We propose a unified framework for hybrid simplifications of Markov models of multiscale stochastic gene networks dynamics. We discuss several possible hybrid simplifications, and provide algorithms to obtain them from pure jump processes. In hybrid simplifications, some components are discrete and evolve by jumps, while other components are continuous. Hybrid simplifications are obtained by partial Kramers-Moyal expansion [1-3] which is equivalent to the application of the central limit theorem to a sub-model. By averaging and variable aggregation we drastically reduce simulation time and eliminate non-critical reactions. Hybrid and averaged simplifications can be used for more effective simulation algorithms and for obtaining general design principles relating noise to topology and time scales. The simplified models reproduce with good accuracy the stochastic properties of the gene networks, including waiting times in intermittence phenomena, fluctuation amplitudes and stationary distributions. The methods are illustrated on several gene network examples. Conclusion Hybrid simplifications can be used for onion-like (multi-layered) approaches to multi-scale biochemical systems, in which various descriptions are used at various scales. Sets of discrete and continuous variables are treated with different methods and are coupled together in a physically justified approach. PMID:19735554

Simulations of noble gases adsorbed on graphene

NASA Astrophysics Data System (ADS)

Maiga, Sidi; Gatica, Silvina

2014-03-01

We present results of Grand Canonical Monte Carlo simulations of adsorption of Kr, Ar and Xe on a suspended graphene sheet. We compute the adsorbate-adsorbate interaction by a Lennard-Jones potential. We adopt a hybrid model for the graphene-adsorbate force; in the hybrid model, the potential interaction with the nearest carbon atoms (within a distance rnn) is computed with an atomistic pair potential Ua; for the atoms at r>rnn, we compute the interaction energy as a continuous integration over a carbon uniform sheet with the density of graphene. For the atomistic potential Ua, we assume the anisotropic LJ potential adapted from the graphite-He interaction proposed by Cole et.al. This interaction includes the anisotropy of the C atoms on graphene, which originates in the anisotropic π-bonds. The adsorption isotherms, energy and structure of the layer are obtained and compared with experimental results. We also compare with the adsorption on graphite and carbon nanotubes. This research was supported by NSF/PRDM (Howard University) and NSF (DMR 1006010).

Multi-GPU hybrid programming accelerated three-dimensional phase-field model in binary alloy

NASA Astrophysics Data System (ADS)

Zhu, Changsheng; Liu, Jieqiong; Zhu, Mingfang; Feng, Li

2018-03-01

In the process of dendritic growth simulation, the computational efficiency and the problem scales have extremely important influence on simulation efficiency of three-dimensional phase-field model. Thus, seeking for high performance calculation method to improve the computational efficiency and to expand the problem scales has a great significance to the research of microstructure of the material. A high performance calculation method based on MPI+CUDA hybrid programming model is introduced. Multi-GPU is used to implement quantitative numerical simulations of three-dimensional phase-field model in binary alloy under the condition of multi-physical processes coupling. The acceleration effect of different GPU nodes on different calculation scales is explored. On the foundation of multi-GPU calculation model that has been introduced, two optimization schemes, Non-blocking communication optimization and overlap of MPI and GPU computing optimization, are proposed. The results of two optimization schemes and basic multi-GPU model are compared. The calculation results show that the use of multi-GPU calculation model can improve the computational efficiency of three-dimensional phase-field obviously, which is 13 times to single GPU, and the problem scales have been expanded to 8193. The feasibility of two optimization schemes is shown, and the overlap of MPI and GPU computing optimization has better performance, which is 1.7 times to basic multi-GPU model, when 21 GPUs are used.

Vehicle routing problem with time windows using natural inspired algorithms

NASA Astrophysics Data System (ADS)

Pratiwi, A. B.; Pratama, A.; Sa’diyah, I.; Suprajitno, H.

2018-03-01

Process of distribution of goods needs a strategy to make the total cost spent for operational activities minimized. But there are several constrains have to be satisfied which are the capacity of the vehicles and the service time of the customers. This Vehicle Routing Problem with Time Windows (VRPTW) gives complex constrains problem. This paper proposes natural inspired algorithms for dealing with constrains of VRPTW which involves Bat Algorithm and Cat Swarm Optimization. Bat Algorithm is being hybrid with Simulated Annealing, the worst solution of Bat Algorithm is replaced by the solution from Simulated Annealing. Algorithm which is based on behavior of cats, Cat Swarm Optimization, is improved using Crow Search Algorithm to make simplier and faster convergence. From the computational result, these algorithms give good performances in finding the minimized total distance. Higher number of population causes better computational performance. The improved Cat Swarm Optimization with Crow Search gives better performance than the hybridization of Bat Algorithm and Simulated Annealing in dealing with big data.

A hybrid genetic-simulated annealing algorithm for the location-inventory-routing problem considering returns under e-supply chain environment.

PubMed

Li, Yanhui; Guo, Hao; Wang, Lin; Fu, Jing

2013-01-01

Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA) is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment.

Hybrid Grid Techniques for Propulsion Applications

NASA Technical Reports Server (NTRS)

Koomullil, Roy P.; Soni, Bharat K.; Thornburg, Hugh J.

1996-01-01

During the past decade, computational simulation of fluid flow for propulsion activities has progressed significantly, and many notable successes have been reported in the literature. However, the generation of a high quality mesh for such problems has often been reported as a pacing item. Hence, much effort has been expended to speed this portion of the simulation process. Several approaches have evolved for grid generation. Two of the most common are structured multi-block, and unstructured based procedures. Structured grids tend to be computationally efficient, and have high aspect ratio cells necessary for efficently resolving viscous layers. Structured multi-block grids may or may not exhibit grid line continuity across the block interface. This relaxation of the continuity constraint at the interface is intended to ease the grid generation process, which is still time consuming. Flow solvers supporting non-contiguous interfaces require specialized interpolation procedures which may not ensure conservation at the interface. Unstructured or generalized indexing data structures offer greater flexibility, but require explicit connectivity information and are not easy to generate for three dimensional configurations. In addition, unstructured mesh based schemes tend to be less efficient and it is difficult to resolve viscous layers. Recently hybrid or generalized element solution and grid generation techniques have been developed with the objective of combining the attractive features of both structured and unstructured techniques. In the present work, recently developed procedures for hybrid grid generation and flow simulation are critically evaluated, and compared to existing structured and unstructured procedures in terms of accuracy and computational requirements.

Hybrid deterministic/stochastic simulation of complex biochemical systems.

PubMed

Lecca, Paola; Bagagiolo, Fabio; Scarpa, Marina

2017-11-21

In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects. Moreover, it should be implemented by efficient algorithms requiring the shortest possible execution time, to avoid enlarging excessively the time elapsing between data analysis and any subsequent experiment. Besides the features of their topological structure, the complexity of biological networks also refers to their dynamics, that is often non-linear and stiff. The stiffness is due to the presence of molecular species whose abundance fluctuates by many orders of magnitude. A fully stochastic simulation of a stiff system is computationally time-expensive. On the other hand, continuous models are less costly, but they fail to capture the stochastic behaviour of small populations of molecular species. We introduce a new efficient hybrid stochastic-deterministic computational model and the software tool MoBioS (MOlecular Biology Simulator) implementing it. The mathematical model of MoBioS uses continuous differential equations to describe the deterministic reactions and a Gillespie-like algorithm to describe the stochastic ones. Unlike the majority of current hybrid methods, the MoBioS algorithm divides the reactions' set into fast reactions, moderate reactions, and slow reactions and implements a hysteresis switching between the stochastic model and the deterministic model. Fast reactions are approximated as continuous-deterministic processes and modelled by deterministic rate equations. Moderate reactions are those whose reaction waiting time is greater than the fast reaction waiting time but smaller than the slow reaction waiting time. A moderate reaction is approximated as a stochastic (deterministic) process if it was classified as a stochastic (deterministic) process at the time at which it crosses the threshold of low (high) waiting time. A Gillespie First Reaction Method is implemented to select and execute the slow reactions. The performances of MoBios were tested on a typical example of hybrid dynamics: that is the DNA transcription regulation. The simulated dynamic profile of the reagents' abundance and the estimate of the error introduced by the fully deterministic approach were used to evaluate the consistency of the computational model and that of the software tool.

A computer simulation of Skylab dynamics and attitude control for performance verification and operational support

NASA Technical Reports Server (NTRS)

Buchanan, H.; Nixon, D.; Joyce, R.

1974-01-01

A simulation of the Skylab attitude and pointing control system (APCS) is outlined and discussed. Implementation is via a large hybrid computer and includes those factors affecting system momentum management, propellant consumption, and overall vehicle performance. The important features of the flight system are discussed; the mathematical models necessary for this treatment are outlined; and the decisions involved in implementation are discussed. A brief summary of the goals and capabilities of this tool is also included.

Quiet Clean Short-haul Experimental Engine (QCSEE) under-the-wing engine simulation report

NASA Technical Reports Server (NTRS)

1977-01-01

Hybrid computer simulations of the under-the-wing engine were constructed to develop the dynamic design of the controls. The engine and control system includes a variable pitch fan and a digital electronic control. Simulation results for throttle bursts from 62 to 100 percent net thrust predict that the engine will accelerate 62 to 95 percent net thrust in one second.

Development of Simulation Methods in the Gibbs Ensemble to Predict Polymer-Solvent Phase Equilibria

NASA Astrophysics Data System (ADS)

Gartner, Thomas; Epps, Thomas; Jayaraman, Arthi

Solvent vapor annealing (SVA) of polymer thin films is a promising method for post-deposition polymer film morphology control. The large number of important parameters relevant to SVA (polymer, solvent, and substrate chemistries, incoming film condition, annealing and solvent evaporation conditions) makes systematic experimental study of SVA a time-consuming endeavor, motivating the application of simulation and theory to the SVA system to provide both mechanistic insight and scans of this wide parameter space. However, to rigorously treat the phase equilibrium between polymer film and solvent vapor while still probing the dynamics of SVA, new simulation methods must be developed. In this presentation, we compare two methods to study polymer-solvent phase equilibrium-Gibbs Ensemble Molecular Dynamics (GEMD) and Hybrid Monte Carlo/Molecular Dynamics (Hybrid MC/MD). Liquid-vapor equilibrium results are presented for the Lennard Jones fluid and for coarse-grained polymer-solvent systems relevant to SVA. We found that the Hybrid MC/MD method is more stable and consistent than GEMD, but GEMD has significant advantages in computational efficiency. We propose that Hybrid MC/MD simulations be used for unfamiliar systems in certain choice conditions, followed by much faster GEMD simulations to map out the remainder of the phase window.

A Generalized Hybrid Multiscale Modeling Approach for Flow and Reactive Transport in Porous Media

NASA Astrophysics Data System (ADS)

Yang, X.; Meng, X.; Tang, Y. H.; Guo, Z.; Karniadakis, G. E.

2017-12-01

Using emerging understanding of biological and environmental processes at fundamental scales to advance predictions of the larger system behavior requires the development of multiscale approaches, and there is strong interest in coupling models at different scales together in a hybrid multiscale simulation framework. A limited number of hybrid multiscale simulation methods have been developed for subsurface applications, mostly using application-specific approaches for model coupling. The proposed generalized hybrid multiscale approach is designed with minimal intrusiveness to the at-scale simulators (pre-selected) and provides a set of lightweight C++ scripts to manage a complex multiscale workflow utilizing a concurrent coupling approach. The workflow includes at-scale simulators (using the lattice-Boltzmann method, LBM, at the pore and Darcy scale, respectively), scripts for boundary treatment (coupling and kriging), and a multiscale universal interface (MUI) for data exchange. The current study aims to apply the generalized hybrid multiscale modeling approach to couple pore- and Darcy-scale models for flow and mixing-controlled reaction with precipitation/dissolution in heterogeneous porous media. The model domain is packed heterogeneously that the mixing front geometry is more complex and not known a priori. To address those challenges, the generalized hybrid multiscale modeling approach is further developed to 1) adaptively define the locations of pore-scale subdomains, 2) provide a suite of physical boundary coupling schemes and 3) consider the dynamic change of the pore structures due to mineral precipitation/dissolution. The results are validated and evaluated by comparing with single-scale simulations in terms of velocities, reactive concentrations and computing cost.

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

PubMed Central

Yu, Yun; Degnan, James H.; Nakhleh, Luay

2012-01-01

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. PMID:22536161

State estimation of stochastic non-linear hybrid dynamic system using an interacting multiple model algorithm.

PubMed

Elenchezhiyan, M; Prakash, J

2015-09-01

In this work, state estimation schemes for non-linear hybrid dynamic systems subjected to stochastic state disturbances and random errors in measurements using interacting multiple-model (IMM) algorithms are formulated. In order to compute both discrete modes and continuous state estimates of a hybrid dynamic system either an IMM extended Kalman filter (IMM-EKF) or an IMM based derivative-free Kalman filters is proposed in this study. The efficacy of the proposed IMM based state estimation schemes is demonstrated by conducting Monte-Carlo simulation studies on the two-tank hybrid system and switched non-isothermal continuous stirred tank reactor system. Extensive simulation studies reveal that the proposed IMM based state estimation schemes are able to generate fairly accurate continuous state estimates and discrete modes. In the presence and absence of sensor bias, the simulation studies reveal that the proposed IMM unscented Kalman filter (IMM-UKF) based simultaneous state and parameter estimation scheme outperforms multiple-model UKF (MM-UKF) based simultaneous state and parameter estimation scheme. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling

DOE PAGES

Kilina, Svetlana; Yarotski, Dzmitry A.; Talin, A. Alec; ...

2011-01-01

We present a combined approach that relies on computational simulations and scanning tunneling microscopy (STM) measurements to reveal morphological properties and stability criteria of carbon nanotube-DNA (CNT-DNA) constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4 ° and a coiling period of 3.3 nm. Using force field simulations, we determine how the DNA-CNT binding energy depends on the sequence and binding geometry of a single strand DNA. This dependence allows us to quantitatively characterize the stability of a hybrid structure with an optimal π-stacking between DNA nucleotides and themore » tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5) CNT as evidenced by the presence of a well-defined minimum in the binding energy as a function of an angle between DNA strand and the nanotube chiral vector. This novel approach demonstrates the feasibility of CNT-DNA geometry studies with subnanometer resolution and paves the way towards complete characterization of the structural and electronic properties of drug-delivering systems based on DNA-CNT hybrids as a function of DNA sequence and a nanotube chirality.« less

Quantum Computation Based on Photons with Three Degrees of Freedom

PubMed Central

Luo, Ming-Xing; Li, Hui-Ran; Lai, Hong; Wang, Xiaojun

2016-01-01

Quantum systems are important resources for quantum computer. Different from previous encoding forms using quantum systems with one degree of freedom (DoF) or two DoFs, we investigate the possibility of photon systems encoding with three DoFs consisting of the polarization DoF and two spatial DoFs. By exploring the optical circular birefringence induced by an NV center in a diamond embedded in the photonic crystal cavity, we propose several hybrid controlled-NOT (hybrid CNOT) gates operating on the two-photon or one-photon system. These hybrid CNOT gates show that three DoFs may be encoded as independent qubits without auxiliary DoFs. Our result provides a useful way to reduce quantum simulation resources by exploring complex quantum systems for quantum applications requiring large qubit systems. PMID:27174302

Quantum Computation Based on Photons with Three Degrees of Freedom.

PubMed

Luo, Ming-Xing; Li, Hui-Ran; Lai, Hong; Wang, Xiaojun

2016-05-13

Quantum systems are important resources for quantum computer. Different from previous encoding forms using quantum systems with one degree of freedom (DoF) or two DoFs, we investigate the possibility of photon systems encoding with three DoFs consisting of the polarization DoF and two spatial DoFs. By exploring the optical circular birefringence induced by an NV center in a diamond embedded in the photonic crystal cavity, we propose several hybrid controlled-NOT (hybrid CNOT) gates operating on the two-photon or one-photon system. These hybrid CNOT gates show that three DoFs may be encoded as independent qubits without auxiliary DoFs. Our result provides a useful way to reduce quantum simulation resources by exploring complex quantum systems for quantum applications requiring large qubit systems.

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.

SiSeRHMap v1.0: a simulator for mapped seismic response using a hybrid model

NASA Astrophysics Data System (ADS)

Grelle, Gerardo; Bonito, Laura; Lampasi, Alessandro; Revellino, Paola; Guerriero, Luigi; Sappa, Giuseppe; Guadagno, Francesco Maria

2016-04-01

The SiSeRHMap (simulator for mapped seismic response using a hybrid model) is a computerized methodology capable of elaborating prediction maps of seismic response in terms of acceleration spectra. It was realized on the basis of a hybrid model which combines different approaches and models in a new and non-conventional way. These approaches and models are organized in a code architecture composed of five interdependent modules. A GIS (geographic information system) cubic model (GCM), which is a layered computational structure based on the concept of lithodynamic units and zones, aims at reproducing a parameterized layered subsoil model. A meta-modelling process confers a hybrid nature to the methodology. In this process, the one-dimensional (1-D) linear equivalent analysis produces acceleration response spectra for a specified number of site profiles using one or more input motions. The shear wave velocity-thickness profiles, defined as trainers, are randomly selected in each zone. Subsequently, a numerical adaptive simulation model (Emul-spectra) is optimized on the above trainer acceleration response spectra by means of a dedicated evolutionary algorithm (EA) and the Levenberg-Marquardt algorithm (LMA) as the final optimizer. In the final step, the GCM maps executor module produces a serial map set of a stratigraphic seismic response at different periods, grid solving the calibrated Emul-spectra model. In addition, the spectra topographic amplification is also computed by means of a 3-D validated numerical prediction model. This model is built to match the results of the numerical simulations related to isolate reliefs using GIS morphometric data. In this way, different sets of seismic response maps are developed on which maps of design acceleration response spectra are also defined by means of an enveloping technique.

Novel hybrid GPU-CPU implementation of parallelized Monte Carlo parametric expectation maximization estimation method for population pharmacokinetic data analysis.

PubMed

Ng, C M

2013-10-01

The development of a population PK/PD model, an essential component for model-based drug development, is both time- and labor-intensive. A graphical-processing unit (GPU) computing technology has been proposed and used to accelerate many scientific computations. The objective of this study was to develop a hybrid GPU-CPU implementation of parallelized Monte Carlo parametric expectation maximization (MCPEM) estimation algorithm for population PK data analysis. A hybrid GPU-CPU implementation of the MCPEM algorithm (MCPEMGPU) and identical algorithm that is designed for the single CPU (MCPEMCPU) were developed using MATLAB in a single computer equipped with dual Xeon 6-Core E5690 CPU and a NVIDIA Tesla C2070 GPU parallel computing card that contained 448 stream processors. Two different PK models with rich/sparse sampling design schemes were used to simulate population data in assessing the performance of MCPEMCPU and MCPEMGPU. Results were analyzed by comparing the parameter estimation and model computation times. Speedup factor was used to assess the relative benefit of parallelized MCPEMGPU over MCPEMCPU in shortening model computation time. The MCPEMGPU consistently achieved shorter computation time than the MCPEMCPU and can offer more than 48-fold speedup using a single GPU card. The novel hybrid GPU-CPU implementation of parallelized MCPEM algorithm developed in this study holds a great promise in serving as the core for the next-generation of modeling software for population PK/PD analysis.

Further validation of artificial neural network-based emissions simulation models for conventional and hybrid electric vehicles.

PubMed

Tóth-Nagy, Csaba; Conley, John J; Jarrett, Ronald P; Clark, Nigel N

2006-07-01

With the advent of hybrid electric vehicles, computer-based vehicle simulation becomes more useful to the engineer and designer trying to optimize the complex combination of control strategy, power plant, drive train, vehicle, and driving conditions. With the desire to incorporate emissions as a design criterion, researchers at West Virginia University have developed artificial neural network (ANN) models for predicting emissions from heavy-duty vehicles. The ANN models were trained on engine and exhaust emissions data collected from transient dynamometer tests of heavy-duty diesel engines then used to predict emissions based on engine speed and torque data from simulated operation of a tractor truck and hybrid electric bus. Simulated vehicle operation was performed with the ADVISOR software package. Predicted emissions (carbon dioxide [CO2] and oxides of nitrogen [NO(x)]) were then compared with actual emissions data collected from chassis dynamometer tests of similar vehicles. This paper expands on previous research to include different driving cycles for the hybrid electric bus and varying weights of the conventional truck. Results showed that different hybrid control strategies had a significant effect on engine behavior (and, thus, emissions) and may affect emissions during different driving cycles. The ANN models underpredicted emissions of CO2 and NO(x) in the case of a class-8 truck but were more accurate as the truck weight increased.

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

Evacuation simulation using Hybrid Space Discretisation and Application to Large Underground Rail Tunnel Station

NASA Astrophysics Data System (ADS)

Chooramun, N.; Lawrence, P. J.; Galea, E. R.

2017-08-01

In all evacuation simulation tools, the space through which agents navigate and interact is represented by one the following methods, namely Coarse regions, Fine nodes and Continuous regions. Each of the spatial representation methods has its benefits and limitations. For instance, the Coarse approach allows simulations to be processed very rapidly, but is unable to represent the interactions of the agents from an individual perspective; the Continuous approach provides a detailed representation of agent movement and interaction but suffers from relatively poor computational performance. The Fine nodal approach presents a compromise between the Continuous and Coarse approaches such that it allows agent interaction to be modelled while providing good computational performance. Our approach for representing space in an evacuation simulation tool differs such that it allows evacuation simulations to be run using a combination of Coarse regions, Fine nodes and Continuous regions. This approach, which we call Hybrid Spatial Discretisation (HSD), is implemented within the buildingEXODUS evacuation simulation software. The HSD incorporates the benefits of each of the spatial representation methods whilst providing an optimal environment for representing agent movement and interaction. In this work, we demonstrate the effectiveness of the HSD through its application to a moderately large case comprising of an underground rail tunnel station with a population of 2,000 agents.

Extending atomistic simulation timescale in solid/liquid systems: crystal growth from solution by a parallel-replica dynamics and continuum hybrid method.

PubMed

Lu, Chun-Yaung; Voter, Arthur F; Perez, Danny

2014-01-28

Deposition of solid material from solution is ubiquitous in nature. However, due to the inherent complexity of such systems, this process is comparatively much less understood than deposition from a gas or vacuum. Further, the accurate atomistic modeling of such systems is computationally expensive, therefore leaving many intriguing long-timescale phenomena out of reach. We present an atomistic/continuum hybrid method for extending the simulation timescales of dynamics at solid/liquid interfaces. We demonstrate the method by simulating the deposition of Ag on Ag (001) from solution with a significant speedup over standard MD. The results reveal specific features of diffusive deposition dynamics, such as a dramatic increase in the roughness of the film.

Numerical investigation of field enhancement by metal nano-particles using a hybrid FDTD-PSTD algorithm.

PubMed

Pernice, W H; Payne, F P; Gallagher, D F

2007-09-03

We present a novel numerical scheme for the simulation of the field enhancement by metal nano-particles in the time domain. The algorithm is based on a combination of the finite-difference time-domain method and the pseudo-spectral time-domain method for dispersive materials. The hybrid solver leads to an efficient subgridding algorithm that does not suffer from spurious field spikes as do FDTD schemes. Simulation of the field enhancement by gold particles shows the expected exponential field profile. The enhancement factors are computed for single particles and particle arrays. Due to the geometry conforming mesh the algorithm is stable for long integration times and thus suitable for the simulation of resonance phenomena in coupled nano-particle structures.

Patient-Specific Geometry Modeling and Mesh Generation for Simulating Obstructive Sleep Apnea Syndrome Cases by Maxillomandibular Advancement

PubMed Central

Ito, Yasushi; Cheng, Gary C.; Shih, Alan M.; Koomullil, Roy P.; Soni, Bharat K.; Sittitavornwong, Somsak; Waite, Peter D.

2011-01-01

The objective of this paper is the reconstruction of upper airway geometric models as hybrid meshes from clinically used Computed Tomography (CT) data sets in order to understand the dynamics and behaviors of the pre- and postoperative upper airway systems of Obstructive Sleep Apnea Syndrome (OSAS) patients by viscous Computational Fluid Dynamics (CFD) simulations. The selection criteria for OSAS cases studied are discussed because two reasonable pre- and postoperative upper airway models for CFD simulations may not be created for every case without a special protocol for CT scanning. The geometry extraction and manipulation methods are presented with technical barriers that must be overcome so that they can be used along with computational simulation software as a daily clinical evaluation tool. Eight cases are presented in this paper, and each case consists of pre- and postoperative configurations. The results of computational simulations of two cases are included in this paper as demonstration. PMID:21625395

Kalman Filtered Bio Heat Transfer Model Based Self-adaptive Hybrid Magnetic Resonance Thermometry.

PubMed

Zhang, Yuxin; Chen, Shuo; Deng, Kexin; Chen, Bingyao; Wei, Xing; Yang, Jiafei; Wang, Shi; Ying, Kui

2017-01-01

To develop a self-adaptive and fast thermometry method by combining the original hybrid magnetic resonance thermometry method and the bio heat transfer equation (BHTE) model. The proposed Kalman filtered Bio Heat Transfer Model Based Self-adaptive Hybrid Magnetic Resonance Thermometry, abbreviated as KalBHT hybrid method, introduced the BHTE model to synthesize a window on the regularization term of the hybrid algorithm, which leads to a self-adaptive regularization both spatially and temporally with change of temperature. Further, to decrease the sensitivity to accuracy of the BHTE model, Kalman filter is utilized to update the window at each iteration time. To investigate the effect of the proposed model, computer heating simulation, phantom microwave heating experiment and dynamic in-vivo model validation of liver and thoracic tumor were conducted in this study. The heating simulation indicates that the KalBHT hybrid algorithm achieves more accurate results without adjusting λ to a proper value in comparison to the hybrid algorithm. The results of the phantom heating experiment illustrate that the proposed model is able to follow temperature changes in the presence of motion and the temperature estimated also shows less noise in the background and surrounding the hot spot. The dynamic in-vivo model validation with heating simulation demonstrates that the proposed model has a higher convergence rate, more robustness to susceptibility problem surrounding the hot spot and more accuracy of temperature estimation. In the healthy liver experiment with heating simulation, the RMSE of the hot spot of the proposed model is reduced to about 50% compared to the RMSE of the original hybrid model and the convergence time becomes only about one fifth of the hybrid model. The proposed model is able to improve the accuracy of the original hybrid algorithm and accelerate the convergence rate of MR temperature estimation.

Evaluation of integration methods for hybrid simulation of complex structural systems through collapse

NASA Astrophysics Data System (ADS)

Del Carpio R., Maikol; Hashemi, M. Javad; Mosqueda, Gilberto

2017-10-01

This study examines the performance of integration methods for hybrid simulation of large and complex structural systems in the context of structural collapse due to seismic excitations. The target application is not necessarily for real-time testing, but rather for models that involve large-scale physical sub-structures and highly nonlinear numerical models. Four case studies are presented and discussed. In the first case study, the accuracy of integration schemes including two widely used methods, namely, modified version of the implicit Newmark with fixed-number of iteration (iterative) and the operator-splitting (non-iterative) is examined through pure numerical simulations. The second case study presents the results of 10 hybrid simulations repeated with the two aforementioned integration methods considering various time steps and fixed-number of iterations for the iterative integration method. The physical sub-structure in these tests consists of a single-degree-of-freedom (SDOF) cantilever column with replaceable steel coupons that provides repeatable highlynonlinear behavior including fracture-type strength and stiffness degradations. In case study three, the implicit Newmark with fixed-number of iterations is applied for hybrid simulations of a 1:2 scale steel moment frame that includes a relatively complex nonlinear numerical substructure. Lastly, a more complex numerical substructure is considered by constructing a nonlinear computational model of a moment frame coupled to a hybrid model of a 1:2 scale steel gravity frame. The last two case studies are conducted on the same porotype structure and the selection of time steps and fixed number of iterations are closely examined in pre-test simulations. The generated unbalance forces is used as an index to track the equilibrium error and predict the accuracy and stability of the simulations.

Auralization of concert hall acoustics using finite difference time domain methods and wave field synthesis

NASA Astrophysics Data System (ADS)

Hochgraf, Kelsey

Auralization methods have been used for a long time to simulate the acoustics of a concert hall for different seat positions. The goal of this thesis was to apply the concept of auralization to a larger audience area that the listener could walk through to compare differences in acoustics for a wide range of seat positions. For this purpose, the acoustics of Rensselaer's Experimental Media and Performing Arts Center (EMPAC) Concert Hall were simulated to create signals for a 136 channel wave field synthesis (WFS) system located at Rensselaer's Collaborative Research Augmented Immersive Virtual Environment (CRAIVE) Laboratory. By allowing multiple people to dynamically experience the concert hall's acoustics at the same time, this research gained perspective on what is important for achieving objective accuracy and subjective plausibility in an auralization. A finite difference time domain (FDTD) simulation on a three-dimensional face-centered cubic grid, combined at a crossover frequency of 800 Hz with a CATT-Acoustic(TM) simulation, was found to have a reverberation time, direct to reverberant sound energy ratio, and early reflection pattern that more closely matched measured data from the hall compared to a CATT-Acoustic(TM) simulation and other hybrid simulations. In the CRAIVE lab, nine experienced listeners found all hybrid auralizations (with varying source location, grid resolution, crossover frequency, and number of loudspeakers) to be more perceptually plausible than the CATT-Acoustic(TM) auralization. The FDTD simulation required two days to compute, while the CATT-Acoustic(TM) simulation required three separate TUCT(TM) computations, each taking four hours, to accommodate the large number of receivers. Given the perceptual advantages realized with WFS for auralization of a large, inhomogeneous sound field, it is recommended that hybrid simulations be used in the future to achieve more accurate and plausible auralizations. Predictions are made for a parallelized version of the simulation code that could achieve such auralizations in less than one hour, making the tool practical for everyday application.

A Hybrid Genetic-Simulated Annealing Algorithm for the Location-Inventory-Routing Problem Considering Returns under E-Supply Chain Environment

PubMed Central

Guo, Hao; Fu, Jing

2013-01-01

Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA) is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment. PMID:24489489

Hybrid genetic algorithm in the Hopfield network for maximum 2-satisfiability problem

NASA Astrophysics Data System (ADS)

Kasihmuddin, Mohd Shareduwan Mohd; Sathasivam, Saratha; Mansor, Mohd. Asyraf

2017-08-01

Heuristic method was designed for finding optimal solution more quickly compared to classical methods which are too complex to comprehend. In this study, a hybrid approach that utilizes Hopfield network and genetic algorithm in doing maximum 2-Satisfiability problem (MAX-2SAT) was proposed. Hopfield neural network was used to minimize logical inconsistency in interpretations of logic clauses or program. Genetic algorithm (GA) has pioneered the implementation of methods that exploit the idea of combination and reproduce a better solution. The simulation incorporated with and without genetic algorithm will be examined by using Microsoft Visual 2013 C++ Express software. The performance of both searching techniques in doing MAX-2SAT was evaluate based on global minima ratio, ratio of satisfied clause and computation time. The result obtained form the computer simulation demonstrates the effectiveness and acceleration features of genetic algorithm in doing MAX-2SAT in Hopfield network.

Hypersonic simulations using open-source CFD and DSMC solvers

NASA Astrophysics Data System (ADS)

Casseau, V.; Scanlon, T. J.; John, B.; Emerson, D. R.; Brown, R. E.

2016-11-01

Hypersonic hybrid hydrodynamic-molecular gas flow solvers are required to satisfy the two essential requirements of any high-speed reacting code, these being physical accuracy and computational efficiency. The James Weir Fluids Laboratory at the University of Strathclyde is currently developing an open-source hybrid code which will eventually reconcile the direct simulation Monte-Carlo method, making use of the OpenFOAM application called dsmcFoam, and the newly coded open-source two-temperature computational fluid dynamics solver named hy2Foam. In conjunction with employing the CVDV chemistry-vibration model in hy2Foam, novel use is made of the QK rates in a CFD solver. In this paper, further testing is performed, in particular with the CFD solver, to ensure its efficacy before considering more advanced test cases. The hy2Foam and dsmcFoam codes have shown to compare reasonably well, thus providing a useful basis for other codes to compare against.

Methodologies for extracting kinetic constants for multiphase reacting flow simulation

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

Chang, S.L.; Lottes, S.A.; Golchert, B.

1997-03-01

Flows in industrial reactors often involve complex reactions of many species. A computational fluid dynamics (CFD) computer code, ICRKFLO, was developed to simulate multiphase, multi-species reacting flows. The ICRKFLO uses a hybrid technique to calculate species concentration and reaction for a large number of species in a reacting flow. This technique includes a hydrodynamic and reacting flow simulation with a small but sufficient number of lumped reactions to compute flow field properties followed by a calculation of local reaction kinetics and transport of many subspecies (order of 10 to 100). Kinetic rate constants of the numerous subspecies chemical reactions aremore » difficult to determine. A methodology has been developed to extract kinetic constants from experimental data efficiently. A flow simulation of a fluid catalytic cracking (FCC) riser was successfully used to demonstrate this methodology.« less

A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks.

PubMed

Samant, Asawari; Ogunnaike, Babatunde A; Vlachos, Dionisios G

2007-05-24

The fundamental role that intrinsic stochasticity plays in cellular functions has been shown via numerous computational and experimental studies. In the face of such evidence, it is important that intracellular networks are simulated with stochastic algorithms that can capture molecular fluctuations. However, separation of time scales and disparity in species population, two common features of intracellular networks, make stochastic simulation of such networks computationally prohibitive. While recent work has addressed each of these challenges separately, a generic algorithm that can simultaneously tackle disparity in time scales and population scales in stochastic systems is currently lacking. In this paper, we propose the hybrid, multiscale Monte Carlo (HyMSMC) method that fills in this void. The proposed HyMSMC method blends stochastic singular perturbation concepts, to deal with potential stiffness, with a hybrid of exact and coarse-grained stochastic algorithms, to cope with separation in population sizes. In addition, we introduce the computational singular perturbation (CSP) method as a means of systematically partitioning fast and slow networks and computing relaxation times for convergence. We also propose a new criteria of convergence of fast networks to stochastic low-dimensional manifolds, which further accelerates the algorithm. We use several prototype and biological examples, including a gene expression model displaying bistability, to demonstrate the efficiency, accuracy and applicability of the HyMSMC method. Bistable models serve as stringent tests for the success of multiscale MC methods and illustrate limitations of some literature methods.

elsA-Hybrid: an all-in-one structured/unstructured solver for the simulation of internal and external flows. Application to turbomachinery

NASA Astrophysics Data System (ADS)

de la Llave Plata, M.; Couaillier, V.; Le Pape, M.-C.; Marmignon, C.; Gazaix, M.

2013-03-01

This paper reports recent work on the extension of the multiblock structured solver elsA to deal with hybrid grids. The new hybrid-grid solver is called elsA-H (elsA-Hybrid), is based on the investigation of a new unstructured-grid module has been built within the original elsA CFD (computational fluid dynamics) system. The implementation benefits from the flexibility of the object-oriented design. The aim of elsA-H is to take advantage of the full potential of structured solvers and unstructured mesh generation by allowing any type of grid to be used within the same simulation process. The main challenge lies in the numerical treatment of the hybrid-grid interfaces where blocks of different type meet. In particular, one must pay attention to the transfer of information across these boundaries, so that the accuracy of the numerical scheme is preserved and flux conservation is guaranteed. In this paper, the numerical approach allowing to achieve this is presented. A comparison between the hybrid and the structured-grid methods is also carried out by considering a fully hexahedral multiblock mesh for which a few blocks have been transformed into unstructured. The performance of elsA-H for the simulation of internal flows will be demonstrated on a number of turbomachinery configurations.

Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

2013-06-01

Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations

PubMed Central

Bachega, José Fernando R.; Timmers, Luís Fernando S.M.; Assirati, Lucas; Bachega, Leonardo R.; Field, Martin J.; Wymore, Troy

2014-01-01

Hybrid quantum chemical (QC)/molecular mechanical (MM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions, that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use we have developed an open-source graphical plug-in, GTKDynamo, that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. PMID:24137667

Multiscale Simulations of Reactive Transport

NASA Astrophysics Data System (ADS)

Tartakovsky, D. M.; Bakarji, J.

2014-12-01

Discrete, particle-based simulations offer distinct advantages when modeling solute transport and chemical reactions. For example, Brownian motion is often used to model diffusion in complex pore networks, and Gillespie-type algorithms allow one to handle multicomponent chemical reactions with uncertain reaction pathways. Yet such models can be computationally more intensive than their continuum-scale counterparts, e.g., advection-dispersion-reaction equations. Combining the discrete and continuum models has a potential to resolve the quantity of interest with a required degree of physicochemical granularity at acceptable computational cost. We present computational examples of such "hybrid models" and discuss the challenges associated with coupling these two levels of description.

Time-domain hybrid method for simulating large amplitude motions of ships advancing in waves

NASA Astrophysics Data System (ADS)

Liu, Shukui; Papanikolaou, Apostolos D.

2011-03-01

Typical results obtained by a newly developed, nonlinear time domain hybrid method for simulating large amplitude motions of ships advancing with constant forward speed in waves are presented. The method is hybrid in the way of combining a time-domain transient Green function method and a Rankine source method. The present approach employs a simple double integration algorithm with respect to time to simulate the free-surface boundary condition. During the simulation, the diffraction and radiation forces are computed by pressure integration over the mean wetted surface, whereas the incident wave and hydrostatic restoring forces/moments are calculated on the instantaneously wetted surface of the hull. Typical numerical results of application of the method to the seakeeping performance of a standard containership, namely the ITTC S175, are herein presented. Comparisons have been made between the results from the present method, the frequency domain 3D panel method (NEWDRIFT) of NTUA-SDL and available experimental data and good agreement has been observed for all studied cases between the results of the present method and comparable other data.

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.

Turbulence modeling for Francis turbine water passages simulation

NASA Astrophysics Data System (ADS)

Maruzewski, P.; Hayashi, H.; Munch, C.; Yamaishi, K.; Hashii, T.; Mombelli, H. P.; Sugow, Y.; Avellan, F.

2010-08-01

The applications of Computational Fluid Dynamics, CFD, to hydraulic machines life require the ability to handle turbulent flows and to take into account the effects of turbulence on the mean flow. Nowadays, Direct Numerical Simulation, DNS, is still not a good candidate for hydraulic machines simulations due to an expensive computational time consuming. Large Eddy Simulation, LES, even, is of the same category of DNS, could be an alternative whereby only the small scale turbulent fluctuations are modeled and the larger scale fluctuations are computed directly. Nevertheless, the Reynolds-Averaged Navier-Stokes, RANS, model have become the widespread standard base for numerous hydraulic machine design procedures. However, for many applications involving wall-bounded flows and attached boundary layers, various hybrid combinations of LES and RANS are being considered, such as Detached Eddy Simulation, DES, whereby the RANS approximation is kept in the regions where the boundary layers are attached to the solid walls. Furthermore, the accuracy of CFD simulations is highly dependent on the grid quality, in terms of grid uniformity in complex configurations. Moreover any successful structured and unstructured CFD codes have to offer a wide range to the variety of classic RANS model to hybrid complex model. The aim of this study is to compare the behavior of turbulent simulations for both structured and unstructured grids topology with two different CFD codes which used the same Francis turbine. Hence, the study is intended to outline the encountered discrepancy for predicting the wake of turbine blades by using either the standard k-epsilon model, or the standard k-epsilon model or the SST shear stress model in a steady CFD simulation. Finally, comparisons are made with experimental data from the EPFL Laboratory for Hydraulic Machines reduced scale model measurements.

Portable implementation model for CFD simulations. Application to hybrid CPU/GPU supercomputers

NASA Astrophysics Data System (ADS)

Oyarzun, Guillermo; Borrell, Ricard; Gorobets, Andrey; Oliva, Assensi

2017-10-01

Nowadays, high performance computing (HPC) systems experience a disruptive moment with a variety of novel architectures and frameworks, without any clarity of which one is going to prevail. In this context, the portability of codes across different architectures is of major importance. This paper presents a portable implementation model based on an algebraic operational approach for direct numerical simulation (DNS) and large eddy simulation (LES) of incompressible turbulent flows using unstructured hybrid meshes. The strategy proposed consists in representing the whole time-integration algorithm using only three basic algebraic operations: sparse matrix-vector product, a linear combination of vectors and dot product. The main idea is based on decomposing the nonlinear operators into a concatenation of two SpMV operations. This provides high modularity and portability. An exhaustive analysis of the proposed implementation for hybrid CPU/GPU supercomputers has been conducted with tests using up to 128 GPUs. The main objective consists in understanding the challenges of implementing CFD codes on new architectures.

Optimal Shape Design of Mail-Slot Nacelle on N3-X Hybrid Wing-Body Configuration

NASA Technical Reports Server (NTRS)

Kim, Hyoungjin; Liou, Meng-Sing

2013-01-01

System studies show that a N3-X hybrid wing-body aircraft with a turboelectric distributed propulsion system using a mail-slot inlet/nozzle nacelle can meet the environmental and performance goals for N+3 generation transports (three generations beyond the current air transport technology level) set by NASA's Subsonic Fixed Wing Project. In this study, a Navier-Stokes flow simulation of N3-X on hybrid unstructured meshes was conducted, including the mail-slot propulsor. The geometry of the mail-slot propulsor was generated by a CAD (Computer-Aided Design)-free shape parameterization. A novel body force model generation approach was suggested for a more realistic and efficient simulation of the flow turning, pressure rise and loss effects of the fan blades and the inlet-fan interactions. Flow simulation results of the N3-X demonstrates the validity of the present approach. An optimal Shape design of the mail-slot nacelle surface was conducted to reduce strength of shock waves and flow separations on the cowl surface.

A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations

DOE PAGES

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

2015-06-01

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

Optimization of PV/WIND/DIESEL Hybrid Power System in HOMER for Rural Electrification

NASA Astrophysics Data System (ADS)

Hassan, Q.; Jaszczur, M.; Abdulateef, J.

2016-09-01

A large proportion of the world's population lives in remote rural areas that are geographically isolated and sparsely populated. The present study is based on modeling, computer simulation and optimization of hybrid power generation system in the rural area in Muqdadiyah district of Diyala state, Iraq. Two renewable resources, namely, solar photovoltaic (PV) and wind turbine (WT) are considered. The HOMER software is used to study and design the proposed hybrid energy system model. Based on simulation results, it has been found that renewable energy sources perhaps replace the conventional energy sources and would be a feasible solution for the generation of electric power at remote locations with a reasonable investment. The hybrid power system solution to electrify the selected area resulted in a least-cost combination of the hybrid power system that can meet the demand in a dependable manner at a cost about (0.321/kWh). If the wind resources in the study area at the lower stage, it's not economically viable for a wind turbine to generate the electricity.

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

PubMed

Salis, Howard; Sotiropoulos, Vassilios; Kaznessis, Yiannis N

2006-02-24

Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations produce a more accurate picture of single cell dynamics, including interesting phenomena missed by deterministic methods, such as noise-induced oscillations and transitions between stable states. However, the computational cost of the original stochastic simulation algorithm can be high, motivating the use of hybrid stochastic methods. Hybrid stochastic methods partition the system into multiple subsets and describe each subset as a different representation, such as a jump Markov, Poisson, continuous Markov, or deterministic process. By applying valid approximations and self-consistently merging disparate descriptions, a method can be considerably faster, while retaining accuracy. In this paper, we describe Hy3S, a collection of multiscale simulation programs. Building on our previous work on developing novel hybrid stochastic algorithms, we have created the Hy3S software package to enable scientists and engineers to both study and design extremely large well-mixed biological systems with many thousands of reactions and chemical species. We have added adaptive stochastic numerical integrators to permit the robust simulation of dynamically stiff biological systems. In addition, Hy3S has many useful features, including embarrassingly parallelized simulations with MPI; special discrete events, such as transcriptional and translation elongation and cell division; mid-simulation perturbations in both the number of molecules of species and reaction kinetic parameters; combinatorial variation of both initial conditions and kinetic parameters to enable sensitivity analysis; use of NetCDF optimized binary format to quickly read and write large datasets; and a simple graphical user interface, written in Matlab, to help users create biological systems and analyze data. We demonstrate the accuracy and efficiency of Hy3S with examples, including a large-scale system benchmark and a complex bistable biochemical network with positive feedback. The software itself is open-sourced under the GPL license and is modular, allowing users to modify it for their own purposes. Hy3S is a powerful suite of simulation programs for simulating the stochastic dynamics of networks of biochemical reactions. Its first public version enables computational biologists to more efficiently investigate the dynamics of realistic biological systems.

Phase I of the Near Term Hybrid Passenger Vehicle Development Program. Final report

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

Not Available

1980-10-01

The results of Phase I of the Near-Term Hybrid Vehicle Program are summarized. This phase of the program ws a study leading to the preliminary design of a 5-passenger hybrid vehicle utilizing two energy sources (electricity and gasoline/diesel fuel) to minimize petroleum usage on a fleet basis. This report presents the following: overall summary of the Phase I activity; summary of the individual tasks; summary of the hybrid vehicle design; summary of the alternative design options; summary of the computer simulations; summary of the economic analysis; summary of the maintenance and reliability considerations; summary of the design for crash safety;more » and bibliography.« less

Solving Fuzzy Optimization Problem Using Hybrid Ls-Sa Method

NASA Astrophysics Data System (ADS)

Vasant, Pandian

2011-06-01

Fuzzy optimization problem has been one of the most and prominent topics inside the broad area of computational intelligent. It's especially relevant in the filed of fuzzy non-linear programming. It's application as well as practical realization can been seen in all the real world problems. In this paper a large scale non-linear fuzzy programming problem has been solved by hybrid optimization techniques of Line Search (LS), Simulated Annealing (SA) and Pattern Search (PS). As industrial production planning problem with cubic objective function, 8 decision variables and 29 constraints has been solved successfully using LS-SA-PS hybrid optimization techniques. The computational results for the objective function respect to vagueness factor and level of satisfaction has been provided in the form of 2D and 3D plots. The outcome is very promising and strongly suggests that the hybrid LS-SA-PS algorithm is very efficient and productive in solving the large scale non-linear fuzzy programming problem.

Hybrid Seminumerical Simulation Scheme to Predict Transducer Outputs of Acoustic Microscopes.

PubMed

Nierla, Michael; Rupitsch, Stefan J

2016-02-01

We present a seminumerical simulation method called SIRFEM, which enables the efficient prediction of high-frequency transducer outputs. In particular, this is important for acoustic microscopy where the specimen under investigation is immersed in a coupling fluid. Conventional finite-element (FE) simulations for such applications would consume too much computational power due to the required spatial and temporal discretization, especially for the coupling fluid between ultrasonic transducer and specimen. However, FE simulations are in most cases essential to consider the mode conversion at and inside the solid specimen as well as the wave propagation in its interior. SIRFEM reduces the computational effort of pure FE simulations by treating only the solid specimen and a small part of the fluid layer with FE. The propagation in the coupling fluid from transducer to specimen and back is processed by the so-called spatial impulse response (SIR). Through this hybrid approach, the number of elements as well as the number of time steps for the FE simulation can be reduced significantly, as it is presented for an axis-symmetric setup. Three B-mode images of a plane 2-D setup-computed at a transducer center frequency of 20 MHz-show that SIRFEM is, furthermore, able to predict reflections at inner structures as well as multiple reflections between those structures and the specimen's surface. For the purpose of a pure 2-D setup, the SIR of a curved-line transducer is derived and compared to the response function of a cylindrically focused aperture of negligible extend in the third spatial dimension.

A Hybrid Approach for Efficient Modeling of Medium-Frequency Propagation in Coal Mines

PubMed Central

Brocker, Donovan E.; Sieber, Peter E.; Waynert, Joseph A.; Li, Jingcheng; Werner, Pingjuan L.; Werner, Douglas H.

2015-01-01

An efficient procedure for modeling medium frequency (MF) communications in coal mines is introduced. In particular, a hybrid approach is formulated and demonstrated utilizing ideal transmission line equations to model MF propagation in combination with full-wave sections used for accurate simulation of local antenna-line coupling and other near-field effects. This work confirms that the hybrid method accurately models signal propagation from a source to a load for various system geometries and material compositions, while significantly reducing computation time. With such dramatic improvement to solution times, it becomes feasible to perform large-scale optimizations with the primary motivation of improving communications in coal mines both for daily operations and emergency response. Furthermore, it is demonstrated that the hybrid approach is suitable for modeling and optimizing large communication networks in coal mines that may otherwise be intractable to simulate using traditional full-wave techniques such as moment methods or finite-element analysis. PMID:26478686

PHoToNs–A parallel heterogeneous and threads oriented code for cosmological N-body simulation

NASA Astrophysics Data System (ADS)

Wang, Qiao; Cao, Zong-Yan; Gao, Liang; Chi, Xue-Bin; Meng, Chen; Wang, Jie; Wang, Long

2018-06-01

We introduce a new code for cosmological simulations, PHoToNs, which incorporates features for performing massive cosmological simulations on heterogeneous high performance computer (HPC) systems and threads oriented programming. PHoToNs adopts a hybrid scheme to compute gravitational force, with the conventional Particle-Mesh (PM) algorithm to compute the long-range force, the Tree algorithm to compute the short range force and the direct summation Particle-Particle (PP) algorithm to compute gravity from very close particles. A self-similar space filling a Peano-Hilbert curve is used to decompose the computing domain. Threads programming is advantageously used to more flexibly manage the domain communication, PM calculation and synchronization, as well as Dual Tree Traversal on the CPU+MIC platform. PHoToNs scales well and efficiency of the PP kernel achieves 68.6% of peak performance on MIC and 74.4% on CPU platforms. We also test the accuracy of the code against the much used Gadget-2 in the community and found excellent agreement.

2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching.

PubMed

Matsumoto, Atsushi; Miyazaki, Naoyuki; Takagi, Junichi; Iwasaki, Kenji

2017-03-23

In this study, we develop an approach termed "2D hybrid analysis" for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.

High-Fidelity Computational Aerodynamics of Multi-Rotor Unmanned Aerial Vehicles

NASA Technical Reports Server (NTRS)

Ventura Diaz, Patricia; Yoon, Seokkwan

2018-01-01

High-fidelity Computational Fluid Dynamics (CFD) simulations have been carried out for several multi-rotor Unmanned Aerial Vehicles (UAVs). Three vehicles have been studied: the classic quadcopter DJI Phantom 3, an unconventional quadcopter specialized for forward flight, the SUI Endurance, and an innovative concept for Urban Air Mobility (UAM), the Elytron 4S UAV. The three-dimensional unsteady Navier-Stokes equations are solved on overset grids using high-order accurate schemes, dual-time stepping, and a hybrid turbulence model. The DJI Phantom 3 is simulated with different rotors and with both a simplified airframe and the real airframe including landing gear and a camera. The effects of weather are studied for the DJI Phantom 3 quadcopter in hover. The SUI En- durance original design is compared in forward flight to a new configuration conceived by the authors, the hybrid configuration, which gives a large improvement in forward thrust. The Elytron 4S UAV is simulated in helicopter mode and in airplane mode. Understanding the complex flows in multi-rotor vehicles will help design quieter, safer, and more efficient future drones and UAM vehicles.

Imaging performance of a hybrid x-ray computed tomography-fluorescence molecular tomography system using priors.

PubMed

Ale, Angelique; Schulz, Ralf B; Sarantopoulos, Athanasios; Ntziachristos, Vasilis

2010-05-01

The performance is studied of two newly introduced and previously suggested methods that incorporate priors into inversion schemes associated with data from a recently developed hybrid x-ray computed tomography and fluorescence molecular tomography system, the latter based on CCD camera photon detection. The unique data set studied attains accurately registered data of high spatially sampled photon fields propagating through tissue along 360 degrees projections. Approaches that incorporate structural prior information were included in the inverse problem by adding a penalty term to the minimization function utilized for image reconstructions. Results were compared as to their performance with simulated and experimental data from a lung inflammation animal model and against the inversions achieved when not using priors. The importance of using priors over stand-alone inversions is also showcased with high spatial sampling simulated and experimental data. The approach of optimal performance in resolving fluorescent biodistribution in small animals is also discussed. Inclusion of prior information from x-ray CT data in the reconstruction of the fluorescence biodistribution leads to improved agreement between the reconstruction and validation images for both simulated and experimental data.

Stochastic hybrid systems for studying biochemical processes.

PubMed

Singh, Abhyudai; Hespanha, João P

2010-11-13

Many protein and mRNA species occur at low molecular counts within cells, and hence are subject to large stochastic fluctuations in copy numbers over time. Development of computationally tractable frameworks for modelling stochastic fluctuations in population counts is essential to understand how noise at the cellular level affects biological function and phenotype. We show that stochastic hybrid systems (SHSs) provide a convenient framework for modelling the time evolution of population counts of different chemical species involved in a set of biochemical reactions. We illustrate recently developed techniques that allow fast computations of the statistical moments of the population count, without having to run computationally expensive Monte Carlo simulations of the biochemical reactions. Finally, we review different examples from the literature that illustrate the benefits of using SHSs for modelling biochemical processes.

An accurate, compact and computationally efficient representation of orbitals for quantum Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Luo, Ye; Esler, Kenneth; Kent, Paul; Shulenburger, Luke

Quantum Monte Carlo (QMC) calculations of giant molecules, surface and defect properties of solids have been feasible recently due to drastically expanding computational resources. However, with the most computationally efficient basis set, B-splines, these calculations are severely restricted by the memory capacity of compute nodes. The B-spline coefficients are shared on a node but not distributed among nodes, to ensure fast evaluation. A hybrid representation which incorporates atomic orbitals near the ions and B-spline ones in the interstitial regions offers a more accurate and less memory demanding description of the orbitals because they are naturally more atomic like near ions and much smoother in between, thus allowing coarser B-spline grids. We will demonstrate the advantage of hybrid representation over pure B-spline and Gaussian basis sets and also show significant speed-up like computing the non-local pseudopotentials with our new scheme. Moreover, we discuss a new algorithm for atomic orbital initialization which used to require an extra workflow step taking a few days. With this work, the highly efficient hybrid representation paves the way to simulate large size even in-homogeneous systems using QMC. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Computational Materials Sciences Program.

Indirect adaptive soft computing based wavelet-embedded control paradigms for WT/PV/SOFC in a grid/charging station connected hybrid power system.

PubMed

Mumtaz, Sidra; Khan, Laiq; Ahmed, Saghir; Bader, Rabiah

2017-01-01

This paper focuses on the indirect adaptive tracking control of renewable energy sources in a grid-connected hybrid power system. The renewable energy systems have low efficiency and intermittent nature due to unpredictable meteorological conditions. The domestic load and the conventional charging stations behave in an uncertain manner. To operate the renewable energy sources efficiently for harvesting maximum power, instantaneous nonlinear dynamics should be captured online. A Chebyshev-wavelet embedded NeuroFuzzy indirect adaptive MPPT (maximum power point tracking) control paradigm is proposed for variable speed wind turbine-permanent synchronous generator (VSWT-PMSG). A Hermite-wavelet incorporated NeuroFuzzy indirect adaptive MPPT control strategy for photovoltaic (PV) system to extract maximum power and indirect adaptive tracking control scheme for Solid Oxide Fuel Cell (SOFC) is developed. A comprehensive simulation test-bed for a grid-connected hybrid power system is developed in Matlab/Simulink. The robustness of the suggested indirect adaptive control paradigms are evaluated through simulation results in a grid-connected hybrid power system test-bed by comparison with conventional and intelligent control techniques. The simulation results validate the effectiveness of the proposed control paradigms.

Indirect adaptive soft computing based wavelet-embedded control paradigms for WT/PV/SOFC in a grid/charging station connected hybrid power system

PubMed Central

Khan, Laiq; Ahmed, Saghir; Bader, Rabiah

2017-01-01

This paper focuses on the indirect adaptive tracking control of renewable energy sources in a grid-connected hybrid power system. The renewable energy systems have low efficiency and intermittent nature due to unpredictable meteorological conditions. The domestic load and the conventional charging stations behave in an uncertain manner. To operate the renewable energy sources efficiently for harvesting maximum power, instantaneous nonlinear dynamics should be captured online. A Chebyshev-wavelet embedded NeuroFuzzy indirect adaptive MPPT (maximum power point tracking) control paradigm is proposed for variable speed wind turbine-permanent synchronous generator (VSWT-PMSG). A Hermite-wavelet incorporated NeuroFuzzy indirect adaptive MPPT control strategy for photovoltaic (PV) system to extract maximum power and indirect adaptive tracking control scheme for Solid Oxide Fuel Cell (SOFC) is developed. A comprehensive simulation test-bed for a grid-connected hybrid power system is developed in Matlab/Simulink. The robustness of the suggested indirect adaptive control paradigms are evaluated through simulation results in a grid-connected hybrid power system test-bed by comparison with conventional and intelligent control techniques. The simulation results validate the effectiveness of the proposed control paradigms. PMID:28877191

Hybrid method to estimate two-layered superficial tissue optical properties from simulated data of diffuse reflectance spectroscopy.

PubMed

Hsieh, Hong-Po; Ko, Fan-Hua; Sung, Kung-Bin

2018-04-20

An iterative curve fitting method has been applied in both simulation [J. Biomed. Opt.17, 107003 (2012)JBOPFO1083-366810.1117/1.JBO.17.10.107003] and phantom [J. Biomed. Opt.19, 077002 (2014)JBOPFO1083-366810.1117/1.JBO.19.7.077002] studies to accurately extract optical properties and the top layer thickness of a two-layered superficial tissue model from diffuse reflectance spectroscopy (DRS) data. This paper describes a hybrid two-step parameter estimation procedure to address two main issues of the previous method, including (1) high computational intensity and (2) converging to local minima. The parameter estimation procedure contained a novel initial estimation step to obtain an initial guess, which was used by a subsequent iterative fitting step to optimize the parameter estimation. A lookup table was used in both steps to quickly obtain reflectance spectra and reduce computational intensity. On simulated DRS data, the proposed parameter estimation procedure achieved high estimation accuracy and a 95% reduction of computational time compared to previous studies. Furthermore, the proposed initial estimation step led to better convergence of the following fitting step. Strategies used in the proposed procedure could benefit both the modeling and experimental data processing of not only DRS but also related approaches such as near-infrared spectroscopy.

A review of hybrid implicit explicit finite difference time domain method

NASA Astrophysics Data System (ADS)

Chen, Juan

2018-06-01

The finite-difference time-domain (FDTD) method has been extensively used to simulate varieties of electromagnetic interaction problems. However, because of its Courant-Friedrich-Levy (CFL) condition, the maximum time step size of this method is limited by the minimum size of cell used in the computational domain. So the FDTD method is inefficient to simulate the electromagnetic problems which have very fine structures. To deal with this problem, the Hybrid Implicit Explicit (HIE)-FDTD method is developed. The HIE-FDTD method uses the hybrid implicit explicit difference in the direction with fine structures to avoid the confinement of the fine spatial mesh on the time step size. So this method has much higher computational efficiency than the FDTD method, and is extremely useful for the problems which have fine structures in one direction. In this paper, the basic formulations, time stability condition and dispersion error of the HIE-FDTD method are presented. The implementations of several boundary conditions, including the connect boundary, absorbing boundary and periodic boundary are described, then some applications and important developments of this method are provided. The goal of this paper is to provide an historical overview and future prospects of the HIE-FDTD method.

Scramjet test flow reconstruction for a large-scale expansion tube, Part 2: axisymmetric CFD analysis

NASA Astrophysics Data System (ADS)

Gildfind, D. E.; Jacobs, P. A.; Morgan, R. G.; Chan, W. Y. K.; Gollan, R. J.

2018-07-01

This paper presents the second part of a study aiming to accurately characterise a Mach 10 scramjet test flow generated using a large free-piston-driven expansion tube. Part 1 described the experimental set-up, the quasi-one-dimensional simulation of the full facility, and the hybrid analysis technique used to compute the nozzle exit test flow properties. The second stage of the hybrid analysis applies the computed 1-D shock tube flow history as an inflow to a high-fidelity two-dimensional-axisymmetric analysis of the acceleration tube. The acceleration tube exit flow history is then applied as an inflow to a further refined axisymmetric nozzle model, providing the final nozzle exit test flow properties and thereby completing the analysis. This paper presents the results of the axisymmetric analyses. These simulations are shown to closely reproduce experimentally measured shock speeds and acceleration tube static pressure histories, as well as nozzle centreline static and impact pressure histories. The hybrid scheme less successfully predicts the diameter of the core test flow; however, this property is readily measured through experimental pitot surveys. In combination, the full test flow history can be accurately determined.

Numerical optimization of actuator trajectories for ITER hybrid scenario profile evolution

NASA Astrophysics Data System (ADS)

van Dongen, J.; Felici, F.; Hogeweij, G. M. D.; Geelen, P.; Maljaars, E.

2014-12-01

Optimal actuator trajectories for an ITER hybrid scenario ramp-up are computed using a numerical optimization method. For both L-mode and H-mode scenarios, the time trajectory of plasma current, EC heating and current drive distribution is determined that minimizes a chosen cost function, while satisfying constraints. The cost function is formulated to reflect two desired properties of the plasma q profile at the end of the ramp-up. The first objective is to maximize the ITG turbulence threshold by maximizing the volume-averaged s/q ratio. The second objective is to achieve a stationary q profile by having a flat loop voltage profile. Actuator and physics-derived constraints are included, imposing limits on plasma current, ramp rates, internal inductance and q profile. This numerical method uses the fast control-oriented plasma profile evolution code RAPTOR, which is successfully benchmarked against more complete CRONOS simulations for L-mode and H-mode mode ITER hybrid scenarios. It is shown that the optimized trajectories computed using RAPTOR also result in an improved ramp-up scenario for CRONOS simulations using the same input trajectories. Furthermore, the optimal trajectories are shown to vary depending on the precise timing of the L-H transition.

Scramjet test flow reconstruction for a large-scale expansion tube, Part 2: axisymmetric CFD analysis

NASA Astrophysics Data System (ADS)

Gildfind, D. E.; Jacobs, P. A.; Morgan, R. G.; Chan, W. Y. K.; Gollan, R. J.

2017-11-01

This paper presents the second part of a study aiming to accurately characterise a Mach 10 scramjet test flow generated using a large free-piston-driven expansion tube. Part 1 described the experimental set-up, the quasi-one-dimensional simulation of the full facility, and the hybrid analysis technique used to compute the nozzle exit test flow properties. The second stage of the hybrid analysis applies the computed 1-D shock tube flow history as an inflow to a high-fidelity two-dimensional-axisymmetric analysis of the acceleration tube. The acceleration tube exit flow history is then applied as an inflow to a further refined axisymmetric nozzle model, providing the final nozzle exit test flow properties and thereby completing the analysis. This paper presents the results of the axisymmetric analyses. These simulations are shown to closely reproduce experimentally measured shock speeds and acceleration tube static pressure histories, as well as nozzle centreline static and impact pressure histories. The hybrid scheme less successfully predicts the diameter of the core test flow; however, this property is readily measured through experimental pitot surveys. In combination, the full test flow history can be accurately determined.

An Object-Oriented Serial DSMC Simulation Package

NASA Astrophysics Data System (ADS)

Liu, Hongli; Cai, Chunpei

2011-05-01

A newly developed three-dimensional direct simulation Monte Carlo (DSMC) simulation package, named GRASP ("Generalized Rarefied gAs Simulation Package"), is reported in this paper. This package utilizes the concept of simulation engine, many C++ features and software design patterns. The package has an open architecture which can benefit further development and maintenance of the code. In order to reduce the engineering time for three-dimensional models, a hybrid grid scheme, combined with a flexible data structure compiled by C++ language, are implemented in this package. This scheme utilizes a local data structure based on the computational cell to achieve high performance on workstation processors. This data structure allows the DSMC algorithm to be very efficiently parallelized with domain decomposition and it provides much flexibility in terms of grid types. This package can utilize traditional structured, unstructured or hybrid grids within the framework of a single code to model arbitrarily complex geometries and to simulate rarefied gas flows. Benchmark test cases indicate that this package has satisfactory accuracy for complex rarefied gas flows.

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.

Evaluation of the UF/NCI hybrid computational phantoms for use in organ dosimetry of pediatric patients undergoing fluoroscopically guided cardiac procedures

NASA Astrophysics Data System (ADS)

Marshall, Emily L.; Borrego, David; Tran, Trung; Fudge, James C.; Bolch, Wesley E.

2018-03-01

Epidemiologic data demonstrate that pediatric patients face a higher relative risk of radiation induced cancers than their adult counterparts at equivalent exposures. Infants and children with congenital heart defects are a critical patient population exposed to ionizing radiation during life-saving procedures. These patients will likely incur numerous procedures throughout their lifespan, each time increasing their cumulative radiation absorbed dose. As continued improvements in long-term prognosis of congenital heart defect patients is achieved, a better understanding of organ radiation dose following treatment becomes increasingly vital. Dosimetry of these patients can be accomplished using Monte Carlo radiation transport simulations, coupled with modern anatomical patient models. The aim of this study was to evaluate the performance of the University of Florida/National Cancer Institute (UF/NCI) pediatric hybrid computational phantom library for organ dose assessment of patients that have undergone fluoroscopically guided cardiac catheterizations. In this study, two types of simulations were modeled. A dose assessment was performed on 29 patient-specific voxel phantoms (taken as representing the patient’s true anatomy), height/weight-matched hybrid library phantoms, and age-matched reference phantoms. Two exposure studies were conducted for each phantom type. First, a parametric study was constructed by the attending pediatric interventional cardiologist at the University of Florida to model the range of parameters seen clinically. Second, four clinical cardiac procedures were simulated based upon internal logfiles captured by a Toshiba Infinix-i Cardiac Bi-Plane fluoroscopic unit. Performance of the phantom library was quantified by computing both the percent difference in individual organ doses, as well as the organ dose root mean square values for overall phantom assessment between the matched phantoms (UF/NCI library or reference) and the patient-specific phantoms. The UF/NCI hybrid phantoms performed at percent differences of between 15% and 30% for the parametric set of irradiation events. Among internal logfile reconstructed procedures, the UF/NCI hybrid phantoms performed with RMS organ dose values between 7% and 29%. Percent improvement in organ dosimetry via the use of hybrid library phantoms over the reference phantoms ranged from 6.6% to 93%. The use of a hybrid phantom library, Monte Carlo radiation transport methods, and clinical information on irradiation events provide a means for tracking organ dose in these radiosensitive patients undergoing fluoroscopically guided cardiac procedures. This work was supported by Advanced Laboratory for Radiation Dosimetry Studies, University of Florida, American Association of University Women, National Cancer Institute Grant 1F31 CA159464.

Introduction of Shear-Based Transport Mechanisms in Radial-Axial Hybrid Hall Thruster Simulations

NASA Astrophysics Data System (ADS)

Scharfe, Michelle; Gascon, Nicolas; Scharfe, David; Cappelli, Mark; Fernandez, Eduardo

2007-11-01

Electron diffusion across magnetic field lines in Hall effect thrusters is experimentally observed to be higher than predicted by classical diffusion theory. Motivated by theoretical work for fusion applications and experimental measurements of Hall thrusters, numerical models for the electron transport are implemented in radial-axial hybrid simulations in order to compute the electron mobility using simulated plasma properties and fitting parameters. These models relate the cross-field transport to the imposed magnetic field distribution through shear suppression of turbulence-enhanced transport. While azimuthal waves likely enhance cross field mobility, axial shear in the electron fluid may reduce transport due to a reduction in turbulence amplitudes and modification of phase shifts between fluctuating properties. The sensitivity of the simulation results to the fitting parameters is evaluated and an examination is made of the transportability of these parameters to several Hall thruster devices.

A Hybrid Cloud Computing Service for Earth Sciences

NASA Astrophysics Data System (ADS)

Yang, C. P.

2016-12-01

Cloud Computing is becoming a norm for providing computing capabilities for advancing Earth sciences including big Earth data management, processing, analytics, model simulations, and many other aspects. A hybrid spatiotemporal cloud computing service is bulit at George Mason NSF spatiotemporal innovation center to meet this demands. This paper will report the service including several aspects: 1) the hardware includes 500 computing services and close to 2PB storage as well as connection to XSEDE Jetstream and Caltech experimental cloud computing environment for sharing the resource; 2) the cloud service is geographically distributed at east coast, west coast, and central region; 3) the cloud includes private clouds managed using open stack and eucalyptus, DC2 is used to bridge these and the public AWS cloud for interoperability and sharing computing resources when high demands surfing; 4) the cloud service is used to support NSF EarthCube program through the ECITE project, ESIP through the ESIP cloud computing cluster, semantics testbed cluster, and other clusters; 5) the cloud service is also available for the earth science communities to conduct geoscience. A brief introduction about how to use the cloud service will be included.

Advances and trends in computational structural mechanics

NASA Technical Reports Server (NTRS)

Noor, A. K.

1986-01-01

Recent developments in computational structural mechanics are reviewed with reference to computational needs for future structures technology, advances in computational models for material behavior, discrete element technology, assessment and control of numerical simulations of structural response, hybrid analysis, and techniques for large-scale optimization. Research areas in computational structural mechanics which have high potential for meeting future technological needs are identified. These include prediction and analysis of the failure of structural components made of new materials, development of computational strategies and solution methodologies for large-scale structural calculations, and assessment of reliability and adaptive improvement of response predictions.

Probabilistic Analysis of Solid Oxide Fuel Cell Based Hybrid Gas Turbine System

NASA Technical Reports Server (NTRS)

Gorla, Rama S. R.; Pai, Shantaram S.; Rusick, Jeffrey J.

2003-01-01

The emergence of fuel cell systems and hybrid fuel cell systems requires the evolution of analysis strategies for evaluating thermodynamic performance. A gas turbine thermodynamic cycle integrated with a fuel cell was computationally simulated and probabilistically evaluated in view of the several uncertainties in the thermodynamic performance parameters. Cumulative distribution functions and sensitivity factors were computed for the overall thermal efficiency and net specific power output due to the uncertainties in the thermodynamic random variables. These results can be used to quickly identify the most critical design variables in order to optimize the design and make it cost effective. The analysis leads to the selection of criteria for gas turbine performance.

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;

Time-Dependent Simulation of Incompressible Flow in a Turbopump Using Overset Grid Approach

NASA Technical Reports Server (NTRS)

Kiris, Cetin; Kwak, Dochan

2001-01-01

This paper reports the progress being made towards complete unsteady turbopump simulation capability by using overset grid systems. A computational model of a turbo-pump impeller is used as a test case for the performance evaluation of the MPI, hybrid MPI/Open-MP, and MLP versions of the INS3D code. Relative motion of the grid system for rotor-stator interaction was obtained by employing overset grid techniques. Unsteady computations for a turbo-pump, which contains 114 zones with 34.3 Million grid points, are performed on Origin 2000 systems at NASA Ames Research Center. The approach taken for these simulations, and the performance of the parallel versions of the code are presented.

Dynamic Test Program, Contact Power Collection for High Speed Tracked Vehicles

DOT National Transportation Integrated Search

1973-01-01

A laboratory test program is defined for determining the dynamic characteristics of a contact power collection system for a high speed tracked vehicle. The use of a hybrid computer is conjuntion with hydraulic exciters to simulate the expected dynami...

Spatially extended hybrid methods: a review

PubMed Central

2018-01-01

Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as partial differential equations are typically fast to simulate, they lack the individual-level detail that may be required in regions of low concentration or small spatial scale. However, to simulate at such an individual level throughout a domain and in regions where concentrations are high can be computationally expensive. Spatially coupled hybrid methods provide a bridge, allowing for multiple representations of the same species in one spatial domain by partitioning space into distinct modelling subdomains. Over the past 20 years, such hybrid methods have risen to prominence, leading to what is now a very active research area across multiple disciplines including chemistry, physics and mathematics. There are three main motivations for undertaking this review. Firstly, we have collated a large number of spatially extended hybrid methods and presented them in a single coherent document, while comparing and contrasting them, so that anyone who requires a multiscale hybrid method will be able to find the most appropriate one for their need. Secondly, we have provided canonical examples with algorithms and accompanying code, serving to demonstrate how these types of methods work in practice. Finally, we have presented papers that employ these methods on real biological and physical problems, demonstrating their utility. We also consider some open research questions in the area of hybrid method development and the future directions for the field. PMID:29491179

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.

Simulating adsorptive expansion of zeolites: application to biomass-derived solutions in contact with silicalite.

PubMed

Santander, Julian E; Tsapatsis, Michael; Auerbach, Scott M

2013-04-16

We have constructed and applied an algorithm to simulate the behavior of zeolite frameworks during liquid adsorption. We applied this approach to compute the adsorption isotherms of furfural-water and hydroxymethyl furfural (HMF)-water mixtures adsorbing in silicalite zeolite at 300 K for comparison with experimental data. We modeled these adsorption processes under two different statistical mechanical ensembles: the grand canonical (V-Nz-μg-T or GC) ensemble keeping volume fixed, and the P-Nz-μg-T (osmotic) ensemble allowing volume to fluctuate. To optimize accuracy and efficiency, we compared pure Monte Carlo (MC) sampling to hybrid MC-molecular dynamics (MD) simulations. For the external furfural-water and HMF-water phases, we assumed the ideal solution approximation and employed a combination of tabulated data and extended ensemble simulations for computing solvation free energies. We found that MC sampling in the V-Nz-μg-T ensemble (i.e., standard GCMC) does a poor job of reproducing both the Henry's law regime and the saturation loadings of these systems. Hybrid MC-MD sampling of the V-Nz-μg-T ensemble, which includes framework vibrations at fixed total volume, provides better results in the Henry's law region, but this approach still does not reproduce experimental saturation loadings. Pure MC sampling of the osmotic ensemble was found to approach experimental saturation loadings more closely, whereas hybrid MC-MD sampling of the osmotic ensemble quantitatively reproduces such loadings because the MC-MD approach naturally allows for locally anisotropic volume changes wherein some pores expand whereas others contract.

Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

PubMed Central

2016-01-01

A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys.2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD–MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD–MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems. PMID:26300709

Next Processor Module: A Hardware Accelerator of UT699 LEON3-FT System for On-Board Computer Software Simulation

NASA Astrophysics Data System (ADS)

Langlois, Serge; Fouquet, Olivier; Gouy, Yann; Riant, David

2014-08-01

On-Board Computers (OBC) are more and more using integrated systems on-chip (SOC) that embed processors running from 50MHz up to several hundreds of MHz, and around which are plugged some dedicated communication controllers together with other Input/Output channels.For ground testing and On-Board SoftWare (OBSW) validation purpose, a representative simulation of these systems, faster than real-time and with cycle-true timing of execution, is not achieved with current purely software simulators.Since a few years some hybrid solutions where put in place ([1], [2]), including hardware in the loop so as to add accuracy and performance in the computer software simulation.This paper presents the results of the works engaged by Thales Alenia Space (TAS-F) at the end of 2010, that led to a validated HW simulator of the UT699 by mid- 2012 and that is now qualified and fully used in operational contexts.

Evaluation of an F100 multivariable control using a real-time engine simulation

NASA Technical Reports Server (NTRS)

Szuch, J. R.; Soeder, J. F.; Skira, C.

1977-01-01

The control evaluated has been designed for the F100-PW-100 turbofan engine. The F100 engine represents the current state-of-the-art in aircraft gas turbine technology. The control makes use of a multivariable, linear quadratic regulator. The evaluation procedure employed utilized a real-time hybrid computer simulation of the F100 engine and an implementation of the control logic on the NASA LeRC digital computer/controller. The results of the evaluation indicated that the control logic and its implementation will be capable of controlling the engine throughout its operating range.

Infusion of a Gaming Paradigm into Computer-Aided Engineering Design Tools

DTIC Science & Technology

2012-05-03

Virtual Test Bed (VTB), and the gaming tool, Unity3D . This hybrid gaming environment coupled a three-dimensional (3D) multibody vehicle system model...from Google Earth to the 3D visual front-end fabricated around Unity3D . The hybrid environment was sufficiently developed to support analyses of the...ndFr Cti3r4 G’OjrdFr ctior-2 The VTB simulation of the vehicle dynamics ran concurrently with and interacted with the gaming engine, Unity3D which

Computer Simulation Studies of the Tearing Mode Instability in a Field-Reversed Ion Layer.

DTIC Science & Technology

1980-09-15

CLASSIFICATION OF THIS PAGE (when Date Entered) 20. (Abstract continued) .those of the linear theory. In addition, it has been demonstrated that when...However, all the results obtained so far are very encouraging. Using the energy prin- ciple Sudan and Rosenbluth5 have shown with a hybrid model that a...found that finite length layers are stable to tearing modes as a consequence of axial kinetic pressure. Using a hybrid model , in which the ion layer is

Modeling a Wireless Network for International Space Station

NASA Technical Reports Server (NTRS)

Alena, Richard; Yaprak, Ece; Lamouri, Saad

2000-01-01

This paper describes the application of wireless local area network (LAN) simulation modeling methods to the hybrid LAN architecture designed for supporting crew-computing tools aboard the International Space Station (ISS). These crew-computing tools, such as wearable computers and portable advisory systems, will provide crew members with real-time vehicle and payload status information and access to digital technical and scientific libraries, significantly enhancing human capabilities in space. A wireless network, therefore, will provide wearable computer and remote instruments with the high performance computational power needed by next-generation 'intelligent' software applications. Wireless network performance in such simulated environments is characterized by the sustainable throughput of data under different traffic conditions. This data will be used to help plan the addition of more access points supporting new modules and more nodes for increased network capacity as the ISS grows.

Arbitrarily shaped dual-stacked patch antennas: A hybrid FEM simulation

NASA Technical Reports Server (NTRS)

Gong, Jian; Volakis, John L.

1995-01-01

A dual-stacked patch antenna is analyzed using a hybrid finite element - boundary integral (FE-BI) method. The metallic patches of the antenna are modeled as perfectly electric conducting (PEC) plates stacked on top of two different dielectric layers. The antenna patches may be of any shape and the lower patch is fed by a coaxial cable from underneath the ground plane or by an aperture coupled microstrip line. The ability of the hybrid FEM technique for the stacked patch antenna characterization will be stressed, and the EM coupling mechanism is also discussed with the aid of the computed near field patterns around the patches.

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling.

PubMed

Kane, Patrick; Zollman, Kevin J S

2015-01-01

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the "hybrid equilibrium," to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith's Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory.

Nonlinear mode coupling theory of the lower-hybrid-drift instability

NASA Technical Reports Server (NTRS)

Drake, J. F.; Guzdar, P. N.; Hassam, A. B.; Huba, J. D.

1984-01-01

A nonlinear mode coupling theory of the lower-hybrid-drift instability is presented. A two-dimensional nonlinear wave equation is derived which describes lower-hybrid drift wave turbulence in the plane transverse to B (k.B = 0), and which is valid for finite beta, collisional and collisionless plasmas. The instability saturates by transferring energy from growing, long wavelength modes to damped, short wavelength modes. Detailed numerical results are presented which compare favorably to both recent computer simulations and experimental observations. Applications of this theory to space plasmas, the earth's magnetotail and the equatorial F region ionosphere, are discussed. Previously announced in STAR as N84-17734

Computer simulations of electromagnetic cool ion beam instabilities. [in near earth space

NASA Technical Reports Server (NTRS)

Gary, S. P.; Madland, C. D.; Schriver, D.; Winske, D.

1986-01-01

Electromagnetic ion beam instabilities driven by cool ion beams at propagation parallel or antiparallel to a uniform magnetic field are studied using computer simulations. The elements of linear theory applicable to electromagnetic ion beam instabilities and the simulations derived from a one-dimensional hybrid computer code are described. The quasi-linear regime of the right-hand resonant ion beam instability, and the gyrophase bunching of the nonlinear regime of the right-hand resonant and nonresonant instabilities are examined. It is detected that in the quasi-linear regime the instability saturation is due to a reduction in the beam core relative drift speed and an increase in the perpendicular-to-parallel beam temperature; in the nonlinear regime the instabilities saturate when half the initial beam drift kinetic energy density is converted to fluctuating magnetic field energy density.

Applications of hybrid and digital computation methods in aerospace-related sciences and engineering. [problem solving methods at the University of Houston

NASA Technical Reports Server (NTRS)

Huang, C. J.; Motard, R. L.

1978-01-01

The computing equipment in the engineering systems simulation laboratory of the Houston University Cullen College of Engineering is described and its advantages are summarized. The application of computer techniques in aerospace-related research psychology and in chemical, civil, electrical, industrial, and mechanical engineering is described in abstracts of 84 individual projects and in reprints of published reports. Research supports programs in acoustics, energy technology, systems engineering, and environment management as well as aerospace engineering.

Survey of computer programs for prediction of crash response and of its experimental validation

NASA Technical Reports Server (NTRS)

Kamat, M. P.

1976-01-01

The author seeks to critically assess the potentialities of the mathematical and hybrid simulators which predict post-impact response of transportation vehicles. A strict rigorous numerical analysis of a complex phenomenon like crash may leave a lot to be desired with regard to the fidelity of mathematical simulation. Hybrid simulations on the other hand which exploit experimentally observed features of deformations appear to hold a lot of promise. MARC, ANSYS, NONSAP, DYCAST, ACTION, WHAM II and KRASH are among some of the simulators examined for their capabilities with regard to prediction of post impact response of vehicles. A review of these simulators reveals that much more by way of an analysis capability may be desirable than what is currently available. NASA's crashworthiness testing program in conjunction with similar programs of various other agencies, besides generating a large data base, will be equally useful in the validation of new mathematical concepts of nonlinear analysis and in the successful extension of other techniques in crashworthiness.

Monte Carlo simulation of simultaneous radiation detection in the hybrid tomography system ClearPET-XPAD3/CT

NASA Astrophysics Data System (ADS)

Dávila, H. Olaya; Sevilla, A. C.; Castro, H. F.; Martínez, S. A.

2016-07-01

Using the Geant4 based simulation framework SciFW1, a detailed simulation was performed for a detector array in the hybrid tomography prototype for small animals called ClearPET / XPAD, which was built in the Centre de Physique des Particules de Marseille. The detector system consists of an array of phoswich scintillation detectors: LSO (Lutetium Oxy-ortosilicate doped with cerium Lu2SiO5:Ce) and LuYAP (Lutetium Ortoaluminate of Yttrium doped with cerium Lu0.7Y0.3AlO3:Ce) for Positron Emission Tomography (PET) and hybrid pixel detector XPAD for Computed Tomography (CT). Simultaneous acquisition of deposited energy and the corresponding time - position for each recorded event were analyzed, independently, for both detectors. interference between detection modules for PET and CT. Information about amount of radiation reaching each phoswich crystal and XPAD detector using a phantom in order to study the effectiveness by radiation attenuation and influence the positioning of the radioactive source 22Na was obtained. The simulation proposed will improve distribution of detectors rings and interference values will be taken into account in the new versions of detectors.

Fast and Accurate Hybrid Stream PCRTMSOLAR Radiative Transfer Model for Reflected Solar Spectrum Simulation in the Cloudy Atmosphere

NASA Technical Reports Server (NTRS)

Yang, Qiguang; Liu, Xu; Wu, Wan; Kizer, Susan; Baize, Rosemary R.

2016-01-01

A hybrid stream PCRTM-SOLAR model has been proposed for fast and accurate radiative transfer simulation. It calculates the reflected solar (RS) radiances with a fast coarse way and then, with the help of a pre-saved matrix, transforms the results to obtain the desired high accurate RS spectrum. The methodology has been demonstrated with the hybrid stream discrete ordinate (HSDO) radiative transfer (RT) model. The HSDO method calculates the monochromatic radiances using a 4-stream discrete ordinate method, where only a small number of monochromatic radiances are simulated with both 4-stream and a larger N-stream (N = 16) discrete ordinate RT algorithm. The accuracy of the obtained channel radiance is comparable to the result from N-stream moderate resolution atmospheric transmission version 5 (MODTRAN5). The root-mean-square errors are usually less than 5x10(exp -4) mW/sq cm/sr/cm. The computational speed is three to four-orders of magnitude faster than the medium speed correlated-k option MODTRAN5. This method is very efficient to simulate thousands of RS spectra under multi-layer clouds/aerosols and solar radiation conditions for climate change study and numerical weather prediction applications.

Scheduling of hybrid types of machines with two-machine flowshop as the first type and a single machine as the second type

NASA Astrophysics Data System (ADS)

Hsiao, Ming-Chih; Su, Ling-Huey

2018-02-01

This research addresses the problem of scheduling hybrid machine types, in which one type is a two-machine flowshop and another type is a single machine. A job is either processed on the two-machine flowshop or on the single machine. The objective is to determine a production schedule for all jobs so as to minimize the makespan. The problem is NP-hard since the two parallel machines problem was proved to be NP-hard. Simulated annealing algorithms are developed to solve the problem optimally. A mixed integer programming (MIP) is developed and used to evaluate the performance for two SAs. Computational experiments demonstrate the efficiency of the simulated annealing algorithms, the quality of the simulated annealing algorithms will also be reported.

A hybrid method for X-ray optics simulation: combining geometric ray-tracing and wavefront propagation

DOE PAGES

Shi, Xianbo; Reininger, Ruben; Sanchez del Rio, Manuel; ...

2014-05-15

A new method for beamline simulation combining ray-tracing and wavefront propagation is described. The 'Hybrid Method' computes diffraction effects when the beam is clipped by an aperture or mirror length and can also simulate the effect of figure errors in the optical elements when diffraction is present. The effect of different spatial frequencies of figure errors on the image is compared withSHADOWresults pointing to the limitations of the latter. The code has been benchmarked against the multi-electron version ofSRWin one dimension to show its validity in the case of fully, partially and non-coherent beams. The results demonstrate that the codemore » is considerably faster than the multi-electron version ofSRWand is therefore a useful tool for beamline design and optimization.« less

Simulation Concept - How to Exploit Tools for Computing Hybrids

DTIC Science & Technology

2010-06-01

biomolecular reactions ................................................................ 42  Figure 30: Overview of MATLAB Implementation...Figure 50: Adenine graphed using MATLAB (left) and OpenGL (right) ........................ 70  Figure 51: An overhead view of a thymine and adenine base...93  Figure 68: Response frequency solution from MATLAB

Refinements to the Graves and Pitarka (2010) Broadband Ground-Motion Simulation Method

DOE PAGES

Graves, Robert; Pitarka, Arben

2014-12-17

This brief article describes refinements to the Graves and Pitarka (2010) broadband ground-motion simulation methodology (GP2010 hereafter) that have been implemented in version 14.3 of the Southern California Earthquake Center (SCEC) Broadband Platform (BBP). The updated version of our method on the current SCEC BBP is referred to as GP14.3. Here, our simulation technique is a hybrid approach that combines low- and high-frequency motions computed with different methods into a single broadband response.

Micro- and meso-scale simulations of magnetospheric processes related to the aurora and substorm morphology

NASA Technical Reports Server (NTRS)

Swift, Daniel W.

1991-01-01

The primary methodology during the grant period has been the use of micro or meso-scale simulations to address specific questions concerning magnetospheric processes related to the aurora and substorm morphology. This approach, while useful in providing some answers, has its limitations. Many of the problems relating to the magnetosphere are inherently global and kinetic. Effort during the last year of the grant period has increasingly focused on development of a global-scale hybrid code to model the entire, coupled magnetosheath - magnetosphere - ionosphere system. In particular, numerical procedures for curvilinear coordinate generation and exactly conservative differencing schemes for hybrid codes in curvilinear coordinates have been developed. The new computer algorithms and the massively parallel computer architectures now make this global code a feasible proposition. Support provided by this project has played an important role in laying the groundwork for the eventual development or a global-scale code to model and forecast magnetospheric weather.

Bioinspired decision architectures containing host and microbiome processing units.

PubMed

Heyde, K C; Gallagher, P W; Ruder, W C

2016-09-27

Biomimetic robots have been used to explore and explain natural phenomena ranging from the coordination of ants to the locomotion of lizards. Here, we developed a series of decision architectures inspired by the information exchange between a host organism and its microbiome. We first modeled the biochemical exchanges of a population of synthetically engineered E. coli. We then built a physical, differential drive robot that contained an integrated, onboard computer vision system. A relay was established between the simulated population of cells and the robot's microcontroller. By placing the robot within a target-containing a two-dimensional arena, we explored how different aspects of the simulated cells and the robot's microcontroller could be integrated to form hybrid decision architectures. We found that distinct decision architectures allow for us to develop models of computation with specific strengths such as runtime efficiency or minimal memory allocation. Taken together, our hybrid decision architectures provide a new strategy for developing bioinspired control systems that integrate both living and nonliving components.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

PubMed

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-07-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

Computer-aided design comparisons of monolithic and hybrid MEM-tunable VCSELs

NASA Astrophysics Data System (ADS)

Ochoa, Edward M.; Nelson, Thomas R., Jr.; Blum-Spahn, Olga; Lott, James A.

2003-07-01

We report and use our micro-electro-mechanically tunable vertical cavity surface emitting laser (MEM-TVCSEL) computer-aided design methodology to investigate the resonant frequency design space for monolithic and hybrid MEM-TVCSELs. For various initial optical air gap thickness, we examine the sensitivity of monolithic or hybrid MEM-TVCSEL resonant frequency by simulating zero, two, and four percent variations in III-V material growth thickness. As expected, as initial optical airgap increases, tuning range decreases due to less coupling between the active region and the tuning mirror. However, each design has different resonant frequency sensitivity to variations in III-V growth parameters. In particular, since the monolithic design is comprised of III-V material, the shift in all growth thicknesses significantly shifts the resonant frequency response. However, for hybrid MEMTVCSELs, less shift results, since the lower reflector is an Au mirror with reflectivity independent of III-V growth variations. Finally, since the hybrid design is comprised of a MUMPS polysilicon mechanical actuator, pull-in voltage remains independent of the initial optical airgap between the tuning reflector and the III-V material. Conversely, as the initial airgap increases in the monolithic design, the pull-in voltage significantly increases.

Hybrid Reynolds-Averaged/Large-Eddy Simulations of a Coaxial Supersonic Free-Jet Experiment

NASA Technical Reports Server (NTRS)

Baurle, Robert A.; Edwards, Jack R.

2010-01-01

Reynolds-averaged and hybrid Reynolds-averaged/large-eddy simulations have been applied to a supersonic coaxial jet flow experiment. The experiment was designed to study compressible mixing flow phenomenon under conditions that are representative of those encountered in scramjet combustors. The experiment utilized either helium or argon as the inner jet nozzle fluid, and the outer jet nozzle fluid consisted of laboratory air. The inner and outer nozzles were designed and operated to produce nearly pressure-matched Mach 1.8 flow conditions at the jet exit. The purpose of the computational effort was to assess the state-of-the-art for each modeling approach, and to use the hybrid Reynolds-averaged/large-eddy simulations to gather insight into the deficiencies of the Reynolds-averaged closure models. The Reynolds-averaged simulations displayed a strong sensitivity to choice of turbulent Schmidt number. The initial value chosen for this parameter resulted in an over-prediction of the mixing layer spreading rate for the helium case, but the opposite trend was observed when argon was used as the injectant. A larger turbulent Schmidt number greatly improved the comparison of the results with measurements for the helium simulations, but variations in the Schmidt number did not improve the argon comparisons. The hybrid Reynolds-averaged/large-eddy simulations also over-predicted the mixing layer spreading rate for the helium case, while under-predicting the rate of mixing when argon was used as the injectant. The primary reason conjectured for the discrepancy between the hybrid simulation results and the measurements centered around issues related to the transition from a Reynolds-averaged state to one with resolved turbulent content. Improvements to the inflow conditions were suggested as a remedy to this dilemma. Second-order turbulence statistics were also compared to their modeled Reynolds-averaged counterparts to evaluate the effectiveness of common turbulence closure assumptions.

Investigation of thermal energy transport interface of hybrid graphene-carbon nanotube/polyethylene nanocomposites.

PubMed

Liu, Feng; Liu, Xuyang; Hu, Ning; Ning, Huiming; Atobe, Satoshi; Yan, Cheng; Mo, Fuhao; Fu, Shaoyun; Zhang, Jianyu; Wang, Yu; Mu, Xiaojing

2017-10-31

It is well known the thermal properties of three-dimensional (3-D) hybrid graphene (GR)-carbon nanotube (CNT) structures are not superior to that of the individual GR and CNT, however, the 3-D hybrid GR-CNT structures can effectively improve the thermal properties of polymer matrix. Therefore, understanding the thermal energy transport in the interface between polymer matrix and 3-D hybrid GR-CNT structure is essential. Here, the enhancement mechanism of interfacial thermal transport of hybrid GR-CNT structure was explored by applying non-equilibrium molecular dynamics (NEMD) simulations. Three different types of hybrid GR-CNT structures were built. The influences of CNT radius and CNT type for the hybrid GR-CNT on the interfacial thermal properties were also analyzed. Computational results show that among the three different types of hybrid GR-CNT structures, the Model-I, i.e., the covalent bond hybrid GR-CNT structures are of the best interfacial thermal properties. Meanwhile, the CNT radius of hybrid GR-CNT structure has a great influence on the interfacial thermal properties.

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

A New Approach to Modeling Jupiter's Magnetosphere

NASA Astrophysics Data System (ADS)

Fukazawa, K.; Katoh, Y.; Walker, R. J.; Kimura, T.; Tsuchiya, F.; Murakami, G.; Kita, H.; Tao, C.; Murata, K. T.

2017-12-01

The scales in planetary magnetospheres range from 10s of planetary radii to kilometers. For a number of years we have studied the magnetospheres of Jupiter and Saturn by using 3-dimensional magnetohydrodynamic (MHD) simulations. However, we have not been able to reach even the limits of the MHD approximation because of the large amount of computer resources required. Recently thanks to the progress in supercomputer systems, we have obtained the capability to simulate Jupiter's magnetosphere with 1000 times the number of grid points used in our previous simulations. This has allowed us to combine the high resolution global simulation with a micro-scale simulation of the Jovian magnetosphere. In particular we can combine a hybrid (kinetic ions and fluid electrons) simulation with the MHD simulation. In addition, the new capability enables us to run multi-parameter survey simulations of the Jupiter-solar wind system. In this study we performed a high-resolution simulation of Jovian magnetosphere to connect with the hybrid simulation, and lower resolution simulations under the various solar wind conditions to compare with Hisaki and Juno observations. In the high-resolution simulation we used a regular Cartesian gird with 0.15 RJ grid spacing and placed the inner boundary at 7 RJ. From these simulation settings, we provide the magnetic field out to around 20 RJ from Jupiter as a background field for the hybrid simulation. For the first time we have been able to resolve Kelvin Helmholtz waves on the magnetopause. We have investigated solar wind dynamic pressures between 0.01 and 0.09 nPa for a number of IMF values. These simulation data are open for the registered users to download the raw data. We have compared the results of these simulations with Hisaki auroral observations.

High-resolution multi-code implementation of unsteady Navier-Stokes flow solver based on paralleled overset adaptive mesh refinement and high-order low-dissipation hybrid schemes

NASA Astrophysics Data System (ADS)

Li, Gaohua; Fu, Xiang; Wang, Fuxin

2017-10-01

The low-dissipation high-order accurate hybrid up-winding/central scheme based on fifth-order weighted essentially non-oscillatory (WENO) and sixth-order central schemes, along with the Spalart-Allmaras (SA)-based delayed detached eddy simulation (DDES) turbulence model, and the flow feature-based adaptive mesh refinement (AMR), are implemented into a dual-mesh overset grid infrastructure with parallel computing capabilities, for the purpose of simulating vortex-dominated unsteady detached wake flows with high spatial resolutions. The overset grid assembly (OGA) process based on collection detection theory and implicit hole-cutting algorithm achieves an automatic coupling for the near-body and off-body solvers, and the error-and-try method is used for obtaining a globally balanced load distribution among the composed multiple codes. The results of flows over high Reynolds cylinder and two-bladed helicopter rotor show that the combination of high-order hybrid scheme, advanced turbulence model, and overset adaptive mesh refinement can effectively enhance the spatial resolution for the simulation of turbulent wake eddies.

Problems Related to Parallelization of CFD Algorithms on GPU, Multi-GPU and Hybrid Architectures

NASA Astrophysics Data System (ADS)

Biazewicz, Marek; Kurowski, Krzysztof; Ludwiczak, Bogdan; Napieraia, Krystyna

2010-09-01

Computational Fluid Dynamics (CFD) is one of the branches of fluid mechanics, which uses numerical methods and algorithms to solve and analyze fluid flows. CFD is used in various domains, such as oil and gas reservoir uncertainty analysis, aerodynamic body shapes optimization (e.g. planes, cars, ships, sport helmets, skis), natural phenomena analysis, numerical simulation for weather forecasting or realistic visualizations. CFD problem is very complex and needs a lot of computational power to obtain the results in a reasonable time. We have implemented a parallel application for two-dimensional CFD simulation with a free surface approximation (MAC method) using new hardware architectures, in particular multi-GPU and hybrid computing environments. For this purpose we decided to use NVIDIA graphic cards with CUDA environment due to its simplicity of programming and good computations performance. We used finite difference discretization of Navier-Stokes equations, where fluid is propagated over an Eulerian Grid. In this model, the behavior of the fluid inside the cell depends only on the properties of local, surrounding cells, therefore it is well suited for the GPU-based architecture. In this paper we demonstrate how to use efficiently the computing power of GPUs for CFD. Additionally, we present some best practices to help users analyze and improve the performance of CFD applications executed on GPU. Finally, we discuss various challenges around the multi-GPU implementation on the example of matrix multiplication.

Computational Modeling of Inflammation and Wound Healing

PubMed Central

Ziraldo, Cordelia; Mi, Qi; An, Gary; Vodovotz, Yoram

2013-01-01

Objective Inflammation is both central to proper wound healing and a key driver of chronic tissue injury via a positive-feedback loop incited by incidental cell damage. We seek to derive actionable insights into the role of inflammation in wound healing in order to improve outcomes for individual patients. Approach To date, dynamic computational models have been used to study the time evolution of inflammation in wound healing. Emerging clinical data on histo-pathological and macroscopic images of evolving wounds, as well as noninvasive measures of blood flow, suggested the need for tissue-realistic, agent-based, and hybrid mechanistic computational simulations of inflammation and wound healing. Innovation We developed a computational modeling system, Simple Platform for Agent-based Representation of Knowledge, to facilitate the construction of tissue-realistic models. Results A hybrid equation–agent-based model (ABM) of pressure ulcer formation in both spinal cord-injured and -uninjured patients was used to identify control points that reduce stress caused by tissue ischemia/reperfusion. An ABM of arterial restenosis revealed new dynamics of cell migration during neointimal hyperplasia that match histological features, but contradict the currently prevailing mechanistic hypothesis. ABMs of vocal fold inflammation were used to predict inflammatory trajectories in individuals, possibly allowing for personalized treatment. Conclusions The intertwined inflammatory and wound healing responses can be modeled computationally to make predictions in individuals, simulate therapies, and gain mechanistic insights. PMID:24527362

Computational Insights into the Stability and Folding Pathways of Human Telomeric DNA G-Quadruplexes.

PubMed

Luo, Di; Mu, Yuguang

2016-06-09

G-quadruplex is a noncanonical yet crucial secondary structure of nucleic acids, which has proven its importance in cell aging, anticancer therapies, gene expression, and genome stability. In this study, the stability and folding dynamics of human telomeric DNA G-quadruplexes were investigated via enhanced sampling techniques. First, temperature-replica exchange MD (REMD) simulations were employed to compare the thermal stabilities among the five established folding topologies. The hybrid-2 type adopted by extended human telomeric sequence is revealed to be the most stable conformation in our simulations. Next, the free energy landscapes and folding intermediates of the hybrid-1 and -2 types were investigated with parallel tempering metadynamics simulations in the well-tempered ensemble. It was observed that the N-glycosidic conformations of guanines can flip over to accommodate into the cyclic Hoogsteen H-bonding on G-tetrads in which they were not originally involved. Furthermore, a hairpin and a triplex intermediate were identified for the folding of the hybrid-1 type conformation, whereas for the hybrid-2 type, there were no folding intermediates observed from its free energy surface. However, the energy barrier from its native topology to the transition structure is found to be extremely high compared to that of the hybrid-1 type, which is consistent with our stability predictions from the REMD simulations. We hope the insights presented in this work can help to complement current understanding on the stability and dynamics of G-quadruplexes, which is necessary not only to stabilize the structures but also to intervene their formation in genome.

Numerical simulation and validation of SI-CAI hybrid combustion in a CAI/HCCI gasoline engine

NASA Astrophysics Data System (ADS)

Wang, Xinyan; Xie, Hui; Xie, Liyan; Zhang, Lianfang; Li, Le; Chen, Tao; Zhao, Hua

2013-02-01

SI-CAI hybrid combustion, also known as spark-assisted compression ignition (SACI), is a promising concept to extend the operating range of CAI (Controlled Auto-Ignition) and achieve the smooth transition between spark ignition (SI) and CAI in the gasoline engine. In this study, a SI-CAI hybrid combustion model (HCM) has been constructed on the basis of the 3-Zones Extended Coherent Flame Model (ECFM3Z). An ignition model is included to initiate the ECFM3Z calculation and induce the flame propagation. In order to precisely depict the subsequent auto-ignition process of the unburned fuel and air mixture independently after the initiation of flame propagation, the tabulated chemistry concept is adopted to describe the auto-ignition chemistry. The methodology for extracting tabulated parameters from the chemical kinetics calculations is developed so that both cool flame reactions and main auto-ignition combustion can be well captured under a wider range of thermodynamic conditions. The SI-CAI hybrid combustion model (HCM) is then applied in the three-dimensional computational fluid dynamics (3-D CFD) engine simulation. The simulation results are compared with the experimental data obtained from a single cylinder VVA engine. The detailed analysis of the simulations demonstrates that the SI-CAI hybrid combustion process is characterised with the early flame propagation and subsequent multi-site auto-ignition around the main flame front, which is consistent with the optical results reported by other researchers. Besides, the systematic study of the in-cylinder condition reveals the influence mechanism of the early flame propagation on the subsequent auto-ignition.

Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

PubMed

Chen, Yunjie; Roux, Benoît

2014-09-21

Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct equilibrium probability distribution with this prescription.

Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

NASA Astrophysics Data System (ADS)

Chen, Yunjie; Roux, Benoît

2014-09-01

Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct equilibrium probability distribution with this prescription.

Validation of High-Fidelity CFD/CAA Framework for Launch Vehicle Acoustic Environment Simulation against Scale Model Test Data

NASA Technical Reports Server (NTRS)

Liever, Peter A.; West, Jeffrey S.

2016-01-01

A hybrid Computational Fluid Dynamics and Computational Aero-Acoustics (CFD/CAA) modeling framework has been developed for launch vehicle liftoff acoustic environment predictions. The framework couples the existing highly-scalable NASA production CFD code, Loci/CHEM, with a high-order accurate discontinuous Galerkin solver developed in the same production framework, Loci/THRUST, to accurately resolve and propagate acoustic physics across the entire launch environment. Time-accurate, Hybrid RANS/LES CFD modeling is applied for predicting the acoustic generation physics at the plume source, and a high-order accurate unstructured discontinuous Galerkin (DG) method is employed to propagate acoustic waves away from the source across large distances using high-order accurate schemes. The DG solver is capable of solving 2nd, 3rd, and 4th order Euler solutions for non-linear, conservative acoustic field propagation. Initial application testing and validation has been carried out against high resolution acoustic data from the Ares Scale Model Acoustic Test (ASMAT) series to evaluate the capabilities and production readiness of the CFD/CAA system to resolve the observed spectrum of acoustic frequency content. This paper presents results from this validation and outlines efforts to mature and improve the computational simulation framework.

An innovative hybrid 3D analytic-numerical model for air breathing parallel channel counter-flow PEM fuel cells.

PubMed

Tavčar, Gregor; Katrašnik, Tomaž

2014-01-01

The parallel straight channel PEM fuel cell model presented in this paper extends the innovative hybrid 3D analytic-numerical (HAN) approach previously published by the authors with capabilities to address ternary diffusion systems and counter-flow configurations. The model's core principle is modelling species transport by obtaining a 2D analytic solution for species concentration distribution in the plane perpendicular to the cannel gas-flow and coupling consecutive 2D solutions by means of a 1D numerical pipe-flow model. Electrochemical and other nonlinear phenomena are coupled to the species transport by a routine that uses derivative approximation with prediction-iteration. The latter is also the core of the counter-flow computation algorithm. A HAN model of a laboratory test fuel cell is presented and evaluated against a professional 3D CFD simulation tool showing very good agreement between results of the presented model and those of the CFD simulation. Furthermore, high accuracy results are achieved at moderate computational times, which is owed to the semi-analytic nature and to the efficient computational coupling of electrochemical kinetics and species transport.

Surface passivation for tight-binding calculations of covalent solids.

PubMed

Bernstein, N

2007-07-04

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp(3) hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Surface passivation for tight-binding calculations of covalent solids

NASA Astrophysics Data System (ADS)

Bernstein, N.

2007-07-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Large Eddy/Reynolds-Averaged Navier-Stokes Simulations of CUBRC Base Heating Experiments

NASA Technical Reports Server (NTRS)

Salazar, Giovanni; Edwards, Jack R.; Amar, Adam J.

2012-01-01

ven with great advances in computational techniques and computing power during recent decades, the modeling of unsteady separated flows, such as those encountered in the wake of a re-entry vehicle, continues to be one of the most challenging problems in CFD. Of most interest to the aerothermodynamics community is accurately predicting transient heating loads on the base of a blunt body, which would result in reduced uncertainties and safety margins when designing a re-entry vehicle. However, the prediction of heat transfer can vary widely depending on the turbulence model employed. Therefore, selecting a turbulence model which realistically captures as much of the flow physics as possible will result in improved results. Reynolds Averaged Navier Stokes (RANS) models have become increasingly popular due to their good performance with attached flows, and the relatively quick turnaround time to obtain results. However, RANS methods cannot accurately simulate unsteady separated wake flows, and running direct numerical simulation (DNS) on such complex flows is currently too computationally expensive. Large Eddy Simulation (LES) techniques allow for the computation of the large eddies, which contain most of the Reynolds stress, while modeling the smaller (subgrid) eddies. This results in models which are more computationally expensive than RANS methods, but not as prohibitive as DNS. By complimenting an LES approach with a RANS model, a hybrid LES/RANS method resolves the larger turbulent scales away from surfaces with LES, and switches to a RANS model inside boundary layers. As pointed out by Bertin et al., this type of hybrid approach has shown a lot of promise for predicting turbulent flows, but work is needed to verify that these models work well in hypersonic flows. The very limited amounts of flight and experimental data available presents an additional challenge for researchers. Recently, a joint study by NASA and CUBRC has focused on collecting heat transfer data on the backshell of a scaled model of the Orion Multi-Purpose Crew Vehicle (MPCV). Heat augmentation effects due to the presence of cavities and RCS jet firings were also investigated. The high quality data produced by this effort presents a new set of data which can be used to assess the performance of CFD methods. In this work, a hybrid LES/RANS model developed at North Carolina State University (NCSU) is used to simulate several runs from these experiments, and evaluate the performance of high fidelity methods as compared to more typical RANS models. .

Village power options

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

Lilienthal, P.

1997-12-01

This paper describes three different computer codes which have been written to model village power applications. The reasons which have driven the development of these codes include: the existance of limited field data; diverse applications can be modeled; models allow cost and performance comparisons; simulations generate insights into cost structures. The models which are discussed are: Hybrid2, a public code which provides detailed engineering simulations to analyze the performance of a particular configuration; HOMER - the hybrid optimization model for electric renewables - which provides economic screening for sensitivity analyses; and VIPOR the village power model - which is amore » network optimization model for comparing mini-grids to individual systems. Examples of the output of these codes are presented for specific applications.« less

Parametric decay of oblique Alfvén waves in two-dimensional hybrid simulations.

PubMed

Verscharen, D; Marsch, E; Motschmann, U; Müller, J

2012-08-01

Certain types of plasma waves are known to become parametrically unstable under specific plasma conditions, in which the pump wave will decay into several daughter waves with different wavenumbers and frequencies. In the past, the related plasma instabilities have been treated analytically for various parameter regimes and by use of various numerical methods, yet the oblique propagation with respect to the background magnetic field has rarely been dealt with in two dimensions, mainly because of the high computational demand. Here we present a hybrid-simulation study of the parametric decay of a moderately oblique Alfvén wave having elliptical polarization. It is found that such a compressive wave can decay into waves with higher and lower wavenumbers than the pump.

A hybrid CS-SA intelligent approach to solve uncertain dynamic facility layout problems considering dependency of demands

NASA Astrophysics Data System (ADS)

Moslemipour, Ghorbanali

2018-07-01

This paper aims at proposing a quadratic assignment-based mathematical model to deal with the stochastic dynamic facility layout problem. In this problem, product demands are assumed to be dependent normally distributed random variables with known probability density function and covariance that change from period to period at random. To solve the proposed model, a novel hybrid intelligent algorithm is proposed by combining the simulated annealing and clonal selection algorithms. The proposed model and the hybrid algorithm are verified and validated using design of experiment and benchmark methods. The results show that the hybrid algorithm has an outstanding performance from both solution quality and computational time points of view. Besides, the proposed model can be used in both of the stochastic and deterministic situations.

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

Parallel Multivariate Spatio-Temporal Clustering of Large Ecological Datasets on Hybrid Supercomputers

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

Sreepathi, Sarat; Kumar, Jitendra; Mills, Richard T.

A proliferation of data from vast networks of remote sensing platforms (satellites, unmanned aircraft systems (UAS), airborne etc.), observational facilities (meteorological, eddy covariance etc.), state-of-the-art sensors, and simulation models offer unprecedented opportunities for scientific discovery. Unsupervised classification is a widely applied data mining approach to derive insights from such data. However, classification of very large data sets is a complex computational problem that requires efficient numerical algorithms and implementations on high performance computing (HPC) platforms. Additionally, increasing power, space, cooling and efficiency requirements has led to the deployment of hybrid supercomputing platforms with complex architectures and memory hierarchies like themore » Titan system at Oak Ridge National Laboratory. The advent of such accelerated computing architectures offers new challenges and opportunities for big data analytics in general and specifically, large scale cluster analysis in our case. Although there is an existing body of work on parallel cluster analysis, those approaches do not fully meet the needs imposed by the nature and size of our large data sets. Moreover, they had scaling limitations and were mostly limited to traditional distributed memory computing platforms. We present a parallel Multivariate Spatio-Temporal Clustering (MSTC) technique based on k-means cluster analysis that can target hybrid supercomputers like Titan. We developed a hybrid MPI, CUDA and OpenACC implementation that can utilize both CPU and GPU resources on computational nodes. We describe performance results on Titan that demonstrate the scalability and efficacy of our approach in processing large ecological data sets.« less

Crash simulation of hybrid structures considering the stress and strain rate dependent material behavior of thermoplastic materials

NASA Astrophysics Data System (ADS)

Hopmann, Ch.; Schöngart, M.; Weber, M.; Klein, J.

2015-05-01

Thermoplastic materials are more and more used as a light weight replacement for metal, especially in the automotive industry. Since these materials do not provide the mechanical properties, which are required to manufacture supporting elements like an auto body or a cross bearer, plastics are combined with metals in so called hybrid structures. Normally, the plastics components are joined to the metal structures using different technologies like welding or screwing. Very often, the hybrid structures are made of flat metal parts, which are stiffened by a reinforcement structure made of thermoplastic materials. The loads on these structures are very often impulsive, for example in the crash situation of an automobile. Due to the large stiffness variation of metal and thermoplastic materials, complex states of stress and very high local strain rates occur in the contact zone under impact conditions. Since the mechanical behavior of thermoplastic materials is highly dependent on these types of load, the crash failure of metal plastic hybrid parts is very complex. The problem is that the normally used strain rate dependent elastic/plastic material models are not capable to simulate the mechanical behavior of thermoplastic materials depended on the state of stress. As part of a research project, a method to simulate the mechanical behavior of hybrid structures under impact conditions is developed at the IKV. For this purpose, a specimen for the measurement of mechanical properties dependet on the state of stress and a method for the strain rate depended characterization of thermoplastic materials were developed. In the second step impact testing is performed. A hybrid structure made from a metal sheet and a reinforcement structure of a Polybutylenterephthalat Polycarbonate blend is tested under impact conditions. The measured stress and strain rate depended material data are used to simulate the mechanical behavior of the hybrid structure under highly dynamic load with impact velocities up to 5 m/s. The mechanical behavior of the plastics structure is simulated using a quadratic yield surface, which takes the state of stress and the strain rate into account. The FE model is made from mid surface elements to reduce the computing time.

Modeling and Validation of Lithium-ion Automotive Battery Packs (SAE 2013-01-1539)

EPA Science Inventory

The Advanced Light-Duty Powertrain and Hybrid Analysis (ALPHA) tool was created by EPA to evaluate the Greenhouse Gas (GHG) emissions of Light-Duty (LD) vehicles. It is a physics-based, forward-looking, full vehicle computer simulator capable of analyzing various vehicle types c...

When Worlds Collide: An Augmented Reality Check

ERIC Educational Resources Information Center

Villano, Matt

2008-01-01

The technology is simple: Mobile technologies such as handheld computers and global positioning systems work in sync to create an alternate, hybrid world that mixes virtual characters with the actual physical environment. The result is a digital simulation that offers powerful game-playing opportunities and allows students to become more engaged…

Benchmarking and Modeling of a Conventional Mid-Size Car Using ALPHA (SAE Paper 2015-01-1140)

EPA Science Inventory

The Advanced Light-Duty Powertrain and Hybrid Analysis (ALPHA) modeling tool was created by EPA to estimate greenhouse gas (GHG) emissions of light-duty vehicles. ALPHA is a physics-based, forward-looking, full vehicle computer simulation capable of analyzing various vehicle type...

Analysis of hydrodynamic fluctuations in heterogeneous adjacent multidomains in shear flow

NASA Astrophysics Data System (ADS)

Bian, Xin; Deng, Mingge; Tang, Yu-Hang; Karniadakis, George Em

2016-03-01

We analyze hydrodynamic fluctuations of a hybrid simulation under shear flow. The hybrid simulation is based on the Navier-Stokes (NS) equations on one domain and dissipative particle dynamics (DPD) on the other. The two domains overlap, and there is an artificial boundary for each one within the overlapping region. To impose the artificial boundary of the NS solver, a simple spatial-temporal averaging is performed on the DPD simulation. In the artificial boundary of the particle simulation, four popular strategies of constraint dynamics are implemented, namely the Maxwell buffer [Hadjiconstantinou and Patera, Int. J. Mod. Phys. C 08, 967 (1997), 10.1142/S0129183197000837], the relaxation dynamics [O'Connell and Thompson, Phys. Rev. E 52, R5792 (1995), 10.1103/PhysRevE.52.R5792], the least constraint dynamics [Nie et al., J. Fluid Mech. 500, 55 (2004), 10.1017/S0022112003007225; Werder et al., J. Comput. Phys. 205, 373 (2005), 10.1016/j.jcp.2004.11.019], and the flux imposition [Flekkøy et al., Europhys. Lett. 52, 271 (2000), 10.1209/epl/i2000-00434-8], to achieve a target mean value given by the NS solver. Going beyond the mean flow field of the hybrid simulations, we investigate the hydrodynamic fluctuations in the DPD domain. Toward that end, we calculate the transversal autocorrelation functions of the fluctuating variables in k space to evaluate the generation, transport, and dissipation of fluctuations in the presence of a hybrid interface. We quantify the unavoidable errors in the fluctuations, due to both the truncation of the domain and the constraint dynamics performed in the artificial boundary. Furthermore, we compare the four methods of constraint dynamics and demonstrate how to reduce the errors in fluctuations. The analysis and findings of this work are directly applicable to other hybrid simulations of fluid flow with thermal fluctuations.

Aeroacoustic Simulation of a Nose Landing Gear in an Open Jet Facility Using FUN3D

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Lockard, David P.; Khorrami, Mehdi R.; Carlson, Jan-Renee

2012-01-01

Numerical simulations have been performed for a partially-dressed, cavity-closed nose landing gear configuration that was tested in NASA Langley s closed-wall Basic Aerodynamic Research Tunnel (BART) and in the University of Florida s open-jet acoustic facility known as UFAFF. The unstructured-grid flow solver, FUN3D, developed at NASA Langley Research center is used to compute the unsteady flow field for this configuration. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these computations. Time-averaged and instantaneous solutions compare favorably with the measured data. Unsteady flowfield data obtained from the FUN3D code are used as input to a Ffowcs Williams-Hawkings noise propagation code to compute the sound pressure levels at microphones placed in the farfield. Significant improvement in predicted noise levels is obtained when the flowfield data from the open jet UFAFF simulations is used as compared to the case using flowfield data from the closed-wall BART configuration.

Structured Overlapping Grid Simulations of Contra-rotating Open Rotor Noise

NASA Technical Reports Server (NTRS)

Housman, Jeffrey A.; Kiris, Cetin C.

2015-01-01

Computational simulations using structured overlapping grids with the Launch Ascent and Vehicle Aerodynamics (LAVA) solver framework are presented for predicting tonal noise generated by a contra-rotating open rotor (CROR) propulsion system. A coupled Computational Fluid Dynamics (CFD) and Computational AeroAcoustics (CAA) numerical approach is applied. Three-dimensional time-accurate hybrid Reynolds Averaged Navier-Stokes/Large Eddy Simulation (RANS/LES) CFD simulations are performed in the inertial frame, including dynamic moving grids, using a higher-order accurate finite difference discretization on structured overlapping grids. A higher-order accurate free-stream preserving metric discretization with discrete enforcement of the Geometric Conservation Law (GCL) on moving curvilinear grids is used to create an accurate, efficient, and stable numerical scheme. The aeroacoustic analysis is based on a permeable surface Ffowcs Williams-Hawkings (FW-H) approach, evaluated in the frequency domain. A time-step sensitivity study was performed using only the forward row of blades to determine an adequate time-step. The numerical approach is validated against existing wind tunnel measurements.

Improving precipitation forecast with hybrid 3DVar and time-lagged ensembles in a heavy rainfall event

NASA Astrophysics Data System (ADS)

Wang, Yuanbing; Min, Jinzhong; Chen, Yaodeng; Huang, Xiang-Yu; Zeng, Mingjian; Li, Xin

2017-01-01

This study evaluates the performance of three-dimensional variational (3DVar) and a hybrid data assimilation system using time-lagged ensembles in a heavy rainfall event. The time-lagged ensembles are constructed by sampling from a moving time window of 3 h along a model trajectory, which is economical and easy to implement. The proposed hybrid data assimilation system introduces flow-dependent error covariance derived from time-lagged ensemble into variational cost function without significantly increasing computational cost. Single observation tests are performed to document characteristic of the hybrid system. The sensitivity of precipitation forecasts to ensemble covariance weight and localization scale is investigated. Additionally, the TLEn-Var is evaluated and compared to the ETKF(ensemble transformed Kalman filter)-based hybrid assimilation within a continuously cycling framework, through which new hybrid analyses are produced every 3 h over 10 days. The 24 h accumulated precipitation, moisture, wind are analyzed between 3DVar and the hybrid assimilation using time-lagged ensembles. Results show that model states and precipitation forecast skill are improved by the hybrid assimilation using time-lagged ensembles compared with 3DVar. Simulation of the precipitable water and structure of the wind are also improved. Cyclonic wind increments are generated near the rainfall center, leading to an improved precipitation forecast. This study indicates that the hybrid data assimilation using time-lagged ensembles seems like a viable alternative or supplement in the complex models for some weather service agencies that have limited computing resources to conduct large size of ensembles.

The control of a parallel hybrid-electric propulsion system for a small unmanned aerial vehicle using a CMAC neural network.

PubMed

Harmon, Frederick G; Frank, Andrew A; Joshi, Sanjay S

2005-01-01

A Simulink model, a propulsion energy optimization algorithm, and a CMAC controller were developed for a small parallel hybrid-electric unmanned aerial vehicle (UAV). The hybrid-electric UAV is intended for military, homeland security, and disaster-monitoring missions involving intelligence, surveillance, and reconnaissance (ISR). The Simulink model is a forward-facing simulation program used to test different control strategies. The flexible energy optimization algorithm for the propulsion system allows relative importance to be assigned between the use of gasoline, electricity, and recharging. A cerebellar model arithmetic computer (CMAC) neural network approximates the energy optimization results and is used to control the parallel hybrid-electric propulsion system. The hybrid-electric UAV with the CMAC controller uses 67.3% less energy than a two-stroke gasoline-powered UAV during a 1-h ISR mission and 37.8% less energy during a longer 3-h ISR mission.

Hybrid 3-D rocket trajectory program. Part 1: Formulation and analysis. Part 2: Computer programming and user's instruction. [computerized simulation using three dimensional motion analysis

NASA Technical Reports Server (NTRS)

Huang, L. C. P.; Cook, R. A.

1973-01-01

Models utilizing various sub-sets of the six degrees of freedom are used in trajectory simulation. A 3-D model with only linear degrees of freedom is especially attractive, since the coefficients for the angular degrees of freedom are the most difficult to determine and the angular equations are the most time consuming for the computer to evaluate. A computer program is developed that uses three separate subsections to predict trajectories. A launch rail subsection is used until the rocket has left its launcher. The program then switches to a special 3-D section which computes motions in two linear and one angular degrees of freedom. When the rocket trims out, the program switches to the standard, three linear degrees of freedom model.

A model-reduction approach in micromechanics of materials preserving the variational structure of constitutive relations

NASA Astrophysics Data System (ADS)

Michel, Jean-Claude; Suquet, Pierre

2016-05-01

In 2003 the authors proposed a model-reduction technique, called the Nonuniform Transformation Field Analysis (NTFA), based on a decomposition of the local fields of internal variables on a reduced basis of modes, to analyze the effective response of composite materials. The present study extends and improves on this approach in different directions. It is first shown that when the constitutive relations of the constituents derive from two potentials, this structure is passed to the NTFA model. Another structure-preserving model, the hybrid NTFA model of Fritzen and Leuschner, is analyzed and found to differ (slightly) from the primal NTFA model (it does not exhibit the same variational upper bound character). To avoid the "on-line" computation of local fields required by the hybrid model, new reduced evolution equations for the reduced variables are proposed, based on an expansion to second order (TSO) of the potential of the hybrid model. The coarse dynamics can then be entirely expressed in terms of quantities which can be pre-computed once for all. Roughly speaking, these pre-computed quantities depend only on the average and fluctuations per phase of the modes and of the associated stress fields. The accuracy of the new NTFA-TSO model is assessed by comparison with full-field simulations. The acceleration provided by the new coarse dynamics over the full-field computations (and over the hybrid model) is then spectacular, larger by three orders of magnitude than the acceleration due to the sole reduction of unknowns.

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling

PubMed Central

Kane, Patrick; Zollman, Kevin J. S.

2015-01-01

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the “hybrid equilibrium,” to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith’s Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory. PMID:26348617

Hybrid Configuration of Darrieus and Savonius Rotors for Stand-alone Power Systems

NASA Astrophysics Data System (ADS)

Wakui, Tetsuya; Tanzawa, Yoshiaki; Hashizume, Takumi; Nagao, Toshio

The suitable hybrid configuration of Darrieus lift-type and Savonius drag-type rotors for stand-alone wind turbine-generator systems is discussed using our dynamic simulation model. Two types of hybrid configurations are taken up: Type-A installs the Savonius rotor inside the Darrieus rotor and Type-B installs the Savonius rotor outside the Darrieus rotor. The computed results of the output characteristics and the dynamic behaviors of the system operated at the maximum power coefficient points show that Type-A, which has fine operating behavior to wind speed changes and can be compactly designed because of a shorter rotational shaft, is an effective way for self-controlled stand-alone small-scale systems.

Comparative study on performances of a continuously variable transmission used in two different powertrain architectures

NASA Astrophysics Data System (ADS)

Sibiceanu, A. R.; Ivan, F.; Nicolae, V.; Iorga, A.; Cioroianu, C.

2017-08-01

Given the importance of reducing carbon emissions from road transport, price and security of oil supply, hybrid electric vehicle can provide a viable alternative solution to conventional vehicles, equipped with thermal engines, which use fossil fuels. Based on the growing trends of new vehicles sales, which include hybrid and electric vehicles closely associated with their use in terms of harmful emissions, strict regulations are established. In this paper were created models of thermal and hybrid electric powertrains groups, using computer simulation program AVL Cruise, making a comparative study using petroleum fuels for continuously variable transmission. The results obtained highlights both fuel consumption as well as pollutant emissions.

A hybrid linear/nonlinear training algorithm for feedforward neural networks.

PubMed

McLoone, S; Brown, M D; Irwin, G; Lightbody, A

1998-01-01

This paper presents a new hybrid optimization strategy for training feedforward neural networks. The algorithm combines gradient-based optimization of nonlinear weights with singular value decomposition (SVD) computation of linear weights in one integrated routine. It is described for the multilayer perceptron (MLP) and radial basis function (RBF) networks and then extended to the local model network (LMN), a new feedforward structure in which a global nonlinear model is constructed from a set of locally valid submodels. Simulation results are presented demonstrating the superiority of the new hybrid training scheme compared to second-order gradient methods. It is particularly effective for the LMN architecture where the linear to nonlinear parameter ratio is large.

An Application of CFD to Guide Forced Boundary-Layer Transition for Low-Speed Tests of a Hybrid Wing-Body Configuration

NASA Technical Reports Server (NTRS)

Luckring, James M.; Deere, Karen A.; Childs, Robert E.; Stremel, Paul M.; Long, Kurtis R.

2016-01-01

A hybrid transition trip-dot sizing and placement test technique was developed in support of recent experimental research on a hybrid wing-body configuration under study for the NASA Environmentally Responsible Aviation project. The approach combines traditional methods with Computational Fluid Dynamics. The application had three-dimensional boundary layers that were simulated with either fully turbulent or transitional flow models using established Reynolds-Averaged Navier-Stokes methods. Trip strip effectiveness was verified experimentally using infrared thermography during a low-speed wind tunnel test. Although the work was performed on one specific configuration, the process was based on fundamental flow physics and could be applicable to other configurations.

Molecular Dynamics Studies of Self-Assembling Biomolecules and DNA-functionalized Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Cho, Vince Y.

This thesis is organized as following. In Chapter 2, we use fully atomistic MD simulations to study the conformation of DNA molecules that link gold nanoparticles to form nanoparticle superlattice crystals. In Chapter 3, we study the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber by using CGMD simulations. Compared to fully atomistic MD simulations, CGMD simulations prove to be computationally cost-efficient and reasonably accurate for exploring self-assembly, and are used in all subsequent chapters. In Chapter 4, we apply CGMD methods to study the self-assembly of small molecule-DNA hybrid (SMDH) building blocks into well-defined cage-like dimers, and reveal the role of kinetics and thermodynamics in this process. In Chapter 5, we extend the CGMD model for this system and find that the assembly of SMDHs can be fine-tuned by changing parameters. In Chapter 6, we explore superlattice crystal structures of DNA-functionalized gold nanoparticles (DNA-AuNP) with the CGMD model and compare the hybridization.

A study of digital holographic filters generation. Phase 2: Digital data communication system, volume 1

NASA Technical Reports Server (NTRS)

Ingels, F. M.; Mo, C. D.

1978-01-01

An empirical study of the performance of the Viterbi decoders in bursty channels was carried out and an improved algebraic decoder for nonsystematic codes was developed. The hybrid algorithm was simulated for the (2,1), k = 7 code on a computer using 20 channels having various error statistics, ranging from pure random error to pure bursty channels. The hybrid system outperformed both the algebraic and the Viterbi decoders in every case, except the 1% random error channel where the Viterbi decoder had one bit less decoding error.

Hybrid transfer-matrix FDTD method for layered periodic structures.

PubMed

Deinega, Alexei; Belousov, Sergei; Valuev, Ilya

2009-03-15

A hybrid transfer-matrix finite-difference time-domain (FDTD) method is proposed for modeling the optical properties of finite-width planar periodic structures. This method can also be applied for calculation of the photonic bands in infinite photonic crystals. We describe the procedure of evaluating the transfer-matrix elements by a special numerical FDTD simulation. The accuracy of the new method is tested by comparing computed transmission spectra of a 32-layered photonic crystal composed of spherical or ellipsoidal scatterers with the results of direct FDTD and layer-multiple-scattering calculations.

GRAPE project

NASA Astrophysics Data System (ADS)

Makino, Junichiro

2002-12-01

We overview our GRAvity PipE (GRAPE) project to develop special-purpose computers for astrophysical N-body simulations. The basic idea of GRAPE is to attach a custom-build computer dedicated to the calculation of gravitational interaction between particles to a general-purpose programmable computer. By this hybrid architecture, we can achieve both a wide range of applications and very high peak performance. Our newest machine, GRAPE-6, achieved the peak speed of 32 Tflops, and sustained performance of 11.55 Tflops, for the total budget of about 4 million USD. We also discuss relative advantages of special-purpose and general-purpose computers and the future of high-performance computing for science and technology.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

PubMed Central

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-01-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 PMID:26753008

Non-linear quantum-classical scheme to simulate non-equilibrium strongly correlated fermionic many-body dynamics

PubMed Central

Kreula, J. M.; Clark, S. R.; Jaksch, D.

2016-01-01

We propose a non-linear, hybrid quantum-classical scheme for simulating non-equilibrium dynamics of strongly correlated fermions described by the Hubbard model in a Bethe lattice in the thermodynamic limit. Our scheme implements non-equilibrium dynamical mean field theory (DMFT) and uses a digital quantum simulator to solve a quantum impurity problem whose parameters are iterated to self-consistency via a classically computed feedback loop where quantum gate errors can be partly accounted for. We analyse the performance of the scheme in an example case. PMID:27609673

Computer Simulations of Ion Transport in Polymer Electrolyte Membranes.

PubMed

Mogurampelly, Santosh; Borodin, Oleg; Ganesan, Venkat

2016-06-07

Understanding the mechanisms and optimizing ion transport in polymer membranes have been the subject of active research for more than three decades. We present an overview of the progress and challenges involved with the modeling and simulation aspects of the ion transport properties of polymer membranes. We are concerned mainly with atomistic and coarser level simulation studies and discuss some salient work in the context of pure binary and single ion conducting polymer electrolytes, polymer nanocomposites, block copolymers, and ionic liquid-based hybrid electrolytes. We conclude with an outlook highlighting future directions.

A computational analysis of the ballistic performance of light-weight hybrid composite armors

NASA Astrophysics Data System (ADS)

Grujicic, M.; Pandurangan, B.; Koudela, K. L.; Cheeseman, B. A.

2006-11-01

The ability of hybrid light-weight fiber-reinforced polymer-matrix composite laminate armor to withstand the impact of a fragment simulating projectile (FSP) is investigated using a non-linear dynamics transient computational analysis. The hybrid armor is constructed using various combinations and stacking sequences of a high-strength/high-stiffness carbon fiber-reinforced epoxy (CFRE) and a high-ductility/high-toughness Kevlar fiber-reinforced epoxy (KFRE) composite laminates of different thicknesses. The results obtained indicate that at a fixed thickness of the armor both the stacking sequence and the number of CFRE/KFRE laminates substantially affect the ballistic performance of the armor. Specifically, it is found that the armor consisting of one layer of KFRE and one layer of CFRE, with KFRE laminate constituting the outer surface of the armor, possesses the maximum resistance towards the projectile-induced damage and failure. The results obtained are rationalized using an analysis of the elastic wave reflection and transmission behavior at the inter-laminate and laminate/air interfaces.

Computed versus measured ion velocity distribution functions in a Hall effect thruster

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

Garrigues, L.; CNRS, LAPLACE, F-31062 Toulouse; Mazouffre, S.

2012-06-01

We compare time-averaged and time-varying measured and computed ion velocity distribution functions in a Hall effect thruster for typical operating conditions. The ion properties are measured by means of laser induced fluorescence spectroscopy. Simulations of the plasma properties are performed with a two-dimensional hybrid model. In the electron fluid description of the hybrid model, the anomalous transport responsible for the electron diffusion across the magnetic field barrier is deduced from the experimental profile of the time-averaged electric field. The use of a steady state anomalous mobility profile allows the hybrid model to capture some properties like the time-averaged ion meanmore » velocity. Yet, the model fails at reproducing the time evolution of the ion velocity. This fact reveals a complex underlying physics that necessitates to account for the electron dynamics over a short time-scale. This study also shows the necessity for electron temperature measurements. Moreover, the strength of the self-magnetic field due to the rotating Hall current is found negligible.« less

Dual learning processes underlying human decision-making in reversal learning tasks: functional significance and evidence from the model fit to human behavior

PubMed Central

Bai, Yu; Katahira, Kentaro; Ohira, Hideki

2014-01-01

Humans are capable of correcting their actions based on actions performed in the past, and this ability enables them to adapt to a changing environment. The computational field of reinforcement learning (RL) has provided a powerful explanation for understanding such processes. Recently, the dual learning system, modeled as a hybrid model that incorporates value update based on reward-prediction error and learning rate modulation based on the surprise signal, has gained attention as a model for explaining various neural signals. However, the functional significance of the hybrid model has not been established. In the present study, we used computer simulation in a reversal learning task to address functional significance in a probabilistic reversal learning task. The hybrid model was found to perform better than the standard RL model in a large parameter setting. These results suggest that the hybrid model is more robust against the mistuning of parameters compared with the standard RL model when decision-makers continue to learn stimulus-reward contingencies, which can create abrupt changes. The parameter fitting results also indicated that the hybrid model fit better than the standard RL model for more than 50% of the participants, which suggests that the hybrid model has more explanatory power for the behavioral data than the standard RL model. PMID:25161635

Simulation of electricity demand in a remote island for optimal planning of a hybrid renewable energy system

NASA Astrophysics Data System (ADS)

Koskinas, Aristotelis; Zacharopoulou, Eleni; Pouliasis, George; Engonopoulos, Ioannis; Mavroyeoryos, Konstantinos; Deligiannis, Ilias; Karakatsanis, Georgios; Dimitriadis, Panayiotis; Iliopoulou, Theano; Koutsoyiannis, Demetris; Tyralis, Hristos

2017-04-01

We simulate the electrical energy demand in the remote island of Astypalaia. To this end we first obtain information regarding the local socioeconomic conditions and energy demand. Secondly, the available hourly demand data are analysed at various time scales (hourly, weekly, daily, seasonal). The cross-correlations between the electrical energy demand and the mean daily temperature as well as other climatic variables for the same time period are computed. Also, we investigate the cross-correlation between those climatic variables and other variables related to renewable energy resources from numerous observations around the globe in order to assess the impact of each one to a hybrid renewable energy system. An exploratory data analysis including all variables is performed with the purpose to find hidden relationships. Finally, the demand is simulated considering all the periodicities found in the analysis. The simulation time series will be used in the development of a framework for planning of a hybrid renewable energy system in Astypalaia. Acknowledgement: This research is conducted within the frame of the undergraduate course "Stochastic Methods in Water Resources" of the National Technical University of Athens (NTUA). The School of Civil Engineering of NTUA provided moral support for the participation of the students in the Assembly.

Throughput and Energy Efficiency of a Cooperative Hybrid ARQ Protocol for Underwater Acoustic Sensor Networks

PubMed Central

Ghosh, Arindam; Lee, Jae-Won; Cho, Ho-Shin

2013-01-01

Due to its efficiency, reliability and better channel and resource utilization, cooperative transmission technologies have been attractive options in underwater as well as terrestrial sensor networks. Their performance can be further improved if merged with forward error correction (FEC) techniques. In this paper, we propose and analyze a retransmission protocol named Cooperative-Hybrid Automatic Repeat reQuest (C-HARQ) for underwater acoustic sensor networks, which exploits both the reliability of cooperative ARQ (CARQ) and the efficiency of incremental redundancy-hybrid ARQ (IR-HARQ) using rate-compatible punctured convolution (RCPC) codes. Extensive Monte Carlo simulations are performed to investigate the performance of the protocol, in terms of both throughput and energy efficiency. The results clearly reveal the enhancement in performance achieved by the C-HARQ protocol, which outperforms both CARQ and conventional stop and wait ARQ (S&W ARQ). Further, using computer simulations, optimum values of various network parameters are estimated so as to extract the best performance out of the C-HARQ protocol. PMID:24217359

Hybrid-PIC Computer Simulation of the Plasma and Erosion Processes in Hall Thrusters

NASA Technical Reports Server (NTRS)

Hofer, Richard R.; Katz, Ira; Mikellides, Ioannis G.; Gamero-Castano, Manuel

2010-01-01

HPHall software simulates and tracks the time-dependent evolution of the plasma and erosion processes in the discharge chamber and near-field plume of Hall thrusters. HPHall is an axisymmetric solver that employs a hybrid fluid/particle-in-cell (Hybrid-PIC) numerical approach. HPHall, originally developed by MIT in 1998, was upgraded to HPHall-2 by the Polytechnic University of Madrid in 2006. The Jet Propulsion Laboratory has continued the development of HPHall-2 through upgrades to the physical models employed in the code, and the addition of entirely new ones. Primary among these are the inclusion of a three-region electron mobility model that more accurately depicts the cross-field electron transport, and the development of an erosion sub-model that allows for the tracking of the erosion of the discharge chamber wall. The code is being developed to provide NASA science missions with a predictive tool of Hall thruster performance and lifetime that can be used to validate Hall thrusters for missions.

Dynamics and Control of Flexible Space Vehicles

NASA Technical Reports Server (NTRS)

Likins, P. W.

1970-01-01

The purpose of this report is twofold: (1) to survey the established analytic procedures for the simulation of controlled flexible space vehicles, and (2) to develop in detail methods that employ a combination of discrete and distributed ("modal") coordinates, i.e., the hybrid-coordinate methods. Analytic procedures are described in three categories: (1) discrete-coordinate methods, (2) hybrid-coordinate methods, and (3) vehicle normal-coordinate methods. Each of these approaches is described and analyzed for its advantages and disadvantages, and each is found to have an area of applicability. The hybrid-coordinate method combines the efficiency of the vehicle normal-coordinate method with the versatility of the discrete-coordinate method, and appears to have the widest range of practical application. The results in this report have practical utility in two areas: (1) complex digital computer simulation of flexible space vehicles of arbitrary configuration subject to realistic control laws, and (2) preliminary control system design based on transfer functions for linearized models of dynamics and control laws.

Multi-objective component sizing of a power-split plug-in hybrid electric vehicle powertrain using Pareto-based natural optimization machines

NASA Astrophysics Data System (ADS)

Mozaffari, Ahmad; Vajedi, Mahyar; Chehresaz, Maryyeh; Azad, Nasser L.

2016-03-01

The urgent need to meet increasingly tight environmental regulations and new fuel economy requirements has motivated system science researchers and automotive engineers to take advantage of emerging computational techniques to further advance hybrid electric vehicle and plug-in hybrid electric vehicle (PHEV) designs. In particular, research has focused on vehicle powertrain system design optimization, to reduce the fuel consumption and total energy cost while improving the vehicle's driving performance. In this work, two different natural optimization machines, namely the synchronous self-learning Pareto strategy and the elitism non-dominated sorting genetic algorithm, are implemented for component sizing of a specific power-split PHEV platform with a Toyota plug-in Prius as the baseline vehicle. To do this, a high-fidelity model of the Toyota plug-in Prius is employed for the numerical experiments using the Autonomie simulation software. Based on the simulation results, it is demonstrated that Pareto-based algorithms can successfully optimize the design parameters of the vehicle powertrain.

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

A hybrid artificial bee colony algorithm and pattern search method for inversion of particle size distribution from spectral extinction data

NASA Astrophysics Data System (ADS)

Wang, Li; Li, Feng; Xing, Jian

2017-10-01

In this paper, a hybrid artificial bee colony (ABC) algorithm and pattern search (PS) method is proposed and applied for recovery of particle size distribution (PSD) from spectral extinction data. To be more useful and practical, size distribution function is modelled as the general Johnson's ? function that can overcome the difficulty of not knowing the exact type beforehand encountered in many real circumstances. The proposed hybrid algorithm is evaluated through simulated examples involving unimodal, bimodal and trimodal PSDs with different widths and mean particle diameters. For comparison, all examples are additionally validated by the single ABC algorithm. In addition, the performance of the proposed algorithm is further tested by actual extinction measurements with real standard polystyrene samples immersed in water. Simulation and experimental results illustrate that the hybrid algorithm can be used as an effective technique to retrieve the PSDs with high reliability and accuracy. Compared with the single ABC algorithm, our proposed algorithm can produce more accurate and robust inversion results while taking almost comparative CPU time over ABC algorithm alone. The superiority of ABC and PS hybridization strategy in terms of reaching a better balance of estimation accuracy and computation effort increases its potentials as an excellent inversion technique for reliable and efficient actual measurement of PSD.

Intra-Beam and Touschek Scattering Computations for Beam with Non-Gaussian Longitudinal Distributions

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

Xiao, A.; Borland, M.

Both intra-beamscattering (IBS) and the Touschek effect become prominent formulti-bend-achromat- (MBA-) based ultra-low-emittance storage rings. To mitigate the transverse emittance degradation and obtain a reasonably long beam lifetime, a higher harmonic rf cavity (HHC) is often proposed to lengthen the bunch. The use of such a cavity results in a non-gaussian longitudinal distribution. However, common methods for computing IBS and Touschek scattering assume Gaussian distributions. Modifications have been made to several simulation codes that are part of the elegant [1] toolkit to allow these computations for arbitrary longitudinal distributions. After describing thesemodifications, we review the results of detailed simulations formore » the proposed hybrid seven-bend-achromat (H7BA) upgrade lattice [2] for the Advanced Photon Source.« less

Hybrid Metaheuristics for Solving a Fuzzy Single Batch-Processing Machine Scheduling Problem

PubMed Central

Molla-Alizadeh-Zavardehi, S.; Tavakkoli-Moghaddam, R.; Lotfi, F. Hosseinzadeh

2014-01-01

This paper deals with a problem of minimizing total weighted tardiness of jobs in a real-world single batch-processing machine (SBPM) scheduling in the presence of fuzzy due date. In this paper, first a fuzzy mixed integer linear programming model is developed. Then, due to the complexity of the problem, which is NP-hard, we design two hybrid metaheuristics called GA-VNS and VNS-SA applying the advantages of genetic algorithm (GA), variable neighborhood search (VNS), and simulated annealing (SA) frameworks. Besides, we propose three fuzzy earliest due date heuristics to solve the given problem. Through computational experiments with several random test problems, a robust calibration is applied on the parameters. Finally, computational results on different-scale test problems are presented to compare the proposed algorithms. PMID:24883359

Enhanced Electric Power Transmission by Hybrid Compensation Technique

NASA Astrophysics Data System (ADS)

Palanichamy, C.; Kiu, G. Q.

2015-04-01

In today's competitive environment, new power system engineers are likely to contribute immediately to the task, without years of seasoning via on-the-job training, mentoring, and rotation assignments. At the same time it is becoming obligatory to train power system engineering graduates for an increasingly quality-minded corporate environment. In order to achieve this, there is a need to make available better-quality tools for educating and training power system engineering students and in-service system engineers too. As a result of the swift advances in computer hardware and software, many windows-based computer software packages were developed for the purpose of educating and training. In line with those packages, a simulation package called Hybrid Series-Shunt Compensators (HSSC) has been developed and presented in this paper for educational purposes.

Leveraging Gibbs Ensemble Molecular Dynamics and Hybrid Monte Carlo/Molecular Dynamics for Efficient Study of Phase Equilibria.

PubMed

Gartner, Thomas E; Epps, Thomas H; Jayaraman, Arthi

2016-11-08

We describe an extension of the Gibbs ensemble molecular dynamics (GEMD) method for studying phase equilibria. Our modifications to GEMD allow for direct control over particle transfer between phases and improve the method's numerical stability. Additionally, we found that the modified GEMD approach had advantages in computational efficiency in comparison to a hybrid Monte Carlo (MC)/MD Gibbs ensemble scheme in the context of the single component Lennard-Jones fluid. We note that this increase in computational efficiency does not compromise the close agreement of phase equilibrium results between the two methods. However, numerical instabilities in the GEMD scheme hamper GEMD's use near the critical point. We propose that the computationally efficient GEMD simulations can be used to map out the majority of the phase window, with hybrid MC/MD used as a follow up for conditions under which GEMD may be unstable (e.g., near-critical behavior). In this manner, we can capitalize on the contrasting strengths of these two methods to enable the efficient study of phase equilibria for systems that present challenges for a purely stochastic GEMC method, such as dense or low temperature systems, and/or those with complex molecular topologies.

SiSeRHMap v1.0: a simulator for mapped seismic response using a hybrid model

NASA Astrophysics Data System (ADS)

Grelle, G.; Bonito, L.; Lampasi, A.; Revellino, P.; Guerriero, L.; Sappa, G.; Guadagno, F. M.

2015-06-01

SiSeRHMap is a computerized methodology capable of drawing up prediction maps of seismic response. It was realized on the basis of a hybrid model which combines different approaches and models in a new and non-conventional way. These approaches and models are organized in a code-architecture composed of five interdependent modules. A GIS (Geographic Information System) Cubic Model (GCM), which is a layered computational structure based on the concept of lithodynamic units and zones, aims at reproducing a parameterized layered subsoil model. A metamodeling process confers a hybrid nature to the methodology. In this process, the one-dimensional linear equivalent analysis produces acceleration response spectra of shear wave velocity-thickness profiles, defined as trainers, which are randomly selected in each zone. Subsequently, a numerical adaptive simulation model (Spectra) is optimized on the above trainer acceleration response spectra by means of a dedicated Evolutionary Algorithm (EA) and the Levenberg-Marquardt Algorithm (LMA) as the final optimizer. In the final step, the GCM Maps Executor module produces a serial map-set of a stratigraphic seismic response at different periods, grid-solving the calibrated Spectra model. In addition, the spectra topographic amplification is also computed by means of a numerical prediction model. This latter is built to match the results of the numerical simulations related to isolate reliefs using GIS topographic attributes. In this way, different sets of seismic response maps are developed, on which, also maps of seismic design response spectra are defined by means of an enveloping technique.

Experimental analysis of computer system dependability

NASA Technical Reports Server (NTRS)

Iyer, Ravishankar, K.; Tang, Dong

1993-01-01

This paper reviews an area which has evolved over the past 15 years: experimental analysis of computer system dependability. Methodologies and advances are discussed for three basic approaches used in the area: simulated fault injection, physical fault injection, and measurement-based analysis. The three approaches are suited, respectively, to dependability evaluation in the three phases of a system's life: design phase, prototype phase, and operational phase. Before the discussion of these phases, several statistical techniques used in the area are introduced. For each phase, a classification of research methods or study topics is outlined, followed by discussion of these methods or topics as well as representative studies. The statistical techniques introduced include the estimation of parameters and confidence intervals, probability distribution characterization, and several multivariate analysis methods. Importance sampling, a statistical technique used to accelerate Monte Carlo simulation, is also introduced. The discussion of simulated fault injection covers electrical-level, logic-level, and function-level fault injection methods as well as representative simulation environments such as FOCUS and DEPEND. The discussion of physical fault injection covers hardware, software, and radiation fault injection methods as well as several software and hybrid tools including FIAT, FERARI, HYBRID, and FINE. The discussion of measurement-based analysis covers measurement and data processing techniques, basic error characterization, dependency analysis, Markov reward modeling, software-dependability, and fault diagnosis. The discussion involves several important issues studies in the area, including fault models, fast simulation techniques, workload/failure dependency, correlated failures, and software fault tolerance.

Hybrid Voronoi diagrams, their computation and reduction for applications in computational biochemistry.

PubMed

Manak, Martin; Zemek, Michal; Szkandera, Jakub; Kolingerova, Ivana; Papaleo, Elena; Lambrughi, Matteo

2017-06-01

Geometric models of molecular structures are often described as a set of balls, where balls represent individual atoms. The ability to describe and explore the empty space among these balls is important, e.g., in the analysis of the interaction of enzymes with substrates, ligands and solvent molecules. Voronoi diagrams from the field of computational geometry are often used here, because they provide a mathematical description of how the whole space can be divided into regions assigned to individual atoms. This paper introduces a combination of two different types of Voronoi diagrams into a new hybrid Voronoi diagram - one part of this diagram belongs to the additively weighted (aw-Voronoi) diagram and the other to the power diagram. The boundary between them is controlled by a user-defined constant (the probe radius). Both parts are computed by different algorithms, which are already known. The reduced aw-Voronoi diagram is then obtained by removing the power diagram part from the hybrid diagram. Reduced aw-Voronoi diagrams are perfectly tailored for the analysis of dynamic molecular structures, their computation is faster and storage requirements are lower than in the case of complete aw-Voronoi diagrams. Here, we showed their application to key proteins in cancer research such as p53 and ARID proteins as case study. We identified a biologically relevant cavity in p53 structural ensembles generated by molecular dynamics simulations and analyzed its accessibility, attesting the potential of our approach. This method is relevant for cancer research since it permits to depict a dynamical view of cavities and pockets in proteins that could be affected by mutations in the disease. Our approach opens novel prospects for the study of cancer-related proteins by molecular simulations and the identification of novel targets for drug design. Copyright © 2017 Elsevier Inc. All rights reserved.

SKIRT: Hybrid parallelization of radiative transfer simulations

NASA Astrophysics Data System (ADS)

Verstocken, S.; Van De Putte, D.; Camps, P.; Baes, M.

2017-07-01

We describe the design, implementation and performance of the new hybrid parallelization scheme in our Monte Carlo radiative transfer code SKIRT, which has been used extensively for modelling the continuum radiation of dusty astrophysical systems including late-type galaxies and dusty tori. The hybrid scheme combines distributed memory parallelization, using the standard Message Passing Interface (MPI) to communicate between processes, and shared memory parallelization, providing multiple execution threads within each process to avoid duplication of data structures. The synchronization between multiple threads is accomplished through atomic operations without high-level locking (also called lock-free programming). This improves the scaling behaviour of the code and substantially simplifies the implementation of the hybrid scheme. The result is an extremely flexible solution that adjusts to the number of available nodes, processors and memory, and consequently performs well on a wide variety of computing architectures.

Broadband ground motion simulation using a paralleled hybrid approach of Frequency Wavenumber and Finite Difference method

NASA Astrophysics Data System (ADS)

Chen, M.; Wei, S.

2016-12-01

The serious damage of Mexico City caused by the 1985 Michoacan earthquake 400 km away indicates that urban areas may be affected by remote earthquakes. To asses earthquake risk of urban areas imposed by distant earthquakes, we developed a hybrid Frequency Wavenumber (FK) and Finite Difference (FD) code implemented with MPI, since the computation of seismic wave propagation from a distant earthquake using a single numerical method (e.g. Finite Difference, Finite Element or Spectral Element) is very expensive. In our approach, we compute the incident wave field (ud) at the boundaries of the excitation box, which surrounding the local structure, using a paralleled FK method (Zhu and Rivera, 2002), and compute the total wave field (u) within the excitation box using a parallelled 2D FD method. We apply perfectly matched layer (PML) absorbing condition to the diffracted wave field (u-ud). Compared to previous Generalized Ray Theory and Finite Difference (Wen and Helmberger, 1998), Frequency Wavenumber and Spectral Element (Tong et al., 2014), and Direct Solution Method and Spectral Element hybrid method (Monteiller et al., 2013), our absorbing boundary condition dramatically suppress the numerical noise. The MPI implementation of our method can greatly speed up the calculation. Besides, our hybrid method also has a potential use in high resolution array imaging similar to Tong et al. (2014).

An Analysis Platform for Multiscale Hydrogeologic Modeling with Emphasis on Hybrid Multiscale Methods

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

Scheibe, Timothy D.; Murphy, Ellyn M.; Chen, Xingyuan

2015-01-01

One of the most significant challenges facing hydrogeologic modelers is the disparity between those spatial and temporal scales at which fundamental flow, transport and reaction processes can best be understood and quantified (e.g., microscopic to pore scales, seconds to days) and those at which practical model predictions are needed (e.g., plume to aquifer scales, years to centuries). While the multiscale nature of hydrogeologic problems is widely recognized, technological limitations in computational and characterization restrict most practical modeling efforts to fairly coarse representations of heterogeneous properties and processes. For some modern problems, the necessary level of simplification is such that modelmore » parameters may lose physical meaning and model predictive ability is questionable for any conditions other than those to which the model was calibrated. Recently, there has been broad interest across a wide range of scientific and engineering disciplines in simulation approaches that more rigorously account for the multiscale nature of systems of interest. In this paper, we review a number of such approaches and propose a classification scheme for defining different types of multiscale simulation methods and those classes of problems to which they are most applicable. Our classification scheme is presented in terms of a flow chart (Multiscale Analysis Platform or MAP), and defines several different motifs of multiscale simulation. Within each motif, the member methods are reviewed and example applications are discussed. We focus attention on hybrid multiscale methods, in which two or more models with different physics described at fundamentally different scales are directly coupled within a single simulation. Very recently these methods have begun to be applied to groundwater flow and transport simulations, and we discuss these applications in the context of our classification scheme. As computational and characterization capabilities continue to improve, we envision that hybrid multiscale modeling will become more common and may become a viable alternative to conventional single-scale models in the near future.« less

An analysis platform for multiscale hydrogeologic modeling with emphasis on hybrid multiscale methods.

PubMed

Scheibe, Timothy D; Murphy, Ellyn M; Chen, Xingyuan; Rice, Amy K; Carroll, Kenneth C; Palmer, Bruce J; Tartakovsky, Alexandre M; Battiato, Ilenia; Wood, Brian D

2015-01-01

One of the most significant challenges faced by hydrogeologic modelers is the disparity between the spatial and temporal scales at which fundamental flow, transport, and reaction processes can best be understood and quantified (e.g., microscopic to pore scales and seconds to days) and at which practical model predictions are needed (e.g., plume to aquifer scales and years to centuries). While the multiscale nature of hydrogeologic problems is widely recognized, technological limitations in computation and characterization restrict most practical modeling efforts to fairly coarse representations of heterogeneous properties and processes. For some modern problems, the necessary level of simplification is such that model parameters may lose physical meaning and model predictive ability is questionable for any conditions other than those to which the model was calibrated. Recently, there has been broad interest across a wide range of scientific and engineering disciplines in simulation approaches that more rigorously account for the multiscale nature of systems of interest. In this article, we review a number of such approaches and propose a classification scheme for defining different types of multiscale simulation methods and those classes of problems to which they are most applicable. Our classification scheme is presented in terms of a flowchart (Multiscale Analysis Platform), and defines several different motifs of multiscale simulation. Within each motif, the member methods are reviewed and example applications are discussed. We focus attention on hybrid multiscale methods, in which two or more models with different physics described at fundamentally different scales are directly coupled within a single simulation. Very recently these methods have begun to be applied to groundwater flow and transport simulations, and we discuss these applications in the context of our classification scheme. As computational and characterization capabilities continue to improve, we envision that hybrid multiscale modeling will become more common and also a viable alternative to conventional single-scale models in the near future. © 2014, National Ground Water Association.

The role of deleterious mutations in the stability of hybridogenetic water frog complexes

PubMed Central

2014-01-01

Background Some species of water frogs originated from hybridization between different species. Such hybrid populations have a particular reproduction system called hybridogenesis. In this paper we consider the two species Pelophylax ridibundus and Pelophylax lessonae, and their hybrids Pelophylax esculentus. P. lessonae and P. esculentus form stable complexes (L-E complexes) in which P. esculentus are hemiclonal. In L-E complexes all the transmitted genomes by P. esculentus carry deleterious mutations which are lethal in homozygosity. Results We analyze, by means of an individual based computational model, L-E complexes. The results of simulations based on the model show that, by eliminating deleterious mutations, L-E complexes collapse. In addition, simulations show that particular female preferences can contribute to the diffusion of deleterious mutations among all P. esculentus frogs. Finally, simulations show how L-E complexes react to the introduction of translocated P. ridibundus. Conclusions The conclusions are the following: (i) deleterious mutations (combined with sexual preferences) strongly contribute to the stability of L-E complexes; (ii) female sexual choice can contribute to the diffusion of deleterious mutations; and (iii) the introduction of P. ridibundus can destabilize L-E complexes. PMID:24885008

A generic framework to simulate realistic lung, liver and renal pathologies in CT imaging

NASA Astrophysics Data System (ADS)

Solomon, Justin; Samei, Ehsan

2014-11-01

Realistic three-dimensional (3D) mathematical models of subtle lesions are essential for many computed tomography (CT) studies focused on performance evaluation and optimization. In this paper, we develop a generic mathematical framework that describes the 3D size, shape, contrast, and contrast-profile characteristics of a lesion, as well as a method to create lesion models based on CT data of real lesions. Further, we implemented a technique to insert the lesion models into CT images in order to create hybrid CT datasets. This framework was used to create a library of realistic lesion models and corresponding hybrid CT images. The goodness of fit of the models was assessed using the coefficient of determination (R2) and the visual appearance of the hybrid images was assessed with an observer study using images of both real and simulated lesions and receiver operator characteristic (ROC) analysis. The average R2 of the lesion models was 0.80, implying that the models provide a good fit to real lesion data. The area under the ROC curve was 0.55, implying that the observers could not readily distinguish between real and simulated lesions. Therefore, we conclude that the lesion-modeling framework presented in this paper can be used to create realistic lesion models and hybrid CT images. These models could be instrumental in performance evaluation and optimization of novel CT systems.

Towards Cloud-Resolving European-Scale Climate Simulations using a fully GPU-enabled Prototype of the COSMO Regional Model

NASA Astrophysics Data System (ADS)

Leutwyler, David; Fuhrer, Oliver; Cumming, Benjamin; Lapillonne, Xavier; Gysi, Tobias; Lüthi, Daniel; Osuna, Carlos; Schär, Christoph

2014-05-01

The representation of moist convection is a major shortcoming of current global and regional climate models. State-of-the-art global models usually operate at grid spacings of 10-300 km, and therefore cannot fully resolve the relevant upscale and downscale energy cascades. Therefore parametrization of the relevant sub-grid scale processes is required. Several studies have shown that this approach entails major uncertainties for precipitation processes, which raises concerns about the model's ability to represent precipitation statistics and associated feedback processes, as well as their sensitivities to large-scale conditions. Further refining the model resolution to the kilometer scale allows representing these processes much closer to first principles and thus should yield an improved representation of the water cycle including the drivers of extreme events. Although cloud-resolving simulations are very useful tools for climate simulations and numerical weather prediction, their high horizontal resolution and consequently the small time steps needed, challenge current supercomputers to model large domains and long time scales. The recent innovations in the domain of hybrid supercomputers have led to mixed node designs with a conventional CPU and an accelerator such as a graphics processing unit (GPU). GPUs relax the necessity for cache coherency and complex memory hierarchies, but have a larger system memory-bandwidth. This is highly beneficial for low compute intensity codes such as atmospheric stencil-based models. However, to efficiently exploit these hybrid architectures, climate models need to be ported and/or redesigned. Within the framework of the Swiss High Performance High Productivity Computing initiative (HP2C) a project to port the COSMO model to hybrid architectures has recently come to and end. The product of these efforts is a version of COSMO with an improved performance on traditional x86-based clusters as well as hybrid architectures with GPUs. We present our redesign and porting approach as well as our experience and lessons learned. Furthermore, we discuss relevant performance benchmarks obtained on the new hybrid Cray XC30 system "Piz Daint" installed at the Swiss National Supercomputing Centre (CSCS), both in terms of time-to-solution as well as energy consumption. We will demonstrate a first set of short cloud-resolving climate simulations at the European-scale using the GPU-enabled COSMO prototype and elaborate our future plans on how to exploit this new model capability.

Magnetic resonance imaging and computational fluid dynamics (CFD) simulations of rabbit nasal airflows for the development of hybrid CFD/PBPK models.

PubMed

Corley, R A; Minard, K R; Kabilan, S; Einstein, D R; Kuprat, A P; Harkema, J R; Kimbell, J S; Gargas, M L; Kinzell, John H

2009-05-01

The percentages of total airflows over the nasal respiratory and olfactory epithelium of female rabbits were calculated from computational fluid dynamics (CFD) simulations of steady-state inhalation. These airflow calculations, along with nasal airway geometry determinations, are critical parameters for hybrid CFD/physiologically based pharmacokinetic models that describe the nasal dosimetry of water-soluble or reactive gases and vapors in rabbits. CFD simulations were based upon three-dimensional computational meshes derived from magnetic resonance images of three adult female New Zealand White (NZW) rabbits. In the anterior portion of the nose, the maxillary turbinates of rabbits are considerably more complex than comparable regions in rats, mice, monkeys, or humans. This leads to a greater surface area to volume ratio in this region and thus the potential for increased extraction of water soluble or reactive gases and vapors in the anterior portion of the nose compared to many other species. Although there was considerable interanimal variability in the fine structures of the nasal turbinates and airflows in the anterior portions of the nose, there was remarkable consistency between rabbits in the percentage of total inspired airflows that reached the ethmoid turbinate region (approximately 50%) that is presumably lined with olfactory epithelium. These latter results (airflows reaching the ethmoid turbinate region) were higher than previous published estimates for the male F344 rat (19%) and human (7%). These differences in regional airflows can have significant implications in interspecies extrapolations of nasal dosimetry.

Improved treatment of exact exchange in Quantum ESPRESSO

DOE PAGES

Barnes, Taylor A.; Kurth, Thorsten; Carrier, Pierre; ...

2017-01-18

Here, we present an algorithm and implementation for the parallel computation of exact exchange in Quantum ESPRESSO (QE) that exhibits greatly improved strong scaling. QE is an open-source software package for electronic structure calculations using plane wave density functional theory, and supports the use of local, semi-local, and hybrid DFT functionals. Wider application of hybrid functionals is desirable for the improved simulation of electronic band energy alignments and thermodynamic properties, but the computational complexity of evaluating the exact exchange potential limits the practical application of hybrid functionals to large systems and requires efficient implementations. We demonstrate that existing implementations ofmore » hybrid DFT that utilize a single data structure for both the local and exact exchange regions of the code are significantly limited in the degree of parallelization achievable. We present a band-pair parallelization approach, in which the calculation of exact exchange is parallelized and evaluated independently from the parallelization of the remainder of the calculation, with the wavefunction data being efficiently transformed on-the-fly into a form that is optimal for each part of the calculation. For a 64 water molecule supercell, our new algorithm reduces the overall time to solution by nearly an order of magnitude.« less

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

Barnes, Taylor A.; Kurth, Thorsten; Carrier, Pierre

Here, we present an algorithm and implementation for the parallel computation of exact exchange in Quantum ESPRESSO (QE) that exhibits greatly improved strong scaling. QE is an open-source software package for electronic structure calculations using plane wave density functional theory, and supports the use of local, semi-local, and hybrid DFT functionals. Wider application of hybrid functionals is desirable for the improved simulation of electronic band energy alignments and thermodynamic properties, but the computational complexity of evaluating the exact exchange potential limits the practical application of hybrid functionals to large systems and requires efficient implementations. We demonstrate that existing implementations ofmore » hybrid DFT that utilize a single data structure for both the local and exact exchange regions of the code are significantly limited in the degree of parallelization achievable. We present a band-pair parallelization approach, in which the calculation of exact exchange is parallelized and evaluated independently from the parallelization of the remainder of the calculation, with the wavefunction data being efficiently transformed on-the-fly into a form that is optimal for each part of the calculation. For a 64 water molecule supercell, our new algorithm reduces the overall time to solution by nearly an order of magnitude.« less

Dynamical analysis of Parkinsonian state emulated by hybrid Izhikevich neuron models

NASA Astrophysics Data System (ADS)

Liu, Chen; Wang, Jiang; Yu, Haitao; Deng, Bin; Wei, Xile; Li, Huiyan; Loparo, Kenneth A.; Fietkiewicz, Chris

2015-11-01

Computational models play a significant role in exploring novel theories to complement the findings of physiological experiments. Various computational models have been developed to reveal the mechanisms underlying brain functions. Particularly, in the development of therapies to modulate behavioral and pathological abnormalities, computational models provide the basic foundations to exhibit transitions between physiological and pathological conditions. Considering the significant roles of the intrinsic properties of the globus pallidus and the coupling connections between neurons in determining the firing patterns and the dynamical activities of the basal ganglia neuronal network, we propose a hypothesis that pathological behaviors under the Parkinsonian state may originate from combined effects of intrinsic properties of globus pallidus neurons and synaptic conductances in the whole neuronal network. In order to establish a computational efficient network model, hybrid Izhikevich neuron model is used due to its capacity of capturing the dynamical characteristics of the biological neuronal activities. Detailed analysis of the individual Izhikevich neuron model can assist in understanding the roles of model parameters, which then facilitates the establishment of the basal ganglia-thalamic network model, and contributes to a further exploration of the underlying mechanisms of the Parkinsonian state. Simulation results show that the hybrid Izhikevich neuron model is capable of capturing many of the dynamical properties of the basal ganglia-thalamic neuronal network, such as variations of the firing rates and emergence of synchronous oscillations under the Parkinsonian condition, despite the simplicity of the two-dimensional neuronal model. It may suggest that the computational efficient hybrid Izhikevich neuron model can be used to explore basal ganglia normal and abnormal functions. Especially it provides an efficient way of emulating the large-scale neuron network and potentially contributes to development of improved therapy for neurological disorders such as Parkinson's disease.

Molecular dynamics simulations through GPU video games technologies

PubMed Central

Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

2016-01-01

Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251

Validation of High-Fidelity CFD/CAA Framework for Launch Vehicle Acoustic Environment Simulation against Scale Model Test Data

NASA Technical Reports Server (NTRS)

Liever, Peter A.; West, Jeffrey S.; Harris, Robert E.

2016-01-01

A hybrid Computational Fluid Dynamics and Computational Aero-Acoustics (CFD/CAA) modeling framework has been developed for launch vehicle liftoff acoustic environment predictions. The framework couples the existing highly-scalable NASA production CFD code, Loci/CHEM, with a high-order accurate Discontinuous Galerkin solver developed in the same production framework, Loci/THRUST, to accurately resolve and propagate acoustic physics across the entire launch environment. Time-accurate, Hybrid RANS/LES CFD modeling is applied for predicting the acoustic generation physics at the plume source, and a high-order accurate unstructured mesh Discontinuous Galerkin (DG) method is employed to propagate acoustic waves away from the source across large distances using high-order accurate schemes. The DG solver is capable of solving 2nd, 3rd, and 4th order Euler solutions for non-linear, conservative acoustic field propagation. Initial application testing and validation has been carried out against high resolution acoustic data from the Ares Scale Model Acoustic Test (ASMAT) series to evaluate the capabilities and production readiness of the CFD/CAA system to resolve the observed spectrum of acoustic frequency content. This paper presents results from this validation and outlines efforts to mature and improve the computational simulation framework.

Efficient Wideband Numerical Simulations for Nanostructures Employing a Drude-Critical Points (DCP) Dispersive Model.

PubMed

Ren, Qiang; Nagar, Jogender; Kang, Lei; Bian, Yusheng; Werner, Ping; Werner, Douglas H

2017-05-18

A highly efficient numerical approach for simulating the wideband optical response of nano-architectures comprised of Drude-Critical Points (DCP) media (e.g., gold and silver) is proposed and validated through comparing with commercial computational software. The kernel of this algorithm is the subdomain level discontinuous Galerkin time domain (DGTD) method, which can be viewed as a hybrid of the spectral-element time-domain method (SETD) and the finite-element time-domain (FETD) method. An hp-refinement technique is applied to decrease the Degrees-of-Freedom (DoFs) and computational requirements. The collocated E-J scheme facilitates solving the auxiliary equations by converting the inversions of matrices to simpler vector manipulations. A new hybrid time stepping approach, which couples the Runge-Kutta and Newmark methods, is proposed to solve the temporal auxiliary differential equations (ADEs) with a high degree of efficiency. The advantages of this new approach, in terms of computational resource overhead and accuracy, are validated through comparison with well-known commercial software for three diverse cases, which cover both near-field and far-field properties with plane wave and lumped port sources. The presented work provides the missing link between DCP dispersive models and FETD and/or SETD based algorithms. It is a competitive candidate for numerically studying the wideband plasmonic properties of DCP media.

High-Performance Reactive Particle Tracking with Adaptive Representation

NASA Astrophysics Data System (ADS)

Schmidt, M.; Benson, D. A.; Pankavich, S.

2017-12-01

Lagrangian particle tracking algorithms have been shown to be effective tools for modeling chemical reactions in imperfectly-mixed media. One disadvantage of these algorithms is the possible need to employ large numbers of particles in simulations, depending on the concentration covariance structure, and these large particle numbers can lead to long computation times. Two distinct approaches have recently arisen to overcome this. One method employs spatial kernels that are related to a specified, reduced particle number; however, over-wide kernels, dictated by a very low particle number, lead to an excess of reaction calculations and cause a reduction in performance. Another formulation involves hybrid particles that carry multiple species of reactant, wherein each particle is treated as its own well-mixed volume, obviating the need for large numbers of particles for each species but still requiring a fixed number of hybrid particles. Here, we combine these two approaches and demonstrate an improved method for simulating a given system in a computationally efficient manner. Additionally, the independent nature of transport and reaction calculations in this approach allows for significant gains via parallelization in an MPI or OpenMP context. For benchmarking, we choose a CO2 injection simulation with dissolution and precipitation of calcite and dolomite, allowing us to derive the proper treatment of interaction between solid and aqueous phases.

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

A fast analytical undulator model for realistic high-energy FEL simulations

NASA Astrophysics Data System (ADS)

Tatchyn, R.; Cremer, T.

1997-02-01

A number of leading FEL simulation codes used for modeling gain in the ultralong undulators required for SASE saturation in the <100 Å range employ simplified analytical models both for field and error representations. Although it is recognized that both the practical and theoretical validity of such codes could be enhanced by incorporating realistic undulator field calculations, the computational cost of doing this can be prohibitive, especially for point-to-point integration of the equations of motion through each undulator period. In this paper we describe a simple analytical model suitable for modeling realistic permanent magnet (PM), hybrid/PM, and non-PM undulator structures, and discuss selected techniques for minimizing computation time.

Digital hardware implementation of a stochastic two-dimensional neuron model.

PubMed

Grassia, F; Kohno, T; Levi, T

2016-11-01

This study explores the feasibility of stochastic neuron simulation in digital systems (FPGA), which realizes an implementation of a two-dimensional neuron model. The stochasticity is added by a source of current noise in the silicon neuron using an Ornstein-Uhlenbeck process. This approach uses digital computation to emulate individual neuron behavior using fixed point arithmetic operation. The neuron model's computations are performed in arithmetic pipelines. It was designed in VHDL language and simulated prior to mapping in the FPGA. The experimental results confirmed the validity of the developed stochastic FPGA implementation, which makes the implementation of the silicon neuron more biologically plausible for future hybrid experiments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interpretation of TOF SIMS depth profiles from ultrashallow high-k dielectric stacks assisted by hybrid collisional computer simulation

NASA Astrophysics Data System (ADS)

Ignatova, V. A.; Möller, W.; Conard, T.; Vandervorst, W.; Gijbels, R.

2005-06-01

The TRIDYN collisional computer simulation has been modified to account for emission of ionic species and molecules during sputter depth profiling, by introducing a power law dependence of the ion yield as a function of the oxygen surface concentration and by modelling the sputtering of monoxide molecules. The results are compared to experimental data obtained with dual beam TOF SIMS depth profiling of ZrO2/SiO2/Si high-k dielectric stacks with thicknesses of the SiO2 interlayer of 0.5, 1, and 1.5 nm. Reasonable agreement between the experiment and the computer simulation is obtained for most of the experimental features, demonstrating the effects of ion-induced atomic relocation, i.e., atomic mixing and recoil implantation, and preferential sputtering. The depth scale of the obtained profiles is significantly distorted by recoil implantation and the depth-dependent ionization factor. A pronounced double-peak structure in the experimental profiles related to Zr is not explained by the computer simulation, and is attributed to ion-induced bond breaking and diffusion, followed by a decoration of the interfaces by either mobile Zr or O.

General Monte Carlo reliability simulation code including common mode failures and HARP fault/error-handling

NASA Technical Reports Server (NTRS)

Platt, M. E.; Lewis, E. E.; Boehm, F.

1991-01-01

A Monte Carlo Fortran computer program was developed that uses two variance reduction techniques for computing system reliability applicable to solving very large highly reliable fault-tolerant systems. The program is consistent with the hybrid automated reliability predictor (HARP) code which employs behavioral decomposition and complex fault-error handling models. This new capability is called MC-HARP which efficiently solves reliability models with non-constant failures rates (Weibull). Common mode failure modeling is also a specialty.

Plane-Wave DFT Methods for Chemistry

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

Bylaska, Eric J.

A detailed description of modern plane-wave DFT methods and software (contained in the NWChem package) are described that allow for both geometry optimization and ab initio molecular dynamics simulations. Significant emphasis is placed on aspects of these methods that are of interest to computational chemists and useful for simulating chemistry, including techniques for calculating charged systems, exact exchange (i.e. hybrid DFT methods), and highly efficient AIMD/MM methods. Sample applications on the structure of the goethite+water interface and the hydrolysis of nitroaromatic molecules are described.

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

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

F100 multivariable control synthesis program: Evaluation of a multivariable control using a real-time engine simulation

NASA Technical Reports Server (NTRS)

Szuch, J. R.; Soeder, J. F.; Seldner, K.; Cwynar, D. S.

1977-01-01

The design, evaluation, and testing of a practical, multivariable, linear quadratic regulator control for the F100 turbofan engine were accomplished. NASA evaluation of the multivariable control logic and implementation are covered. The evaluation utilized a real time, hybrid computer simulation of the engine. Results of the evaluation are presented, and recommendations concerning future engine testing of the control are made. Results indicated that the engine testing of the control should be conducted as planned.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

Hybrid Large Eddy Simulation / Reynolds Averaged Navier-Stokes Modeling in Directed Energy Applications

NASA Astrophysics Data System (ADS)

Zilberter, Ilya Alexandrovich

In this work, a hybrid Large Eddy Simulation / Reynolds-Averaged Navier Stokes (LES/RANS) turbulence model is applied to simulate two flows relevant to directed energy applications. The flow solver blends the Menter Baseline turbulence closure near solid boundaries with a Lenormand-type subgrid model in the free-stream with a blending function that employs the ratio of estimated inner and outer turbulent length scales. A Mach 2.2 mixing nozzle/diffuser system representative of a gas laser is simulated under a range of exit pressures to assess the ability of the model to predict the dynamics of the shock train. The simulation captures the location of the shock train responsible for pressure recovery but under-predicts the rate of pressure increase. Predicted turbulence production at the wall is found to be highly sensitive to the behavior of the RANS turbulence model. A Mach 2.3, high-Reynolds number, three-dimensional cavity flow is also simulated in order to compute the wavefront aberrations of an optical beam passing thorough the cavity. The cavity geometry is modeled using an immersed boundary method, and an auxiliary flat plate simulation is performed to replicate the effects of the wind-tunnel boundary layer on the computed optical path difference. Pressure spectra extracted on the cavity walls agree with empirical predictions based on Rossiter's formula. Proper orthogonal modes of the wavefront aberrations in a beam originating from the cavity center agree well with experimental data despite uncertainty about in flow turbulence levels and boundary layer thicknesses over the wind tunnel window. Dynamic mode decomposition of a planar wavefront spanning the cavity reveals that wavefront distortions are driven by shear layer oscillations at the Rossiter frequencies; these disturbances create eddy shocklets that propagate into the free-stream, creating additional optical wavefront distortion.

ITER Simulations Using the PEDESTAL Module in the PTRANSP Code

NASA Astrophysics Data System (ADS)

Halpern, F. D.; Bateman, G.; Kritz, A. H.; Pankin, A. Y.; Budny, R. V.; Kessel, C.; McCune, D.; Onjun, T.

2006-10-01

PTRANSP simulations with a computed pedestal height are carried out for ITER scenarios including a standard ELMy H-mode (15 MA discharge) and a hybrid scenario (12MA discharge). It has been found that fusion power production predicted in simulations of ITER discharges depends sensitively on the height of the H-mode temperature pedestal [1]. In order to study this effect, the NTCC PEDESTAL module [2] has been implemented in PTRANSP code to provide boundary conditions used for the computation of the projected performance of ITER. The PEDESTAL module computes both the temperature and width of the pedestal at the edge of type I ELMy H-mode discharges once the threshold conditions for the H-mode are satisfied. The anomalous transport in the plasma core is predicted using the GLF23 or MMM95 transport models. To facilitate the steering of lengthy PTRANSP computations, the PTRANSP code has been modified to allow changes in the transport model when simulations are restarted. The PTRANSP simulation results are compared with corresponding results obtained using other integrated modeling codes.[1] G. Bateman, T. Onjun and A.H. Kritz, Plasma Physics and Controlled Fusion, 45, 1939 (2003).[2] T. Onjun, G. Bateman, A.H. Kritz, and G. Hammett, Phys. Plasmas 9, 5018 (2002).

A new hybrid-Lagrangian numerical scheme for gyrokinetic simulation of tokamak edge plasma

DOE PAGES

Ku, S.; Hager, R.; Chang, C. S.; ...

2016-04-01

In order to enable kinetic simulation of non-thermal edge plasmas at a reduced computational cost, a new hybrid-Lagrangian δf scheme has been developed that utilizes the phase space grid in addition to the usual marker particles, taking advantage of the computational strengths from both sides. The new scheme splits the particle distribution function of a kinetic equation into two parts. Marker particles contain the fast space-time varying, δf, part of the distribution function and the coarse-grained phase-space grid contains the slow space-time varying part. The coarse-grained phase-space grid reduces the memory-requirement and the computing cost, while the marker particles providemore » scalable computing ability for the fine-grained physics. Weights of the marker particles are determined by a direct weight evolution equation instead of the differential form weight evolution equations that the conventional delta-f schemes use. The particle weight can be slowly transferred to the phase space grid, thereby reducing the growth of the particle weights. The non-Lagrangian part of the kinetic equation – e.g., collision operation, ionization, charge exchange, heat-source, radiative cooling, and others – can be operated directly on the phase space grid. Deviation of the particle distribution function on the velocity grid from a Maxwellian distribution function – driven by ionization, charge exchange and wall loss – is allowed to be arbitrarily large. In conclusion, the numerical scheme is implemented in the gyrokinetic particle code XGC1, which specializes in simulating the tokamak edge plasma that crosses the magnetic separatrix and is in contact with the material wall.« less

A new hybrid-Lagrangian numerical scheme for gyrokinetic simulation of tokamak edge plasma

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

Ku, S.; Hager, R.; Chang, C. S.

In order to enable kinetic simulation of non-thermal edge plasmas at a reduced computational cost, a new hybrid-Lagrangian δf scheme has been developed that utilizes the phase space grid in addition to the usual marker particles, taking advantage of the computational strengths from both sides. The new scheme splits the particle distribution function of a kinetic equation into two parts. Marker particles contain the fast space-time varying, δf, part of the distribution function and the coarse-grained phase-space grid contains the slow space-time varying part. The coarse-grained phase-space grid reduces the memory-requirement and the computing cost, while the marker particles providemore » scalable computing ability for the fine-grained physics. Weights of the marker particles are determined by a direct weight evolution equation instead of the differential form weight evolution equations that the conventional delta-f schemes use. The particle weight can be slowly transferred to the phase space grid, thereby reducing the growth of the particle weights. The non-Lagrangian part of the kinetic equation – e.g., collision operation, ionization, charge exchange, heat-source, radiative cooling, and others – can be operated directly on the phase space grid. Deviation of the particle distribution function on the velocity grid from a Maxwellian distribution function – driven by ionization, charge exchange and wall loss – is allowed to be arbitrarily large. In conclusion, the numerical scheme is implemented in the gyrokinetic particle code XGC1, which specializes in simulating the tokamak edge plasma that crosses the magnetic separatrix and is in contact with the material wall.« less

A new hybrid-Lagrangian numerical scheme for gyrokinetic simulation of tokamak edge plasma

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

Ku, S., E-mail: sku@pppl.gov; Hager, R.; Chang, C.S.

In order to enable kinetic simulation of non-thermal edge plasmas at a reduced computational cost, a new hybrid-Lagrangian δf scheme has been developed that utilizes the phase space grid in addition to the usual marker particles, taking advantage of the computational strengths from both sides. The new scheme splits the particle distribution function of a kinetic equation into two parts. Marker particles contain the fast space-time varying, δf, part of the distribution function and the coarse-grained phase-space grid contains the slow space-time varying part. The coarse-grained phase-space grid reduces the memory-requirement and the computing cost, while the marker particles providemore » scalable computing ability for the fine-grained physics. Weights of the marker particles are determined by a direct weight evolution equation instead of the differential form weight evolution equations that the conventional delta-f schemes use. The particle weight can be slowly transferred to the phase space grid, thereby reducing the growth of the particle weights. The non-Lagrangian part of the kinetic equation – e.g., collision operation, ionization, charge exchange, heat-source, radiative cooling, and others – can be operated directly on the phase space grid. Deviation of the particle distribution function on the velocity grid from a Maxwellian distribution function – driven by ionization, charge exchange and wall loss – is allowed to be arbitrarily large. The numerical scheme is implemented in the gyrokinetic particle code XGC1, which specializes in simulating the tokamak edge plasma that crosses the magnetic separatrix and is in contact with the material wall.« less

NASA Environmentally Responsible Aviation Hybrid Wing Body Flow-Through Nacelle Wind Tunnel CFD

NASA Technical Reports Server (NTRS)

Schuh, Michael J.; Garcia, Jospeh A.; Carter, Melissa B.; Deere, Karen A.; Stremel, Paul M.; Tompkins, Daniel M.

2016-01-01

Wind tunnel tests of a 5.75% scale model of the Boeing Hybrid Wing Body (HWB) configuration were conducted in the NASA Langley Research Center (LaRC) 14'x22' and NASA Ames Research Center (ARC) 40'x80' low speed wind tunnels as part of the NASA Environmentally Responsible Aviation (ERA) Project. Computational fluid dynamics (CFD) simulations of the flow-through nacelle (FTN) configuration of this model were performed before and after the testing. This paper presents a summary of the experimental and CFD results for the model in the cruise and landing configurations.

NASA Environmentally Responsible Aviation Hybrid Wing Body Flow-Through Nacelle Wind Tunnel CFD

NASA Technical Reports Server (NTRS)

Schuh, Michael J.; Garcia, Joseph A.; Carter, Melissa B.; Deere, Karen A.; Tompkins, Daniel M.; Stremel, Paul M.

2016-01-01

Wind tunnel tests of a 5.75 scale model of the Boeing Hybrid Wing Body (HWB) configuration were conducted in the NASA Langley Research Center (LaRC) 14x22 and NASA Ames Research Center (ARC) 40x80 low speed wind tunnels as part of the NASA Environmentally Responsible Aviation (ERA) Project. Computational fluid dynamics (CFD) simulations of the flow-through nacelle (FTN) configuration of this model were performed before and after the testing. This paper presents a summary of the experimental and CFD results for the model in the cruise and landing configurations.

Sensing circuits for multiwire proportional chambers

NASA Technical Reports Server (NTRS)

Peterson, H. T.; Worley, E. R.

1977-01-01

Integrated sensing circuits were designed, fabricated, and packaged for use in determining the direction and fluence of ionizing radiation passing through a multiwire proportional chamber. CMOS on sapphire was selected because of its high speed and low power capabilities. The design of the proposed circuits is described and the results of computer simulations are presented. The fabrication processes for the CMOS on sapphire sensing circuits and hybrid substrates are outlined. Several design options are described and the cost implications of each discussed. To be most effective, each chip should handle not more than 32 inputs, and should be mounted on its own hybrid substrate.

Probabilistic assessment of uncertain adaptive hybrid composites

NASA Technical Reports Server (NTRS)

Shiao, Michael C.; Singhal, Surendra N.; Chamis, Christos C.

1994-01-01

Adaptive composite structures using actuation materials, such as piezoelectric fibers, were assessed probabilistically utilizing intraply hybrid composite mechanics in conjunction with probabilistic composite structural analysis. Uncertainties associated with the actuation material as well as the uncertainties in the regular (traditional) composite material properties were quantified and considered in the assessment. Static and buckling analyses were performed for rectangular panels with various boundary conditions and different control arrangements. The probability density functions of the structural behavior, such as maximum displacement and critical buckling load, were computationally simulated. The results of the assessment indicate that improved design and reliability can be achieved with actuation material.

Integration of Extended MHD and Kinetic Effects in Global Magnetosphere Models

NASA Astrophysics Data System (ADS)

Germaschewski, K.; Wang, L.; Maynard, K. R. M.; Raeder, J.; Bhattacharjee, A.

2015-12-01

Computational models of Earth's geospace environment are an important tool to investigate the science of the coupled solar-wind -- magnetosphere -- ionosphere system, complementing satellite and ground observations with a global perspective. They are also crucial in understanding and predicting space weather, in particular under extreme conditions. Traditionally, global models have employed the one-fluid MHD approximation, which captures large-scale dynamics quite well. However, in Earth's nearly collisionless plasma environment it breaks down on small scales, where ion and electron dynamics and kinetic effects become important, and greatly change the reconnection dynamics. A number of approaches have recently been taken to advance global modeling, e.g., including multiple ion species, adding Hall physics in a Generalized Ohm's Law, embedding local PIC simulations into a larger fluid domain and also some work on simulating the entire system with hybrid or fully kinetic models, the latter however being to computationally expensive to be run at realistic parameters. We will present an alternate approach, ie., a multi-fluid moment model that is derived rigorously from the Vlasov-Maxwell system. The advantage is that the computational cost remains managable, as we are still solving fluid equations. While the evolution equation for each moment is exact, it depends on the next higher-order moment, so that truncating the hiearchy and closing the system to capture the essential kinetic physics is crucial. We implement 5-moment (density, momentum, scalar pressure) and 10-moment (includes pressure tensor) versions of the model, and use local approximations for the heat flux to close the system. We test these closures by local simulations where we can compare directly to PIC / hybrid codes, and employ them in global simulations using the next-generation OpenGGCM to contrast them to MHD / Hall-MHD results and compare with observations.

Computational Cosmology at the Bleeding Edge

NASA Astrophysics Data System (ADS)

Habib, Salman

2013-04-01

Large-area sky surveys are providing a wealth of cosmological information to address the mysteries of dark energy and dark matter. Observational probes based on tracking the formation of cosmic structure are essential to this effort, and rely crucially on N-body simulations that solve the Vlasov-Poisson equation in an expanding Universe. As statistical errors from survey observations continue to shrink, and cosmological probes increase in number and complexity, simulations are entering a new regime in their use as tools for scientific inference. Changes in supercomputer architectures provide another rationale for developing new parallel simulation and analysis capabilities that can scale to computational concurrency levels measured in the millions to billions. In this talk I will outline the motivations behind the development of the HACC (Hardware/Hybrid Accelerated Cosmology Code) extreme-scale cosmological simulation framework and describe its essential features. By exploiting a novel algorithmic structure that allows flexible tuning across diverse computer architectures, including accelerated and many-core systems, HACC has attained a performance of 14 PFlops on the IBM BG/Q Sequoia system at 69% of peak, using more than 1.5 million cores.

Photoconductivity enhancement and charge transport properties in ruthenium-containing block copolymer/carbon nanotube hybrids.

PubMed

Lo, Kin Cheung; Hau, King In; Chan, Wai Kin

2018-04-05

Functional polymer/carbon nanotube (CNT) hybrid materials can serve as a good model for light harvesting systems based on CNTs. This paper presents the synthesis of block copolymer/CNT hybrids and the characterization of their photocurrent responses by both experimental and computational approaches. A series of functional diblock copolymers was synthesized by reversible addition-fragmentation chain transfer polymerizations for the dispersion and functionalization of CNTs. The block copolymers contain photosensitizing ruthenium complexes and modified pyrene-based anchoring units. The photocurrent responses of the polymer/CNT hybrids were measured by photoconductive atomic force microscopy (PCAFM), from which the experimental data were analyzed by vigorous statistical models. The difference in photocurrent response among different hybrids was correlated to the conformations of the hybrids, which were elucidated by molecular dynamics simulations, and the electronic properties of polymers. The photoresponse of the block copolymer/CNT hybrids can be enhanced by introducing an electron-accepting block between the photosensitizing block and the CNT. We have demonstrated that the application of a rigorous statistical methodology can unravel the charge transport properties of these hybrid materials and provide general guidelines for the design of molecular light harvesting systems.

Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees.

PubMed

Mirzaei, Sajad; Wu, Yufeng

2016-01-01

Hybridization networks represent plausible evolutionary histories of species that are affected by reticulate evolutionary processes. An established computational problem on hybridization networks is constructing the most parsimonious hybridization network such that each of the given phylogenetic trees (called gene trees) is "displayed" in the network. There have been several previous approaches, including an exact method and several heuristics, for this NP-hard problem. However, the exact method is only applicable to a limited range of data, and heuristic methods can be less accurate and also slow sometimes. In this paper, we develop a new algorithm for constructing near parsimonious networks for multiple binary gene trees. This method is more efficient for large numbers of gene trees than previous heuristics. This new method also produces more parsimonious results on many simulated datasets as well as a real biological dataset than a previous method. We also show that our method produces topologically more accurate networks for many datasets.

A Hybrid Soft-computing Method for Image Analysis of Digital Plantar Scanners.

PubMed

Razjouyan, Javad; Khayat, Omid; Siahi, Mehdi; Mansouri, Ali Alizadeh

2013-01-01

Digital foot scanners have been developed in recent years to yield anthropometrists digital image of insole with pressure distribution and anthropometric information. In this paper, a hybrid algorithm containing gray level spatial correlation (GLSC) histogram and Shanbag entropy is presented for analysis of scanned foot images. An evolutionary algorithm is also employed to find the optimum parameters of GLSC and transform function of the membership values. Resulting binary images as the thresholded images are undergone anthropometric measurements taking in to account the scale factor of pixel size to metric scale. The proposed method is finally applied to plantar images obtained through scanning feet of randomly selected subjects by a foot scanner system as our experimental setup described in the paper. Running computation time and the effects of GLSC parameters are investigated in the simulation results.

Combining Computational Fluid Dynamics and Agent-Based Modeling: A New Approach to Evacuation Planning

PubMed Central

Epstein, Joshua M.; Pankajakshan, Ramesh; Hammond, Ross A.

2011-01-01

We introduce a novel hybrid of two fields—Computational Fluid Dynamics (CFD) and Agent-Based Modeling (ABM)—as a powerful new technique for urban evacuation planning. CFD is a predominant technique for modeling airborne transport of contaminants, while ABM is a powerful approach for modeling social dynamics in populations of adaptive individuals. The hybrid CFD-ABM method is capable of simulating how large, spatially-distributed populations might respond to a physically realistic contaminant plume. We demonstrate the overall feasibility of CFD-ABM evacuation design, using the case of a hypothetical aerosol release in Los Angeles to explore potential effectiveness of various policy regimes. We conclude by arguing that this new approach can be powerfully applied to arbitrary population centers, offering an unprecedented preparedness and catastrophic event response tool. PMID:21687788

Scattering properties of electromagnetic waves from metal object in the lower terahertz region

NASA Astrophysics Data System (ADS)

Chen, Gang; Dang, H. X.; Hu, T. Y.; Su, Xiang; Lv, R. C.; Li, Hao; Tan, X. M.; Cui, T. J.

2018-01-01

An efficient hybrid algorithm is proposed to analyze the electromagnetic scattering properties of metal objects in the lower terahertz (THz) frequency. The metal object can be viewed as perfectly electrical conducting object with a slightly rough surface in the lower THz region. Hence the THz scattered field from metal object can be divided into coherent and incoherent parts. The physical optics and truncated-wedge incremental-length diffraction coefficients methods are combined to compute the coherent part; while the small perturbation method is used for the incoherent part. With the MonteCarlo method, the radar cross section of the rough metal surface is computed by the multilevel fast multipole algorithm and the proposed hybrid algorithm, respectively. The numerical results show that the proposed algorithm has good accuracy to simulate the scattering properties rapidly in the lower THz region.

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

Bakosi, Jozsef; Christon, Mark A.; Francois, Marianne M.

This report describes the work carried out for completion of the Thermal Hydraulics Methods (THM) Level 3 Milestone THM.CFD.P5.05 for the Consortium for Advanced Simulation of Light Water Reactors (CASL). A series body-fitted computational meshes have been generated by Numeca's Hexpress/Hybrid, a.k.a. 'Spider', meshing technology for the V5H 3x3 and 5x5 rod bundle geometry used to compute the fluid dynamics of grid-to-rod fretting (GTRF). Spider is easy to use, fast, and automatically generates high-quality meshes for extremely complex geometries, required for the GTRF problem. Hydra-TH has been used to carry out large-eddy simulations on both 3x3 and 5x5 geometries, usingmore » different mesh resolutions. The results analyzed show good agreement with Star-CCM+ simulations and experimental data.« less

Architecture design of resistor/FET-logic demultiplexer for hybrid CMOS/nanodevice circuit interconnect.

PubMed

Li, Shu; Zhang, Tong

2008-05-07

Hybrid nanoelectronics consisting of nanodevice crossbars on top of CMOS backplane circuits is emerging as one viable option to sustain Moore's law after the CMOS scaling limit is reached. One main design challenge in such hybrid nanoelectronics is the interface between the highly dense nanowires in nanodevice crossbars and relatively coarse microwires in the CMOS domain. Such an interface can be realized through a logic circuit called a demultiplexer (demux). In this context, all the prior work on demux design uses a single type of device, such as resistor, diode or field effect transistor (FET), to realize the demultiplexing function. However, different types of devices have their own advantages and disadvantages in terms of functionality, manufacturability, speed and power consumption. This makes none of them provide a satisfactory solution. To tackle this challenge, this work proposes to combine resistor with FET to implement the demux, leading to the hybrid resistor/FET-logic demux. Such hybrid demux architecture can make these two types of devices complement each other well to improve the overall demux design effectiveness. Furthermore, due to the inevitable fabrication process variations at the nanoscale, the effects of resistor conductance and FET threshold voltage variability are analyzed and evaluated based on computer simulations. The simulation results provide the requirement on the fabrication process to ensure a high demux reliability, and promise the hybrid resistor/FET-logic demux an improved addressability and process variance tolerance.

Hybrid Computation at Louisiana State University.

ERIC Educational Resources Information Center

Corripio, Armando B.

Hybrid computation facilities have been in operation at Louisiana State University since the spring of 1969. In part, they consist of an Electronics Associates, Inc. (EAI) Model 680 analog computer, an EAI Model 693 interface, and a Xerox Data Systems (XDS) Sigma 5 digital computer. The hybrid laboratory is used in a course on hybrid computation…

Electric dipole-quadrupole hybridization induced enhancement of second-harmonic generation in T-shaped plasmonic heterodimers.

PubMed

Guo, Kai; Zhang, Yong-Liang; Qian, Cheng; Fung, Kin-Hung

2018-04-30

In this work, we demonstrate computationally that electric dipole-quadrupole hybridization (EDQH) could be utilized to enhance plasmonic SHG efficiency. To this end, we construct T-shaped plasmonic heterodimers consisting of a short and a long gold nanorod with finite element method simulation. By controlling the strength of capacitive coupling between two gold nanorods, we explore the effect of EDQH evolution on the SHG process, including the SHG efficiency enhancement, corresponding near-field distribution, and far-field radiation pattern. Simulation results demonstrate that EDQH could enhance the SHG efficiency by a factor >100 in comparison with that achieved by an isolated gold nanorod. Additionally, the far-field pattern of the SHG could be adjusted beyond the well-known quadrupolar distribution and confirms that EDQH plays an important role in the SHG process.

A hybrid gyrokinetic ion and isothermal electron fluid code for astrophysical plasma

NASA Astrophysics Data System (ADS)

Kawazura, Y.; Barnes, M.

2018-05-01

This paper describes a new code for simulating astrophysical plasmas that solves a hybrid model composed of gyrokinetic ions (GKI) and an isothermal electron fluid (ITEF) Schekochihin et al. (2009) [9]. This model captures ion kinetic effects that are important near the ion gyro-radius scale while electron kinetic effects are ordered out by an electron-ion mass ratio expansion. The code is developed by incorporating the ITEF approximation into AstroGK, an Eulerian δf gyrokinetics code specialized to a slab geometry Numata et al. (2010) [41]. The new code treats the linear terms in the ITEF equations implicitly while the nonlinear terms are treated explicitly. We show linear and nonlinear benchmark tests to prove the validity and applicability of the simulation code. Since the fast electron timescale is eliminated by the mass ratio expansion, the Courant-Friedrichs-Lewy condition is much less restrictive than in full gyrokinetic codes; the present hybrid code runs ∼ 2√{mi /me } ∼ 100 times faster than AstroGK with a single ion species and kinetic electrons where mi /me is the ion-electron mass ratio. The improvement of the computational time makes it feasible to execute ion scale gyrokinetic simulations with a high velocity space resolution and to run multiple simulations to determine the dependence of turbulent dynamics on parameters such as electron-ion temperature ratio and plasma beta.

Full-band quantum simulation of electron devices with the pseudopotential method: Theory, implementation, and applications

NASA Astrophysics Data System (ADS)

Pala, M. G.; Esseni, D.

2018-03-01

This paper presents the theory, implementation, and application of a quantum transport modeling approach based on the nonequilibrium Green's function formalism and a full-band empirical pseudopotential Hamiltonian. We here propose to employ a hybrid real-space/plane-wave basis that results in a significant reduction of the computational complexity compared to a full plane-wave basis. To this purpose, we provide a theoretical formulation in the hybrid basis of the quantum confinement, the self-energies of the leads, and the coupling between the device and the leads. After discussing the theory and the implementation of the new simulation methodology, we report results for complete, self-consistent simulations of different electron devices, including a silicon Esaki diode, a thin-body silicon field effect transistor (FET), and a germanium tunnel FET. The simulated transistors have technologically relevant geometrical features with a semiconductor film thickness of about 4 nm and a channel length ranging from 10 to 17 nm. We believe that the newly proposed formalism may find applications also in transport models based on ab initio Hamiltonians, as those employed in density functional theory methods.

Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.

PubMed

Doi, Atsushi; Nagasaki, Masao; Matsuno, Hiroshi; Miyano, Satoru

2011-01-01

MDM2 and p19ARF are essential proteins in cancer pathways forming a complex with protein p53 to control the transcriptional activity of protein p53. It is confirmed that protein p53 loses its transcriptional activity by forming the functional dimer with protein MDM2. However, it is still unclear that protein p53 keeps its transcriptional activity when it forms the trimer with proteins MDM2 and p19ARF. We have observed mutual behaviors among genes p53, MDM2, p19ARF and their products on a computational model with hybrid functional Petri net (HFPN) which is constructed based on information described in the literature. The simulation results suggested that protein p53 should have the transcriptional activity in the forms of the trimer of proteins p53, MDM2, and p19ARF. This paper also discusses the advantages of HFPN based modeling method in terms of pathway description for simulations.

Advanced particle-in-cell simulation techniques for modeling the Lockheed Martin Compact Fusion Reactor

NASA Astrophysics Data System (ADS)

Welch, Dale; Font, Gabriel; Mitchell, Robert; Rose, David

2017-10-01

We report on particle-in-cell developments of the study of the Compact Fusion Reactor. Millisecond, two and three-dimensional simulations (cubic meter volume) of confinement and neutral beam heating of the magnetic confinement device requires accurate representation of the complex orbits, near perfect energy conservation, and significant computational power. In order to determine initial plasma fill and neutral beam heating, these simulations include ionization, elastic and charge exchange hydrogen reactions. To this end, we are pursuing fast electromagnetic kinetic modeling algorithms including a two implicit techniques and a hybrid quasi-neutral algorithm with kinetic ions. The kinetic modeling includes use of the Poisson-corrected direct implicit, magnetic implicit, as well as second-order cloud-in-cell techniques. The hybrid algorithm, ignoring electron inertial effects, is two orders of magnitude faster than kinetic but not as accurate with respect to confinement. The advantages and disadvantages of these techniques will be presented. Funded by Lockheed Martin.

Application of hybrid methodology to rotors in steady and maneuvering flight

NASA Astrophysics Data System (ADS)

Rajmohan, Nischint

Helicopters are versatile flying machines that have capabilities that are unparalleled by fixed wing aircraft, such as operating in hover, performing vertical takeoff and landing on unprepared sites. This makes their use especially desirable in military and search-and-rescue operations. However, modern helicopters still suffer from high levels of noise and vibration caused by the physical phenomena occurring in the vicinity of the rotor blades. Therefore, improvement in rotorcraft design to reduce the noise and vibration levels requires understanding of the underlying physical phenomena, and accurate prediction capabilities of the resulting rotorcraft aeromechanics. The goal of this research is to study the aeromechanics of rotors in steady and maneuvering flight using hybrid Computational Fluid Dynamics (CFD) methodology. The hybrid CFD methodology uses the Navier-Stokes equations to solve the flow near the blade surface but the effect of the far wake is computed through the wake model. The hybrid CFD methodology is computationally efficient and its wake modeling approach is nondissipative making it an attractive tool to study rotorcraft aeromechanics. Several enhancements were made to the CFD methodology and it was coupled to a Computational Structural Dynamics (CSD) methodology to perform a trimmed aeroelastic analysis of a rotor in forward flight. The coupling analyses, both loose and tight were used to identify the key physical phenomena that affect rotors in different steady flight regimes. The modeling enhancements improved the airloads predictions for a variety of flight conditions. It was found that the tightly coupled method did not impact the loads significantly for steady flight conditions compared to the loosely coupled method. The coupling methodology was extended to maneuvering flight analysis by enhancing the computational and structural models to handle non-periodic flight conditions and vehicle motions in time accurate mode. The flight test control angles were employed to enable the maneuvering flight analysis. The fully coupled model provided the presence of three dynamic stall cycles on the rotor in maneuver. It is important to mention that analysis of maneuvering flight requires knowledge of the pilot input control pitch settings, and the vehicle states. As the result, these computational tools cannot be used for analysis of loads in a maneuver that has not been duplicated in a real flight. This is a significant limitation if these tools are to be selected during the design phase of a helicopter where its handling qualities are evaluated in different trajectories. Therefore, a methodology was developed to couple the CFD/CSD simulation with an inverse flight mechanics simulation to perform the maneuver analysis without using the flight test control input. The methodology showed reasonable convergence in steady flight regime and control angles predictions compared fairly well with test data. In the maneuvering flight regions, the convergence was slower due to relaxation techniques used for the numerical stability. The subsequent computed control angles for the maneuvering flight regions compared well with test data. Further, the enhancement of the rotor inflow computations in the inverse simulation through implementation of a Lagrangian wake model improved the convergence of the coupling methodology.

PAB3D: Its History in the Use of Turbulence Models in the Simulation of Jet and Nozzle Flows

NASA Technical Reports Server (NTRS)

Abdol-Hamid, Khaled S.; Pao, S. Paul; Hunter, Craig A.; Deere, Karen A.; Massey, Steven J.; Elmiligui, Alaa

2006-01-01

This is a review paper for PAB3D s history in the implementation of turbulence models for simulating jet and nozzle flows. We describe different turbulence models used in the simulation of subsonic and supersonic jet and nozzle flows. The time-averaged simulations use modified linear or nonlinear two-equation models to account for supersonic flow as well as high temperature mixing. Two multiscale-type turbulence models are used for unsteady flow simulations. These models require modifications to the Reynolds Averaged Navier-Stokes (RANS) equations. The first scheme is a hybrid RANS/LES model utilizing the two-equation (k-epsilon) model with a RANS/LES transition function, dependent on grid spacing and the computed turbulence length scale. The second scheme is a modified version of the partially averaged Navier-Stokes (PANS) formulation. All of these models are implemented in the three-dimensional Navier-Stokes code PAB3D. This paper discusses computational methods, code implementation, computed results for a wide range of nozzle configurations at various operating conditions, and comparisons with available experimental data. Very good agreement is shown between the numerical solutions and available experimental data over a wide range of operating conditions.

Aeroacoustic Simulations of a Nose Landing Gear Using FUN3D on Pointwise Unstructured Grids

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Khorrami, Mehdi R.; Rhoads, John; Lockard, David P.

2015-01-01

Numerical simulations have been performed for a partially-dressed, cavity-closed (PDCC) nose landing gear configuration that was tested in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D is used to compute the unsteady flow field for this configuration. Mixed-element grids generated using the Pointwise(TradeMark) grid generation software are used for these simulations. Particular care is taken to ensure quality cells and proper resolution in critical areas of interest in an effort to minimize errors introduced by numerical artifacts. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these simulations. Solutions are also presented for a wall function model coupled to the standard turbulence model. Time-averaged and instantaneous solutions obtained on these Pointwise grids are compared with the measured data and previous numerical solutions. The resulting CFD solutions are used as input to a Ffowcs Williams-Hawkings noise propagation code to compute the farfield noise levels in the flyover and sideline directions. The computed noise levels compare well with previous CFD solutions and experimental data.

Effect of nonlinearity in hybrid kinetic Monte Carlo-continuum models.

PubMed

Balter, Ariel; Lin, Guang; Tartakovsky, Alexandre M

2012-01-01

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a kinetic Monte Carlo (KMC) model for a surface to a finite-difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition-dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition-dissolution model including competitive adsorption, which leads to a nonlinear rate, and show that in this case the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.

Effect of Nonlinearity in Hybrid Kinetic Monte Carlo-Continuum Models

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

Balter, Ariel I.; Lin, Guang; Tartakovsky, Alexandre M.

2012-04-23

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a KMC model for a surface to a finite difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and also show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition/dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition/dissolution model including competitive adsorption, which leadsmore » to a nonlinear rate, and show that, in this case, the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.« less

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.

Fuel consumption optimization for smart hybrid electric vehicle during a car-following process

NASA Astrophysics Data System (ADS)

Li, Liang; Wang, Xiangyu; Song, Jian

2017-03-01

Hybrid electric vehicles (HEVs) provide large potential to save energy and reduce emission, and smart vehicles bring out great convenience and safety for drivers. By combining these two technologies, vehicles may achieve excellent performances in terms of dynamic, economy, environmental friendliness, safety, and comfort. Hence, a smart hybrid electric vehicle (s-HEV) is selected as a platform in this paper to study a car-following process with optimizing the fuel consumption. The whole process is a multi-objective optimal problem, whose optimal solution is not just adding an energy management strategy (EMS) to an adaptive cruise control (ACC), but a deep fusion of these two methods. The problem has more restricted conditions, optimal objectives, and system states, which may result in larger computing burden. Therefore, a novel fuel consumption optimization algorithm based on model predictive control (MPC) is proposed and some search skills are adopted in receding horizon optimization to reduce computing burden. Simulations are carried out and the results indicate that the fuel consumption of proposed method is lower than that of the ACC+EMS method on the condition of ensuring car-following performances.

Computational fluid dynamics challenges for hybrid air vehicle applications

NASA Astrophysics Data System (ADS)

Carrin, M.; Biava, M.; Steijl, R.; Barakos, G. N.; Stewart, D.

2017-06-01

This paper begins by comparing turbulence models for the prediction of hybrid air vehicle (HAV) flows. A 6 : 1 prolate spheroid is employed for validation of the computational fluid dynamics (CFD) method. An analysis of turbulent quantities is presented and the Shear Stress Transport (SST) k-ω model is compared against a k-ω Explicit Algebraic Stress model (EASM) within the unsteady Reynolds-Averaged Navier-Stokes (RANS) framework. Further comparisons involve Scale Adaptative Simulation models and a local transition transport model. The results show that the flow around the vehicle at low pitch angles is sensitive to transition effects. At high pitch angles, the vortices generated on the suction side provide substantial lift augmentation and are better resolved by EASMs. The validated CFD method is employed for the flow around a shape similar to the Airlander aircraft of Hybrid Air Vehicles Ltd. The sensitivity of the transition location to the Reynolds number is demonstrated and the role of each vehicle£s component is analyzed. It was found that the ¦ns contributed the most to increase the lift and drag.

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

PubMed Central

Stover, Lori J.; Nair, Niketh S.; Faeder, James R.

2014-01-01

Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This “network-free” approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of “partial network expansion” into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility. PMID:24699269

Exact hybrid particle/population simulation of rule-based models of biochemical systems.

PubMed

Hogg, Justin S; Harris, Leonard A; Stover, Lori J; Nair, Niketh S; Faeder, James R

2014-04-01

Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility.

Scattering of Acoustic Energy from Rough Deep Ocean Seafloor: a Numerical Modeling Approach.

NASA Astrophysics Data System (ADS)

Robertsson, Johan Olof Anders

1995-01-01

The highly heterogeneous and anelastic nature of deep ocean seafloor results in complex reverberation as acoustic energy incident from the overlaying water column interacts and scatters from it. To gain a deeper understanding of the mechanisms causing the reverberation in sonar and seafloor scattering experiments, we have developed numerical simulation techniques that are capable of modeling the principal physical properties of complex seafloor structures. A new viscoelastic finite-difference technique for modeling anelastic wave propagation in 2-D and 3-D heterogeneous media, as well as a computationally optimally efficient method for quantifying the anelastic properties in terms of viscoelastic mechanics are presented. A method for reducing numerical dispersion using a Galerkin-wavelet formulation that enables large computational savings is also presented. The widely different regimes of wave propagation occurring in ocean acoustic problems motivate the use of hybrid simulation techniques. HARVEST (Hybrid Adaptive Regime Visco-Elastic Simulation Technique) combines solutions from Gaussian beams, viscoelastic finite-differences, and Kirchhoff extrapolation, to simulate large offset scattering problems. Several scattering hypotheses based on finite -difference simulations of short-range acoustic scattering from realistic seafloor models are presented. Anelastic sediments on the seafloor are found to have a significant impact on the backscattered field from low grazing angle scattering experiments. In addition, small perturbations in the sediment compressional velocity can also dramatically alter the backscattered field due to transitions between pre- and post-critical reflection regimes. The hybrid techniques are employed to simulate deep ocean acoustic reverberation data collected in the vicinity of the northern mid-Atlantic ridge. In general, the simulated data compare well to the real data. Noise partly due to side-lobes in the beam-pattern of the receiver -array is the principal source of reverberation at lower levels. Overall, the employed seafloor models were found to model the real seafloor well. Inaccurately predicted events may partly be attributed to the intrinsic uncertainty in the stochastic seafloor models. For optimal comparison between real and HARVEST simulated data the experimental geometry should be chosen so that 3-D effects may be ignored, and to yield a cross-range resolution in the beam-formed acoustic data that is small relative to the lineation of the seafloor.

Hybrid DG/FV schemes for magnetohydrodynamics and relativistic hydrodynamics

NASA Astrophysics Data System (ADS)

Núñez-de la Rosa, Jonatan; Munz, Claus-Dieter

2018-01-01

This paper presents a high order hybrid discontinuous Galerkin/finite volume scheme for solving the equations of the magnetohydrodynamics (MHD) and of the relativistic hydrodynamics (SRHD) on quadrilateral meshes. In this approach, for the spatial discretization, an arbitrary high order discontinuous Galerkin spectral element (DG) method is combined with a finite volume (FV) scheme in order to simulate complex flow problems involving strong shocks. Regarding the time discretization, a fourth order strong stability preserving Runge-Kutta method is used. In the proposed hybrid scheme, a shock indicator is computed at the beginning of each Runge-Kutta stage in order to flag those elements containing shock waves or discontinuities. Subsequently, the DG solution in these troubled elements and in the current time step is projected onto a subdomain composed of finite volume subcells. Right after, the DG operator is applied to those unflagged elements, which, in principle, are oscillation-free, meanwhile the troubled elements are evolved with a robust second/third order FV operator. With this approach we are able to numerically simulate very challenging problems in the context of MHD and SRHD in one, and two space dimensions and with very high order polynomials. We make convergence tests and show a comprehensive one- and two dimensional testbench for both equation systems, focusing in problems with strong shocks. The presented hybrid approach shows that numerical schemes of very high order of accuracy are able to simulate these complex flow problems in an efficient and robust manner.

Multiscale Mathematics for Biomass Conversion to Renewable Hydrogen

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

Plechac, Petr; Vlachos, Dionisios; Katsoulakis, Markos

2013-09-05

The overall objective of this project is to develop multiscale models for understanding and eventually designing complex processes for renewables. To the best of our knowledge, our work is the first attempt at modeling complex reacting systems, whose performance relies on underlying multiscale mathematics. Our specific application lies at the heart of biofuels initiatives of DOE and entails modeling of catalytic systems, to enable economic, environmentally benign, and efficient conversion of biomass into either hydrogen or valuable chemicals. Specific goals include: (i) Development of rigorous spatio-temporal coarse-grained kinetic Monte Carlo (KMC) mathematics and simulation for microscopic processes encountered in biomassmore » transformation. (ii) Development of hybrid multiscale simulation that links stochastic simulation to a deterministic partial differential equation (PDE) model for an entire reactor. (iii) Development of hybrid multiscale simulation that links KMC simulation with quantum density functional theory (DFT) calculations. (iv) Development of parallelization of models of (i)-(iii) to take advantage of Petaflop computing and enable real world applications of complex, multiscale models. In this NCE period, we continued addressing these objectives and completed the proposed work. Main initiatives, key results, and activities are outlined.« less

Fast Flows in the Magnetotail and Energetic Particle Transport: Multiscale Coupling in the Magnetosphere

NASA Astrophysics Data System (ADS)

Lin, Y.; Wang, X.; Fok, M. C. H.; Buzulukova, N.; Perez, J. D.; Chen, L. J.

2017-12-01

The interaction between the Earth's inner and outer magnetospheric regions associated with the tail fast flows is calculated by coupling the Auburn 3-D global hybrid simulation code (ANGIE3D) to the Comprehensive Inner Magnetosphere/Ionosphere (CIMI) model. The global hybrid code solves fully kinetic equations governing the ions and a fluid model for electrons in the self-consistent electromagnetic field of the dayside and night side outer magnetosphere. In the integrated computation model, the hybrid simulation provides the CIMI model with field data in the CIMI 3-D domain and particle data at its boundary, and the transport in the inner magnetosphere is calculated by the CIMI model. By joining the two existing codes, effects of the solar wind on particle transport through the outer magnetosphere into the inner magnetosphere are investigated. Our simulation shows that fast flows and flux ropes are localized transients in the magnetotail plasma sheet and their overall structures have a dawn-dusk asymmetry. Strong perpendicular ion heating is found at the fast flow braking, which affects the earthward transport of entropy-depleted bubbles. We report on the impacts from the temperature anisotropy and non-Maxwellian ion distributions associated with the fast flows on the ring current and the convection electric field.

Development of a Hybrid RANS/LES Method for Turbulent Mixing Layers

NASA Technical Reports Server (NTRS)

Georgiadis, Nicholas J.; Alexander, J. Iwan D.; Reshotko, Eli

2001-01-01

Significant research has been underway for several years in NASA Glenn Research Center's nozzle branch to develop advanced computational methods for simulating turbulent flows in exhaust nozzles. The primary efforts of this research have concentrated on improving our ability to calculate the turbulent mixing layers that dominate flows both in the exhaust systems of modern-day aircraft and in those of hypersonic vehicles under development. As part of these efforts, a hybrid numerical method was recently developed to simulate such turbulent mixing layers. The method developed here is intended for configurations in which a dominant structural feature provides an unsteady mechanism to drive the turbulent development in the mixing layer. Interest in Large Eddy Simulation (LES) methods have increased in recent years, but applying an LES method to calculate the wide range of turbulent scales from small eddies in the wall-bounded regions to large eddies in the mixing region is not yet possible with current computers. As a result, the hybrid method developed here uses a Reynolds-averaged Navier-Stokes (RANS) procedure to calculate wall-bounded regions entering a mixing section and uses a LES procedure to calculate the mixing-dominated regions. A numerical technique was developed to enable the use of the hybrid RANS-LES method on stretched, non-Cartesian grids. With this technique, closure for the RANS equations is obtained by using the Cebeci-Smith algebraic turbulence model in conjunction with the wall-function approach of Ota and Goldberg. The LES equations are closed using the Smagorinsky subgrid scale model. Although the function of the Cebeci-Smith model to replace all of the turbulent stresses is quite different from that of the Smagorinsky subgrid model, which only replaces the small subgrid turbulent stresses, both are eddy viscosity models and both are derived at least in part from mixing-length theory. The similar formulation of these two models enables the RANS and LES equations to be solved with a single solution scheme and computational grid. The hybrid RANS-LES method has been applied to a benchmark compressible mixing layer experiment in which two isolated supersonic streams, separated by a splitter plate, provide the flows to a constant-area mixing section. Although the configuration is largely two dimensional in nature, three-dimensional calculations were found to be necessary to enable disturbances to develop in three spatial directions and to transition to turbulence. The flow in the initial part of the mixing section consists of a periodic vortex shedding downstream of the splitter plate trailing edge. This organized vortex shedding then rapidly transitions to a turbulent structure, which is very similar to the flow development observed in the experiments. Although the qualitative nature of the large-scale turbulent development in the entire mixing section is captured well by the LES part of the current hybrid method, further efforts are planned to directly calculate a greater portion of the turbulence spectrum and to limit the subgrid scale modeling to only the very small scales. This will be accomplished by the use of higher accuracy solution schemes and more powerful computers, measured both in speed and memory capabilities.

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul

2016-03-01

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

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

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de

2016-03-21

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). Formore » the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “first-principles” DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.« less

Genome-Wide Prediction of the Performance of Three-Way Hybrids in Barley.

PubMed

Li, Zuo; Philipp, Norman; Spiller, Monika; Stiewe, Gunther; Reif, Jochen C; Zhao, Yusheng

2017-03-01

Predicting the grain yield performance of three-way hybrids is challenging. Three-way crosses are relevant for hybrid breeding in barley ( L.) and maize ( L.) adapted to East Africa. The main goal of our study was to implement and evaluate genome-wide prediction approaches of the performance of three-way hybrids using data of single-cross hybrids for a scenario in which parental lines of the three-way hybrids originate from three genetically distinct subpopulations. We extended the ridge regression best linear unbiased prediction (RRBLUP) and devised a genomic selection model allowing for subpopulation-specific marker effects (GSA-RRBLUP: general and subpopulation-specific additive RRBLUP). Using an empirical barley data set, we showed that applying GSA-RRBLUP tripled the prediction ability of three-way hybrids from 0.095 to 0.308 compared with RRBLUP, modeling one additive effect for all three subpopulations. The experimental findings were further substantiated with computer simulations. Our results emphasize the potential of GSA-RRBLUP to improve genome-wide hybrid prediction of three-way hybrids for scenarios of genetically diverse parental populations. Because of the advantages of the GSA-RRBLUP model in dealing with hybrids from different parental populations, it may also be a promising approach to boost the prediction ability for hybrid breeding programs based on genetically diverse heterotic groups. Copyright © 2017 Crop Science Society of America.

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.

A Two-Stage Procedure Toward the Efficient Implementation of PANS and Other Hybrid Turbulence Models

NASA Technical Reports Server (NTRS)

Abdol-Hamid, Khaled S.; Girimaji, Sharath S.

2004-01-01

The main objective of this article is to introduce and to show the implementation of a novel two-stage procedure to efficiently estimate the level of scale resolution possible for a given flow on a given grid for Partial Averaged Navier-Stokes (PANS) and other hybrid models. It has been found that the prescribed scale resolution can play a major role in obtaining accurate flow solutions. The first step is to solve the unsteady or steady Reynolds Averaged Navier-Stokes (URANS/RANS) equations. From this preprocessing step, the turbulence length-scale field is obtained. This is then used to compute the characteristic length-scale ratio between the turbulence scale and the grid spacing. Based on this ratio, we can assess the finest scale resolution that a given grid for a given flow can support. Along with other additional criteria, we are able to analytically identify the appropriate hybrid solver resolution for different regions of the flow. This procedure removes the grid dependency issue that affects the results produced by different hybrid procedures in solving unsteady flows. The formulation, implementation methodology, and validation example are presented. We implemented this capability in a production Computational Fluid Dynamics (CFD) code, PAB3D, for the simulation of unsteady flows.

Efficiently passing messages in distributed spiking neural network simulation.

PubMed

Thibeault, Corey M; Minkovich, Kirill; O'Brien, Michael J; Harris, Frederick C; Srinivasa, Narayan

2013-01-01

Efficiently passing spiking messages in a neural model is an important aspect of high-performance simulation. As the scale of networks has increased so has the size of the computing systems required to simulate them. In addition, the information exchange of these resources has become more of an impediment to performance. In this paper we explore spike message passing using different mechanisms provided by the Message Passing Interface (MPI). A specific implementation, MVAPICH, designed for high-performance clusters with Infiniband hardware is employed. The focus is on providing information about these mechanisms for users of commodity high-performance spiking simulators. In addition, a novel hybrid method for spike exchange was implemented and benchmarked.

Hybrid multiscale modeling and prediction of cancer cell behavior

PubMed Central

Habibi, Jafar

2017-01-01

Background Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. Methods In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods. The purpose of this simulation is to create a dataset that can be used for prediction of cell phenotypes. By using a proposed Q-learning based on SVR-NSGA-II method, the cells have the capability to predict their phenotypes autonomously that is, to act on its own without external direction in response to situations it encounters. Results Computational simulations of the model were performed in order to analyze its performance. The most striking feature of our results is that each cell can select its phenotype at each time step according to its condition. We provide evidence that the prediction of cell phenotypes is reliable. Conclusion Our proposed model, which we term a hybrid multiscale modeling of cancer cell behavior, has the potential to combine the best features of both continuum and discrete models. The in silico results indicate that the 3D model can represent key features of cancer growth, angiogenesis, and its related micro-environment and show that the findings are in good agreement with biological tumor behavior. To the best of our knowledge, this paper is the first hybrid vascular multiscale modeling of cancer cell behavior that has the capability to predict cell phenotypes individually by a self-generated dataset. PMID:28846712

A Hybrid Numerical Method for Turbulent Mixing Layers. Degree awarded by Case Western Reserve Univ.

NASA Technical Reports Server (NTRS)

Georgiadis, Nicholas J.

2001-01-01

A hybrid method has been developed for simulations of compressible turbulent mixing layers. Such mixing layers dominate the flows in exhaust systems of modern day aircraft and also those of hypersonic vehicles currently under development. The method configurations in which a dominant structural feature provides an unsteady mechanism to drive the turbulent development in the mixing layer. The hybrid method uses a Reynolds-averaged Navier-Stokes (RANS) procedure to calculate wall bounded regions entering a mixing section, and a Large Eddy Simulation (LES) procedure to calculate the mixing dominated regions. A numerical technique was developed to enable the use of the hybrid RANS-LES method on stretched, non-Cartesian grids. Closure for the RANS equations was obtained using the Cebeci-Smith algebraic turbulence model in conjunction with the wall-function approach of Ota and Goldberg. The wall-function approach enabled a continuous computational grid from the RANS regions to the LES region. The LES equations were closed using the Smagorinsky subgrid scale model. The hybrid RANS-LES method is applied to a benchmark compressible mixing layer experiment. Preliminary two dimensional calculations are used to investigate the effects of axial grid density and boundary conditions. Vortex shedding from the base region of a splitter plate separating the upstream flows was observed to eventually transition to turbulence. The location of the transition, however, was much further downstream than indicated by experiments. Actual LES calculations, performed in three spatial directions, also indicated vortex shedding, but the transition to turbulence was found to occur much closer to the beginning of the mixing section. which is in agreement with experimental observations. These calculations demonstrated that LES simulations must be performed in three dimensions. Comparisons of time-averaged axial velocities and turbulence intensities indicated reasonable agreement with experimental data.

Hybrid multiscale modeling and prediction of cancer cell behavior.

PubMed

Zangooei, Mohammad Hossein; Habibi, Jafar

2017-01-01

Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods. The purpose of this simulation is to create a dataset that can be used for prediction of cell phenotypes. By using a proposed Q-learning based on SVR-NSGA-II method, the cells have the capability to predict their phenotypes autonomously that is, to act on its own without external direction in response to situations it encounters. Computational simulations of the model were performed in order to analyze its performance. The most striking feature of our results is that each cell can select its phenotype at each time step according to its condition. We provide evidence that the prediction of cell phenotypes is reliable. Our proposed model, which we term a hybrid multiscale modeling of cancer cell behavior, has the potential to combine the best features of both continuum and discrete models. The in silico results indicate that the 3D model can represent key features of cancer growth, angiogenesis, and its related micro-environment and show that the findings are in good agreement with biological tumor behavior. To the best of our knowledge, this paper is the first hybrid vascular multiscale modeling of cancer cell behavior that has the capability to predict cell phenotypes individually by a self-generated dataset.

A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

NASA Astrophysics Data System (ADS)

Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M.

1999-06-01

We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane-wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be spoiled by the lower quality force field of the solvent is checked, including cases in which the two fragments are covalently joined. The results demonstrate that our QM/MM hybrid method is especially well suited for the vibrational analysis of molecules in condensed phase.

Unsteady Three-Dimensional Simulation of a Shear Coaxial GO2/GH2 Rocket Injector with RANS and Hybrid-RAN-LES/DES Using Flamelet Models

NASA Technical Reports Server (NTRS)

Westra, Doug G.; West, Jeffrey S.; Richardson, Brian R.

2015-01-01

Historically, the analysis and design of liquid rocket engines (LREs) has relied on full-scale testing and one-dimensional empirical tools. The testing is extremely expensive and the one-dimensional tools are not designed to capture the highly complex, and multi-dimensional features that are inherent to LREs. Recent advances in computational fluid dynamics (CFD) tools have made it possible to predict liquid rocket engine performance, stability, to assess the effect of complex flow features, and to evaluate injector-driven thermal environments, to mitigate the cost of testing. Extensive efforts to verify and validate these CFD tools have been conducted, to provide confidence for using them during the design cycle. Previous validation efforts have documented comparisons of predicted heat flux thermal environments with test data for a single element gaseous oxygen (GO2) and gaseous hydrogen (GH2) injector. The most notable validation effort was a comprehensive validation effort conducted by Tucker et al. [1], in which a number of different groups modeled a GO2/GH2 single element configuration by Pal et al [2]. The tools used for this validation comparison employed a range of algorithms, from both steady and unsteady Reynolds Averaged Navier-Stokes (U/RANS) calculations, large-eddy simulations (LES), detached eddy simulations (DES), and various combinations. A more recent effort by Thakur et al. [3] focused on using a state-of-the-art CFD simulation tool, Loci/STREAM, on a two-dimensional grid. Loci/STREAM was chosen because it has a unique, very efficient flamelet parameterization of combustion reactions that are too computationally expensive to simulate with conventional finite-rate chemistry calculations. The current effort focuses on further advancement of validation efforts, again using the Loci/STREAM tool with the flamelet parameterization, but this time with a three-dimensional grid. Comparisons to the Pal et al. heat flux data will be made for both RANS and Hybrid RANSLES/ Detached Eddy simulations (DES). Computation costs will be reported, along with comparison of accuracy and cost to much less expensive two-dimensional RANS simulations of the same geometry.

Computational analysis on plug-in hybrid electric motorcycle chassis

NASA Astrophysics Data System (ADS)

Teoh, S. J.; Bakar, R. A.; Gan, L. M.

2013-12-01

Plug-in hybrid electric motorcycle (PHEM) is an alternative to promote sustainability lower emissions. However, the PHEM overall system packaging is constrained by limited space in a motorcycle chassis. In this paper, a chassis applying the concept of a Chopper is analysed to apply in PHEM. The chassis 3dimensional (3D) modelling is built with CAD software. The PHEM power-train components and drive-train mechanisms are intergraded into the 3D modelling to ensure the chassis provides sufficient space. Besides that, a human dummy model is built into the 3D modelling to ensure the rider?s ergonomics and comfort. The chassis 3D model then undergoes stress-strain simulation. The simulation predicts the stress distribution, displacement and factor of safety (FOS). The data are used to identify the critical point, thus suggesting the chassis design is applicable or need to redesign/ modify to meet the require strength. Critical points mean highest stress which might cause the chassis to fail. This point occurs at the joints at triple tree and bracket rear absorber for a motorcycle chassis. As a conclusion, computational analysis predicts the stress distribution and guideline to develop a safe prototype chassis.

Numerical Methods of Computational Electromagnetics for Complex Inhomogeneous Systems

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

Cai, Wei

Understanding electromagnetic phenomena is the key in many scientific investigation and engineering designs such as solar cell designs, studying biological ion channels for diseases, and creating clean fusion energies, among other things. The objectives of the project are to develop high order numerical methods to simulate evanescent electromagnetic waves occurring in plasmon solar cells and biological ion-channels, where local field enhancement within random media in the former and long range electrostatic interactions in the latter are of major challenges for accurate and efficient numerical computations. We have accomplished these objectives by developing high order numerical methods for solving Maxwell equationsmore » such as high order finite element basis for discontinuous Galerkin methods, well-conditioned Nedelec edge element method, divergence free finite element basis for MHD, and fast integral equation methods for layered media. These methods can be used to model the complex local field enhancement in plasmon solar cells. On the other hand, to treat long range electrostatic interaction in ion channels, we have developed image charge based method for a hybrid model in combining atomistic electrostatics and continuum Poisson-Boltzmann electrostatics. Such a hybrid model will speed up the molecular dynamics simulation of transport in biological ion-channels.« less

UT simulation using a fully automated 3D hybrid model: Application to planar backwall breaking defects inspection

NASA Astrophysics Data System (ADS)

Imperiale, Alexandre; Chatillon, Sylvain; Darmon, Michel; Leymarie, Nicolas; Demaldent, Edouard

2018-04-01

The high frequency models gathered in the CIVA software allow fast computations and provide satisfactory quantitative predictions in a wide range of situations. However, the domain of validity of these models is limited since they do not accurately predict the ultrasound response in configurations involving subwavelength complex phenomena. In addition, when modelling backwall breaking defects inspection, an important challenge remains to capture the propagation of the creeping waves that are generated at the critical angle. Hybrid models combining numerical and asymptotic methods have already been shown to be an effective strategy to overcome these limitations in 2D [1]. However, 3D simulations remain a crucial issue for industrial applications because of the computational cost of the numerical solver. A dedicated three dimensional high order finite element model combined with a domain decomposition method has been recently proposed to tackle 3D limitations [2]. In this communication, we will focus on the specific case of planar backwall breaking defects, with an adapted coupling strategy in order to efficiently model the propagation of creeping waves. Numerical and experimental validations will be proposed on various configurations.

A hybrid stochastic model of folate-mediated one-carbon metabolism: Effect of the common C677T MTHFR variant on de novo thymidylate biosynthesis.

PubMed

Misselbeck, Karla; Marchetti, Luca; Field, Martha S; Scotti, Marco; Priami, Corrado; Stover, Patrick J

2017-04-11

Folate-mediated one-carbon metabolism (FOCM) is an interconnected network of metabolic pathways, including those required for the de novo synthesis of dTMP and purine nucleotides and for remethylation of homocysteine to methionine. Mouse models of folate-responsive neural tube defects (NTDs) indicate that impaired de novo thymidylate (dTMP) synthesis through changes in SHMT expression is causative in folate-responsive NTDs. We have created a hybrid computational model comprised of ordinary differential equations and stochastic simulation. We investigated whether the de novo dTMP synthesis pathway was sensitive to perturbations in FOCM that are known to be associated with human NTDs. This computational model shows that de novo dTMP synthesis is highly sensitive to the common MTHFR C677T polymorphism and that the effect of the polymorphism on FOCM is greater in folate deficiency. Computational simulations indicate that the MTHFR C677T polymorphism and folate deficiency interact to increase the stochastic behavior of the FOCM network, with the greatest instability observed for reactions catalyzed by serine hydroxymethyltransferase (SHMT). Furthermore, we show that de novo dTMP synthesis does not occur in the cytosol at rates sufficient for DNA replication, supporting empirical data indicating that impaired nuclear de novo dTMP synthesis results in uracil misincorporation into DNA.

Cardiovascular system simulation in biomedical engineering education.

NASA Technical Reports Server (NTRS)

Rideout, V. C.

1972-01-01

Use of complex cardiovascular system models, in conjunction with a large hybrid computer, in biomedical engineering courses. A cardiovascular blood pressure-flow model, driving a compartment model for the study of dye transport, was set up on the computer for use as a laboratory exercise by students who did not have the computer experience or skill to be able to easily set up such a simulation involving some 27 differential equations running at 'real time' rate. The students were given detailed instructions regarding the model, and were then able to study effects such as those due to septal and valve defects upon the pressure, flow, and dye dilution curves. The success of this experiment in the use of involved models in engineering courses was such that it seems that this type of laboratory exercise might be considered for use in physiology courses as an adjunct to animal experiments.

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Parallel Unsteady Turbopump Simulations for Liquid Rocket Engines

NASA Technical Reports Server (NTRS)

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

2000-01-01

This paper reports the progress being made towards complete turbo-pump simulation capability for liquid rocket engines. Space Shuttle Main Engine (SSME) turbo-pump impeller is used as a test case for the performance evaluation of the MPI and hybrid MPI/Open-MP versions of the INS3D code. Then, a computational model of a turbo-pump has been developed for the shuttle upgrade program. Relative motion of the grid system for rotor-stator interaction was obtained by employing overset grid techniques. Time-accuracy of the scheme has been evaluated by using simple test cases. Unsteady computations for SSME turbo-pump, which contains 136 zones with 35 Million grid points, are currently underway on Origin 2000 systems at NASA Ames Research Center. Results from time-accurate simulations with moving boundary capability, and the performance of the parallel versions of the code will be presented in the final paper.

QSPIN: A High Level Java API for Quantum Computing Experimentation

NASA Technical Reports Server (NTRS)

Barth, Tim

2017-01-01

QSPIN is a high level Java language API for experimentation in QC models used in the calculation of Ising spin glass ground states and related quadratic unconstrained binary optimization (QUBO) problems. The Java API is intended to facilitate research in advanced QC algorithms such as hybrid quantum-classical solvers, automatic selection of constraint and optimization parameters, and techniques for the correction and mitigation of model and solution errors. QSPIN includes high level solver objects tailored to the D-Wave quantum annealing architecture that implement hybrid quantum-classical algorithms [Booth et al.] for solving large problems on small quantum devices, elimination of variables via roof duality, and classical computing optimization methods such as GPU accelerated simulated annealing and tabu search for comparison. A test suite of documented NP-complete applications ranging from graph coloring, covering, and partitioning to integer programming and scheduling are provided to demonstrate current capabilities.

Hybrid expert system for decision supporting in the medical area: complexity and cognitive computing.

PubMed

Brasil, L M; de Azevedo, F M; Barreto, J M

2001-09-01

This paper proposes a hybrid expert system (HES) to minimise some complexity problems pervasive to the artificial intelligence such as: the knowledge elicitation process, known as the bottleneck of expert systems; the model choice for knowledge representation to code human reasoning; the number of neurons in the hidden layer and the topology used in the connectionist approach; the difficulty to obtain the explanation on how the network arrived to a conclusion. Two algorithms applied to developing of HES are also suggested. One of them is used to train the fuzzy neural network and the other to obtain explanations on how the fuzzy neural network attained a conclusion. To overcome these difficulties the cognitive computing was integrated to the developed system. A case study is presented (e.g. epileptic crisis) with the problem definition and simulations. Results are also discussed.

Applications of the hybrid coordinate method to the TOPS autopilot

NASA Technical Reports Server (NTRS)

Fleischer, G. E.

1978-01-01

Preliminary results are presented from the application of the hybrid coordinate method to modeling TOPS (thermoelectric outer planet spacecraft) structural dynamics. Computer simulated responses of the vehicle are included which illustrate the interaction of relatively flexible appendages with an autopilot control system. Comparisons were made between simplified single-axis models of the control loop, with spacecraft flexibility represented by hinged rigid bodies, and a very detailed three-axis spacecraft model whose flexible portions are described by modal coordinates. While single-axis system, root loci provided reasonable qualitative indications of stability margins in this case, they were quantitatively optimistic when matched against responses of the detailed model.

Characterization of hybrid lighting systems of the Electrical Engineering Building in the Industrial University of Santander

NASA Astrophysics Data System (ADS)

Galvis, D.; Exposito, C.; Osma, G.; Amado, L.; Ordóñez, G.

2016-07-01

This paper presents an analysis of hybrid lighting systems of Electrical Engineering Building in the Industrial University of Santander, which is a pilot of green building for warm- tropical conditions. Analysis of lighting performance of inner spaces is based on lighting curves obtained from characterization of daylighting systems of these spaces. A computation tool was made in Excel-Visual Basic to simulate the behaviour of artificial lighting system considering artificial control system, user behaviour and solar condition. Also, this tool allows to estimate the electrical energy consumption of the lighting system for a day, a month and a year.

Aeroacoustic Simulation of Nose Landing Gear on Adaptive Unstructured Grids With FUN3D

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Khorrami, Mehdi R.; Park, Michael A.; Lockard, David P.

2013-01-01

Numerical simulations have been performed for a partially-dressed, cavity-closed nose landing gear configuration that was tested in NASA Langley s closed-wall Basic Aerodynamic Research Tunnel (BART) and in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D, developed at NASA Langley Research center, is used to compute the unsteady flow field for this configuration. Starting with a coarse grid, a series of successively finer grids were generated using the adaptive gridding methodology available in the FUN3D code. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these computations. Time-averaged and instantaneous solutions obtained on these grids are compared with the measured data. In general, the correlation with the experimental data improves with grid refinement. A similar trend is observed for sound pressure levels obtained by using these CFD solutions as input to a FfowcsWilliams-Hawkings noise propagation code to compute the farfield noise levels. In general, the numerical solutions obtained on adapted grids compare well with the hand-tuned enriched fine grid solutions and experimental data. In addition, the grid adaption strategy discussed here simplifies the grid generation process, and results in improved computational efficiency of CFD simulations.

PENTACLE: Parallelized particle-particle particle-tree code for planet formation

NASA Astrophysics Data System (ADS)

Iwasawa, Masaki; Oshino, Shoichi; Fujii, Michiko S.; Hori, Yasunori

2017-10-01

We have newly developed a parallelized particle-particle particle-tree code for planet formation, PENTACLE, which is a parallelized hybrid N-body integrator executed on a CPU-based (super)computer. PENTACLE uses a fourth-order Hermite algorithm to calculate gravitational interactions between particles within a cut-off radius and a Barnes-Hut tree method for gravity from particles beyond. It also implements an open-source library designed for full automatic parallelization of particle simulations, FDPS (Framework for Developing Particle Simulator), to parallelize a Barnes-Hut tree algorithm for a memory-distributed supercomputer. These allow us to handle 1-10 million particles in a high-resolution N-body simulation on CPU clusters for collisional dynamics, including physical collisions in a planetesimal disc. In this paper, we show the performance and the accuracy of PENTACLE in terms of \\tilde{R}_cut and a time-step Δt. It turns out that the accuracy of a hybrid N-body simulation is controlled through Δ t / \\tilde{R}_cut and Δ t / \\tilde{R}_cut ˜ 0.1 is necessary to simulate accurately the accretion process of a planet for ≥106 yr. For all those interested in large-scale particle simulations, PENTACLE, customized for planet formation, will be freely available from https://github.com/PENTACLE-Team/PENTACLE under the MIT licence.

Low noise SQUIDs

NASA Astrophysics Data System (ADS)

de Waal, V. J.

1983-02-01

The present investigation deals with the design, fabrication, and limitations of very sensitive SQUID (Superconducting Quantum Interference Device) magnetometers. The SQUID magnetometer is based on a utilization of the Josephson effect. A description of the theoretical background is provided, and high performance DC SQUIDs with submicron niobium Josephson junctions are discussed, taking into account design considerations, fabrication, junction characterization, the performance of the SQUID and input coil, and the gradiometer performance. The simulation and optimization of a DC SQUID with finite capacitance is considered, giving attention to the implementation of a simulation procedure on a hybrid computer.

Simulating groundwater flow in karst aquifers with distributed parameter models—Comparison of porous-equivalent media and hybrid flow approaches

USGS Publications Warehouse

Kuniansky, Eve L.

2016-09-22

Understanding karst aquifers, for purposes of their management and protection, poses unique challenges. Karst aquifers are characterized by groundwater flow through conduits (tertiary porosity), and (or) layers with interconnected pores (secondary porosity) and through intergranular porosity (primary or matrix porosity). Since the late 1960s, advances have been made in the development of numerical computer codes and the use of mathematical model applications towards the understanding of dual (primary [matrix] and secondary [fractures and conduits]) porosity groundwater flow processes, as well as characterization and management of karst aquifers. The Floridan aquifer system (FAS) in Florida and parts of Alabama, Georgia, and South Carolina is composed of a thick sequence of predominantly carbonate rocks. Karst features are present over much of its area, especially in Florida where more than 30 first-magnitude springs occur, numerous sinkholes and submerged conduits have been mapped, and numerous circular lakes within sinkhole depressions are present. Different types of mathematical models have been applied for simulation of the FAS. Most of these models are distributed parameter models based on the assumption that, like a sponge, water flows through connected pores within the aquifer system and can be simulated with the same mathematical methods applied to flow through sand and gravel aquifers; these models are usually referred to as porous-equivalent media models. The partial differential equation solved for groundwater flow is the potential flow equation of fluid mechanics, which is used when flow is dominated by potential energy and has been applied for many fluid problems in which kinetic energy terms are dropped from the differential equation solved. In many groundwater model codes (basic MODFLOW), it is assumed that the water has a constant temperature and density and that flow is laminar, such that kinetic energy has minimal impact on flow. Some models have been developed that incorporate the submerged conduits as a one-dimensional pipe network within the aquifer rather than as discrete, extremely transmissive features in a porous-equivalent medium; these submerged conduit models are usually referred to as hybrid models and may include the capability to simulate both laminar and turbulent flow in the one-dimensional pipe network. Comparisons of the application of a porous-equivalent media model with and without turbulence (MODFLOW-Conduit Flow Process mode 2 and basic MODFLOW, respectively) and a hybrid (MODFLOW-Conduit Flow Process mode 1) model to the Woodville Karst Plain near Tallahassee, Florida, indicated that for annual, monthly, or seasonal average hydrologic conditions, all methods met calibration criteria (matched observed groundwater levels and average flows). Thus, the increased effort required, such as the collection of data on conduit location, to develop a hybrid model and its increased computational burden, is not necessary for simulation of average hydrologic conditions (non-laminar flow effects on simulated head and spring discharge were minimal). However, simulation of a large storm event in the Woodville Karst Plain with daily stress periods indicated that turbulence is important for matching daily springflow hydrographs. Thus, if matching streamflow hydrographs over a storm event is required, the simulation of non-laminar flow and the location of conduits are required. The main challenge in application of the methods and approaches for developing hybrid models relates to the difficulty of mapping conduit networks or having high-quality datasets to calibrate these models. Additionally, hybrid models have long simulation times, which can preclude the use of parameter estimation for calibration. Simulation of contaminant transport that does not account for preferential flow through conduits or extremely permeable zones in any approach is ill-advised. Simulation results in other karst aquifers or other parts of the FAS may differ from the comparison demonstrated herein.

Hybrid stochastic and deterministic simulations of calcium blips.

PubMed

Rüdiger, S; Shuai, J W; Huisinga, W; Nagaiah, C; Warnecke, G; Parker, I; Falcke, M

2007-09-15

Intracellular calcium release is a prime example for the role of stochastic effects in cellular systems. Recent models consist of deterministic reaction-diffusion equations coupled to stochastic transitions of calcium channels. The resulting dynamics is of multiple time and spatial scales, which complicates far-reaching computer simulations. In this article, we introduce a novel hybrid scheme that is especially tailored to accurately trace events with essential stochastic variations, while deterministic concentration variables are efficiently and accurately traced at the same time. We use finite elements to efficiently resolve the extreme spatial gradients of concentration variables close to a channel. We describe the algorithmic approach and we demonstrate its efficiency compared to conventional methods. Our single-channel model matches experimental data and results in intriguing dynamics if calcium is used as charge carrier. Random openings of the channel accumulate in bursts of calcium blips that may be central for the understanding of cellular calcium dynamics.

Large-deformation modal coordinates for nonrigid vehicle dynamics

NASA Technical Reports Server (NTRS)

Likins, P. W.; Fleischer, G. E.

1972-01-01

The derivation of minimum-dimension sets of discrete-coordinate and hybrid-coordinate equations of motion of a system consisting of an arbitrary number of hinge-connected rigid bodies assembled in tree topology is presented. These equations are useful for the simulation of dynamical systems that can be idealized as tree-like arrangements of substructures, with each substructure consisting of either a rigid body or a collection of elastically interconnected rigid bodies restricted to small relative rotations at each connection. Thus, some of the substructures represent elastic bodies subjected to small strains or local deformations, but possibly large gross deformations, in the hybrid formulation, distributed coordinates referred to herein as large-deformation modal coordinates, are used for the deformations of these substructures. The equations are in a form suitable for incorporation into one or more computer programs to be used as multipurpose tools in the simulation of spacecraft and other complex electromechanical systems.

Hybrid multiphase CFD simulation for liquid-liquid interfacial area prediction in annular centrifugal contactors

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

Wardle, K.E.

2013-07-01

Liquid-liquid contacting equipment used in solvent extraction processes has the dual purpose of mixing and separating two immiscible fluids. Consequently, such devices inherently encompass a wide variety of multiphase flow regimes. A hybrid multiphase computational fluid dynamics (CFD) solver which combines the Eulerian multi-fluid method with VOF (volume of fluid) sharp interface capturing has been developed for application to annular centrifugal contactors. This solver has been extended to enable prediction of mean droplet size and liquid-liquid interfacial area through a single moment population balance method. Simulations of liquid-liquid mixing in a simplified geometry and a model annular centrifugal contactor aremore » reported with droplet breakup/coalescence models being calibrated versus available experimental data. Quantitative comparison is made for two different housing vane geometries and it is found that the predicted droplet size is significantly smaller for vane geometries which result in higher annular liquid holdup.« less

A Generic Simulation Framework for Non-Entangled based Experimental Quantum Cryptography and Communication: Quantum Cryptography and Communication Simulator (QuCCs)

NASA Astrophysics Data System (ADS)

Buhari, Abudhahir; Zukarnain, Zuriati Ahmad; Khalid, Roszelinda; Zakir Dato', Wira Jaafar Ahmad

2016-11-01

The applications of quantum information science move towards bigger and better heights for the next generation technology. Especially, in the field of quantum cryptography and quantum computation, the world already witnessed various ground-breaking tangible product and promising results. Quantum cryptography is one of the mature field from quantum mechanics and already available in the markets. The current state of quantum cryptography is still under various researches in order to reach the heights of digital cryptography. The complexity of quantum cryptography is higher due to combination of hardware and software. The lack of effective simulation tool to design and analyze the quantum cryptography experiments delays the reaching distance of the success. In this paper, we propose a framework to achieve an effective non-entanglement based quantum cryptography simulation tool. We applied hybrid simulation technique i.e. discrete event, continuous event and system dynamics. We also highlight the limitations of a commercial photonic simulation tool based experiments. Finally, we discuss ideas for achieving one-stop simulation package for quantum based secure key distribution experiments. All the modules of simulation framework are viewed from the computer science perspective.

Quiet Clean Short-haul Experimental Engine (QCSEE) over-the-wing engine and control simulation results

NASA Technical Reports Server (NTRS)

1978-01-01

A hybrid-computer simulation of the over the wing turbofan engine was constructed to develop the dynamic design of the control. This engine and control system includes a full authority digital electronic control using compressor stator reset to achieve fast thrust response and a modified Kalman filter to correct for sensor failures. Fast thrust response for powered-lift operations and accurate, fast responding, steady state control of the engine is provided. Simulation results for throttle bursts from 62 to 100 percent takeoff thrust predict that the engine will accelerate from 62 to 95 percent takeoff thrust in one second.

Simulation of Foam Impact Effects on Components of the Space Shuttle Thermal Protection System. Chapter 7

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.; Park, Young-Keun

2004-01-01

A series of three dimensional simulations has been performed to investigate analytically the effect of insulating foam impacts on ceramic tile and reinforced carbon-carbon components of the Space Shuttle thermal protection system. The simulations employed a hybrid particle-finite element method and a parallel code developed for use in spacecraft design applications. The conclusions suggested by the numerical study are in general consistent with experiment. The results emphasize the need for additional material testing work on the dynamic mechanical response of thermal protection system materials, and additional impact experiments for use in validating computational models of impact effects.

Large-eddy simulation/Reynolds-averaged Navier-Stokes hybrid schemes for high speed flows

NASA Astrophysics Data System (ADS)

Xiao, Xudong

Three LES/RANS hybrid schemes have been proposed for the prediction of high speed separated flows. Each method couples the k-zeta (Enstrophy) BANS model with an LES subgrid scale one-equation model by using a blending function that is coordinate system independent. Two of these functions are based on turbulence dissipation length scale and grid size, while the third one has no explicit dependence on the grid. To implement the LES/RANS hybrid schemes, a new rescaling-reintroducing method is used to generate time-dependent turbulent inflow conditions. The hybrid schemes have been tested on a Mach 2.88 flow over 25 degree compression-expansion ramp and a Mach 2.79 flow over 20 degree compression ramp. A special computation procedure has been designed to prevent the separation zone from expanding upstream to the recycle-plane. The code is parallelized using Message Passing Interface (MPI) and is optimized for running on IBM-SP3 parallel machine. The scheme was validated first for a flat plate. It was shown that the blending function has to be monotonic to prevent the RANS region from appearing in the LES region. In the 25 deg ramp case, the hybrid schemes provided better agreement with experiment in the recovery region. Grid refinement studies demonstrated the importance of using a grid independent blend function and further improvement with experiment in the recovery region. In the 20 deg ramp case, with a relatively finer grid, the hybrid scheme characterized by grid independent blending function well predicted the flow field in both the separation region and the recovery region. Therefore, with "appropriately" fine grid, current hybrid schemes are promising for the simulation of shock wave/boundary layer interaction problems.

Numerical Simulation of Transitional, Hypersonic Flows using a Hybrid Particle-Continuum Method

NASA Astrophysics Data System (ADS)

Verhoff, Ashley Marie

Analysis of hypersonic flows requires consideration of multiscale phenomena due to the range of flight regimes encountered, from rarefied conditions in the upper atmosphere to fully continuum flow at low altitudes. At transitional Knudsen numbers there are likely to be localized regions of strong thermodynamic nonequilibrium effects that invalidate the continuum assumptions of the Navier-Stokes equations. Accurate simulation of these regions, which include shock waves, boundary and shear layers, and low-density wakes, requires a kinetic theory-based approach where no prior assumptions are made regarding the molecular distribution function. Because of the nature of these types of flows, there is much to be gained in terms of both numerical efficiency and physical accuracy by developing hybrid particle-continuum simulation approaches. The focus of the present research effort is the continued development of the Modular Particle-Continuum (MPC) method, where the Navier-Stokes equations are solved numerically using computational fluid dynamics (CFD) techniques in regions of the flow field where continuum assumptions are valid, and the direct simulation Monte Carlo (DSMC) method is used where strong thermodynamic nonequilibrium effects are present. Numerical solutions of transitional, hypersonic flows are thus obtained with increased physical accuracy relative to CFD alone, and improved numerical efficiency is achieved in comparison to DSMC alone because this more computationally expensive method is restricted to those regions of the flow field where it is necessary to maintain physical accuracy. In this dissertation, a comprehensive assessment of the physical accuracy of the MPC method is performed, leading to the implementation of a non-vacuum supersonic outflow boundary condition in particle domains, and more consistent initialization of DSMC simulator particles along hybrid interfaces. The relative errors between MPC and full DSMC results are greatly reduced as a direct result of these improvements. Next, a new parameter for detecting rotational nonequilibrium effects is proposed and shown to offer advantages over other continuum breakdown parameters, achieving further accuracy gains. Lastly, the capabilities of the MPC method are extended to accommodate multiple chemical species in rotational nonequilibrium, each of which is allowed to equilibrate independently, enabling application of the MPC method to more realistic atmospheric flows.

Hamiltonian adaptive resolution molecular dynamics simulation of infrared dielectric functions of liquids

NASA Astrophysics Data System (ADS)

Wang, C. C.; Tan, J. Y.; Liu, L. H.

2018-05-01

Hamiltonian adaptive resolution scheme (H-AdResS), which allows to simulate materials by treating different domains of the system at different levels of resolution, is a recently proposed atomistic/coarse-grained multiscale model. In this work, a scheme to calculate the dielectric functions of liquids on account of H-AdResS is presented. In the proposed H-AdResS dielectric-function calculation scheme (DielectFunctCalS), the corrected molecular dipole moments are calculated by multiplying molecular dipole moment by the weighting fraction of the molecular mapping point. As the widths of all-atom and hybrid regions show different degrees of influence on the dielectric functions, a prefactor is multiplied to eliminate the effects of all-atom and hybrid region widths. Since one goal of using the H-AdResS method is to reduce computational costs, widths of the all-atom region and the hybrid region can be reduced considering that the coarse-grained simulation is much more timesaving compared to atomistic simulation. Liquid water and ethanol are taken as test cases to validate the DielectFunctCalS. The H-AdResS DielectFunctCalS results are in good agreement with all-atom molecular dynamics simulations. The accuracy of the H-AdResS results, together with all-atom molecular dynamics results, depends heavily on the choice of the force field and force field parameters. The H-AdResS DielectFunctCalS allows us to calculate the dielectric functions of macromolecule systems with high efficiency and makes the dielectric function calculations of large biomolecular systems possible.

The advanced role of computational mechanics and visualization in science and technology: analysis of the Germanwings Flight 9525 crash

NASA Astrophysics Data System (ADS)

Chen, Goong; Wang, Yi-Ching; Perronnet, Alain; Gu, Cong; Yao, Pengfei; Bin-Mohsin, Bandar; Hajaiej, Hichem; Scully, Marlan O.

2017-03-01

Computational mathematics, physics and engineering form a major constituent of modern computational science, which now stands on an equal footing with the established branches of theoretical and experimental sciences. Computational mechanics solves problems in science and engineering based upon mathematical modeling and computing, bypassing the need for expensive and time-consuming laboratory setups and experimental measurements. Furthermore, it allows the numerical simulations of large scale systems, such as the formation of galaxies that could not be done in any earth bound laboratories. This article is written as part of the 21st Century Frontiers Series to illustrate some state-of-the-art computational science. We emphasize how to do numerical modeling and visualization in the study of a contemporary event, the pulverizing crash of the Germanwings Flight 9525 on March 24, 2015, as a showcase. Such numerical modeling and the ensuing simulation of aircraft crashes into land or mountain are complex tasks as they involve both theoretical study and supercomputing of a complex physical system. The most tragic type of crash involves ‘pulverization’ such as the one suffered by this Germanwings flight. Here, we show pulverizing airliner crashes by visualization through video animations from supercomputer applications of the numerical modeling tool LS-DYNA. A sound validation process is challenging but essential for any sophisticated calculations. We achieve this by validation against the experimental data from a crash test done in 1993 of an F4 Phantom II fighter jet into a wall. We have developed a method by hybridizing two primary methods: finite element analysis and smoothed particle hydrodynamics. This hybrid method also enhances visualization by showing a ‘debris cloud’. Based on our supercomputer simulations and the visualization, we point out that prior works on this topic based on ‘hollow interior’ modeling can be quite problematic and, thus, not likely to be correct. We discuss the effects of terrain on pulverization using the information from the recovered flight-data-recorder and show our forensics and assessments of what may have happened during the final moments of the crash. Finally, we point out that our study has potential for being made into real-time flight crash simulators to help the study of crashworthiness and survivability for future aviation safety. Some forward-looking statements are also made.

Calculations of High-Temperature Jet Flow Using Hybrid Reynolds-Average Navier-Stokes Formulations

NASA Technical Reports Server (NTRS)

Abdol-Hamid, Khaled S.; Elmiligui, Alaa; Giriamaji, Sharath S.

2008-01-01

Two multiscale-type turbulence models are implemented in the PAB3D solver. The models are based on modifying the Reynolds-averaged Navier Stokes equations. The first scheme is a hybrid Reynolds-averaged- Navier Stokes/large-eddy-simulation model using the two-equation k(epsilon) model with a Reynolds-averaged-Navier Stokes/large-eddy-simulation transition function dependent on grid spacing and the computed turbulence length scale. The second scheme is a modified version of the partially averaged Navier Stokes model in which the unresolved kinetic energy parameter f(sub k) is allowed to vary as a function of grid spacing and the turbulence length scale. This parameter is estimated based on a novel two-stage procedure to efficiently estimate the level of scale resolution possible for a given flow on a given grid for partially averaged Navier Stokes. It has been found that the prescribed scale resolution can play a major role in obtaining accurate flow solutions. The parameter f(sub k) varies between zero and one and is equal to one in the viscous sublayer and when the Reynolds-averaged Navier Stokes turbulent viscosity becomes smaller than the large-eddy-simulation viscosity. The formulation, usage methodology, and validation examples are presented to demonstrate the enhancement of PAB3D's time-accurate turbulence modeling capabilities. The accurate simulations of flow and turbulent quantities will provide a valuable tool for accurate jet noise predictions. Solutions from these models are compared with Reynolds-averaged Navier Stokes results and experimental data for high-temperature jet flows. The current results show promise for the capability of hybrid Reynolds-averaged Navier Stokes and large eddy simulation and partially averaged Navier Stokes in simulating such flow phenomena.

New hybrid voxelized/analytical primitive in Monte Carlo simulations for medical applications

NASA Astrophysics Data System (ADS)

Bert, Julien; Lemaréchal, Yannick; Visvikis, Dimitris

2016-05-01

Monte Carlo simulations (MCS) applied in particle physics play a key role in medical imaging and particle therapy. In such simulations, particles are transported through voxelized phantoms derived from predominantly patient CT images. However, such voxelized object representation limits the incorporation of fine elements, such as artificial implants from CAD modeling or anatomical and functional details extracted from other imaging modalities. In this work we propose a new hYbrid Voxelized/ANalytical primitive (YVAN) that combines both voxelized and analytical object descriptions within the same MCS, without the need to simultaneously run two parallel simulations, which is the current gold standard methodology. Given that YVAN is simply a new primitive object, it does not require any modifications on the underlying MC navigation code. The new proposed primitive was assessed through a first simple MCS. Results from the YVAN primitive were compared against an MCS using a pure analytical geometry and the layer mass geometry concept. A perfect agreement was found between these simulations, leading to the conclusion that the new hybrid primitive is able to accurately and efficiently handle phantoms defined by a mixture of voxelized and analytical objects. In addition, two application-based evaluation studies in coronary angiography and intra-operative radiotherapy showed that the use of YVAN was 6.5% and 12.2% faster than the layered mass geometry method, respectively, without any associated loss of accuracy. However, the simplification advantages and differences in computational time improvements obtained with YVAN depend on the relative proportion of the analytical and voxelized structures used in the simulation as well as the size and number of triangles used in the description of the analytical object meshes.

A comparative study of ground motion hybrid simulations and the modified NGA ground motion predictive equations for directivity and its application to the the Marmara Sea region (Turkey)

NASA Astrophysics Data System (ADS)

Pischiutta, M.; Akinci, A.; Spagnuolo, E.; Taroni, M.; Herrero, A.; Aochi, H.

2016-12-01

We have simulated strong ground motions for two Mw>7.0 rupture scenarios on the North Anatolian Fault, in the Marmara Sea within 10-20 km from Istanbul. This city is characterized by one of the highest levels of seismic risk in Europe and the Mediterranean region. The increased risk in Istanbul is due to eight destructive earthquakes that ruptured the fault system and left a seismic gap at the western portion of the 1000km-long North Anatolian Fault Zone. To estimate the ground motion characteristics and its variability in the region we have simulated physics-based rupture scenarios, producing hybrid broadband time histories. We have merged two simulation techniques: a full 3D wave propagation method to generate low-frequency seismograms (Aochi and Ulrich, 2015) and the stochastic finite-fault model approach based on a dynamic corner frequency (Motazedian and Atkinson, 2005) to simulate high-frequency seismograms (Akinci et al., 2016, submitted to BSSA, 2016). They are merged to compute realistic broadband hybrid time histories. The comparison of ground motion intensity measures (PGA, PGV, SA) resulting from our simulations with those predicted by the recent Ground Motion Prediction Equations (GMPEs) in the region (Boore & Atkinson, 2008; Chiou & Young, 2008; Akkar & Bommer, 2010; Akkar & Cagnan, 2010) seems to indicate that rupture directivity and super-shear rupture effects affect the ground motion in the Marmara Sea region. In order to account for the rupture directivity we improve the comparison using the directivity predictor proposed by Spudich & Chiu (2008). This study highlights the importance of the rupture directivity for the hazard estimation in the Marmara Sea region, especially for the city of Istanbul.

Effects of stochastic sodium channels on extracellular excitation of myelinated nerve fibers.

PubMed

Mino, Hiroyuki; Grill, Warren M

2002-06-01

The effects of the stochastic gating properties of sodium channels on the extracellular excitation properties of mammalian nerve fibers was determined by computer simulation. To reduce computation time, a hybrid multicompartment cable model including five central nodes of Ranvier containing stochastic sodium channels and 16 flanking nodes containing detenninistic membrane dynamics was developed. The excitation properties of the hybrid cable model were comparable with those of a full stochastic cable model including 21 nodes of Ranvier containing stochastic sodium channels, indicating the validity of the hybrid cable model. The hybrid cable model was used to investigate whether or not the excitation properties of extracellularly activated fibers were influenced by the stochastic gating of sodium channels, including spike latencies, strength-duration (SD), current-distance (IX), and recruitment properties. The stochastic properties of the sodium channels in the hybrid cable model had the greatest impact when considering the temporal dynamics of nerve fibers, i.e., a large variability in latencies, while they did not influence the SD, IX, or recruitment properties as compared with those of the conventional deterministic cable model. These findings suggest that inclusion of stochastic nodes is not important for model-based design of stimulus waveforms for activation of motor nerve fibers. However, in cases where temporal fine structure is important, for example in sensory neural prostheses in the auditory and visual systems, the stochastic properties of the sodium channels may play a key role in the design of stimulus waveforms.

A new hybrid numerical scheme for modelling elastodynamics in unbounded media with near-source heterogeneities

NASA Astrophysics Data System (ADS)

Hajarolasvadi, Setare; Elbanna, Ahmed E.

2017-11-01

The finite difference (FD) and the spectral boundary integral (SBI) methods have been used extensively to model spontaneously-propagating shear cracks in a variety of engineering and geophysical applications. In this paper, we propose a new modelling approach in which these two methods are combined through consistent exchange of boundary tractions and displacements. Benefiting from the flexibility of FD and the efficiency of SBI methods, the proposed hybrid scheme will solve a wide range of problems in a computationally efficient way. We demonstrate the validity of the approach using two examples for dynamic rupture propagation: one in the presence of a low-velocity layer and the other in which off-fault plasticity is permitted. We discuss possible potential uses of the hybrid scheme in earthquake cycle simulations as well as an exact absorbing boundary condition.

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

Omelchenko, Yuri A.

Global interactions of energetic ions with magnetoplasmas and neutral gases lie at the core of many space and laboratory plasma phenomena ranging from solar wind entry into and transport within planetary magnetospheres and exospheres to fast-ion driven instabilities in fusion devices to astrophysics-in-lab experiments. The ability of computational models to properly account for physical effects that underlie such interactions, namely ion kinetic, ion cyclotron, Hall, collisional and ionization processes is important for the success and planning of experimental research in plasma physics. Understanding the physics of energetic ions, in particular their nonlinear resonance interactions with Alfvén waves, is central tomore » improving the heating performance of magnetically confined plasmas for future energy generation. Fluid models are not adequate for high-beta plasmas as they cannot fully capture ion kinetic and cyclotron physics (e.g., ion behavior in the presence of magnetic nulls, shock structures, plasma interpenetration, etc.). Recent results from global reconnection simulations show that even in a MHD-like regime there may be significant differences between kinetic and MHD simulations. Therefore, kinetic modeling becomes essential for meeting modern day challenges in plasma physics. The hybrid approximation is an intermediate approximation between the fluid and fully kinetic approximations. It eliminates light waves, removes the electron inertial temporal and spatial scales from the problem and enables full-orbit ion kinetics. As a result, hybrid codes have become effective tools for exploring ion-scale driven phenomena associated with ion beams, shocks, reconnection and turbulence that control the large-scale behavior of laboratory and space magnetoplasmas. A number of numerical issues, however, make three-dimensional (3D) large-scale hybrid simulations of inhomogeneous magnetized plasmas prohibitively expensive or even impossible. To resolve these difficulties we have developed a novel Event-driven Multiscale Asynchronous Parallel Simulation (EMAPS) technology that replaces time stepping with self-adaptive update events. Local calculations are carried out only on an “as needed basis”. EMAPS (i) guarantees accurate and stable processing of physical variables in time accurate simulations, and (ii) eliminates unnecessary computation. Applying EMAPS to the hybrid model has resulted in the development of a unique parallel code, dimension-independent (compile-time-configurable) HYPERS (Hybrid Parallel Event-Resolved Simulator) that scales to hundreds of thousands of parallel processors. HYPERS advances electromagnetic fields and particles asynchronously on time scales determined by local physical laws and mesh properties. To achieve high computational accuracy in complex device geometries, HYPERS employs high-fidelity Cartesian grids with masked conductive cells. The HYPERS model includes multiple ion species, energy and momentum conserving ion-ion collisions, and provides a number of approximations for plasma resistivity and vacuum regions. Both local and periodic boundary conditions are allowed. The HYPERS solver preserves zero divergence of magnetic field. The project has demonstrated HYPERS capabilities on a number of applications of interest to fusion and astrophysical plasma physics applications listed below. 1. Theta-pinch formation of FRCs The formation, spontaneous spin-up, and stability of theta-pinch formed field-reversed configurations have been studied self-consistently in 3D. The end-to-end hybrid simulations reveal poloidal profiles of implosion-driven fast toroidal plasma rotation and demonstrate three discharge regimes as a function of experimental parameters: the decaying stable configuration, the tilt unstable configuration, and the nonlinear evolution of a fast growing tearing mode. 2. FRC collisions with magnetic mirrors Interactions of fast plasma streams and objects with magnetic obstacles (dipoles, mirrors, etc) lie at the core of many space and laboratory plasma phenomena ranging from magnetoshells and solar wind interactions with planetary magnetospheres to compact fusion plasmas. HYPERS simulations are compared with data from the MSX experiment (LANL) that focuses on the physics of magnetized collisionless shocks through the acceleration and subsequent stagnation of FRC plasmoids against a strong magnetic mirrors and flux-conserving boundaries. 3. Exploding magnetoplasmas Results from hybrid simulations of two experiments at the LAPD and Nevada Terawatt Facility are discussed where short-pulse lasers are used to ablate solid targets to produce plasmas that expand across external magnetic fields. The first simulation recreates flutelike density striations observed at the leading edge of a carbon plasma and predicts an early destruction of the magnetic cavity in agreement with experimental evidence. In the second simulation a polyethylene target is ablated into a mixture of protons and carbon ions. A mechanism is demonstrated that allows protons to penetrate the magnetic field in the form of a collimated flow. The results are compared to experimental data and single-fluid MHD simulations. The EMAPS framework has the potential for wide application in many other engineering and scientific fields, such as climate models, biological systems, electronic devices, seismic events, oil reservation simulators that all involve advancing solutions of partial differential equations in time where the rate of activity can be adapted widely over the spatial domain depending on locally space/time phenomena (“events”).« less

Hybrid Symbiotic Organisms Search Optimization Algorithm for Scheduling of Tasks on Cloud Computing Environment.

PubMed

Abdullahi, Mohammed; Ngadi, Md Asri

2016-01-01

Cloud computing has attracted significant attention from research community because of rapid migration rate of Information Technology services to its domain. Advances in virtualization technology has made cloud computing very popular as a result of easier deployment of application services. Tasks are submitted to cloud datacenters to be processed on pay as you go fashion. Task scheduling is one the significant research challenges in cloud computing environment. The current formulation of task scheduling problems has been shown to be NP-complete, hence finding the exact solution especially for large problem sizes is intractable. The heterogeneous and dynamic feature of cloud resources makes optimum task scheduling non-trivial. Therefore, efficient task scheduling algorithms are required for optimum resource utilization. Symbiotic Organisms Search (SOS) has been shown to perform competitively with Particle Swarm Optimization (PSO). The aim of this study is to optimize task scheduling in cloud computing environment based on a proposed Simulated Annealing (SA) based SOS (SASOS) in order to improve the convergence rate and quality of solution of SOS. The SOS algorithm has a strong global exploration capability and uses fewer parameters. The systematic reasoning ability of SA is employed to find better solutions on local solution regions, hence, adding exploration ability to SOS. Also, a fitness function is proposed which takes into account the utilization level of virtual machines (VMs) which reduced makespan and degree of imbalance among VMs. CloudSim toolkit was used to evaluate the efficiency of the proposed method using both synthetic and standard workload. Results of simulation showed that hybrid SOS performs better than SOS in terms of convergence speed, response time, degree of imbalance, and makespan.

Hybrid Symbiotic Organisms Search Optimization Algorithm for Scheduling of Tasks on Cloud Computing Environment

PubMed Central

Abdullahi, Mohammed; Ngadi, Md Asri

2016-01-01

Cloud computing has attracted significant attention from research community because of rapid migration rate of Information Technology services to its domain. Advances in virtualization technology has made cloud computing very popular as a result of easier deployment of application services. Tasks are submitted to cloud datacenters to be processed on pay as you go fashion. Task scheduling is one the significant research challenges in cloud computing environment. The current formulation of task scheduling problems has been shown to be NP-complete, hence finding the exact solution especially for large problem sizes is intractable. The heterogeneous and dynamic feature of cloud resources makes optimum task scheduling non-trivial. Therefore, efficient task scheduling algorithms are required for optimum resource utilization. Symbiotic Organisms Search (SOS) has been shown to perform competitively with Particle Swarm Optimization (PSO). The aim of this study is to optimize task scheduling in cloud computing environment based on a proposed Simulated Annealing (SA) based SOS (SASOS) in order to improve the convergence rate and quality of solution of SOS. The SOS algorithm has a strong global exploration capability and uses fewer parameters. The systematic reasoning ability of SA is employed to find better solutions on local solution regions, hence, adding exploration ability to SOS. Also, a fitness function is proposed which takes into account the utilization level of virtual machines (VMs) which reduced makespan and degree of imbalance among VMs. CloudSim toolkit was used to evaluate the efficiency of the proposed method using both synthetic and standard workload. Results of simulation showed that hybrid SOS performs better than SOS in terms of convergence speed, response time, degree of imbalance, and makespan. PMID:27348127

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

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.

Efficient Development of High Fidelity Structured Volume Grids for Hypersonic Flow Simulations

NASA Technical Reports Server (NTRS)

Alter, Stephen J.

2003-01-01

A new technique for the control of grid line spacing and intersection angles of a structured volume grid, using elliptic partial differential equations (PDEs) is presented. Existing structured grid generation algorithms make use of source term hybridization to provide control of grid lines, imposing orthogonality implicitly at the boundary and explicitly on the interior of the domain. A bridging function between the two types of grid line control is typically used to blend the different orthogonality formulations. It is shown that utilizing such a bridging function with source term hybridization can result in the excessive use of computational resources and diminishes robustness. A new approach, Anisotropic Lagrange Based Trans-Finite Interpolation (ALBTFI), is offered as a replacement to source term hybridization. The ALBTFI technique captures the essence of the desired grid controls while improving the convergence rate of the elliptic PDEs when compared with source term hybridization. Grid generation on a blunt cone and a Shuttle Orbiter is used to demonstrate and assess the ALBTFI technique, which is shown to be as much as 50% faster, more robust, and produces higher quality grids than source term hybridization.

Using a Ventilation Controller to Optimize Residential Passive Ventilation For Energy and Indoor Air Quality

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

Turner, William; Walker, Iain

One way to reduce the energy impact of providing residential ventilation is to use passive and hybrid systems. However, these passive and hybrid (sometimes called mixed-mode) systems must still meet chronic and acute health standards for ventilation. This study uses a computer simulation approach to examine the energy and indoor air quality (IAQ) implications of passive and hybrid ventilation systems, in 16 California climate zones. Both uncontrolled and flow controlled passive stacks are assessed. A new hybrid ventilation system is outlined that uses an intelligent ventilation controller to minimise energy use, while ensuring chronic and acute IAQ standards are met.more » ASHRAE Standard 62.2-2010 – the United States standard for residential ventilation - is used as the chronic standard, and exposure limits for PM 2.5, formaldehyde and NO 2 are used as the acute standards.The results show that controlled passive ventilation and hybrid ventilation can be used in homes to provide equivalent IAQ to continuous mechanical ventilation, for less use of energy.« less

A simplified computational fluid-dynamic approach to the oxidizer injector design in hybrid rockets

NASA Astrophysics Data System (ADS)

Di Martino, Giuseppe D.; Malgieri, Paolo; Carmicino, Carmine; Savino, Raffaele

2016-12-01

Fuel regression rate in hybrid rockets is non-negligibly affected by the oxidizer injection pattern. In this paper a simplified computational approach developed in an attempt to optimize the oxidizer injector design is discussed. Numerical simulations of the thermo-fluid-dynamic field in a hybrid rocket are carried out, with a commercial solver, to investigate into several injection configurations with the aim of increasing the fuel regression rate and minimizing the consumption unevenness, but still favoring the establishment of flow recirculation at the motor head end, which is generated with an axial nozzle injector and has been demonstrated to promote combustion stability, and both larger efficiency and regression rate. All the computations have been performed on the configuration of a lab-scale hybrid rocket motor available at the propulsion laboratory of the University of Naples with typical operating conditions. After a preliminary comparison between the two baseline limiting cases of an axial subsonic nozzle injector and a uniform injection through the prechamber, a parametric analysis has been carried out by varying the oxidizer jet flow divergence angle, as well as the grain port diameter and the oxidizer mass flux to study the effect of the flow divergence on heat transfer distribution over the fuel surface. Some experimental firing test data are presented, and, under the hypothesis that fuel regression rate and surface heat flux are proportional, the measured fuel consumption axial profiles are compared with the predicted surface heat flux showing fairly good agreement, which allowed validating the employed design approach. Finally an optimized injector design is proposed.

Fast Dynamic Simulation-Based Small Signal Stability Assessment and Control

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

Acharya, Naresh; Baone, Chaitanya; Veda, Santosh

2014-12-31

Power grid planning and operation decisions are made based on simulation of the dynamic behavior of the system. Enabling substantial energy savings while increasing the reliability of the aging North American power grid through improved utilization of existing transmission assets hinges on the adoption of wide-area measurement systems (WAMS) for power system stabilization. However, adoption of WAMS alone will not suffice if the power system is to reach its full entitlement in stability and reliability. It is necessary to enhance predictability with "faster than real-time" dynamic simulations that will enable the dynamic stability margins, proactive real-time control, and improve gridmore » resiliency to fast time-scale phenomena such as cascading network failures. Present-day dynamic simulations are performed only during offline planning studies, considering only worst case conditions such as summer peak, winter peak days, etc. With widespread deployment of renewable generation, controllable loads, energy storage devices and plug-in hybrid electric vehicles expected in the near future and greater integration of cyber infrastructure (communications, computation and control), monitoring and controlling the dynamic performance of the grid in real-time would become increasingly important. The state-of-the-art dynamic simulation tools have limited computational speed and are not suitable for real-time applications, given the large set of contingency conditions to be evaluated. These tools are optimized for best performance of single-processor computers, but the simulation is still several times slower than real-time due to its computational complexity. With recent significant advances in numerical methods and computational hardware, the expectations have been rising towards more efficient and faster techniques to be implemented in power system simulators. This is a natural expectation, given that the core solution algorithms of most commercial simulators were developed decades ago, when High Performance Computing (HPC) resources were not commonly available.« less

Aeroacoustic Simulations of a Nose Landing Gear with FUN3D: A Grid Refinement Study

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Khorrami, Mehdi R.; Lockard, David P.

2017-01-01

A systematic grid refinement study is presented for numerical simulations of a partially-dressed, cavity-closed (PDCC) nose landing gear configuration that was tested in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D is used to compute the unsteady flow field for this configuration. Mixed-element grids generated using the Pointwise (Registered Trademark) grid generation software are used for numerical simulations. Particular care is taken to ensure quality cells and proper resolution in critical areas of interest in an effort to minimize errors introduced by numerical artifacts. A set of grids was generated in this manner to create a family of uniformly refined grids. The finest grid was then modified to coarsen the wall-normal spacing to create a grid suitable for the wall-function implementation in FUN3D code. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence modeling approach is used for these simulations. Time-averaged and instantaneous solutions obtained on these grids are compared with the measured data. These CFD solutions are used as input to a FfowcsWilliams-Hawkings (FW-H) noise propagation code to compute the farfield noise levels. The agreement of the computed results with the experimental data improves as the grid is refined.

Digital flight control research

NASA Technical Reports Server (NTRS)

Potter, J. E.; Stern, R. G.; Smith, T. B.; Sinha, P.

1974-01-01

The results of studies which were undertaken to contribute to the design of digital flight control systems, particularly for transport aircraft are presented. In addition to the overall design considerations for a digital flight control system, the following topics are discussed in detail: (1) aircraft attitude reference system design, (2) the digital computer configuration, (3) the design of a typical digital autopilot for transport aircraft, and (4) a hybrid flight simulator.

Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations.

PubMed

Zhong, Ellen D; Shirts, Michael R

2014-05-06

A better understanding of changes in protein stability upon adsorption can improve the design of protein separation processes. In this study, we examine the coupling of the folding and the adsorption of a model protein, the B1 domain of streptococcal protein G, as a function of surface attraction using a hybrid Monte Carlo (HMC) approach with temperature replica exchange and umbrella sampling. In our HMC implementation, we are able to use a molecular dynamics (MD) time step that is an order of magnitude larger than in a traditional MD simulation protocol and observe a factor of 2 enhancement in the folding and unfolding rate. To demonstrate the convergence of our systems, we measure the travel of our order parameter the fraction of native contacts between folded and unfolded states throughout the length of our simulations. Thermodynamic quantities are extracted with minimum statistical variance using multistate reweighting between simulations at different temperatures and harmonic distance restraints from the surface. The resultant free energies, enthalpies, and entropies of the coupled unfolding and absorption processes are in qualitative agreement with previous experimental and computational observations, including entropic stabilization of the adsorbed, folded state relative to the bulk on surfaces with low attraction.

Modeling bioluminescent photon transport in tissue based on Radiosity-diffusion model

NASA Astrophysics Data System (ADS)

Sun, Li; Wang, Pu; Tian, Jie; Zhang, Bo; Han, Dong; Yang, Xin

2010-03-01

Bioluminescence tomography (BLT) is one of the most important non-invasive optical molecular imaging modalities. The model for the bioluminescent photon propagation plays a significant role in the bioluminescence tomography study. Due to the high computational efficiency, diffusion approximation (DA) is generally applied in the bioluminescence tomography. But the diffusion equation is valid only in highly scattering and weakly absorbing regions and fails in non-scattering or low-scattering tissues, such as a cyst in the breast, the cerebrospinal fluid (CSF) layer of the brain and synovial fluid layer in the joints. A hybrid Radiosity-diffusion model is proposed for dealing with the non-scattering regions within diffusing domains in this paper. This hybrid method incorporates a priori information of the geometry of non-scattering regions, which can be acquired by magnetic resonance imaging (MRI) or x-ray computed tomography (CT). Then the model is implemented using a finite element method (FEM) to ensure the high computational efficiency. Finally, we demonstrate that the method is comparable with Mont Carlo (MC) method which is regarded as a 'gold standard' for photon transportation simulation.

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations.

PubMed

Procacci, Piero

2016-06-27

We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .

Time-ordered product expansions for computational stochastic system biology.

PubMed

Mjolsness, Eric

2013-06-01

The time-ordered product framework of quantum field theory can also be used to understand salient phenomena in stochastic biochemical networks. It is used here to derive Gillespie's stochastic simulation algorithm (SSA) for chemical reaction networks; consequently, the SSA can be interpreted in terms of Feynman diagrams. It is also used here to derive other, more general simulation and parameter-learning algorithms including simulation algorithms for networks of stochastic reaction-like processes operating on parameterized objects, and also hybrid stochastic reaction/differential equation models in which systems of ordinary differential equations evolve the parameters of objects that can also undergo stochastic reactions. Thus, the time-ordered product expansion can be used systematically to derive simulation and parameter-fitting algorithms for stochastic systems.

Normal mode analysis of isotopic shifts in Raman spectrum of TNT-d5

NASA Astrophysics Data System (ADS)

Liu, Yuemin; Tzeng, Nianfeng; Liu, Yucheng; Junk, Thomas

2017-09-01

A combined experimental-computational study was conducted on the Raman spectrum of TNT-d5 in the present study. It was found that among the 24 hybrid density functional theory (DFT) methods, O3LYP, tHCTHhyb, and B3LYP simulations yielded the strongest Raman bands which were closest to those measured from experiments. Simulations of hybrid DFT methods did not show that deuterium replacements alter orientations of 2- and 6-nitro with respect to phenyl ring, considering a larger size of the methyl group. However, the deuterium replacements apparently changed the reduced masses for all deuterium related vibrations. Although no difference of structural parameters was shown between TNT and its deuterated analogue, discrepancy was indicated in vibrational zero energy from our simulations. O3LYP simulation exhibited 24 deuterium involved vibrations, which were coupled into seven Raman bands of TNT-d5. This phenomenon can account for the experimental Raman band shifts or split of TNT-d5 when compared with the corresponding bands of TNT. The present study and its outcomes provide in-depth microchemical insights of Raman characteristics of TNT and may facilitate the design of nano-structures of SERS substrates for detection of TNT and its degradation products. All intensities displayed in this study were calculated from numerical simulations.

Classical force field for hydrofluorocarbon molecular simulations. Application to the study of gas solubility in poly(vinylidene fluoride).

PubMed

Lachet, V; Teuler, J-M; Rousseau, B

2015-01-08

A classical all-atoms force field for molecular simulations of hydrofluorocarbons (HFCs) has been developed. Lennard-Jones force centers plus point charges are used to represent dispersion-repulsion and electrostatic interactions. Parametrization of this force field has been performed iteratively using three target properties of pentafluorobutane: the quantum energy of an isolated molecule, the dielectric constant in the liquid phase, and the compressed liquid density. The accuracy and transferability of this new force field has been demonstrated through the simulation of different thermophysical properties of several fluorinated compounds, showing significant improvements compared to existing models. This new force field has been applied to study solubilities of several gases in poly(vinylidene fluoride) (PVDF) above the melting temperature of this polymer. The solubility of CH4, CO2, H2S, H2, N2, O2, and H2O at infinite dilution has been computed using test particle insertions in the course of a NpT hybrid Monte Carlo simulation. For CH4, CO2, and their mixtures, some calculations beyond the Henry regime have also been performed using hybrid Monte Carlo simulations in the osmotic ensemble, allowing both swelling and solubility determination. An ideal mixing behavior is observed, with identical solubility coefficients in the mixtures and in pure gas systems.

Some Developments of the Equilibrium Particle Simulation Method for the Direct Simulation of Compressible Flows

NASA Technical Reports Server (NTRS)

Macrossan, M. N.

1995-01-01

The direct simulation Monte Carlo (DSMC) method is the established technique for the simulation of rarefied gas flows. In some flows of engineering interest, such as occur for aero-braking spacecraft in the upper atmosphere, DSMC can become prohibitively expensive in CPU time because some regions of the flow, particularly on the windward side of blunt bodies, become collision dominated. As an alternative to using a hybrid DSMC and continuum gas solver (Euler or Navier-Stokes solver) this work is aimed at making the particle simulation method efficient in the high density regions of the flow. A high density, infinite collision rate limit of DSMC, the Equilibrium Particle Simulation method (EPSM) was proposed some 15 years ago. EPSM is developed here for the flow of a gas consisting of many different species of molecules and is shown to be computationally efficient (compared to DSMC) for high collision rate flows. It thus offers great potential as part of a hybrid DSMC/EPSM code which could handle flows in the transition regime between rarefied gas flows and fully continuum flows. As a first step towards this goal a pure EPSM code is described. The next step of combining DSMC and EPSM is not attempted here but should be straightforward. EPSM and DSMC are applied to Taylor-Couette flow with Kn = 0.02 and 0.0133 and S(omega) = 3). Toroidal vortices develop for both methods but some differences are found, as might be expected for the given flow conditions. EPSM appears to be less sensitive to the sequence of random numbers used in the simulation than is DSMC and may also be more dissipative. The question of the origin and the magnitude of the dissipation in EPSM is addressed. It is suggested that this analysis is also relevant to DSMC when the usual accuracy requirements on the cell size and decoupling time step are relaxed in the interests of computational efficiency.

Comparisons of time explicit hybrid kinetic-fluid code Architect for Plasma Wakefield Acceleration with a full PIC code

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

Massimo, F., E-mail: francesco.massimo@ensta-paristech.fr; Dipartimento SBAI, Università di Roma “La Sapienza“, Via A. Scarpa 14, 00161 Roma; Atzeni, S.

Architect, a time explicit hybrid code designed to perform quick simulations for electron driven plasma wakefield acceleration, is described. In order to obtain beam quality acceptable for applications, control of the beam-plasma-dynamics is necessary. Particle in Cell (PIC) codes represent the state-of-the-art technique to investigate the underlying physics and possible experimental scenarios; however PIC codes demand the necessity of heavy computational resources. Architect code substantially reduces the need for computational resources by using a hybrid approach: relativistic electron bunches are treated kinetically as in a PIC code and the background plasma as a fluid. Cylindrical symmetry is assumed for themore » solution of the electromagnetic fields and fluid equations. In this paper both the underlying algorithms as well as a comparison with a fully three dimensional particle in cell code are reported. The comparison highlights the good agreement between the two models up to the weakly non-linear regimes. In highly non-linear regimes the two models only disagree in a localized region, where the plasma electrons expelled by the bunch close up at the end of the first plasma oscillation.« less

Evaluation of logistic and economic impacts of hybrid vehicle propulsion/microgrid concepts: Demonstration of LOCSS applied to HE HMMWV in future unit of action

NASA Astrophysics Data System (ADS)

Farrell, Michael; Tiberi, Lisa; Burns, Joseph; Udvare, Thomas B.

2006-05-01

Computer models have been developed and used to predict the performance of vehicles equipped with advanced fuel and power train technologies such as hybrid electric or fuel cells. However, simulations that describe the interaction of the vehicle with the rest of the vehicle fleet and infrastructure are just emerging. This paper documents the results of an experiment to demonstrate the utility of these types of simulations. The experiment examined the business case of fielding hybrid electric, high-mobility multipurpose wheeled vehicles (HE HMMWVs) in a future Army organization. The hypothesis was that fielding HE vehicles would significantly reduce fuel consumption due to the economy offered by the HE technology and reducing the number of generators as a result of using the vehicles to generate electrical power. The Logistical and Combat Systems Simulation (LOCSS) was used to estimate differences in fuel consumption and associated equipment during a 72-hour operation with and without HE HMMWVs. There was a 25 percent reduction in fuel consumption over the systems examined. However, due to the relatively low density of the HE vehicles in the organization, the total difference in fuel consumption was not operationally significant; and the savings in fuel costs did not overcome the additional procurement costs over a twenty-year life cycle.

Lewis Research Center studies of multiple large wind turbine generators on a utility network

NASA Technical Reports Server (NTRS)

Gilbert, L. J.; Triezenberg, D. M.

1979-01-01

A NASA-Lewis program to study the anticipated performance of a wind turbine generator farm on an electric utility network is surveyed. The paper describes the approach of the Lewis Wind Energy Project Office to developing analysis capabilities in the area of wind turbine generator-utility network computer simulations. Attention is given to areas such as, the Lewis Purdue hybrid simulation, an independent stability study, DOE multiunit plant study, and the WEST simulator. Also covered are the Lewis mod-2 simulation including analog simulation of a two wind turbine system and comparison with Boeing simulation results, and gust response of a two machine model. Finally future work to be done is noted and it is concluded that the study shows little interaction between the generators and between the generators and the bus.

Particle/Continuum Hybrid Simulation in a Parallel Computing Environment

NASA Technical Reports Server (NTRS)

Baganoff, Donald

1996-01-01

The objective of this study was to modify an existing parallel particle code based on the direct simulation Monte Carlo (DSMC) method to include a Navier-Stokes (NS) calculation so that a hybrid solution could be developed. In carrying out this work, it was determined that the following five issues had to be addressed before extensive program development of a three dimensional capability was pursued: (1) find a set of one-sided kinetic fluxes that are fully compatible with the DSMC method, (2) develop a finite volume scheme to make use of these one-sided kinetic fluxes, (3) make use of the one-sided kinetic fluxes together with DSMC type boundary conditions at a material surface so that velocity slip and temperature slip arise naturally for near-continuum conditions, (4) find a suitable sampling scheme so that the values of the one-sided fluxes predicted by the NS solution at an interface between the two domains can be converted into the correct distribution of particles to be introduced into the DSMC domain, (5) carry out a suitable number of tests to confirm that the developed concepts are valid, individually and in concert for a hybrid scheme.

A hybrid continuous-discrete method for stochastic reaction-diffusion processes.

PubMed

Lo, Wing-Cheong; Zheng, Likun; Nie, Qing

2016-09-01

Stochastic fluctuations in reaction-diffusion processes often have substantial effect on spatial and temporal dynamics of signal transductions in complex biological systems. One popular approach for simulating these processes is to divide the system into small spatial compartments assuming that molecules react only within the same compartment and jump between adjacent compartments driven by the diffusion. While the approach is convenient in terms of its implementation, its computational cost may become prohibitive when diffusive jumps occur significantly more frequently than reactions, as in the case of rapid diffusion. Here, we present a hybrid continuous-discrete method in which diffusion is simulated using continuous approximation while reactions are based on the Gillespie algorithm. Specifically, the diffusive jumps are approximated as continuous Gaussian random vectors with time-dependent means and covariances, allowing use of a large time step, even for rapid diffusion. By considering the correlation among diffusive jumps, the approximation is accurate for the second moment of the diffusion process. In addition, a criterion is obtained for identifying the region in which such diffusion approximation is required to enable adaptive calculations for better accuracy. Applications to a linear diffusion system and two nonlinear systems of morphogens demonstrate the effectiveness and benefits of the new hybrid method.

Simulation of Liquid Injection Thrust Vector Control for Mars Ascent Vehicle

NASA Technical Reports Server (NTRS)

Gudenkauf, Jared

2017-01-01

The Jet Propulsion Laboratory is currently in the initial design phase for a potential Mars Ascent Vehicle; which will be landed on Mars, stay on the surface for period of time, collect samples from the Mars 2020 rover, and then lift these samples into orbit around Mars. The engineers at JPL have down selected to a hybrid wax-based fuel rocket using a liquid oxidizer based on nitrogen tetroxide, or a Mixed Oxide of Nitrogen. To lower the gross lift-off mass of the vehicle the thrust vector control system will use liquid injection of the oxidizer to deflect the thrust of the main nozzle instead of using a gimbaled nozzle. The disadvantage of going with the liquid injection system is the low technology readiness level with a hybrid rocket. Presented in this paper is an effort to simulate the Mars Ascent Vehicle hybrid rocket nozzle and liquid injection thrust vector control system using the computational fluid dynamic flow solver Loci/Chem. This effort also includes determining the sensitivity of the thrust vector control system to a number of different design variables for the injection ports; including axial location, number of adjacent ports, injection angle, and distance between the ports.

Thermoelectrics as elements of hybrid-electric vehicle thermal energy systems

NASA Astrophysics Data System (ADS)

Headings, Leon; Washington, Gregory; Jaworski, Christopher M.

2008-03-01

Despite vast technological improvements, the traditional internal combustion powered vehicle still achieves only 25- 30% efficiency, with the remainder lost primarily as heat. While the load leveling offered by hybrid-electric vehicle technology helps to improve this overall efficiency, part of the efficiency gains are achieved by making new systems such as regenerative braking viable. In a similar fashion, thermoelectric (TE) energy recovery has long been considered for traditional vehicles with mixed results, but little has been done to consider thermoelectrics in the framework of the unique energy systems of hybrid vehicles. Systems that may not have been viable or even possible with traditional vehicles may offer improvements to system efficiency as well as emissions, vehicle durability, passenger comfort, and cost. This research describes a simulation developed for evaluating and optimizing thermoelectric energy recovery systems and results for four different system configurations. Two novel system configurations are presented which offer the potential for additional benefits such as emissions reduction that will soon be quantified. In addition, a test setup is presented which was constructed for the testing and validation of various thermoelectric recovery systems. Actual test performance was near the expected theoretical performance and supported the conclusions reached from the computer simulations.

A comparative study based on docking and molecular dynamics simulations over HDAC-tubulin dual inhibitors.

PubMed

Hassanzadeh, Malihe; Bagherzadeh, Kowsar; Amanlou, Massoud

2016-11-01

Nowadays the ability to prediction of complex behavior rationally based on the computational approaches has been a successful technique in drug discovery. In the present study interactions of a new series of hybrids, which were made by linking colchicine as a tubulin inhibitor and suberoylanilide hydroxamic acid (SAHA) as a HDAC inhibitor, with HDAC8 and HDAC1 were investigated and compared. This research has been facilitated by the availability of experimental information besides employing docking methodology as well as classical molecular dynamics simulations and binding free energy calculation were performed. The obtained findings indicate different modes of interactions and inhibition strengths of the studied inhibitors for HDAC8 and HDAC1. HDAC8 binding free energies (-34.35 to -26.27kcal/mol) revealed higher binding affinity to HDAC8 compared to HDAC1 (-33.17 to -7.99kcal/mol). The binding energy contribution of each residue with the hybrid compounds 4a-4e within the active site of HDAC1 and HDAC8 was analyzed and the results confirmed the rule of key amino acids in interaction with the hybrid compounds. Copyright © 2016 Elsevier Inc. All rights reserved.

Hybrid LES/RANS Simulation of Transverse Sonic Injection into a Mach 2 Flow

NASA Technical Reports Server (NTRS)

Boles, John A.; Edwards, Jack R.; Baurle, Robert A.

2008-01-01

A computational study of transverse sonic injection of air and helium into a Mach 1.98 cross-flow is presented. A hybrid large-eddy simulation / Reynolds-averaged Navier-Stokes (LES/RANS) turbulence model is used, with the two-equation Menter baseline (Menter-BSL) closure for the RANS part of the flow and a Smagorinsky-type model for the LES part of the flow. A time-dependent blending function, dependent on modeled turbulence variables, is used to shift the closure from RANS to LES. Turbulent structures are initiated and sustained through the use of a recycling / rescaling technique. Two higher-order discretizations, the Piecewise Parabolic Method (PPM) of Colella and Woodward, and the SONIC-A ENO scheme of Suresh and Huyhn are used in the study. The results using the hybrid model show reasonably good agreement with time-averaged Mie scattering data and with experimental surface pressure distributions, even though the penetration of the jet into the cross-flow is slightly over-predicted. The LES/RANS results are used to examine the validity of commonly-used assumptions of constant Schmidt and Prandtl numbers in the intense mixing zone downstream of the injection location.

A Dual-Beam Irradiation Facility for a Novel Hybrid Cancer Therapy

NASA Astrophysics Data System (ADS)

Sabchevski, Svilen Petrov; Idehara, Toshitaka; Ishiyama, Shintaro; Miyoshi, Norio; Tatsukawa, Toshiaki

2013-01-01

In this paper we present the main ideas and discuss both the feasibility and the conceptual design of a novel hybrid technique and equipment for an experimental cancer therapy based on the simultaneous and/or sequential application of two beams, namely a beam of neutrons and a CW (continuous wave) or intermittent sub-terahertz wave beam produced by a gyrotron for treatment of cancerous tumors. The main simulation tools for the development of the computer aided design (CAD) of the prospective experimental facility for clinical trials and study of such new medical technology are briefly reviewed. Some tasks for a further continuation of this feasibility analysis are formulated as well.

An update on the BQCD Hybrid Monte Carlo program

NASA Astrophysics Data System (ADS)

Haar, Taylor Ryan; Nakamura, Yoshifumi; Stüben, Hinnerk

2018-03-01

We present an update of BQCD, our Hybrid Monte Carlo program for simulating lattice QCD. BQCD is one of the main production codes of the QCDSF collaboration and is used by CSSM and in some Japanese finite temperature and finite density projects. Since the first publication of the code at Lattice 2010 the program has been extended in various ways. New features of the code include: dynamical QED, action modification in order to compute matrix elements by using Feynman-Hellman theory, more trace measurements (like Tr(D-n) for K, cSW and chemical potential reweighting), a more flexible integration scheme, polynomial filtering, term-splitting for RHMC, and a portable implementation of performance critical parts employing SIMD.

A novel chaotic based image encryption using a hybrid model of deoxyribonucleic acid and cellular automata

NASA Astrophysics Data System (ADS)

Enayatifar, Rasul; Sadaei, Hossein Javedani; Abdullah, Abdul Hanan; Lee, Malrey; Isnin, Ismail Fauzi

2015-08-01

Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.

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

An improved data transfer and storage technique for hybrid computation

NASA Technical Reports Server (NTRS)

Hansing, A. M.

1972-01-01

Improved technique was developed for transferring and storing data at faster than real time speeds on hybrid computer. Predominant advantage is combined use of electronic relays, track and store units, and analog-to-digital and digital-to-analog conversion units of hybrid computer.

Supercomputer simulations of structure formation in the Universe

NASA Astrophysics Data System (ADS)

Ishiyama, Tomoaki

2017-06-01

We describe the implementation and performance results of our massively parallel MPI†/OpenMP‡ hybrid TreePM code for large-scale cosmological N-body simulations. For domain decomposition, a recursive multi-section algorithm is used and the size of domains are automatically set so that the total calculation time is the same for all processes. We developed a highly-tuned gravity kernel for short-range forces, and a novel communication algorithm for long-range forces. For two trillion particles benchmark simulation, the average performance on the fullsystem of K computer (82,944 nodes, the total number of core is 663,552) is 5.8 Pflops, which corresponds to 55% of the peak speed.

Simulatng Sawtooth Mixers For Biofouling Mitigation

NASA Astrophysics Data System (ADS)

Waters, James; Balazs, Anna

2017-11-01

We demonstrate how a ridged surface can be used to generate vortices that will break up clusters of cells as they form. This offers an appealing avenue for fouling mitigation, as it relies on a physical mechanism without unintended environmental consequences. By adjusting the shape of these ridges, we can increase the effectiveness of the surface across a range of shear values. We represent such a system computationally using a hybrid of bulk fluid simulated via the lattice Boltzmann method, and deformable vesicles, representing cells, simulated via that lattice spring method. This simulation methodology allows us to rapidly implement and test different surface patterns, and explore how their parameters can most effectively deter the accumulation of biofilms.

An Assessment of CFD/CSD Prediction State-of-the-Art by Using the HART II International Workshop Data

NASA Technical Reports Server (NTRS)

Smith, Marilyn J.; Lim, Joon W.; vanderWall, Berend G.; Baeder, James D.; Biedron, Robert T.; Boyd, D. Douglas, Jr.; Jayaraman, Buvana; Jung, Sung N.; Min, Byung-Young

2012-01-01

Over the past decade, there have been significant advancements in the accuracy of rotor aeroelastic simulations with the application of computational fluid dynamics methods coupled with computational structural dynamics codes (CFD/CSD). The HART II International Workshop database, which includes descent operating conditions with strong blade-vortex interactions (BVI), provides a unique opportunity to assess the ability of CFD/CSD to capture these physics. In addition to a baseline case with BVI, two additional cases with 3/rev higher harmonic blade root pitch control (HHC) are available for comparison. The collaboration during the workshop permits assessment of structured, unstructured, and hybrid overset CFD/CSD methods from across the globe on the dynamics, aerodynamics, and wake structure. Evaluation of the plethora of CFD/CSD methods indicate that the most important numerical variables associated with most accurately capturing BVI are a two-equation or detached eddy simulation (DES)-based turbulence model and a sufficiently small time step. An appropriate trade-off between grid fidelity and spatial accuracy schemes also appears to be pertinent for capturing BVI on the advancing rotor disk. Overall, the CFD/CSD methods generally fall within the same accuracy; cost-effective hybrid Navier-Stokes/Lagrangian wake methods provide accuracies within 50% the full CFD/CSD methods for most parameters of interest, except for those highly influenced by torsion. The importance of modeling the fuselage is observed, and other computational requirements are discussed.

Modelling realistic TiO2 nanospheres: A benchmark study of SCC-DFTB against hybrid DFT

NASA Astrophysics Data System (ADS)

Selli, Daniele; Fazio, Gianluca; Di Valentin, Cristiana

2017-10-01

TiO2 nanoparticles (NPs) are nowadays considered fundamental building blocks for many technological applications. Morphology is found to play a key role with spherical NPs presenting higher binding properties and chemical activity. From the experimental point of view, the characterization of these nano-objects is extremely complex, opening a large room for computational investigations. In this work, TiO2 spherical NPs of different sizes (from 300 to 4000 atoms) have been studied with a two-scale computational approach. Global optimization to obtain stable and equilibrated nanospheres was performed with a self-consistent charge density functional tight-binding (SCC-DFTB) simulated annealing process, causing a considerable atomic rearrangement within the nanospheres. Those SCC-DFTB relaxed structures have been then optimized at the DFT(B3LYP) level of theory. We present a systematic and comparative SCC-DFTB vs DFT(B3LYP) study of the structural properties, with particular emphasis on the surface-to-bulk sites ratio, coordination distribution of surface sites, and surface energy. From the electronic point of view, we compare HOMO-LUMO and Kohn-Sham gaps, total and projected density of states. Overall, the comparisons between DFTB and hybrid density functional theory show that DFTB provides a rather accurate geometrical and electronic description of these nanospheres of realistic size (up to a diameter of 4.4 nm) at an extremely reduced computational cost. This opens for new challenges in simulations of very large systems and more extended molecular dynamics.

A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

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

Nomura, K; Seymour, R; Wang, W

2009-02-17

A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based onmore » hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).« less

A hybrid agent-based approach for modeling microbiological systems.

PubMed

Guo, Zaiyi; Sloot, Peter M A; Tay, Joc Cing

2008-11-21

Models for systems biology commonly adopt Differential Equations or Agent-Based modeling approaches for simulating the processes as a whole. Models based on differential equations presuppose phenomenological intracellular behavioral mechanisms, while models based on Multi-Agent approach often use directly translated, and quantitatively less precise if-then logical rule constructs. We propose an extendible systems model based on a hybrid agent-based approach where biological cells are modeled as individuals (agents) while molecules are represented by quantities. This hybridization in entity representation entails a combined modeling strategy with agent-based behavioral rules and differential equations, thereby balancing the requirements of extendible model granularity with computational tractability. We demonstrate the efficacy of this approach with models of chemotaxis involving an assay of 10(3) cells and 1.2x10(6) molecules. The model produces cell migration patterns that are comparable to laboratory observations.

Hybrid Radar Emitter Recognition Based on Rough k-Means Classifier and Relevance Vector Machine

PubMed Central

Yang, Zhutian; Wu, Zhilu; Yin, Zhendong; Quan, Taifan; Sun, Hongjian

2013-01-01

Due to the increasing complexity of electromagnetic signals, there exists a significant challenge for recognizing radar emitter signals. In this paper, a hybrid recognition approach is presented that classifies radar emitter signals by exploiting the different separability of samples. The proposed approach comprises two steps, namely the primary signal recognition and the advanced signal recognition. In the former step, a novel rough k-means classifier, which comprises three regions, i.e., certain area, rough area and uncertain area, is proposed to cluster the samples of radar emitter signals. In the latter step, the samples within the rough boundary are used to train the relevance vector machine (RVM). Then RVM is used to recognize the samples in the uncertain area; therefore, the classification accuracy is improved. Simulation results show that, for recognizing radar emitter signals, the proposed hybrid recognition approach is more accurate, and presents lower computational complexity than traditional approaches. PMID:23344380

Higher-order spin and charge dynamics in a quantum dot-lead hybrid system.

PubMed

Otsuka, Tomohiro; Nakajima, Takashi; Delbecq, Matthieu R; Amaha, Shinichi; Yoneda, Jun; Takeda, Kenta; Allison, Giles; Stano, Peter; Noiri, Akito; Ito, Takumi; Loss, Daniel; Ludwig, Arne; Wieck, Andreas D; Tarucha, Seigo

2017-09-22

Understanding the dynamics of open quantum systems is important and challenging in basic physics and applications for quantum devices and quantum computing. Semiconductor quantum dots offer a good platform to explore the physics of open quantum systems because we can tune parameters including the coupling to the environment or leads. Here, we apply the fast single-shot measurement techniques from spin qubit experiments to explore the spin and charge dynamics due to tunnel coupling to a lead in a quantum dot-lead hybrid system. We experimentally observe both spin and charge time evolution via first- and second-order tunneling processes, and reveal the dynamics of the spin-flip through the intermediate state. These results enable and stimulate the exploration of spin dynamics in dot-lead hybrid systems, and may offer useful resources for spin manipulation and simulation of open quantum systems.

Mixed-Timescale Per-Group Hybrid Precoding for Multiuser Massive MIMO Systems

NASA Astrophysics Data System (ADS)

Teng, Yinglei; Wei, Min; Liu, An; Lau, Vincent; Zhang, Yong

2018-05-01

Considering the expensive radio frequency (RF) chain, huge training overhead and feedback burden issues in massive MIMO, in this letter, we propose a mixed-timescale per-group hybrid precoding (MPHP) scheme under an adaptive partially-connected RF precoding structure (PRPS), where the RF precoder is implemented using an adaptive connection network (ACN) and M analog phase shifters (APSs), where M is the number of antennas at the base station (BS). Exploiting the mixed-time stage channel state information (CSI) structure, the joint-design of ACN and APSs is formulated as a statistical signal-to-leakage-and-noise ratio (SSLNR) maximization problem, and a heuristic group RF precoding (GRFP) algorithm is proposed to provide a near-optimal solution. Simulation results show that the proposed design advances at better energy efficiency (EE) and lower hardware cost, CSI signaling overhead and computational complexity than the conventional hybrid precoding (HP) schemes.

pmx: Automated protein structure and topology generation for alchemical perturbations

PubMed Central

Gapsys, Vytautas; Michielssens, Servaas; Seeliger, Daniel; de Groot, Bert L

2015-01-01

Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36. PMID:25487359

Near term hybrid passenger vehicle development program, phase 1

NASA Technical Reports Server (NTRS)

1980-01-01

Missions for hybrid vehicles that promise to yield high petroleum impact were identified and a preliminary design, was developed that satisfies the mission requirements and performance specifications. Technologies that are critical to successful vehicle design, development and fabrication were determined. Trade-off studies to maximize fuel savings were used to develop initial design specifications of the near term hybrid vehicle. Various designs were "driven" through detailed computer simulations which calculate the petroleum consumption in standard driving cycles, the petroleum and electricity consumptions over the specified missions, and the vehicle's life cycle costs over a 10 year vehicle lifetime. Particular attention was given to the selection of the electric motor, heat engine, drivetrain, battery pack and control system. The preliminary design reflects a modified current compact car powered by a currently available turbocharged diesel engine and a 24 kW (peak) compound dc electric motor.

Phase 1 of the near term hybrid passenger vehicle development program. Appendix B: Trade-off studies. Volume 2: Appendices

NASA Technical Reports Server (NTRS)

Traversi, M.; Piccolo, R.

1979-01-01

The SPEC '78 computer program which consists of mathematical simulations of any vehicle component and external environment is described as are configuration alternatives for the propulsion system. Preliminary assessments of the fundamental characteristics of the lead-acid and sodium-sulfur batteries are included and procedures are given for estimating the cost of a new vehicle in mass production.

Hybrid approach combining multiple characterization techniques and simulations for microstructural analysis of proton exchange membrane fuel cell electrodes

NASA Astrophysics Data System (ADS)

Cetinbas, Firat C.; Ahluwalia, Rajesh K.; Kariuki, Nancy; De Andrade, Vincent; Fongalland, Dash; Smith, Linda; Sharman, Jonathan; Ferreira, Paulo; Rasouli, Somaye; Myers, Deborah J.

2017-03-01

The cost and performance of proton exchange membrane fuel cells strongly depend on the cathode electrode due to usage of expensive platinum (Pt) group metal catalyst and sluggish reaction kinetics. Development of low Pt content high performance cathodes requires comprehensive understanding of the electrode microstructure. In this study, a new approach is presented to characterize the detailed cathode electrode microstructure from nm to μm length scales by combining information from different experimental techniques. In this context, nano-scale X-ray computed tomography (nano-CT) is performed to extract the secondary pore space of the electrode. Transmission electron microscopy (TEM) is employed to determine primary C particle and Pt particle size distributions. X-ray scattering, with its ability to provide size distributions of orders of magnitude more particles than TEM, is used to confirm the TEM-determined size distributions. The number of primary pores that cannot be resolved by nano-CT is approximated using mercury intrusion porosimetry. An algorithm is developed to incorporate all these experimental data in one geometric representation. Upon validation of pore size distribution against gas adsorption and mercury intrusion porosimetry data, reconstructed ionomer size distribution is reported. In addition, transport related characteristics and effective properties are computed by performing simulations on the hybrid microstructure.

A study on optimization of hybrid drive train using Advanced Vehicle Simulator (ADVISOR)

NASA Astrophysics Data System (ADS)

Same, Adam; Stipe, Alex; Grossman, David; Park, Jae Wan

This study investigates the advantages and disadvantages of three hybrid drive train configurations: series, parallel, and "through-the-ground" parallel. Power flow simulations are conducted with the MATLAB/Simulink-based software ADVISOR. These simulations are then applied in an application for the UC Davis SAE Formula Hybrid vehicle. ADVISOR performs simulation calculations for vehicle position using a combined backward/forward method. These simulations are used to study how efficiency and agility are affected by the motor, fuel converter, and hybrid configuration. Three different vehicle models are developed to optimize the drive train of a vehicle for three stages of the SAE Formula Hybrid competition: autocross, endurance, and acceleration. Input cycles are created based on rough estimates of track geometry. The output from these ADVISOR simulations is a series of plots of velocity profile and energy storage State of Charge that provide a good estimate of how the Formula Hybrid vehicle will perform on the given course. The most noticeable discrepancy between the input cycle and the actual velocity profile of the vehicle occurs during deceleration. A weighted ranking system is developed to organize the simulation results and to determine the best drive train configuration for the Formula Hybrid vehicle. Results show that the through-the-ground parallel configuration with front-mounted motors achieves an optimal balance of efficiency, simplicity, and cost. ADVISOR is proven to be a useful tool for vehicle power train design for the SAE Formula Hybrid competition. This vehicle model based on ADVISOR simulation is applicable to various studies concerning performance and efficiency of hybrid drive trains.

Parallel Computing for Brain Simulation.

PubMed

Pastur-Romay, L A; Porto-Pazos, A B; Cedron, F; Pazos, A

2017-01-01

The human brain is the most complex system in the known universe, it is therefore one of the greatest mysteries. It provides human beings with extraordinary abilities. However, until now it has not been understood yet how and why most of these abilities are produced. For decades, researchers have been trying to make computers reproduce these abilities, focusing on both understanding the nervous system and, on processing data in a more efficient way than before. Their aim is to make computers process information similarly to the brain. Important technological developments and vast multidisciplinary projects have allowed creating the first simulation with a number of neurons similar to that of a human brain. This paper presents an up-to-date review about the main research projects that are trying to simulate and/or emulate the human brain. They employ different types of computational models using parallel computing: digital models, analog models and hybrid models. This review includes the current applications of these works, as well as future trends. It is focused on various works that look for advanced progress in Neuroscience and still others which seek new discoveries in Computer Science (neuromorphic hardware, machine learning techniques). Their most outstanding characteristics are summarized and the latest advances and future plans are presented. In addition, this review points out the importance of considering not only neurons: Computational models of the brain should also include glial cells, given the proven importance of astrocytes in information processing. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Advancing renal education: hybrid simulation, using simulated patients to enhance realism in haemodialysis education.

PubMed

Dunbar-Reid, Kylie; Sinclair, Peter M; Hudson, Denis

2015-06-01

Simulation is a well-established and proven teaching method, yet its use in renal education is not widely reported. Criticisms of simulation-based teaching include limited realism and a lack of authentic patient interaction. This paper discusses the benefits and challenges of high-fidelity simulation and suggests hybrid simulation as a complementary model to existing simulation programmes. Through the use of a simulated patient, hybrid simulation can improve the authenticity of renal simulation-based education while simultaneously teaching and assessing technologically enframed caring. © 2015 European Dialysis and Transplant Nurses Association/European Renal Care Association.

Progress Toward Affordable High Fidelity Combustion Simulations Using Filtered Density Functions for Hypersonic Flows in Complex Geometries

NASA Technical Reports Server (NTRS)

Drozda, Tomasz G.; Quinlan, Jesse R.; Pisciuneri, Patrick H.; Yilmaz, S. Levent

2012-01-01

Significant progress has been made in the development of subgrid scale (SGS) closures based on a filtered density function (FDF) for large eddy simulations (LES) of turbulent reacting flows. The FDF is the counterpart of the probability density function (PDF) method, which has proven effective in Reynolds averaged simulations (RAS). However, while systematic progress is being made advancing the FDF models for relatively simple flows and lab-scale flames, the application of these methods in complex geometries and high speed, wall-bounded flows with shocks remains a challenge. The key difficulties are the significant computational cost associated with solving the FDF transport equation and numerically stiff finite rate chemistry. For LES/FDF methods to make a more significant impact in practical applications a pragmatic approach must be taken that significantly reduces the computational cost while maintaining high modeling fidelity. An example of one such ongoing effort is at the NASA Langley Research Center, where the first generation FDF models, namely the scalar filtered mass density function (SFMDF) are being implemented into VULCAN, a production-quality RAS and LES solver widely used for design of high speed propulsion flowpaths. This effort leverages internal and external collaborations to reduce the overall computational cost of high fidelity simulations in VULCAN by: implementing high order methods that allow reduction in the total number of computational cells without loss in accuracy; implementing first generation of high fidelity scalar PDF/FDF models applicable to high-speed compressible flows; coupling RAS/PDF and LES/FDF into a hybrid framework to efficiently and accurately model the effects of combustion in the vicinity of the walls; developing efficient Lagrangian particle tracking algorithms to support robust solutions of the FDF equations for high speed flows; and utilizing finite rate chemistry parametrization, such as flamelet models, to reduce the number of transported reactive species and remove numerical stiffness. This paper briefly introduces the SFMDF model (highlighting key benefits and challenges), and discusses particle tracking for flows with shocks, the hybrid coupled RAS/PDF and LES/FDF model, flamelet generated manifolds (FGM) model, and the Irregularly Portioned Lagrangian Monte Carlo Finite Difference (IPLMCFD) methodology for scalable simulation of high-speed reacting compressible flows.

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

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

Shimojo, Fuyuki; Hattori, Shinnosuke; Department of Physics, Kumamoto University, Kumamoto 860-8555

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at themore » peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.« less

SpaceCubeX: A Framework for Evaluating Hybrid Multi-Core CPU FPGA DSP Architectures

NASA Technical Reports Server (NTRS)

Schmidt, Andrew G.; Weisz, Gabriel; French, Matthew; Flatley, Thomas; Villalpando, Carlos Y.

2017-01-01

The SpaceCubeX project is motivated by the need for high performance, modular, and scalable on-board processing to help scientists answer critical 21st century questions about global climate change, air quality, ocean health, and ecosystem dynamics, while adding new capabilities such as low-latency data products for extreme event warnings. These goals translate into on-board processing throughput requirements that are on the order of 100-1,000 more than those of previous Earth Science missions for standard processing, compression, storage, and downlink operations. To study possible future architectures to achieve these performance requirements, the SpaceCubeX project provides an evolvable testbed and framework that enables a focused design space exploration of candidate hybrid CPU/FPGA/DSP processing architectures. The framework includes ArchGen, an architecture generator tool populated with candidate architecture components, performance models, and IP cores, that allows an end user to specify the type, number, and connectivity of a hybrid architecture. The framework requires minimal extensions to integrate new processors, such as the anticipated High Performance Spaceflight Computer (HPSC), reducing time to initiate benchmarking by months. To evaluate the framework, we leverage a wide suite of high performance embedded computing benchmarks and Earth science scenarios to ensure robust architecture characterization. We report on our projects Year 1 efforts and demonstrate the capabilities across four simulation testbed models, a baseline SpaceCube 2.0 system, a dual ARM A9 processor system, a hybrid quad ARM A53 and FPGA system, and a hybrid quad ARM A53 and DSP system.

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

Bakosi, Jozsef; Christon, Mark A.; Francois, Marianne M.

This report describes the work carried out for completion of the Thermal Hydraulics Methods (THM) Level 3 Milestone THM.CFD.P5.05 for the Consortium for Advanced Simulation of Light Water Reactors (CASL). A series of body-fitted computational meshes have been generated by Numeca's Hexpress/Hybrid, a.k.a. 'Spider', meshing technology for the V5H 3 x 3 and 5 x 5 rod bundle geometries and subsequently used to compute the fluid dynamics of grid-to-rod fretting (GTRF). Spider is easy to use, fast, and automatically generates high-quality meshes for extremely complex geometries, required for the GTRF problem. Hydra-TH has been used to carry out large-eddy simulationsmore » on both 3 x 3 and 5 x 5 geometries, using different mesh resolutions. The results analyzed show good agreement with Star-CCM+ simulations and experimental data.« less

Tempest - Efficient Computation of Atmospheric Flows Using High-Order Local Discretization Methods

NASA Astrophysics Data System (ADS)

Ullrich, P. A.; Guerra, J. E.

2014-12-01

The Tempest Framework composes several compact numerical methods to easily facilitate intercomparison of atmospheric flow calculations on the sphere and in rectangular domains. This framework includes the implementations of Spectral Elements, Discontinuous Galerkin, Flux Reconstruction, and Hybrid Finite Element methods with the goal of achieving optimal accuracy in the solution of atmospheric problems. Several advantages of this approach are discussed such as: improved pressure gradient calculation, numerical stability by vertical/horizontal splitting, arbitrary order of accuracy, etc. The local numerical discretization allows for high performance parallel computation and efficient inclusion of parameterizations. These techniques are used in conjunction with a non-conformal, locally refined, cubed-sphere grid for global simulations and standard Cartesian grids for simulations at the mesoscale. A complete implementation of the methods described is demonstrated in a non-hydrostatic setting.

Adaptive CFD schemes for aerospace propulsion

NASA Astrophysics Data System (ADS)

Ferrero, A.; Larocca, F.

2017-05-01

The flow fields which can be observed inside several components of aerospace propulsion systems are characterised by the presence of very localised phenomena (boundary layers, shock waves,...) which can deeply influence the performances of the system. In order to accurately evaluate these effects by means of Computational Fluid Dynamics (CFD) simulations, it is necessary to locally refine the computational mesh. In this way the degrees of freedom related to the discretisation are focused in the most interesting regions and the computational cost of the simulation remains acceptable. In the present work, a discontinuous Galerkin (DG) discretisation is used to numerically solve the equations which describe the flow field. The local nature of the DG reconstruction makes it possible to efficiently exploit several adaptive schemes in which the size of the elements (h-adaptivity) and the order of reconstruction (p-adaptivity) are locally changed. After a review of the main adaptation criteria, some examples related to compressible flows in turbomachinery are presented. An hybrid hp-adaptive algorithm is also proposed and compared with a standard h-adaptive scheme in terms of computational efficiency.

Computational Aerodynamic Modeling of Small Quadcopter Vehicles

NASA Technical Reports Server (NTRS)

Yoon, Seokkwan; Ventura Diaz, Patricia; Boyd, D. Douglas; Chan, William M.; Theodore, Colin R.

2017-01-01

High-fidelity computational simulations have been performed which focus on rotor-fuselage and rotor-rotor aerodynamic interactions of small quad-rotor vehicle systems. The three-dimensional unsteady Navier-Stokes equations are solved on overset grids using high-order accurate schemes, dual-time stepping, low Mach number preconditioning, and hybrid turbulence modeling. Computational results for isolated rotors are shown to compare well with available experimental data. Computational results in hover reveal the differences between a conventional configuration where the rotors are mounted above the fuselage and an unconventional configuration where the rotors are mounted below the fuselage. Complex flow physics in forward flight is investigated. The goal of this work is to demonstrate that understanding of interactional aerodynamics can be an important factor in design decisions regarding rotor and fuselage placement for next-generation multi-rotor drones.

Computational fluid dynamics modeling of laminar, transitional, and turbulent flows with sensitivity to streamline curvature and rotational effects

NASA Astrophysics Data System (ADS)

Chitta, Varun

Modeling of complex flows involving the combined effects of flow transition and streamline curvature using two advanced turbulence models, one in the Reynolds-averaged Navier-Stokes (RANS) category and the other in the hybrid RANS-Large eddy simulation (LES) category is considered in this research effort. In the first part of the research, a new scalar eddy-viscosity model (EVM) is proposed, designed to exhibit physically correct responses to flow transition, streamline curvature, and system rotation effects. The four equation model developed herein is a curvature-sensitized version of a commercially available three-equation transition-sensitive model. The physical effects of rotation and curvature (RC) enter the model through the added transport equation, analogous to a transverse turbulent velocity scale. The eddy-viscosity has been redefined such that the proposed model is constrained to reduce to the original transition-sensitive model definition in nonrotating flows or in regions with negligible RC effects. In the second part of the research, the developed four-equation model is combined with a LES technique using a new hybrid modeling framework, dynamic hybrid RANS-LES. The new framework is highly generalized, allowing coupling of any desired LES model with any given RANS model and addresses several deficiencies inherent in most current hybrid models. In the present research effort, the DHRL model comprises of the proposed four-equation model for RANS component and the MILES scheme for LES component. Both the models were implemented into a commercial computational fluid dynamics (CFD) solver and tested on a number of engineering and generic flow problems. Results from both the RANS and hybrid models show successful resolution of the combined effects of transition and curvature with reasonable engineering accuracy, and for only a small increase in computational cost. In addition, results from the hybrid model indicate significant levels of turbulent fluctuations in the flowfield, improved accuracy compared to RANS models predictions, and are obtained at a significant reduction of computational cost compared to full LES models. The results suggest that the advanced turbulence modeling techniques presented in this research effort have potential as practical tools for solving low/high Re flows over blunt/curved bodies for the prediction of transition and RC effects.

Computational materials design of crystalline solids.

PubMed

Butler, Keith T; Frost, Jarvist M; Skelton, Jonathan M; Svane, Katrine L; Walsh, Aron

2016-11-07

The modelling of materials properties and processes from first principles is becoming sufficiently accurate as to facilitate the design and testing of new systems in silico. Computational materials science is both valuable and increasingly necessary for developing novel functional materials and composites that meet the requirements of next-generation technology. A range of simulation techniques are being developed and applied to problems related to materials for energy generation, storage and conversion including solar cells, nuclear reactors, batteries, fuel cells, and catalytic systems. Such techniques may combine crystal-structure prediction (global optimisation), data mining (materials informatics) and high-throughput screening with elements of machine learning. We explore the development process associated with computational materials design, from setting the requirements and descriptors to the development and testing of new materials. As a case study, we critically review progress in the fields of thermoelectrics and photovoltaics, including the simulation of lattice thermal conductivity and the search for Pb-free hybrid halide perovskites. Finally, a number of universal chemical-design principles are advanced.

Numerical investigation of interactions between marine atmospheric boundary layer and offshore wind farm

NASA Astrophysics Data System (ADS)

Lyu, Pin; Chen, Wenli; Li, Hui; Shen, Lian

2017-11-01

In recent studies, Yang, Meneveau & Shen (Physics of Fluids, 2014; Renewable Energy, 2014) developed a hybrid numerical framework for simulation of offshore wind farm. The framework consists of simulation of nonlinear surface waves using a high-order spectral method, large-eddy simulation of wind turbulence on a wave-surface-fitted curvilinear grid, and an actuator disk model for wind turbines. In the present study, several more precise wind turbine models, including the actuator line model, actuator disk model with rotation, and nacelle model, are introduced into the computation. Besides offshore wind turbines on fixed piles, the new computational framework has the capability to investigate the interaction among wind, waves, and floating wind turbines. In this study, onshore, offshore fixed pile, and offshore floating wind farms are compared in terms of flow field statistics and wind turbine power extraction rate. The authors gratefully acknowledge financial support from China Scholarship Council (No. 201606120186) and the Institute on the Environment of University of Minnesota.

Instabilities and Turbulence Generation by Pick-Up Ion Distributions in the Outer Heliosheath

NASA Astrophysics Data System (ADS)

Weichman, K.; Roytershteyn, V.; Delzanno, G. L.; Pogorelov, N.

2017-12-01

Pick-up ions (PUIs) play a significant role in the dynamics of the heliosphere. One problem that has attracted significant attention is the stability of ring-like distributions of PUIs and the electromagnetic fluctuations that could be generated by PUI distributions. For example, PUI stability is relevant to theories attempting to identify the origins of the IBEX ribbon. PUIs have previously been investigated by linear stability analysis of model (e.g. Gaussian) rings and corresponding computer simulations. The majority of these simulations utilized particle-in-cell methods which suffer from accuracy limitations imposed by the statistical noise associated with representing the plasma by a relatively small number of computational particles. In this work, we utilize highly accurate spectral Vlasov simulations conducted using the fully kinetic implicit code SPS (Spectral Plasma Solver) to investigate the PUI distributions inferred from a global heliospheric model (Heerikhuisen et al., 2016). Results are compared with those obtained by hybrid and fully kinetic particle-in-cell methods.

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

PubMed

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

2016-01-01

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

Optimization behavior of brainstem respiratory neurons. A cerebral neural network model.

PubMed

Poon, C S

1991-01-01

A recent model of respiratory control suggested that the steady-state respiratory responses to CO2 and exercise may be governed by an optimal control law in the brainstem respiratory neurons. It was not certain, however, whether such complex optimization behavior could be accomplished by a realistic biological neural network. To test this hypothesis, we developed a hybrid computer-neural model in which the dynamics of the lung, brain and other tissue compartments were simulated on a digital computer. Mimicking the "controller" was a human subject who pedalled on a bicycle with varying speed (analog of ventilatory output) with a view to minimize an analog signal of the total cost of breathing (chemical and mechanical) which was computed interactively and displayed on an oscilloscope. In this manner, the visuomotor cortex served as a proxy (homolog) of the brainstem respiratory neurons in the model. Results in 4 subjects showed a linear steady-state ventilatory CO2 response to arterial PCO2 during simulated CO2 inhalation and a nearly isocapnic steady-state response during simulated exercise. Thus, neural optimization is a plausible mechanism for respiratory control during exercise and can be achieved by a neural network with cognitive computational ability without the need for an exercise stimulus.

Dynamics and Adaptive Control for Stability Recovery of Damaged Aircraft

NASA Technical Reports Server (NTRS)

Nguyen, Nhan; Krishnakumar, Kalmanje; Kaneshige, John; Nespeca, Pascal

2006-01-01

This paper presents a recent study of a damaged generic transport model as part of a NASA research project to investigate adaptive control methods for stability recovery of damaged aircraft operating in off-nominal flight conditions under damage and or failures. Aerodynamic modeling of damage effects is performed using an aerodynamic code to assess changes in the stability and control derivatives of a generic transport aircraft. Certain types of damage such as damage to one of the wings or horizontal stabilizers can cause the aircraft to become asymmetric, thus resulting in a coupling between the longitudinal and lateral motions. Flight dynamics for a general asymmetric aircraft is derived to account for changes in the center of gravity that can compromise the stability of the damaged aircraft. An iterative trim analysis for the translational motion is developed to refine the trim procedure by accounting for the effects of the control surface deflection. A hybrid direct-indirect neural network, adaptive flight control is proposed as an adaptive law for stabilizing the rotational motion of the damaged aircraft. The indirect adaptation is designed to estimate the plant dynamics of the damaged aircraft in conjunction with the direct adaptation that computes the control augmentation. Two approaches are presented 1) an adaptive law derived from the Lyapunov stability theory to ensure that the signals are bounded, and 2) a recursive least-square method for parameter identification. A hardware-in-the-loop simulation is conducted and demonstrates the effectiveness of the direct neural network adaptive flight control in the stability recovery of the damaged aircraft. A preliminary simulation of the hybrid adaptive flight control has been performed and initial data have shown the effectiveness of the proposed hybrid approach. Future work will include further investigations and high-fidelity simulations of the proposed hybrid adaptive Bight control approach.

Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer.

PubMed

Świderek, Katarzyna; Arafet, Kemel; Kohen, Amnon; Moliner, Vicent

2017-03-14

Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these processes. In this paper, the hydride-transfer step catalyzed by thymidylate synthase (TSase) is studied by examining hybrid quantum mechanics/molecular mechanics (QM/MM) potentials via multiple semiempirical methods and the M06-2X hybrid density functional. Calculations of protium and tritium transfer in these reactions across a range of temperatures allowed calculation of the temperature dependence of kinetic isotope effects (KIE). Dynamics and quantum-tunneling effects are revealed to have little effect on the reaction rate, but are significant in determining the KIEs and their temperature dependence. A good agreement with experiments is found, especially when computed for RM1/MM simulations. The small temperature dependence of quantum tunneling corrections and the quasiclassical contribution term cancel each other, while the recrossing transmission coefficient seems to be temperature-independent over the interval of 5-40 °C.

Using hybrid implicit Monte Carlo diffusion to simulate gray radiation hydrodynamics

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

Cleveland, Mathew A., E-mail: cleveland7@llnl.gov; Gentile, Nick

This work describes how to couple a hybrid Implicit Monte Carlo Diffusion (HIMCD) method with a Lagrangian hydrodynamics code to evaluate the coupled radiation hydrodynamics equations. This HIMCD method dynamically applies Implicit Monte Carlo Diffusion (IMD) [1] to regions of a problem that are opaque and diffusive while applying standard Implicit Monte Carlo (IMC) [2] to regions where the diffusion approximation is invalid. We show that this method significantly improves the computational efficiency as compared to a standard IMC/Hydrodynamics solver, when optically thick diffusive material is present, while maintaining accuracy. Two test cases are used to demonstrate the accuracy andmore » performance of HIMCD as compared to IMC and IMD. The first is the Lowrie semi-analytic diffusive shock [3]. The second is a simple test case where the source radiation streams through optically thin material and heats a thick diffusive region of material causing it to rapidly expand. We found that HIMCD proves to be accurate, robust, and computationally efficient for these test problems.« less

A finite-volume module for all-scale Earth-system modelling at ECMWF

NASA Astrophysics Data System (ADS)

Kühnlein, Christian; Malardel, Sylvie; Smolarkiewicz, Piotr

2017-04-01

We highlight recent advancements in the development of the finite-volume module (FVM) (Smolarkiewicz et al., 2016) for the IFS at ECMWF. FVM represents an alternative dynamical core that complements the operational spectral dynamical core of the IFS with new capabilities. Most notably, these include a compact-stencil finite-volume discretisation, flexible meshes, conservative non-oscillatory transport and all-scale governing equations. As a default, FVM solves the compressible Euler equations in a geospherical framework (Szmelter and Smolarkiewicz, 2010). The formulation incorporates a generalised terrain-following vertical coordinate. A hybrid computational mesh, fully unstructured in the horizontal and structured in the vertical, enables efficient global atmospheric modelling. Moreover, a centred two-time-level semi-implicit integration scheme is employed with 3D implicit treatment of acoustic, buoyant, and rotational modes. The associated 3D elliptic Helmholtz problem is solved using a preconditioned Generalised Conjugate Residual approach. The solution procedure employs the non-oscillatory finite-volume MPDATA advection scheme that is bespoke for the compressible dynamics on the hybrid mesh (Kühnlein and Smolarkiewicz, 2017). The recent progress of FVM is illustrated with results of benchmark simulations of intermediate complexity, and comparison to the operational spectral dynamical core of the IFS. C. Kühnlein, P.K. Smolarkiewicz: An unstructured-mesh finite-volume MPDATA for compressible atmospheric dynamics, J. Comput. Phys. (2017), in press. P.K. Smolarkiewicz, W. Deconinck, M. Hamrud, C. Kühnlein, G. Mozdzynski, J. Szmelter, N.P. Wedi: A finite-volume module for simulating global all-scale atmospheric flows, J. Comput. Phys. 314 (2016) 287-304. J. Szmelter, P.K. Smolarkiewicz: An edge-based unstructured mesh discretisation in geospherical framework, J. Comput. Phys. 229 (2010) 4980-4995.

New type side weir discharge coefficient simulation using three novel hybrid adaptive neuro-fuzzy inference systems

NASA Astrophysics Data System (ADS)

Bonakdari, Hossein; Zaji, Amir Hossein

2018-03-01

In many hydraulic structures, side weirs have a critical role. Accurately predicting the discharge coefficient is one of the most important stages in the side weir design process. In the present paper, a new high efficient side weir is investigated. To simulate the discharge coefficient of these side weirs, three novel soft computing methods are used. The process includes modeling the discharge coefficient with the hybrid Adaptive Neuro-Fuzzy Interface System (ANFIS) and three optimization algorithms, namely Differential Evaluation (ANFIS-DE), Genetic Algorithm (ANFIS-GA) and Particle Swarm Optimization (ANFIS-PSO). In addition, sensitivity analysis is done to find the most efficient input variables for modeling the discharge coefficient of these types of side weirs. According to the results, the ANFIS method has higher performance when using simpler input variables. In addition, the ANFIS-DE with RMSE of 0.077 has higher performance than the ANFIS-GA and ANFIS-PSO methods with RMSE of 0.079 and 0.096, respectively.

Hybrid parallelization of the XTOR-2F code for the simulation of two-fluid MHD instabilities in tokamaks

NASA Astrophysics Data System (ADS)

Marx, Alain; Lütjens, Hinrich

2017-03-01

A hybrid MPI/OpenMP parallel version of the XTOR-2F code [Lütjens and Luciani, J. Comput. Phys. 229 (2010) 8130] solving the two-fluid MHD equations in full tokamak geometry by means of an iterative Newton-Krylov matrix-free method has been developed. The present work shows that the code has been parallelized significantly despite the numerical profile of the problem solved by XTOR-2F, i.e. a discretization with pseudo-spectral representations in all angular directions, the stiffness of the two-fluid stability problem in tokamaks, and the use of a direct LU decomposition to invert the physical pre-conditioner at every Krylov iteration of the solver. The execution time of the parallelized version is an order of magnitude smaller than the sequential one for low resolution cases, with an increasing speedup when the discretization mesh is refined. Moreover, it allows to perform simulations with higher resolutions, previously forbidden because of memory limitations.

Optimizing the Performance of Reactive Molecular Dynamics Simulations for Multi-core Architectures

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

Aktulga, Hasan Metin; Coffman, Paul; Shan, Tzu-Ray

2015-12-01

Hybrid parallelism allows high performance computing applications to better leverage the increasing on-node parallelism of modern supercomputers. In this paper, we present a hybrid parallel implementation of the widely used LAMMPS/ReaxC package, where the construction of bonded and nonbonded lists and evaluation of complex ReaxFF interactions are implemented efficiently using OpenMP parallelism. Additionally, the performance of the QEq charge equilibration scheme is examined and a dual-solver is implemented. We present the performance of the resulting ReaxC-OMP package on a state-of-the-art multi-core architecture Mira, an IBM BlueGene/Q supercomputer. For system sizes ranging from 32 thousand to 16.6 million particles, speedups inmore » the range of 1.5-4.5x are observed using the new ReaxC-OMP software. Sustained performance improvements have been observed for up to 262,144 cores (1,048,576 processes) of Mira with a weak scaling efficiency of 91.5% in larger simulations containing 16.6 million particles.« less

A hybrid computational model to explore the topological characteristics of epithelial tissues.

PubMed

González-Valverde, Ismael; García-Aznar, José Manuel

2017-11-01

Epithelial tissues show a particular topology where cells resemble a polygon-like shape, but some biological processes can alter this tissue topology. During cell proliferation, mitotic cell dilation deforms the tissue and modifies the tissue topology. Additionally, cells are reorganized in the epithelial layer and these rearrangements also alter the polygon distribution. We present here a computer-based hybrid framework focused on the simulation of epithelial layer dynamics that combines discrete and continuum numerical models. In this framework, we consider topological and mechanical aspects of the epithelial tissue. Individual cells in the tissue are simulated by an off-lattice agent-based model, which keeps the information of each cell. In addition, we model the cell-cell interaction forces and the cell cycle. Otherwise, we simulate the passive mechanical behaviour of the cell monolayer using a material that approximates the mechanical properties of the cell. This continuum approach is solved by the finite element method, which uses a dynamic mesh generated by the triangulation of cell polygons. Forces generated by cell-cell interaction in the agent-based model are also applied on the finite element mesh. Cell movement in the agent-based model is driven by the displacements obtained from the deformed finite element mesh of the continuum mechanical approach. We successfully compare the results of our simulations with some experiments about the topology of proliferating epithelial tissues in Drosophila. Our framework is able to model the emergent behaviour of the cell monolayer that is due to local cell-cell interactions, which have a direct influence on the dynamics of the epithelial tissue. Copyright © 2017 John Wiley & Sons, Ltd.

A hybrid, coupled approach for modeling charged fluids from the nano to the mesoscale

DOE PAGES

Cheung, James; Frischknecht, Amalie L.; Perego, Mauro; ...

2017-07-20

Here, we develop and demonstrate a new, hybrid simulation approach for charged fluids, which combines the accuracy of the nonlocal, classical density functional theory (cDFT) with the efficiency of the Poisson–Nernst–Planck (PNP) equations. The approach is motivated by the fact that the more accurate description of the physics in the cDFT model is required only near the charged surfaces, while away from these regions the PNP equations provide an acceptable representation of the ionic system. We formulate the hybrid approach in two stages. The first stage defines a coupled hybrid model in which the PNP and cDFT equations act independentlymore » on two overlapping domains, subject to suitable interface coupling conditions. At the second stage we apply the principles of the alternating Schwarz method to the hybrid model by using the interface conditions to define the appropriate boundary conditions and volume constraints exchanged between the PNP and the cDFT subdomains. Numerical examples with two representative examples of ionic systems demonstrate the numerical properties of the method and its potential to reduce the computational cost of a full cDFT calculation, while retaining the accuracy of the latter near the charged surfaces.« less

A hybrid, coupled approach for modeling charged fluids from the nano to the mesoscale

NASA Astrophysics Data System (ADS)

Cheung, James; Frischknecht, Amalie L.; Perego, Mauro; Bochev, Pavel

2017-11-01

We develop and demonstrate a new, hybrid simulation approach for charged fluids, which combines the accuracy of the nonlocal, classical density functional theory (cDFT) with the efficiency of the Poisson-Nernst-Planck (PNP) equations. The approach is motivated by the fact that the more accurate description of the physics in the cDFT model is required only near the charged surfaces, while away from these regions the PNP equations provide an acceptable representation of the ionic system. We formulate the hybrid approach in two stages. The first stage defines a coupled hybrid model in which the PNP and cDFT equations act independently on two overlapping domains, subject to suitable interface coupling conditions. At the second stage we apply the principles of the alternating Schwarz method to the hybrid model by using the interface conditions to define the appropriate boundary conditions and volume constraints exchanged between the PNP and the cDFT subdomains. Numerical examples with two representative examples of ionic systems demonstrate the numerical properties of the method and its potential to reduce the computational cost of a full cDFT calculation, while retaining the accuracy of the latter near the charged surfaces.

A hybrid, coupled approach for modeling charged fluids from the nano to the mesoscale

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

Cheung, James; Frischknecht, Amalie L.; Perego, Mauro

Here, we develop and demonstrate a new, hybrid simulation approach for charged fluids, which combines the accuracy of the nonlocal, classical density functional theory (cDFT) with the efficiency of the Poisson–Nernst–Planck (PNP) equations. The approach is motivated by the fact that the more accurate description of the physics in the cDFT model is required only near the charged surfaces, while away from these regions the PNP equations provide an acceptable representation of the ionic system. We formulate the hybrid approach in two stages. The first stage defines a coupled hybrid model in which the PNP and cDFT equations act independentlymore » on two overlapping domains, subject to suitable interface coupling conditions. At the second stage we apply the principles of the alternating Schwarz method to the hybrid model by using the interface conditions to define the appropriate boundary conditions and volume constraints exchanged between the PNP and the cDFT subdomains. Numerical examples with two representative examples of ionic systems demonstrate the numerical properties of the method and its potential to reduce the computational cost of a full cDFT calculation, while retaining the accuracy of the latter near the charged surfaces.« less

Statistical comparison of a hybrid approach with approximate and exact inference models for Fusion 2+

NASA Astrophysics Data System (ADS)

Lee, K. David; Wiesenfeld, Eric; Gelfand, Andrew

2007-04-01

One of the greatest challenges in modern combat is maintaining a high level of timely Situational Awareness (SA). In many situations, computational complexity and accuracy considerations make the development and deployment of real-time, high-level inference tools very difficult. An innovative hybrid framework that combines Bayesian inference, in the form of Bayesian Networks, and Possibility Theory, in the form of Fuzzy Logic systems, has recently been introduced to provide a rigorous framework for high-level inference. In previous research, the theoretical basis and benefits of the hybrid approach have been developed. However, lacking is a concrete experimental comparison of the hybrid framework with traditional fusion methods, to demonstrate and quantify this benefit. The goal of this research, therefore, is to provide a statistical analysis on the comparison of the accuracy and performance of hybrid network theory, with pure Bayesian and Fuzzy systems and an inexact Bayesian system approximated using Particle Filtering. To accomplish this task, domain specific models will be developed under these different theoretical approaches and then evaluated, via Monte Carlo Simulation, in comparison to situational ground truth to measure accuracy and fidelity. Following this, a rigorous statistical analysis of the performance results will be performed, to quantify the benefit of hybrid inference to other fusion tools.

The Occurrence of Tidal Hybrid Kelvin-Edge Waves in the Global Ocean

NASA Astrophysics Data System (ADS)

Kaur, H.; Buijsman, M. C.; Yankovsky, A. E.; Zhang, T.; Jeon, C. H.

2017-12-01

This study presents the analysis of hybrid Kelvin-edge waves on the continental shelves in a global ocean model. Our objective is to find areas where the transition occurs from Kelvin waves to hybrid Kelvin-edge waves. The change in continental shelf width may convert a Kelvin wave into a hybrid Kelvin-edge wave. In this process the group velocity reaches a minimum and tidal energy is radiated on and/or offshore [Zhang 2016]. We extract M2 SSH (Sea Surface Height) and velocity from the Hybrid Coordinate Ocean Model (HYCOM) and calculate barotropic energy fluxes. We analyze these three areas: the Bay of Biscay, the Amazon Shelf and North West Africa. In these three regions, the continental shelf widens in the propagation direction and the alongshore flux changes its direction towards the coast. A transect is taken at different points in these areas to compute the dispersion relations of the waves on the continental shelf. In model simulations, we change the bathymetry of the Bay of Biscay to study the behavior of the hybrid Kelvin-edge waves. BibliographyZhang, T., and A. E Yankovsky. (2016), On the nature of cross-isobath energy fluxes in topographically modified barotropic semidiurnal Kelvin waves, J. Geophys. Res. Oceans, 121, 3058-3074, doi:10.1002/2015JC011617.

Checkpointing for a hybrid computing node

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

Cher, Chen-Yong

2016-03-08

According to an aspect, a method for checkpointing in a hybrid computing node includes executing a task in a processing accelerator of the hybrid computing node. A checkpoint is created in a local memory of the processing accelerator. The checkpoint includes state data to restart execution of the task in the processing accelerator upon a restart operation. Execution of the task is resumed in the processing accelerator after creating the checkpoint. The state data of the checkpoint are transferred from the processing accelerator to a main processor of the hybrid computing node while the processing accelerator is executing the task.

Accelerating the Gillespie Exact Stochastic Simulation Algorithm using hybrid parallel execution on graphics processing units.

PubMed

Komarov, Ivan; D'Souza, Roshan M

2012-01-01

The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differential equations. The inherent limitations of the GSSA include the time required for executing a single run and the need for multiple runs for parameter sweep exercises due to the stochastic nature of the simulation. Even very efficient variants of GSSA are prohibitively expensive to compute and perform parameter sweeps. Here we present a novel variant of the exact GSSA that is amenable to acceleration by using graphics processing units (GPUs). We parallelize the execution of a single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, which is the bottleneck in computing the GSSA. Our benchmarks show an 8×-120× performance gain over various state-of-the-art serial algorithms when simulating different types of models.

Exact and approximate stochastic simulation of intracellular calcium dynamics.

PubMed

Wieder, Nicolas; Fink, Rainer H A; Wegner, Frederic von

2011-01-01

In simulations of chemical systems, the main task is to find an exact or approximate solution of the chemical master equation (CME) that satisfies certain constraints with respect to computation time and accuracy. While Brownian motion simulations of single molecules are often too time consuming to represent the mesoscopic level, the classical Gillespie algorithm is a stochastically exact algorithm that provides satisfying results in the representation of calcium microdomains. Gillespie's algorithm can be approximated via the tau-leap method and the chemical Langevin equation (CLE). Both methods lead to a substantial acceleration in computation time and a relatively small decrease in accuracy. Elimination of the noise terms leads to the classical, deterministic reaction rate equations (RRE). For complex multiscale systems, hybrid simulations are increasingly proposed to combine the advantages of stochastic and deterministic algorithms. An often used exemplary cell type in this context are striated muscle cells (e.g., cardiac and skeletal muscle cells). The properties of these cells are well described and they express many common calcium-dependent signaling pathways. The purpose of the present paper is to provide an overview of the aforementioned simulation approaches and their mutual relationships in the spectrum ranging from stochastic to deterministic algorithms.

A framework using cluster-based hybrid network architecture for collaborative virtual surgery.

PubMed

Qin, Jing; Choi, Kup-Sze; Poon, Wai-Sang; Heng, Pheng-Ann

2009-12-01

Research on collaborative virtual environments (CVEs) opens the opportunity for simulating the cooperative work in surgical operations. It is however a challenging task to implement a high performance collaborative surgical simulation system because of the difficulty in maintaining state consistency with minimum network latencies, especially when sophisticated deformable models and haptics are involved. In this paper, an integrated framework using cluster-based hybrid network architecture is proposed to support collaborative virtual surgery. Multicast transmission is employed to transmit updated information among participants in order to reduce network latencies, while system consistency is maintained by an administrative server. Reliable multicast is implemented using distributed message acknowledgment based on cluster cooperation and sliding window technique. The robustness of the framework is guaranteed by the failure detection chain which enables smooth transition when participants join and leave the collaboration, including normal and involuntary leaving. Communication overhead is further reduced by implementing a number of management approaches such as computational policies and collaborative mechanisms. The feasibility of the proposed framework is demonstrated by successfully extending an existing standalone orthopedic surgery trainer into a collaborative simulation system. A series of experiments have been conducted to evaluate the system performance. The results demonstrate that the proposed framework is capable of supporting collaborative surgical simulation.

Dynamic Clamp in Cardiac and Neuronal Systems Using RTXI

PubMed Central

Ortega, Francis A.; Butera, Robert J.; Christini, David J.; White, John A.; Dorval, Alan D.

2016-01-01

The injection of computer-simulated conductances through the dynamic clamp technique has allowed researchers to probe the intercellular and intracellular dynamics of cardiac and neuronal systems with great precision. By coupling computational models to biological systems, dynamic clamp has become a proven tool in electrophysiology with many applications, such as generating hybrid networks in neurons or simulating channelopathies in cardiomyocytes. While its applications are broad, the approach is straightforward: synthesizing traditional patch clamp, computational modeling, and closed-loop feedback control to simulate a cellular conductance. Here, we present two example applications: artificial blocking of the inward rectifier potassium current in a cardiomyocyte and coupling of a biological neuron to a virtual neuron through a virtual synapse. The design and implementation of the necessary software to administer these dynamic clamp experiments can be difficult. In this chapter, we provide an overview of designing and implementing a dynamic clamp experiment using the Real-Time eXperiment Interface (RTXI), an open- source software system tailored for real-time biological experiments. We present two ways to achieve this using RTXI’s modular format, through the creation of a custom user-made module and through existing modules found in RTXI’s online library. PMID:25023319

Modeling of anomalous electron mobility in Hall thrusters

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

Koo, Justin W.; Boyd, Iain D.

Accurate modeling of the anomalous electron mobility is absolutely critical for successful simulation of Hall thrusters. In this work, existing computational models for the anomalous electron mobility are used to simulate the UM/AFRL P5 Hall thruster (a 5 kW laboratory model) in a two-dimensional axisymmetric hybrid particle-in-cell Monte Carlo collision code. Comparison to experimental results indicates that, while these computational models can be tuned to reproduce the correct thrust or discharge current, it is very difficult to match all integrated performance parameters (thrust, power, discharge current, etc.) simultaneously. Furthermore, multiple configurations of these computational models can produce reasonable integrated performancemore » parameters. A semiempirical electron mobility profile is constructed from a combination of internal experimental data and modeling assumptions. This semiempirical electron mobility profile is used in the code and results in more accurate simulation of both the integrated performance parameters and the mean potential profile of the thruster. Results indicate that the anomalous electron mobility, while absolutely necessary in the near-field region, provides a substantially smaller contribution to the total electron mobility in the high Hall current region near the thruster exit plane.« less

Multipurpose Educational Modules to Teach Hydraulic Hybrid Vehicle Technologies

DOT National Transportation Integrated Search

2007-09-01

The goal of the overall project is to develop a software simulation for a hydraulic hybrid vehicle. The simulation will enable students to compare various hybrid configurations with conventional IC engine performance.

Kinetic particle simulation of discharge and wall erosion of a Hall thruster

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

Cho, Shinatora; Komurasaki, Kimiya; Arakawa, Yoshihiro

2013-06-15

The primary lifetime limiting factor of Hall thrusters is the wall erosion caused by the ion induced sputtering, which is predominated by dielectric wall sheath and pre-sheath. However, so far only fluid or hybrid simulation models were applied to wall erosion and lifetime studies in which this non-quasi-neutral and non-equilibrium area cannot be treated directly. Thus, in this study, a 2D fully kinetic particle-in-cell model was presented for Hall thruster discharge and lifetime simulation. Because the fully kinetic lifetime simulation was yet to be achieved so far due to the high computational cost, the semi-implicit field solver and the techniquemore » of mass ratio manipulation was employed to accelerate the computation. However, other artificial manipulations like permittivity or geometry scaling were not used in order to avoid unrecoverable change of physics. Additionally, a new physics recovering model for the mass ratio was presented for better preservation of electron mobility at the weakly magnetically confined plasma region. The validity of the presented model was examined by various parametric studies, and the thrust performance and wall erosion rate of a laboratory model magnetic layer type Hall thruster was modeled for different operation conditions. The simulation results successfully reproduced the measurement results with typically less than 10% discrepancy without tuning any numerical parameters. It is also shown that the computational cost was reduced to the level that the Hall thruster fully kinetic lifetime simulation is feasible.« less