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

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

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

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

Validation of the solar heating and cooling high speed performance (HISPER) computer code

NASA Technical Reports Server (NTRS)

Wallace, D. B.

1980-01-01

Developed to give a quick and accurate predictions HISPER, a simplification of the TRNSYS program, achieves its computational speed by not simulating detailed system operations or performing detailed load computations. In order to validate the HISPER computer for air systems the simulation was compared to the actual performance of an operational test site. Solar insolation, ambient temperature, water usage rate, and water main temperatures from the data tapes for an office building in Huntsville, Alabama were used as input. The HISPER program was found to predict the heating loads and solar fraction of the loads with errors of less than ten percent. Good correlation was found on both a seasonal basis and a monthly basis. Several parameters (such as infiltration rate and the outside ambient temperature above which heating is not required) were found to require careful selection for accurate simulation.

Computational Fluid Dynamics of Whole-Body Aircraft

NASA Astrophysics Data System (ADS)

Agarwal, Ramesh

1999-01-01

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

Turbulent Flow Simulation at the Exascale: Opportunities and Challenges Workshop: August 4-5, 2015, Washington, D.C.

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

Sprague, Michael A.; Boldyrev, Stanislav; Fischer, Paul

This report details the impact exascale will bring to turbulent-flow simulations in applied science and technology. The need for accurate simulation of turbulent flows is evident across the DOE applied-science and engineering portfolios, including combustion, plasma physics, nuclear-reactor physics, wind energy, and atmospheric science. The workshop brought together experts in turbulent-flow simulation, computational mathematics, and high-performance computing. Building upon previous ASCR workshops on exascale computing, participants defined a research agenda and path forward that will enable scientists and engineers to continually leverage, engage, and direct advances in computational systems on the path to exascale computing.

Computer simulation results of attitude estimation of earth orbiting satellites

NASA Technical Reports Server (NTRS)

Kou, S. R.

1976-01-01

Computer simulation results of attitude estimation of Earth-orbiting satellites (including Space Telescope) subjected to environmental disturbances and noises are presented. Decomposed linear recursive filter and Kalman filter were used as estimation tools. Six programs were developed for this simulation, and all were written in the basic language and were run on HP 9830A and HP 9866A computers. Simulation results show that a decomposed linear recursive filter is accurate in estimation and fast in response time. Furthermore, for higher order systems, this filter has computational advantages (i.e., less integration errors and roundoff errors) over a Kalman filter.

Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear-Layer. Part 2

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Singer, Bart A.; Lockard, David P.

2002-01-01

Unsteady computational simulations of a multi-element, high-lift configuration are performed. Emphasis is placed on accurate spatiotemporal resolution of the free shear layer in the slat-cove region. The excessive dissipative effects of the turbulence model, so prevalent in previous simulations, are circumvented by switching off the turbulence-production term in the slat cove region. The justifications and physical arguments for taking such a step are explained in detail. The removal of this excess damping allows the shear layer to amplify large-scale structures, to achieve a proper non-linear saturation state, and to permit vortex merging. The large-scale disturbances are self-excited, and unlike our prior fully turbulent simulations, no external forcing of the shear layer is required. To obtain the farfield acoustics, the Ffowcs Williams and Hawkings equation is evaluated numerically using the simulated time-accurate flow data. The present comparison between the computed and measured farfield acoustic spectra shows much better agreement for the amplitude and frequency content than past calculations. The effect of the angle-of-attack on the slat's flow features radiated acoustic field are also simulated presented.

An Accurate and Computationally Efficient Model for Membrane-Type Circular-Symmetric Micro-Hotplates

PubMed Central

Khan, Usman; Falconi, Christian

2014-01-01

Ideally, the design of high-performance micro-hotplates would require a large number of simulations because of the existence of many important design parameters as well as the possibly crucial effects of both spread and drift. However, the computational cost of FEM simulations, which are the only available tool for accurately predicting the temperature in micro-hotplates, is very high. As a result, micro-hotplate designers generally have no effective simulation-tools for the optimization. In order to circumvent these issues, here, we propose a model for practical circular-symmetric micro-hot-plates which takes advantage of modified Bessel functions, computationally efficient matrix-approach for considering the relevant boundary conditions, Taylor linearization for modeling the Joule heating and radiation losses, and external-region-segmentation strategy in order to accurately take into account radiation losses in the entire micro-hotplate. The proposed model is almost as accurate as FEM simulations and two to three orders of magnitude more computationally efficient (e.g., 45 s versus more than 8 h). The residual errors, which are mainly associated to the undesired heating in the electrical contacts, are small (e.g., few degrees Celsius for an 800 °C operating temperature) and, for important analyses, almost constant. Therefore, we also introduce a computationally-easy single-FEM-compensation strategy in order to reduce the residual errors to about 1 °C. As illustrative examples of the power of our approach, we report the systematic investigation of a spread in the membrane thermal conductivity and of combined variations of both ambient and bulk temperatures. Our model enables a much faster characterization of micro-hotplates and, thus, a much more effective optimization prior to fabrication. PMID:24763214

Development of hardware accelerator for molecular dynamics simulations: a computation board that calculates nonbonded interactions in cooperation with fast multipole method.

PubMed

Amisaki, Takashi; Toyoda, Shinjiro; Miyagawa, Hiroh; Kitamura, Kunihiro

2003-04-15

Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle-particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation ("particle processor") are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein-water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 582-592, 2003

Progress in fast, accurate multi-scale climate simulations

DOE PAGES

Collins, W. D.; Johansen, H.; Evans, K. J.; ...

2015-06-01

We present a survey of physical and computational techniques that have the potential to contribute to the next generation of high-fidelity, multi-scale climate simulations. Examples of the climate science problems that can be investigated with more depth with these computational improvements include the capture of remote forcings of localized hydrological extreme events, an accurate representation of cloud features over a range of spatial and temporal scales, and parallel, large ensembles of simulations to more effectively explore model sensitivities and uncertainties. Numerical techniques, such as adaptive mesh refinement, implicit time integration, and separate treatment of fast physical time scales are enablingmore » improved accuracy and fidelity in simulation of dynamics and allowing more complete representations of climate features at the global scale. At the same time, partnerships with computer science teams have focused on taking advantage of evolving computer architectures such as many-core processors and GPUs. As a result, approaches which were previously considered prohibitively costly have become both more efficient and scalable. In combination, progress in these three critical areas is poised to transform climate modeling in the coming decades.« less

Computational Methods for HSCT-Inlet Controls/CFD Interdisciplinary Research

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

Influence of Computational Drop Representation in LES of a Droplet-Laden Mixing Layer

NASA Technical Reports Server (NTRS)

Bellan, Josette; Radhakrishnan, Senthilkumaran

2013-01-01

Multiphase turbulent flows are encountered in many practical applications including turbine engines or natural phenomena involving particle dispersion. Numerical computations of multiphase turbulent flows are important because they provide a cheaper alternative to performing experiments during an engine design process or because they can provide predictions of pollutant dispersion, etc. Two-phase flows contain millions and sometimes billions of particles. For flows with volumetrically dilute particle loading, the most accurate method of numerically simulating the flow is based on direct numerical simulation (DNS) of the governing equations in which all scales of the flow including the small scales that are responsible for the overwhelming amount of dissipation are resolved. DNS, however, requires high computational cost and cannot be used in engineering design applications where iterations among several design conditions are necessary. Because of high computational cost, numerical simulations of such flows cannot track all these drops. The objective of this work is to quantify the influence of the number of computational drops and grid spacing on the accuracy of predicted flow statistics, and to possibly identify the minimum number, or, if not possible, the optimal number of computational drops that provide minimal error in flow prediction. For this purpose, several Large Eddy Simulation (LES) of a mixing layer with evaporating drops have been performed by using coarse, medium, and fine grid spacings and computational drops, rather than physical drops. To define computational drops, an integer NR is introduced that represents the ratio of the number of existing physical drops to the desired number of computational drops; for example, if NR=8, this means that a computational drop represents 8 physical drops in the flow field. The desired number of computational drops is determined by the available computational resources; the larger NR is, the less computationally intensive is the simulation. A set of first order and second order flow statistics, and of drop statistics are extracted from LES predictions and are compared to results obtained by filtering a DNS database. First order statistics such as Favre averaged stream-wise velocity, Favre averaged vapor mass fraction, and the drop stream-wise velocity, are predicted accurately independent of the number of computational drops and grid spacing. Second order flow statistics depend both on the number of computational drops and on grid spacing. The scalar variance and turbulent vapor flux are predicted accurately by the fine mesh LES only when NR is less than 32, and by the coarse mesh LES reasonably accurately for all NR values. This is attributed to the fact that when the grid spacing is coarsened, the number of drops in a computational cell must not be significantly lower than that in the DNS.

Computational Flow Modeling of Human Upper Airway Breathing

NASA Astrophysics Data System (ADS)

Mylavarapu, Goutham

Computational modeling of biological systems have gained a lot of interest in biomedical research, in the recent past. This thesis focuses on the application of computational simulations to study airflow dynamics in human upper respiratory tract. With advancements in medical imaging, patient specific geometries of anatomically accurate respiratory tracts can now be reconstructed from Magnetic Resonance Images (MRI) or Computed Tomography (CT) scans, with better and accurate details than traditional cadaver cast models. Computational studies using these individualized geometrical models have advantages of non-invasiveness, ease, minimum patient interaction, improved accuracy over experimental and clinical studies. Numerical simulations can provide detailed flow fields including velocities, flow rates, airway wall pressure, shear stresses, turbulence in an airway. Interpretation of these physical quantities will enable to develop efficient treatment procedures, medical devices, targeted drug delivery etc. The hypothesis for this research is that computational modeling can predict the outcomes of a surgical intervention or a treatment plan prior to its application and will guide the physician in providing better treatment to the patients. In the current work, three different computational approaches Computational Fluid Dynamics (CFD), Flow-Structure Interaction (FSI) and Particle Flow simulations were used to investigate flow in airway geometries. CFD approach assumes airway wall as rigid, and relatively easy to simulate, compared to the more challenging FSI approach, where interactions of airway wall deformations with flow are also accounted. The CFD methodology using different turbulence models is validated against experimental measurements in an airway phantom. Two case-studies using CFD, to quantify a pre and post-operative airway and another, to perform virtual surgery to determine the best possible surgery in a constricted airway is demonstrated. The unsteady Large Eddy simulations (LES) and a steady Reynolds Averaged Navier Stokes (RANS) approaches in CFD modeling are discussed. The more challenging FSI approach is modeled first in simple two-dimensional anatomical geometry and then extended to simplified three dimensional geometry and finally in three dimensionally accurate geometries. The concepts of virtual surgery and the differences to CFD are discussed. Finally, the influence of various drug delivery parameters on particle deposition efficiency in airway anatomy are investigated through particle-flow simulations in a nasal airway model.

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.

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

PubMed

Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

2015-01-01

Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

Improving Computational Efficiency of Prediction in Model-Based Prognostics Using the Unscented Transform

NASA Technical Reports Server (NTRS)

Daigle, Matthew John; Goebel, Kai Frank

2010-01-01

Model-based prognostics captures system knowledge in the form of physics-based models of components, and how they fail, in order to obtain accurate predictions of end of life (EOL). EOL is predicted based on the estimated current state distribution of a component and expected profiles of future usage. In general, this requires simulations of the component using the underlying models. In this paper, we develop a simulation-based prediction methodology that achieves computational efficiency by performing only the minimal number of simulations needed in order to accurately approximate the mean and variance of the complete EOL distribution. This is performed through the use of the unscented transform, which predicts the means and covariances of a distribution passed through a nonlinear transformation. In this case, the EOL simulation acts as that nonlinear transformation. In this paper, we review the unscented transform, and describe how this concept is applied to efficient EOL prediction. As a case study, we develop a physics-based model of a solenoid valve, and perform simulation experiments to demonstrate improved computational efficiency without sacrificing prediction accuracy.

Computer Simulation of Microwave Devices

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1997-01-01

The accurate simulation of cold-test results including dispersion, on-axis beam interaction impedance, and attenuation of a helix traveling-wave tube (TWT) slow-wave circuit using the three-dimensional code MAFIA (Maxwell's Equations Solved by the Finite Integration Algorithm) was demonstrated for the first time. Obtaining these results is a critical step in the design of TWT's. A well-established procedure to acquire these parameters is to actually build and test a model or a scale model of the circuit. However, this procedure is time-consuming and expensive, and it limits freedom to examine new variations to the basic circuit. These limitations make the need for computational methods crucial since they can lower costs, reduce tube development time, and lessen limitations on novel designs. Computer simulation has been used to accurately obtain cold-test parameters for several slow-wave circuits. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. A new computer modeling technique developed at the NASA Lewis Research Center overcomes these difficulties. The MAFIA three-dimensional mesh for a C-band helix slow-wave circuit is shown.

Analysis of electrophoresis performance

NASA Technical Reports Server (NTRS)

Roberts, Glyn O.

1988-01-01

A flexible efficient computer code is being developed to simulate electrophoretic separation phenomena, in either a cylindrical or a rectangular geometry. The code will computer the evolution in time of the concentrations of an arbitrary number of chemical species, and of the temperature, pH distribution, conductivity, electric field, and fluid motion. Use of nonuniform meshes and fast accurate implicit time-stepping will yield accurate answers at economical cost.

DNS of Low-Pressure Turbine Cascade Flows with Elevated Inflow Turbulence Using a Discontinuous-Galerkin Spectral-Element Method

NASA Technical Reports Server (NTRS)

Garai, Anirban; Diosady, Laslo T.; Murman, Scott M.; Madavan, Nateri K.

2016-01-01

Recent progress towards developing a new computational capability for accurate and efficient high-fidelity direct numerical simulation (DNS) and large-eddy simulation (LES) of turbomachinery is described. This capability is based on an entropy- stable Discontinuous-Galerkin spectral-element approach that extends to arbitrarily high orders of spatial and temporal accuracy, and is implemented in a computationally efficient manner on a modern high performance computer architecture. An inflow turbulence generation procedure based on a linear forcing approach has been incorporated in this framework and DNS conducted to study the effect of inflow turbulence on the suction- side separation bubble in low-pressure turbine (LPT) cascades. The T106 series of airfoil cascades in both lightly (T106A) and highly loaded (T106C) configurations at exit isentropic Reynolds numbers of 60,000 and 80,000, respectively, are considered. The numerical simulations are performed using 8th-order accurate spatial and 4th-order accurate temporal discretization. The changes in separation bubble topology due to elevated inflow turbulence is captured by the present method and the physical mechanisms leading to the changes are explained. The present results are in good agreement with prior numerical simulations but some expected discrepancies with the experimental data for the T106C case are noted and discussed.

BlazeDEM3D-GPU A Large Scale DEM simulation code for GPUs

NASA Astrophysics Data System (ADS)

Govender, Nicolin; Wilke, Daniel; Pizette, Patrick; Khinast, Johannes

2017-06-01

Accurately predicting the dynamics of particulate materials is of importance to numerous scientific and industrial areas with applications ranging across particle scales from powder flow to ore crushing. Computational discrete element simulations is a viable option to aid in the understanding of particulate dynamics and design of devices such as mixers, silos and ball mills, as laboratory scale tests comes at a significant cost. However, the computational time required to simulate an industrial scale simulation which consists of tens of millions of particles can take months to complete on large CPU clusters, making the Discrete Element Method (DEM) unfeasible for industrial applications. Simulations are therefore typically restricted to tens of thousands of particles with highly detailed particle shapes or a few million of particles with often oversimplified particle shapes. However, a number of applications require accurate representation of the particle shape to capture the macroscopic behaviour of the particulate system. In this paper we give an overview of the recent extensions to the open source GPU based DEM code, BlazeDEM3D-GPU, that can simulate millions of polyhedra and tens of millions of spheres on a desktop computer with a single or multiple GPUs.

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

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

Badal, A; Zbijewski, W; Bolch, W

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

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

LOS selective fading and AN/FRC-170(V) radio hybrid computer simulation phase A report

NASA Astrophysics Data System (ADS)

Klukis, M. K.; Lyon, T. I.; Walker, R.

1981-09-01

This report documents results of the first phase of modeling, simulation and study of the dual diversity AN/FRC-170(V) radio and frequency selective fading line of sight channel. Both hybrid computer and circuit technologies were used to develop a fast, accurate and flexible simulation tool to investigate changes and proposed improvements to the design of the AN/FRC-170(V) radio. In addition to the simulation study, a remote hybrid computer terminal was provided to DCEC for interactive study of the modeled radio and channel. Simulated performance of the radio for Rayleigh, line of sight two ray channels, and additive noise are included in the report.

Time-Accurate Unsteady Pressure Loads Simulated for the Space Launch System at Wind Tunnel Conditions

NASA Technical Reports Server (NTRS)

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

2015-01-01

A transonic flow field about a Space Launch System (SLS) configuration was simulated with the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics (CFD) code at wind tunnel conditions. Unsteady, time-accurate computations were performed using second-order Delayed Detached Eddy Simulation (DDES) for up to 1.5 physical seconds. The surface pressure time history was collected at 619 locations, 169 of which matched locations on a 2.5 percent wind tunnel model that was tested in the 11 ft. x 11 ft. test section of the NASA Ames Research Center's Unitary Plan Wind Tunnel. Comparisons between computation and experiment showed that the peak surface pressure RMS level occurs behind the forward attach hardware, and good agreement for frequency and power was obtained in this region. Computational domain, grid resolution, and time step sensitivity studies were performed. These included an investigation of pseudo-time sub-iteration convergence. Using these sensitivity studies and experimental data comparisons, a set of best practices to date have been established for FUN3D simulations for SLS launch vehicle analysis. To the author's knowledge, this is the first time DDES has been used in a systematic approach and establish simulation time needed, to analyze unsteady pressure loads on a space launch vehicle such as the NASA SLS.

Computer Vision Assisted Virtual Reality Calibration

NASA Technical Reports Server (NTRS)

Kim, W.

1999-01-01

A computer vision assisted semi-automatic virtual reality (VR) calibration technology has been developed that can accurately match a virtual environment of graphically simulated three-dimensional (3-D) models to the video images of the real task environment.

Optimal simulations of ultrasonic fields produced by large thermal therapy arrays using the angular spectrum approach

PubMed Central

Zeng, Xiaozheng; McGough, Robert J.

2009-01-01

The angular spectrum approach is evaluated for the simulation of focused ultrasound fields produced by large thermal therapy arrays. For an input pressure or normal particle velocity distribution in a plane, the angular spectrum approach rapidly computes the output pressure field in a three dimensional volume. To determine the optimal combination of simulation parameters for angular spectrum calculations, the effect of the size, location, and the numerical accuracy of the input plane on the computed output pressure is evaluated. Simulation results demonstrate that angular spectrum calculations performed with an input pressure plane are more accurate than calculations with an input velocity plane. Results also indicate that when the input pressure plane is slightly larger than the array aperture and is located approximately one wavelength from the array, angular spectrum simulations have very small numerical errors for two dimensional planar arrays. Furthermore, the root mean squared error from angular spectrum simulations asymptotically approaches a nonzero lower limit as the error in the input plane decreases. Overall, the angular spectrum approach is an accurate and robust method for thermal therapy simulations of large ultrasound phased arrays when the input pressure plane is computed with the fast nearfield method and an optimal combination of input parameters. PMID:19425640

Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions.

PubMed

Isele-Holder, Rolf E; Mitchell, Wayne; Ismail, Ahmed E

2012-11-07

For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation of these contributions, we have implemented a particle-particle particle-mesh Ewald solver for dispersion (r(-6)) interactions into the LAMMPS molecular dynamics package. We demonstrate that the solver's O(N log N) scaling behavior allows its application to large-scale simulations. We carefully determine a set of parameters for the solver that provides accurate results and efficient computation. We perform a series of simulations with Lennard-Jones particles, SPC/E water, and hexane to show that with our choice of parameters the dependence of physical results on the chosen cutoff radius is removed. Physical results and computation time of these simulations are compared to results obtained using either a plain cutoff or a traditional Ewald sum for dispersion.

An integrated computational tool for precipitation simulation

NASA Astrophysics Data System (ADS)

Cao, W.; Zhang, F.; Chen, S.-L.; Zhang, C.; Chang, Y. A.

2011-07-01

Computer aided materials design is of increasing interest because the conventional approach solely relying on experimentation is no longer viable within the constraint of available resources. Modeling of microstructure and mechanical properties during precipitation plays a critical role in understanding the behavior of materials and thus accelerating the development of materials. Nevertheless, an integrated computational tool coupling reliable thermodynamic calculation, kinetic simulation, and property prediction of multi-component systems for industrial applications is rarely available. In this regard, we are developing a software package, PanPrecipitation, under the framework of integrated computational materials engineering to simulate precipitation kinetics. It is seamlessly integrated with the thermodynamic calculation engine, PanEngine, to obtain accurate thermodynamic properties and atomic mobility data necessary for precipitation simulation.

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.

Navier-Stokes simulations of slender axisymmetric shapes in supersonic, turbulent flow

NASA Astrophysics Data System (ADS)

Moran, Kenneth J.; Beran, Philip S.

1994-07-01

Computational fluid dynamics is used to study flows about slender, axisymmetric bodies at very high speeds. Numerical experiments are conducted to simulate a broad range of flight conditions. Mach number is varied from 1.5 to 8 and Reynolds number is varied from 1 X 10(exp 6)/m to 10(exp 8)/m. The primary objective is to develop and validate a computational and methodology for the accurate simulation of a wide variety of flow structures. Accurate results are obtained for detached bow shocks, recompression shocks, corner-point expansions, base-flow recirculations, and turbulent boundary layers. Accuracy is assessed through comparison with theory and experimental data; computed surface pressure, shock structure, base-flow structure, and velocity profiles are within measurement accuracy throughout the range of conditions tested. The methodology is both practical and general: general in its applicability, and practicaal in its performance. To achieve high accuracy, modifications to previously reported techniques are implemented in the scheme. These modifications improve computed results in the vicinity of symmetry lines and in the base flow region, including the turbulent wake.

Outcomes from the DOE Workshop on Turbulent Flow Simulation at the Exascale

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

Sprague, Michael; Boldyrev, Stanislav; Chang, Choong-Seock

This paper summarizes the outcomes from the Turbulent Flow Simulation at the Exascale: Opportunities and Challenges Workshop, which was held 4-5 August 2015, and was sponsored by the U.S. Department of Energy Office of Advanced Scientific Computing Research. The workshop objective was to define and describe the challenges and opportunities that computing at the exascale will bring to turbulent-flow simulations in applied science and technology. The need for accurate simulation of turbulent flows is evident across the U.S. Department of Energy applied-science and engineering portfolios, including combustion, plasma physics, nuclear-reactor physics, wind energy, and atmospheric science. The workshop brought togethermore » experts in turbulent-flow simulation, computational mathematics, and high-performance computing. Building upon previous ASCR workshops on exascale computing, participants defined a research agenda and path forward that will enable scientists and engineers to continually leverage, engage, and direct advances in computational systems on the path to exascale computing.« less

Long-range interactions and parallel scalability in molecular simulations

NASA Astrophysics Data System (ADS)

Patra, Michael; Hyvönen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko

2007-01-01

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes—we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.

Higher Order Time Integration Schemes for the Unsteady Navier-Stokes Equations on Unstructured Meshes

NASA Technical Reports Server (NTRS)

Jothiprasad, Giridhar; Mavriplis, Dimitri J.; Caughey, David A.

2002-01-01

The rapid increase in available computational power over the last decade has enabled higher resolution flow simulations and more widespread use of unstructured grid methods for complex geometries. While much of this effort has been focused on steady-state calculations in the aerodynamics community, the need to accurately predict off-design conditions, which may involve substantial amounts of flow separation, points to the need to efficiently simulate unsteady flow fields. Accurate unsteady flow simulations can easily require several orders of magnitude more computational effort than a corresponding steady-state simulation. For this reason, techniques for improving the efficiency of unsteady flow simulations are required in order to make such calculations feasible in the foreseeable future. The purpose of this work is to investigate possible reductions in computer time due to the choice of an efficient time-integration scheme from a series of schemes differing in the order of time-accuracy, and by the use of more efficient techniques to solve the nonlinear equations which arise while using implicit time-integration schemes. This investigation is carried out in the context of a two-dimensional unstructured mesh laminar Navier-Stokes solver.

Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo.

PubMed

Parsons, Neal; Levin, Deborah A; van Duin, Adri C T; Zhu, Tong

2014-12-21

The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N2(Σg+1)-N2(Σg+1) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections.

Advanced Dynamically Adaptive Algorithms for Stochastic Simulations on Extreme Scales

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

Xiu, Dongbin

2017-03-03

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

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

PubMed Central

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

2013-01-01

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

Molecular dynamics studies of transport properties and equation of state of supercritical fluids

NASA Astrophysics Data System (ADS)

Nwobi, Obika C.

Many chemical propulsion systems operate with one or more of the reactants above the critical point in order to enhance their performance. Most of the computational fluid dynamics (CFD) methods used to predict these flows require accurate information on the transport properties and equation of state at these supercritical conditions. This work involves the determination of transport coefficients and equation of state of supercritical fluids by equilibrium molecular dynamics (MD) simulations on parallel computers using the Green-Kubo formulae and the virial equation of state, respectively. MD involves the solution of equations of motion of a system of molecules that interact with each other through an intermolecular potential. Provided that an accurate potential can be found for the system of interest, MD can be used regardless of the phase and thermodynamic conditions of the substances involved. The MD program uses the effective Lennard-Jones potential, with system sizes of 1000-1200 molecules and, simulations of 2,000,000 time-steps for computing transport coefficients and 200,000 time-steps for pressures. The computer code also uses linked cell lists for efficient sorting of molecules, periodic boundary conditions, and a modified velocity Verlet algorithm for particle displacement. Particle decomposition is used for distributing the molecules to different processors of a parallel computer. Simulations have been carried out on pure argon, nitrogen, oxygen and ethylene at various supercritical conditions, with self-diffusion coefficients, shear viscosity coefficients, thermal conductivity coefficients and pressures computed for most of the conditions. Results compare well with experimental and the National Institute of Standards and Technology (NIST) values. The results show that the number of molecules and the potential cut-off radius have no significant effect on the computed coefficients, while long-time integration is necessary for accurate determination of the coefficients.

Advanced EUV mask and imaging modeling

NASA Astrophysics Data System (ADS)

Evanschitzky, Peter; Erdmann, Andreas

2017-10-01

The exploration and optimization of image formation in partially coherent EUV projection systems with complex source shapes requires flexible, accurate, and efficient simulation models. This paper reviews advanced mask diffraction and imaging models for the highly accurate and fast simulation of EUV lithography systems, addressing important aspects of the current technical developments. The simulation of light diffraction from the mask employs an extended rigorous coupled wave analysis (RCWA) approach, which is optimized for EUV applications. In order to be able to deal with current EUV simulation requirements, several additional models are included in the extended RCWA approach: a field decomposition and a field stitching technique enable the simulation of larger complex structured mask areas. An EUV multilayer defect model including a database approach makes the fast and fully rigorous defect simulation and defect repair simulation possible. A hybrid mask simulation approach combining real and ideal mask parts allows the detailed investigation of the origin of different mask 3-D effects. The image computation is done with a fully vectorial Abbe-based approach. Arbitrary illumination and polarization schemes and adapted rigorous mask simulations guarantee a high accuracy. A fully vectorial sampling-free description of the pupil with Zernikes and Jones pupils and an optimized representation of the diffraction spectrum enable the computation of high-resolution images with high accuracy and short simulation times. A new pellicle model supports the simulation of arbitrary membrane stacks, pellicle distortions, and particles/defects on top of the pellicle. Finally, an extension for highly accurate anamorphic imaging simulations is included. The application of the models is demonstrated by typical use cases.

Understanding Islamist political violence through computational social simulation

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

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

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

Faster Aerodynamic Simulation With Cart3D

NASA Technical Reports Server (NTRS)

2003-01-01

A NASA-developed aerodynamic simulation tool is ensuring the safety of future space operations while providing designers and engineers with an automated, highly accurate computer simulation suite. Cart3D, co-winner of NASA's 2002 Software of the Year award, is the result of over 10 years of research and software development conducted by Michael Aftosmis and Dr. John Melton of Ames Research Center and Professor Marsha Berger of the Courant Institute at New York University. Cart3D offers a revolutionary approach to computational fluid dynamics (CFD), the computer simulation of how fluids and gases flow around an object of a particular design. By fusing technological advancements in diverse fields such as mineralogy, computer graphics, computational geometry, and fluid dynamics, the software provides a new industrial geometry processing and fluid analysis capability with unsurpassed automation and efficiency.

Trends in Programming Languages for Neuroscience Simulations

PubMed Central

Davison, Andrew P.; Hines, Michael L.; Muller, Eilif

2009-01-01

Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing. PMID:20198154

Trends in programming languages for neuroscience simulations.

PubMed

Davison, Andrew P; Hines, Michael L; Muller, Eilif

2009-01-01

Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing.

Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear Layer

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Singer, Bart A.; Berkman, Mert E.

2001-01-01

A detailed computational aeroacoustic analysis of a high-lift flow field is performed. Time-accurate Reynolds Averaged Navier-Stokes (RANS) computations simulate the free shear layer that originates from the slat cusp. Both unforced and forced cases are studied. Preliminary results show that the shear layer is a good amplifier of disturbances in the low to mid-frequency range. The Ffowcs-Williams and Hawkings equation is solved to determine the acoustic field using the unsteady flow data from the RANS calculations. The noise radiated from the excited shear layer has a spectral shape qualitatively similar to that obtained from measurements in a corresponding experimental study of the high-lift system.

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

NASA Technical Reports Server (NTRS)

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

1977-01-01

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

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

2009-03-14

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.; Knepley, Matthew G.; Anitescu, Mihai

2009-03-01

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Sonic Boom Computations for a Mach 1.6 Cruise Low Boom Configuration and Comparisons with Wind Tunnel Data

NASA Technical Reports Server (NTRS)

Elmiligui, Alaa A.; Cliff, Susan E.; Wilcox, Floyd; Nemec, Marian; Bangert, Linda; Aftosmis, Michael J.; Parlette, Edward

2011-01-01

Accurate analysis of sonic boom pressure signatures using computational fluid dynamics techniques remains quite challenging. Although CFD shows accurate predictions of flow around complex configurations, generating grids that can resolve the sonic boom signature far away from the body is a challenge. The test case chosen for this study corresponds to an experimental wind-tunnel test that was conducted to measure the sonic boom pressure signature of a low boom configuration designed by Gulfstream Aerospace Corporation. Two widely used NASA codes, USM3D and AERO, are examined for their ability to accurately capture sonic boom signature. Numerical simulations are conducted for a free-stream Mach number of 1.6, angle of attack of 0.3 and Reynolds number of 3.85x10(exp 6) based on model reference length. Flow around the low boom configuration in free air and inside the Langley Unitary plan wind tunnel are computed. Results from the numerical simulations are compared with wind tunnel data. The effects of viscous and turbulence modeling along with tunnel walls on the computed sonic boom signature are presented and discussed.

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...

Do dichromats see colours in this way? Assessing simulation tools without colorimetric measurements.

PubMed

Lillo Jover, Julio A; Álvaro Llorente, Leticia; Moreira Villegas, Humberto; Melnikova, Anna

2016-11-01

Simulcheck evaluates Colour Simulation Tools (CSTs, they transform colours to mimic those seen by colour vision deficients). Two CSTs (Variantor and Coblis) were used to know if the standard Simulcheck version (direct measurement based, DMB) can be substituted by another (RGB values based) not requiring sophisticated measurement instruments. Ten normal trichromats performed the two psychophysical tasks included in the Simulcheck method. The Pseudoachromatic Stimuli Identification task provided the h uv (hue angle) values of the pseudoachromatic stimuli: colours seen as red or green by normal trichromats but as grey by colour deficient people. The Minimum Achromatic Contrast task was used to compute the L R (relative luminance) values of the pseudoachromatic stimuli. Simulcheck DMB version showed that Variantor was accurate to simulate protanopia but neither Variantor nor Coblis were accurate to simulate deuteranopia. Simulcheck RGB version provided accurate h uv values, so this variable can be adequately estimated when lacking a colorimeter —an expensive and unusual apparatus—. Contrary, the inaccuracy of the L R estimations provided by Simulcheck RGB version makes it advisable to compute this variable from the measurements performed with a photometer, a cheap and easy to find apparatus.

High-resolution subject-specific mitral valve imaging and modeling: experimental and computational methods.

PubMed

Toma, Milan; Bloodworth, Charles H; Einstein, Daniel R; Pierce, Eric L; Cochran, Richard P; Yoganathan, Ajit P; Kunzelman, Karyn S

2016-12-01

The diversity of mitral valve (MV) geometries and multitude of surgical options for correction of MV diseases necessitates the use of computational modeling. Numerical simulations of the MV would allow surgeons and engineers to evaluate repairs, devices, procedures, and concepts before performing them and before moving on to more costly testing modalities. Constructing, tuning, and validating these models rely upon extensive in vitro characterization of valve structure, function, and response to change due to diseases. Micro-computed tomography ([Formula: see text]CT) allows for unmatched spatial resolution for soft tissue imaging. However, it is still technically challenging to obtain an accurate geometry of the diastolic MV. We discuss here the development of a novel technique for treating MV specimens with glutaraldehyde fixative in order to minimize geometric distortions in preparation for [Formula: see text]CT scanning. The technique provides a resulting MV geometry which is significantly more detailed in chordal structure, accurate in leaflet shape, and closer to its physiological diastolic geometry. In this paper, computational fluid-structure interaction (FSI) simulations are used to show the importance of more detailed subject-specific MV geometry with 3D chordal structure to simulate a proper closure validated against [Formula: see text]CT images of the closed valve. Two computational models, before and after use of the aforementioned technique, are used to simulate closure of the MV.

Third-order accurate conservative method on unstructured meshes for gasdynamic simulations

NASA Astrophysics Data System (ADS)

Shirobokov, D. A.

2017-04-01

A third-order accurate finite-volume method on unstructured meshes is proposed for solving viscous gasdynamic problems. The method is described as applied to the advection equation. The accuracy of the method is verified by computing the evolution of a vortex on meshes of various degrees of detail with variously shaped cells. Additionally, unsteady flows around a cylinder and a symmetric airfoil are computed. The numerical results are presented in the form of plots and tables.

Autonomic Closure for Turbulent Flows Using Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Doronina, Olga; Christopher, Jason; Hamlington, Peter; Dahm, Werner

2017-11-01

Autonomic closure is a new technique for achieving fully adaptive and physically accurate closure of coarse-grained turbulent flow governing equations, such as those solved in large eddy simulations (LES). Although autonomic closure has been shown in recent a priori tests to more accurately represent unclosed terms than do dynamic versions of traditional LES models, the computational cost of the approach makes it challenging to implement for simulations of practical turbulent flows at realistically high Reynolds numbers. The optimization step used in the approach introduces large matrices that must be inverted and is highly memory intensive. In order to reduce memory requirements, here we propose to use approximate Bayesian computation (ABC) in place of the optimization step, thereby yielding a computationally-efficient implementation of autonomic closure that trades memory-intensive for processor-intensive computations. The latter challenge can be overcome as co-processors such as general purpose graphical processing units become increasingly available on current generation petascale and exascale supercomputers. In this work, we outline the formulation of ABC-enabled autonomic closure and present initial results demonstrating the accuracy and computational cost of the approach.

A brief overview of computational structures technology related activities at NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Hopkins, Dale A.

1992-01-01

The presentation gives a partial overview of research and development underway in the Structures Division of LeRC, which collectively is referred to as the Computational Structures Technology Program. The activities in the program are diverse and encompass four major categories: (1) composite materials and structures; (2) probabilistic analysis and reliability; (3) design optimization and expert systems; and (4) computational methods and simulation. The approach of the program is comprehensive and entails exploration of fundamental theories of structural mechanics to accurately represent the complex physics governing engine structural performance, formulation, and implementation of computational techniques and integrated simulation strategies to provide accurate and efficient solutions of the governing theoretical models by exploiting the emerging advances in computer technology, and validation and verification through numerical and experimental tests to establish confidence and define the qualities and limitations of the resulting theoretical models and computational solutions. The program comprises both in-house and sponsored research activities. The remainder of the presentation provides a sample of activities to illustrate the breadth and depth of the program and to demonstrate the accomplishments and benefits that have resulted.

Toward high-speed 3D nonlinear soft tissue deformation simulations using Abaqus software.

PubMed

Idkaidek, Ashraf; Jasiuk, Iwona

2015-12-01

We aim to achieve a fast and accurate three-dimensional (3D) simulation of a porcine liver deformation under a surgical tool pressure using the commercial finite element software Abaqus. The liver geometry is obtained using magnetic resonance imaging, and a nonlinear constitutive law is employed to capture large deformations of the tissue. Effects of implicit versus explicit analysis schemes, element type, and mesh density on computation time are studied. We find that Abaqus explicit and implicit solvers are capable of simulating nonlinear soft tissue deformations accurately using first-order tetrahedral elements in a relatively short time by optimizing the element size. This study provides new insights and guidance on accurate and relatively fast nonlinear soft tissue simulations. Such simulations can provide force feedback during robotic surgery and allow visualization of tissue deformations for surgery planning and training of surgical residents.

Procedure for Adapting Direct Simulation Monte Carlo Meshes

NASA Technical Reports Server (NTRS)

Woronowicz, Michael S.; Wilmoth, Richard G.; Carlson, Ann B.; Rault, Didier F. G.

1992-01-01

A technique is presented for adapting computational meshes used in the G2 version of the direct simulation Monte Carlo method. The physical ideas underlying the technique are discussed, and adaptation formulas are developed for use on solutions generated from an initial mesh. The effect of statistical scatter on adaptation is addressed, and results demonstrate the ability of this technique to achieve more accurate results without increasing necessary computational resources.

Comparability of Examinee Proficiency Scores on Computer Adaptive Tests Using Real and Simulated Data

ERIC Educational Resources Information Center

Evans, Josiah Jeremiah

2010-01-01

In measurement research, data simulations are a commonly used analytical technique. While simulation designs have many benefits, it is unclear if these artificially generated datasets are able to accurately capture real examinee item response behaviors. This potential lack of comparability may have important implications for administration of…

A new lumped-parameter model for flow in unsaturated dual-porosity media

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

Zimmerman, Robert W.; Hadgu, Teklu; Bodvarsson, Gudmundur S.

A new lumped-parameter approach to simulating unsaturated flow processes in dual-porosity media such as fractured rocks or aggregated soils is presented. Fluid flow between the fracture network and the matrix blocks is described by a non-linear equation that relates the imbibition rate to the local difference in liquid-phase pressure between the fractures and the matrix blocks. Unlike a Warren-Root-type equation, this equation is accurate in both the early and late time regimes. The fracture/matrix interflow equation has been incorporated into an existing unsaturated flow simulator, to serve as a source/sink term for fracture gridblocks. Flow processes are then simulated usingmore » only fracture gridblocks in the computational grid. This new lumped-parameter approach has been tested on two problems involving transient flow in fractured/porous media, and compared with simulations performed using explicit discretization of the matrix blocks. The new procedure seems to accurately simulate flow processes in unsaturated fractured rocks, and typically requires an order of magnitude less computational time than do simulations using fully-discretized matrix blocks. [References: 37]« less

Accurate Bit Error Rate Calculation for Asynchronous Chaos-Based DS-CDMA over Multipath Channel

NASA Astrophysics Data System (ADS)

Kaddoum, Georges; Roviras, Daniel; Chargé, Pascal; Fournier-Prunaret, Daniele

2009-12-01

An accurate approach to compute the bit error rate expression for multiuser chaosbased DS-CDMA system is presented in this paper. For more realistic communication system a slow fading multipath channel is considered. A simple RAKE receiver structure is considered. Based on the bit energy distribution, this approach compared to others computation methods existing in literature gives accurate results with low computation charge. Perfect estimation of the channel coefficients with the associated delays and chaos synchronization is assumed. The bit error rate is derived in terms of the bit energy distribution, the number of paths, the noise variance, and the number of users. Results are illustrated by theoretical calculations and numerical simulations which point out the accuracy of our approach.

A time accurate prediction of the viscous flow in a turbine stage including a rotor in motion

NASA Astrophysics Data System (ADS)

Shavalikul, Akamol

In this current study, the flow field in the Pennsylvania State University Axial Flow Turbine Research Facility (AFTRF) was simulated. This study examined four sets of simulations. The first two sets are for an individual NGV and for an individual rotor. The last two sets use a multiple reference frames approach for a complete turbine stage with two different interface models: a steady circumferential average approach called a mixing plane model, and a time accurate flow simulation approach called a sliding mesh model. The NGV passage flow field was simulated using a three-dimensional Reynolds Averaged Navier-Stokes finite volume solver (RANS) with a standard kappa -- epsilon turbulence model. The mean flow distributions on the NGV surfaces and endwall surfaces were computed. The numerical solutions indicate that two passage vortices begin to be observed approximately at the mid axial chord of the NGV suction surface. The first vortex is a casing passage vortex which occurs at the corner formed by the NGV suction surface and the casing. This vortex is created by the interaction of the passage flow and the radially inward flow, while the second vortex, the hub passage vortex, is observed near the hub. These two vortices become stronger towards the NGV trailing edge. By comparing the results from the X/Cx = 1.025 plane and the X/Cx = 1.09 plane, it can be concluded that the NGV wake decays rapidly within a short axial distance downstream of the NGV. For the rotor, a set of simulations was carried out to examine the flow fields associated with different pressure side tip extension configurations, which are designed to reduce the tip leakage flow. The simulation results show that significant reductions in tip leakage mass flow rate and aerodynamic loss reduction are possible by using suitable tip platform extensions located near the pressure side corner of the blade tip. The computations used realistic turbine rotor inlet flow conditions in a linear cascade arrangement in the relative frame of reference; the boundary conditions for the computations were obtained from inlet flow measurements performed in the AFTRF. A complete turbine stage, including an NGV and a rotor row was simulated using the RANS solver with the SST kappa -- o turbulence model, with two different computational models for the interface between the rotating component and the stationary component. The first interface model, the circumferentially averaged mixing plane model, was solved for a fixed position of the rotor blades relative to the NGV in the stationary frame of reference. The information transferred between the NGV and rotor domains is obtained by averaging across the entire interface. The quasi-steady state flow characteristics of the AFTRF can be obtained from this interface model. After the model was validated with the existing experimental data, this model was not only used to investigate the flow characteristics in the turbine stage but also the effects of using pressure side rotor tip extensions. The tip leakage flow fields simulated from this model and from the linear cascade model show similar trends. More detailed understanding of unsteady characteristics of a turbine flow field can be obtained using the second type of interface model, the time accurate sliding mesh model. The potential flow interactions, wake characteristics, their effects on secondary flow formation, and the wake mixing process in a rotor passage were examined using this model. Furthermore, turbine stage efficiency and effects of tip clearance height on the turbine stage efficiency were also investigated. A comparison between the results from the circumferential average model and the time accurate flow model results is presented. It was found that the circumferential average model cannot accurately simulate flow interaction characteristics on the interface plane between the NGV trailing edge and the rotor leading edge. However, the circumferential average model does give accurate flow characteristics in the NGV domain and the rotor domain with less computational time and computer memory requirements. In contrast, the time accurate flow simulation can predict all unsteady flow characteristics occurring in the turbine stage, but with high computational resource requirements. (Abstract shortened by UMI.)

Automated Development of Accurate Algorithms and Efficient Codes for Computational Aeroacoustics

NASA Technical Reports Server (NTRS)

Goodrich, John W.; Dyson, Rodger W.

1999-01-01

The simulation of sound generation and propagation in three space dimensions with realistic aircraft components is a very large time dependent computation with fine details. Simulations in open domains with embedded objects require accurate and robust algorithms for propagation, for artificial inflow and outflow boundaries, and for the definition of geometrically complex objects. The development, implementation, and validation of methods for solving these demanding problems is being done to support the NASA pillar goals for reducing aircraft noise levels. Our goal is to provide algorithms which are sufficiently accurate and efficient to produce usable results rapidly enough to allow design engineers to study the effects on sound levels of design changes in propulsion systems, and in the integration of propulsion systems with airframes. There is a lack of design tools for these purposes at this time. Our technical approach to this problem combines the development of new, algorithms with the use of Mathematica and Unix utilities to automate the algorithm development, code implementation, and validation. We use explicit methods to ensure effective implementation by domain decomposition for SPMD parallel computing. There are several orders of magnitude difference in the computational efficiencies of the algorithms which we have considered. We currently have new artificial inflow and outflow boundary conditions that are stable, accurate, and unobtrusive, with implementations that match the accuracy and efficiency of the propagation methods. The artificial numerical boundary treatments have been proven to have solutions which converge to the full open domain problems, so that the error from the boundary treatments can be driven as low as is required. The purpose of this paper is to briefly present a method for developing highly accurate algorithms for computational aeroacoustics, the use of computer automation in this process, and a brief survey of the algorithms that have resulted from this work. A review of computational aeroacoustics has recently been given by Lele.

Probabilistic techniques for obtaining accurate patient counts in Clinical Data Warehouses

PubMed Central

Myers, Risa B.; Herskovic, Jorge R.

2011-01-01

Proposal and execution of clinical trials, computation of quality measures and discovery of correlation between medical phenomena are all applications where an accurate count of patients is needed. However, existing sources of this type of patient information, including Clinical Data Warehouses (CDW) may be incomplete or inaccurate. This research explores applying probabilistic techniques, supported by the MayBMS probabilistic database, to obtain accurate patient counts from a clinical data warehouse containing synthetic patient data. We present a synthetic clinical data warehouse (CDW), and populate it with simulated data using a custom patient data generation engine. We then implement, evaluate and compare different techniques for obtaining patients counts. We model billing as a test for the presence of a condition. We compute billing’s sensitivity and specificity both by conducting a “Simulated Expert Review” where a representative sample of records are reviewed and labeled by experts, and by obtaining the ground truth for every record. We compute the posterior probability of a patient having a condition through a “Bayesian Chain”, using Bayes’ Theorem to calculate the probability of a patient having a condition after each visit. The second method is a “one-shot” approach that computes the probability of a patient having a condition based on whether the patient is ever billed for the condition Our results demonstrate the utility of probabilistic approaches, which improve on the accuracy of raw counts. In particular, the simulated review paired with a single application of Bayes’ Theorem produces the best results, with an average error rate of 2.1% compared to 43.7% for the straightforward billing counts. Overall, this research demonstrates that Bayesian probabilistic approaches improve patient counts on simulated patient populations. We believe that total patient counts based on billing data are one of the many possible applications of our Bayesian framework. Use of these probabilistic techniques will enable more accurate patient counts and better results for applications requiring this metric. PMID:21986292

Physically Based Modeling and Simulation with Dynamic Spherical Volumetric Simplex Splines

PubMed Central

Tan, Yunhao; Hua, Jing; Qin, Hong

2009-01-01

In this paper, we present a novel computational modeling and simulation framework based on dynamic spherical volumetric simplex splines. The framework can handle the modeling and simulation of genus-zero objects with real physical properties. In this framework, we first develop an accurate and efficient algorithm to reconstruct the high-fidelity digital model of a real-world object with spherical volumetric simplex splines which can represent with accuracy geometric, material, and other properties of the object simultaneously. With the tight coupling of Lagrangian mechanics, the dynamic volumetric simplex splines representing the object can accurately simulate its physical behavior because it can unify the geometric and material properties in the simulation. The visualization can be directly computed from the object’s geometric or physical representation based on the dynamic spherical volumetric simplex splines during simulation without interpolation or resampling. We have applied the framework for biomechanic simulation of brain deformations, such as brain shifting during the surgery and brain injury under blunt impact. We have compared our simulation results with the ground truth obtained through intra-operative magnetic resonance imaging and the real biomechanic experiments. The evaluations demonstrate the excellent performance of our new technique. PMID:20161636

Real-time haptic cutting of high-resolution soft tissues.

PubMed

Wu, Jun; Westermann, Rüdiger; Dick, Christian

2014-01-01

We present our systematic efforts in advancing the computational performance of physically accurate soft tissue cutting simulation, which is at the core of surgery simulators in general. We demonstrate a real-time performance of 15 simulation frames per second for haptic soft tissue cutting of a deformable body at an effective resolution of 170,000 finite elements. This is achieved by the following innovative components: (1) a linked octree discretization of the deformable body, which allows for fast and robust topological modifications of the simulation domain, (2) a composite finite element formulation, which thoroughly reduces the number of simulation degrees of freedom and thus enables to carefully balance simulation performance and accuracy, (3) a highly efficient geometric multigrid solver for solving the linear systems of equations arising from implicit time integration, (4) an efficient collision detection algorithm that effectively exploits the composition structure, and (5) a stable haptic rendering algorithm for computing the feedback forces. Considering that our method increases the finite element resolution for physically accurate real-time soft tissue cutting simulation by an order of magnitude, our technique has a high potential to significantly advance the realism of surgery simulators.

Learning a force field for the martensitic phase transformation in Zr

NASA Astrophysics Data System (ADS)

Zong, Hongxiang; Pilania, Ghanshyam; Ramprasad, Rampi; Lookman, Turab

Atomic simulations provide an effective means to understand the underlying physics of martensitic transformations under extreme conditions. However, this is still a challenge for certain phase transforming metals due to the lack of an accurate classical force field. Quantum molecular dynamics (QMD) simulations are accurate but expensive. During the course of QMD simulations, similar configurations are constantly visited and revisited. Machine Learning can effectively learn from past visits and, therefore, eliminate such redundancies. In this talk, we will discuss the development of a hybrid ML-QMD method in which on-demand, on-the-fly quantum mechanical (QM) calculations are performed to accelerate calculations of interatomic forces at much lower computational costs. Using Zirconium as a model system for which accurate atomisctic potentials are currently unvailable we will demonstrate the feasibility and effectiveness of our approach. Specifically, the computed structural phase transformation behavior within the ML-QMD approach will be compared with available experimental results. Furthermore, results on phonons, stacking fault energies, and activation barriers for the homogeneous martensitic transformation in Zr will be presented.

Subgrid or Reynolds stress-modeling for three-dimensional turbulence computations

NASA Technical Reports Server (NTRS)

Rubesin, M. W.

1975-01-01

A review is given of recent advances in two distinct computational methods for evaluating turbulence fields, namely, statistical Reynolds stress modeling and turbulence simulation, where large eddies are followed in time. It is shown that evaluation of the mean Reynolds stresses, rather than use of a scalar eddy viscosity, permits an explanation of streamline curvature effects found in several experiments. Turbulence simulation, with a new volume averaging technique and third-order accurate finite-difference computing is shown to predict the decay of isotropic turbulence in incompressible flow with rather modest computer storage requirements, even at Reynolds numbers of aerodynamic interest.

Parallel Simulation of Unsteady Turbulent Flames

NASA Technical Reports Server (NTRS)

Menon, Suresh

1996-01-01

Time-accurate simulation of turbulent flames in high Reynolds number flows is a challenging task since both fluid dynamics and combustion must be modeled accurately. To numerically simulate this phenomenon, very large computer resources (both time and memory) are required. Although current vector supercomputers are capable of providing adequate resources for simulations of this nature, the high cost and their limited availability, makes practical use of such machines less than satisfactory. At the same time, the explicit time integration algorithms used in unsteady flow simulations often possess a very high degree of parallelism, making them very amenable to efficient implementation on large-scale parallel computers. Under these circumstances, distributed memory parallel computers offer an excellent near-term solution for greatly increased computational speed and memory, at a cost that may render the unsteady simulations of the type discussed above more feasible and affordable.This paper discusses the study of unsteady turbulent flames using a simulation algorithm that is capable of retaining high parallel efficiency on distributed memory parallel architectures. Numerical studies are carried out using large-eddy simulation (LES). In LES, the scales larger than the grid are computed using a time- and space-accurate scheme, while the unresolved small scales are modeled using eddy viscosity based subgrid models. This is acceptable for the moment/energy closure since the small scales primarily provide a dissipative mechanism for the energy transferred from the large scales. However, for combustion to occur, the species must first undergo mixing at the small scales and then come into molecular contact. Therefore, global models cannot be used. Recently, a new model for turbulent combustion was developed, in which the combustion is modeled, within the subgrid (small-scales) using a methodology that simulates the mixing and the molecular transport and the chemical kinetics within each LES grid cell. Finite-rate kinetics can be included without any closure and this approach actually provides a means to predict the turbulent rates and the turbulent flame speed. The subgrid combustion model requires resolution of the local time scales associated with small-scale mixing, molecular diffusion and chemical kinetics and, therefore, within each grid cell, a significant amount of computations must be carried out before the large-scale (LES resolved) effects are incorporated. Therefore, this approach is uniquely suited for parallel processing and has been implemented on various systems such as: Intel Paragon, IBM SP-2, Cray T3D and SGI Power Challenge (PC) using the system independent Message Passing Interface (MPI) compiler. In this paper, timing data on these machines is reported along with some characteristic results.

Application of shell elements in simulation of cans ironing

NASA Astrophysics Data System (ADS)

Andrianov, A. V.; Erisov, Y. A.; Aryshensky, E. V.; Aryshensky, V. Y.

2017-01-01

In the present study, the special shell finite elements are used to simulate the drawing with high ironing ratio of aluminum beverage cans. These elements are implemented in commercial software complex PAM-STAMP 2G by means of T.T.S. normal stress option, which is used for ironing to describe well normal stress. By comparison of simulation and experimental data, it is shown that shell elements with T.T.S. option are capable to provide accurate simulation of deep drawing and ironing. The error of can thickness and height computation agrees with the engineering computation accuracy.

Computer simulation comparison of tripolar, bipolar, and spline Laplacian electrocadiogram estimators.

PubMed

Chen, T; Besio, W; Dai, W

2009-01-01

A comparison of the performance of the tripolar and bipolar concentric as well as spline Laplacian electrocardiograms (LECGs) and body surface Laplacian mappings (BSLMs) for localizing and imaging the cardiac electrical activation has been investigated based on computer simulation. In the simulation a simplified eccentric heart-torso sphere-cylinder homogeneous volume conductor model were developed. Multiple dipoles with different orientations were used to simulate the underlying cardiac electrical activities. Results show that the tripolar concentric ring electrodes produce the most accurate LECG and BSLM estimation among the three estimators with the best performance in spatial resolution.

The impact of 14nm photomask variability and uncertainty on computational lithography solutions

NASA Astrophysics Data System (ADS)

Sturtevant, John; Tejnil, Edita; Buck, Peter D.; Schulze, Steffen; Kalk, Franklin; Nakagawa, Kent; Ning, Guoxiang; Ackmann, Paul; Gans, Fritz; Buergel, Christian

2013-09-01

Computational lithography solutions rely upon accurate process models to faithfully represent the imaging system output for a defined set of process and design inputs. These models rely upon the accurate representation of multiple parameters associated with the scanner and the photomask. Many input variables for simulation are based upon designed or recipe-requested values or independent measurements. It is known, however, that certain measurement methodologies, while precise, can have significant inaccuracies. Additionally, there are known errors associated with the representation of certain system parameters. With shrinking total CD control budgets, appropriate accounting for all sources of error becomes more important, and the cumulative consequence of input errors to the computational lithography model can become significant. In this work, we examine via simulation, the impact of errors in the representation of photomask properties including CD bias, corner rounding, refractive index, thickness, and sidewall angle. The factors that are most critical to be accurately represented in the model are cataloged. CD bias values are based on state of the art mask manufacturing data and other variables changes are speculated, highlighting the need for improved metrology and communication between mask and OPC model experts. The simulations are done by ignoring the wafer photoresist model, and show the sensitivity of predictions to various model inputs associated with the mask. It is shown that the wafer simulations are very dependent upon the 1D/2D representation of the mask and for 3D, that the mask sidewall angle is a very sensitive factor influencing simulated wafer CD results.

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.

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.

Computational Fluid Dynamics Demonstration of Rigid Bodies in Motion

NASA Technical Reports Server (NTRS)

Camarena, Ernesto; Vu, Bruce T.

2011-01-01

The Design Analysis Branch (NE-Ml) at the Kennedy Space Center has not had the ability to accurately couple Rigid Body Dynamics (RBD) and Computational Fluid Dynamics (CFD). OVERFLOW-D is a flow solver that has been developed by NASA to have the capability to analyze and simulate dynamic motions with up to six Degrees of Freedom (6-DOF). Two simulations were prepared over the course of the internship to demonstrate 6DOF motion of rigid bodies under aerodynamic loading. The geometries in the simulations were based on a conceptual Space Launch System (SLS). The first simulation that was prepared and computed was the motion of a Solid Rocket Booster (SRB) as it separates from its core stage. To reduce computational time during the development of the simulation, only half of the physical domain with respect to the symmetry plane was simulated. Then a full solution was prepared and computed. The second simulation was a model of the SLS as it departs from a launch pad under a 20 knot crosswind. This simulation was reduced to Two Dimensions (2D) to reduce both preparation and computation time. By allowing 2-DOF for translations and 1-DOF for rotation, the simulation predicted unrealistic rotation. The simulation was then constrained to only allow translations.

Computational algorithms for simulations in atmospheric optics.

PubMed

Konyaev, P A; Lukin, V P

2016-04-20

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

[The characteristics of computer simulation of traffic accidents].

PubMed

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

2008-12-01

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

A Machine LearningFramework to Forecast Wave Conditions

NASA Astrophysics Data System (ADS)

Zhang, Y.; James, S. C.; O'Donncha, F.

2017-12-01

Recently, significant effort has been undertaken to quantify and extract wave energy because it is renewable, environmental friendly, abundant, and often close to population centers. However, a major challenge is the ability to accurately and quickly predict energy production, especially across a 48-hour cycle. Accurate forecasting of wave conditions is a challenging undertaking that typically involves solving the spectral action-balance equation on a discretized grid with high spatial resolution. The nature of the computations typically demands high-performance computing infrastructure. Using a case-study site at Monterey Bay, California, a machine learning framework was trained to replicate numerically simulated wave conditions at a fraction of the typical computational cost. Specifically, the physics-based Simulating WAves Nearshore (SWAN) model, driven by measured wave conditions, nowcast ocean currents, and wind data, was used to generate training data for machine learning algorithms. The model was run between April 1st, 2013 and May 31st, 2017 generating forecasts at three-hour intervals yielding 11,078 distinct model outputs. SWAN-generated fields of 3,104 wave heights and a characteristic period could be replicated through simple matrix multiplications using the mapping matrices from machine learning algorithms. In fact, wave-height RMSEs from the machine learning algorithms (9 cm) were less than those for the SWAN model-verification exercise where those simulations were compared to buoy wave data within the model domain (>40 cm). The validated machine learning approach, which acts as an accurate surrogate for the SWAN model, can now be used to perform real-time forecasts of wave conditions for the next 48 hours using available forecasted boundary wave conditions, ocean currents, and winds. This solution has obvious applications to wave-energy generation as accurate wave conditions can be forecasted with over a three-order-of-magnitude reduction in computational expense. The low computational cost (and by association low computer-power requirement) means that the machine learning algorithms could be installed on a wave-energy converter as a form of "edge computing" where a device could forecast its own 48-hour energy production.

Hyperbolic heat conduction problems involving non-Fourier effects - Numerical simulations via explicit Lax-Wendroff/Taylor-Galerkin finite element formulations

NASA Technical Reports Server (NTRS)

Tamma, Kumar K.; Namburu, Raju R.

1989-01-01

Numerical simulations are presented for hyperbolic heat-conduction problems that involve non-Fourier effects, using explicit, Lax-Wendroff/Taylor-Galerkin FEM formulations as the principal computational tool. Also employed are smoothing techniques which stabilize the numerical noise and accurately predict the propagating thermal disturbances. The accurate capture of propagating thermal disturbances at characteristic time-step values is achieved; numerical test cases are presented which validate the proposed hyperbolic heat-conduction problem concepts.

Unsteady Full Annulus Simulations of a Transonic Axial Compressor Stage

NASA Technical Reports Server (NTRS)

Herrick, Gregory P.; Hathaway, Michael D.; Chen, Jen-Ping

2009-01-01

Two recent research endeavors in turbomachinery at NASA Glenn Research Center have focused on compression system stall inception and compression system aerothermodynamic performance. Physical experiment and computational research are ongoing in support of these research objectives. TURBO, an unsteady, three-dimensional, Navier-Stokes computational fluid dynamics code commissioned and developed by NASA, has been utilized, enhanced, and validated in support of these endeavors. In the research which follows, TURBO is shown to accurately capture compression system flow range-from choke to stall inception-and also to accurately calculate fundamental aerothermodynamic performance parameters. Rigorous full-annulus calculations are performed to validate TURBO s ability to simulate the unstable, unsteady, chaotic stall inception process; as part of these efforts, full-annulus calculations are also performed at a condition approaching choke to further document TURBO s capabilities to compute aerothermodynamic performance data and support a NASA code assessment effort.

TSaT-MUSIC: a novel algorithm for rapid and accurate ultrasonic 3D localization

NASA Astrophysics Data System (ADS)

Mizutani, Kyohei; Ito, Toshio; Sugimoto, Masanori; Hashizume, Hiromichi

2011-12-01

We describe a fast and accurate indoor localization technique using the multiple signal classification (MUSIC) algorithm. The MUSIC algorithm is known as a high-resolution method for estimating directions of arrival (DOAs) or propagation delays. A critical problem in using the MUSIC algorithm for localization is its computational complexity. Therefore, we devised a novel algorithm called Time Space additional Temporal-MUSIC, which can rapidly and simultaneously identify DOAs and delays of mul-ticarrier ultrasonic waves from transmitters. Computer simulations have proved that the computation time of the proposed algorithm is almost constant in spite of increasing numbers of incoming waves and is faster than that of existing methods based on the MUSIC algorithm. The robustness of the proposed algorithm is discussed through simulations. Experiments in real environments showed that the standard deviation of position estimations in 3D space is less than 10 mm, which is satisfactory for indoor localization.

Multivariable extrapolation of grand canonical free energy landscapes

NASA Astrophysics Data System (ADS)

Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.

2017-12-01

We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat-histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is accomplished by expanding the landscape in a Taylor series at each value of the order parameter which defines its macrostate phase space. The coefficients in each Taylor polynomial are known exactly from fluctuation formulas, which may be computed by measuring the appropriate moments of extensive variables that fluctuate in this ensemble. Here we derive the expressions necessary to define these coefficients up to arbitrary order. In principle, this enables a single flat-histogram simulation to provide complete thermodynamic information over a broad range of temperatures and chemical potentials. Using this, we also show how to combine a small number of simulations, each performed at different conditions, in a thermodynamically consistent fashion to accurately compute properties at arbitrary temperatures and chemical potentials. This method may significantly increase the computational efficiency of biased grand canonical Monte Carlo simulations, especially for multicomponent mixtures. Although approximate, this approach is amenable to high-throughput and data-intensive investigations where it is preferable to have a large quantity of reasonably accurate simulation data, rather than a smaller amount with a higher accuracy.

Computational simulation of laser heat processing of materials

NASA Astrophysics Data System (ADS)

Shankar, Vijaya; Gnanamuthu, Daniel

1987-04-01

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

Proton Upset Monte Carlo Simulation

NASA Technical Reports Server (NTRS)

O'Neill, Patrick M.; Kouba, Coy K.; Foster, Charles C.

2009-01-01

The Proton Upset Monte Carlo Simulation (PROPSET) program calculates the frequency of on-orbit upsets in computer chips (for given orbits such as Low Earth Orbit, Lunar Orbit, and the like) from proton bombardment based on the results of heavy ion testing alone. The software simulates the bombardment of modern microelectronic components (computer chips) with high-energy (.200 MeV) protons. The nuclear interaction of the proton with the silicon of the chip is modeled and nuclear fragments from this interaction are tracked using Monte Carlo techniques to produce statistically accurate predictions.

Flight code validation simulator

NASA Astrophysics Data System (ADS)

Sims, Brent A.

1996-05-01

An End-To-End Simulation capability for software development and validation of missile flight software on the actual embedded computer has been developed utilizing a 486 PC, i860 DSP coprocessor, embedded flight computer and custom dual port memory interface hardware. This system allows real-time interrupt driven embedded flight software development and checkout. The flight software runs in a Sandia Digital Airborne Computer and reads and writes actual hardware sensor locations in which Inertial Measurement Unit data resides. The simulator provides six degree of freedom real-time dynamic simulation, accurate real-time discrete sensor data and acts on commands and discretes from the flight computer. This system was utilized in the development and validation of the successful premier flight of the Digital Miniature Attitude Reference System in January of 1995 at the White Sands Missile Range on a two stage attitude controlled sounding rocket.

A physical-based gas-surface interaction model for rarefied gas flow simulation

NASA Astrophysics Data System (ADS)

Liang, Tengfei; Li, Qi; Ye, Wenjing

2018-01-01

Empirical gas-surface interaction models, such as the Maxwell model and the Cercignani-Lampis model, are widely used as the boundary condition in rarefied gas flow simulations. The accuracy of these models in the prediction of macroscopic behavior of rarefied gas flows is less satisfactory in some cases especially the highly non-equilibrium ones. Molecular dynamics simulation can accurately resolve the gas-surface interaction process at atomic scale, and hence can predict accurate macroscopic behavior. They are however too computationally expensive to be applied in real problems. In this work, a statistical physical-based gas-surface interaction model, which complies with the basic relations of boundary condition, is developed based on the framework of the washboard model. In virtue of its physical basis, this new model is capable of capturing some important relations/trends for which the classic empirical models fail to model correctly. As such, the new model is much more accurate than the classic models, and in the meantime is more efficient than MD simulations. Therefore, it can serve as a more accurate and efficient boundary condition for rarefied gas flow simulations.

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

Walker, Andrew; Lawrence, Earl

The Response Surface Modeling (RSM) Tool Suite is a collection of three codes used to generate an empirical interpolation function for a collection of drag coefficient calculations computed with Test Particle Monte Carlo (TPMC) simulations. The first code, "Automated RSM", automates the generation of a drag coefficient RSM for a particular object to a single command. "Automated RSM" first creates a Latin Hypercube Sample (LHS) of 1,000 ensemble members to explore the global parameter space. For each ensemble member, a TPMC simulation is performed and the object drag coefficient is computed. In the next step of the "Automated RSM" code,more » a Gaussian process is used to fit the TPMC simulations. In the final step, Markov Chain Monte Carlo (MCMC) is used to evaluate the non-analytic probability distribution function from the Gaussian process. The second code, "RSM Area", creates a look-up table for the projected area of the object based on input limits on the minimum and maximum allowed pitch and yaw angles and pitch and yaw angle intervals. The projected area from the look-up table is used to compute the ballistic coefficient of the object based on its pitch and yaw angle. An accurate ballistic coefficient is crucial in accurately computing the drag on an object. The third code, "RSM Cd", uses the RSM generated by the "Automated RSM" code and the projected area look-up table generated by the "RSM Area" code to accurately compute the drag coefficient and ballistic coefficient of the object. The user can modify the object velocity, object surface temperature, the translational temperature of the gas, the species concentrations of the gas, and the pitch and yaw angles of the object. Together, these codes allow for the accurate derivation of an object's drag coefficient and ballistic coefficient under any conditions with only knowledge of the object's geometry and mass.« less

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

PubMed

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

2016-04-01

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

Influence of Contact Angle Boundary Condition on CFD Simulation of T-Junction

NASA Astrophysics Data System (ADS)

Arias, S.; Montlaur, A.

2018-03-01

In this work, we study the influence of the contact angle boundary condition on 3D CFD simulations of the bubble generation process occurring in a capillary T-junction. Numerical simulations have been performed with the commercial Computational Fluid Dynamics solver ANSYS Fluent v15.0.7. Experimental results serve as a reference to validate numerical results for four independent parameters: the bubble generation frequency, volume, velocity and length. CFD simulations accurately reproduce experimental results both from qualitative and quantitative points of view. Numerical results are very sensitive to the gas-liquid-wall contact angle boundary conditions, confirming that this is a fundamental parameter to obtain accurate CFD results for simulations of this kind of problems.

Requirements for Large Eddy Simulation Computations of Variable-Speed Power Turbine Flows

NASA Technical Reports Server (NTRS)

Ameri, Ali A.

2016-01-01

Variable-speed power turbines (VSPTs) operate at low Reynolds numbers and with a wide range of incidence angles. Transition, separation, and the relevant physics leading to them are important to VSPT flow. Higher fidelity tools such as large eddy simulation (LES) may be needed to resolve the flow features necessary for accurate predictive capability and design of such turbines. A survey conducted for this report explores the requirements for such computations. The survey is limited to the simulation of two-dimensional flow cases and endwalls are not included. It suggests that a grid resolution necessary for this type of simulation to accurately represent the physics may be of the order of Delta(x)+=45, Delta(x)+ =2 and Delta(z)+=17. Various subgrid-scale (SGS) models have been used and except for the Smagorinsky model, all seem to perform well and in some instances the simulations worked well without SGS modeling. A method of specifying the inlet conditions such as synthetic eddy modeling (SEM) is necessary to correctly represent the inlet conditions.

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

PubMed

Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

2016-07-15

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Numerical Simulation of a High Mach Number Jet Flow

NASA Technical Reports Server (NTRS)

Hayder, M. Ehtesham; Turkel, Eli; Mankbadi, Reda R.

1993-01-01

The recent efforts to develop accurate numerical schemes for transition and turbulent flows are motivated, among other factors, by the need for accurate prediction of flow noise. The success of developing high speed civil transport plane (HSCT) is contingent upon our understanding and suppression of the jet exhaust noise. The radiated sound can be directly obtained by solving the full (time-dependent) compressible Navier-Stokes equations. However, this requires computational storage that is beyond currently available machines. This difficulty can be overcome by limiting the solution domain to the near field where the jet is nonlinear and then use acoustic analogy (e.g., Lighthill) to relate the far-field noise to the near-field sources. The later requires obtaining the time-dependent flow field. The other difficulty in aeroacoustics computations is that at high Reynolds numbers the turbulent flow has a large range of scales. Direct numerical simulations (DNS) cannot obtain all the scales of motion at high Reynolds number of technological interest. However, it is believed that the large scale structure is more efficient than the small-scale structure in radiating noise. Thus, one can model the small scales and calculate the acoustically active scales. The large scale structure in the noise-producing initial region of the jet can be viewed as a wavelike nature, the net radiated sound is the net cancellation after integration over space. As such, aeroacoustics computations are highly sensitive to errors in computing the sound sources. It is therefore essential to use a high-order numerical scheme to predict the flow field. The present paper presents the first step in a ongoing effort to predict jet noise. The emphasis here is in accurate prediction of the unsteady flow field. We solve the full time-dependent Navier-Stokes equations by a high order finite difference method. Time accurate spatial simulations of both plane and axisymmetric jet are presented. Jet Mach numbers of 1.5 and 2.1 are considered. Reynolds number in the simulations was about a million. Our numerical model is based on the 2-4 scheme by Gottlieb & Turkel. Bayliss et al. applied the 2-4 scheme in boundary layer computations. This scheme was also used by Ragab and Sheen to study the nonlinear development of supersonic instability waves in a mixing layer. In this study, we present two dimensional direct simulation results for both plane and axisymmetric jets. These results are compared with linear theory predictions. These computations were made for near nozzle exit region and velocity in spanwise/azimuthal direction was assumed to be zero.

Computational Challenges of Viscous Incompressible Flows

NASA Technical Reports Server (NTRS)

Kwak, Dochan; Kiris, Cetin; Kim, Chang Sung

2004-01-01

Over the past thirty years, numerical methods and simulation tools for incompressible flows have been advanced as a subset of the computational fluid dynamics (CFD) discipline. Although incompressible flows are encountered in many areas of engineering, simulation of compressible flow has been the major driver for developing computational algorithms and tools. This is probably due to the rather stringent requirements for predicting aerodynamic performance characteristics of flight vehicles, while flow devices involving low-speed or incompressible flow could be reasonably well designed without resorting to accurate numerical simulations. As flow devices are required to be more sophisticated and highly efficient CFD took become increasingly important in fluid engineering for incompressible and low-speed flow. This paper reviews some of the successes made possible by advances in computational technologies during the same period, and discusses some of the current challenges faced in computing incompressible flows.

AdapChem

NASA Technical Reports Server (NTRS)

Oluwole, Oluwayemisi O.; Wong, Hsi-Wu; Green, William

2012-01-01

AdapChem software enables high efficiency, low computational cost, and enhanced accuracy on computational fluid dynamics (CFD) numerical simulations used for combustion studies. The software dynamically allocates smaller, reduced chemical models instead of the larger, full chemistry models to evolve the calculation while ensuring the same accuracy to be obtained for steady-state CFD reacting flow simulations. The software enables detailed chemical kinetic modeling in combustion CFD simulations. AdapChem adapts the reaction mechanism used in the CFD to the local reaction conditions. Instead of a single, comprehensive reaction mechanism throughout the computation, a dynamic distribution of smaller, reduced models is used to capture accurately the chemical kinetics at a fraction of the cost of the traditional single-mechanism approach.

Parallel stochastic simulation of macroscopic calcium currents.

PubMed

González-Vélez, Virginia; González-Vélez, Horacio

2007-06-01

This work introduces MACACO, a macroscopic calcium currents simulator. It provides a parameter-sweep framework which computes macroscopic Ca(2+) currents from the individual aggregation of unitary currents, using a stochastic model for L-type Ca(2+) channels. MACACO uses a simplified 3-state Markov model to simulate the response of each Ca(2+) channel to different voltage inputs to the cell. In order to provide an accurate systematic view for the stochastic nature of the calcium channels, MACACO is composed of an experiment generator, a central simulation engine and a post-processing script component. Due to the computational complexity of the problem and the dimensions of the parameter space, the MACACO simulation engine employs a grid-enabled task farm. Having been designed as a computational biology tool, MACACO heavily borrows from the way cell physiologists conduct and report their experimental work.

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Impact of detector simulation in particle physics collider experiments

NASA Astrophysics Data System (ADS)

Daniel Elvira, V.

2017-06-01

Through the last three decades, accurate simulation of the interactions of particles with matter and modeling of detector geometries has proven to be of critical importance to the success of the international high-energy physics (HEP) experimental programs. For example, the detailed detector modeling and accurate physics of the Geant4-based simulation software of the CMS and ATLAS particle physics experiments at the European Center of Nuclear Research (CERN) Large Hadron Collider (LHC) was a determinant factor for these collaborations to deliver physics results of outstanding quality faster than any hadron collider experiment ever before. This review article highlights the impact of detector simulation on particle physics collider experiments. It presents numerous examples of the use of simulation, from detector design and optimization, through software and computing development and testing, to cases where the use of simulation samples made a difference in the precision of the physics results and publication turnaround, from data-taking to submission. It also presents estimates of the cost and economic impact of simulation in the CMS experiment. Future experiments will collect orders of magnitude more data with increasingly complex detectors, taxing heavily the performance of simulation and reconstruction software. Consequently, exploring solutions to speed up simulation and reconstruction software to satisfy the growing demand of computing resources in a time of flat budgets is a matter that deserves immediate attention. The article ends with a short discussion on the potential solutions that are being considered, based on leveraging core count growth in multicore machines, using new generation coprocessors, and re-engineering HEP code for concurrency and parallel computing.

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

PubMed

Salis, Howard; Kaznessis, Yiannis

2005-02-01

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

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

Assessment of CFD Estimation of Aerodynamic Characteristics of Basic Reusable Rocket Configurations

NASA Astrophysics Data System (ADS)

Fujimoto, Keiichiro; Fujii, Kozo

Flow-fields around the basic SSTO-rocket configurations are numerically simulated by the Reynolds-averaged Navier-Stokes (RANS) computations. Simulations of the Apollo-like configuration is first carried out, where the results are compared with NASA experiments and the prediction ability of the RANS simulation is discussed. The angle of attack of the freestream ranges from 0° to 180° and the freestream Mach number ranges from 0.7 to 2.0. Computed aerodynamic coefficients for the Apollo-like configuration agree well with the experiments under a wide range of flow conditions. The flow simulations around the slender Apollo-type configuration are carried out next and the results are compared with the experiments. Computed aerodynamic coefficients also agree well with the experiments. Flow-fields are dominated by the three-dimensional massively separated flow, which should be captured for accurate aerodynamic prediction. Grid refinement effects on the computed aerodynamic coefficients are investigated comprehensively.

CatSim: a new computer assisted tomography simulation environment

NASA Astrophysics Data System (ADS)

De Man, Bruno; Basu, Samit; Chandra, Naveen; Dunham, Bruce; Edic, Peter; Iatrou, Maria; McOlash, Scott; Sainath, Paavana; Shaughnessy, Charlie; Tower, Brendon; Williams, Eugene

2007-03-01

We present a new simulation environment for X-ray computed tomography, called CatSim. CatSim provides a research platform for GE researchers and collaborators to explore new reconstruction algorithms, CT architectures, and X-ray source or detector technologies. The main requirements for this simulator are accurate physics modeling, low computation times, and geometrical flexibility. CatSim allows simulating complex analytic phantoms, such as the FORBILD phantoms, including boxes, ellipsoids, elliptical cylinders, cones, and cut planes. CatSim incorporates polychromaticity, realistic quantum and electronic noise models, finite focal spot size and shape, finite detector cell size, detector cross-talk, detector lag or afterglow, bowtie filtration, finite detector efficiency, non-linear partial volume, scatter (variance-reduced Monte Carlo), and absorbed dose. We present an overview of CatSim along with a number of validation experiments.

Model Comparison for Electron Thermal Transport

NASA Astrophysics Data System (ADS)

Moses, Gregory; Chenhall, Jeffrey; Cao, Duc; Delettrez, Jacques

2015-11-01

Four electron thermal transport models are compared for their ability to accurately and efficiently model non-local behavior in ICF simulations. Goncharov's transport model has accurately predicted shock timing in implosion simulations but is computationally slow and limited to 1D. The iSNB (implicit Schurtz Nicolai Busquet electron thermal transport method of Cao et al. uses multigroup diffusion to speed up the calculation. Chenhall has expanded upon the iSNB diffusion model to a higher order simplified P3 approximation and a Monte Carlo transport model, to bridge the gap between the iSNB and Goncharov models while maintaining computational efficiency. Comparisons of the above models for several test problems will be presented. This work was supported by Sandia National Laboratory - Albuquerque and the University of Rochester Laboratory for Laser Energetics.

Virtual reality technique to assist measurement of degree of shaking of two minarets of an ancient building

NASA Astrophysics Data System (ADS)

Homainejad, Amir S.; Satari, Mehran

2000-05-01

VR is possible which brings users to the reality by computer and VE is a simulated world which takes users to any points and directions of the object. VR and VE can be very useful if accurate and precise data are sued, and allows users to work with realistic model. Photogrammetry is a technique which is able to collect and provide accurate and precise data for building 3D model in a computer. Data can be collected from various sensor and cameras, and methods of data collector are vary based on the method of image acquiring. Indeed VR includes real-time graphics, 3D model, and display and it has application in the entertainment industry, flight simulators, industrial design.

Measurement and Validation of Bidirectional Reflectance of Space Shuttle and Space Station Materials for Computerized Lighting Models

NASA Technical Reports Server (NTRS)

Fletcher, Lauren E.; Aldridge, Ann M.; Wheelwright, Charles; Maida, James

1997-01-01

Task illumination has a major impact on human performance: What a person can perceive in his environment significantly affects his ability to perform tasks, especially in space's harsh environment. Training for lighting conditions in space has long depended on physical models and simulations to emulate the effect of lighting, but such tests are expensive and time-consuming. To evaluate lighting conditions not easily simulated on Earth, personnel at NASA Johnson Space Center's (JSC) Graphics Research and Analysis Facility (GRAF) have been developing computerized simulations of various illumination conditions using the ray-tracing program, Radiance, developed by Greg Ward at Lawrence Berkeley Laboratory. Because these computer simulations are only as accurate as the data used, accurate information about the reflectance properties of materials and light distributions is needed. JSC's Lighting Environment Test Facility (LETF) personnel gathered material reflectance properties for a large number of paints, metals, and cloths used in the Space Shuttle and Space Station programs, and processed these data into reflectance parameters needed for the computer simulations. They also gathered lamp distribution data for most of the light sources used, and validated the ability to accurately simulate lighting levels by comparing predictions with measurements for several ground-based tests. The result of this study is a database of material reflectance properties for a wide variety of materials, and lighting information for most of the standard light sources used in the Shuttle/Station programs. The combination of the Radiance program and GRAF's graphics capability form a validated computerized lighting simulation capability for NASA.

Multigrid Computations of 3-D Incompressible Internal and External Viscous Rotating Flows

NASA Technical Reports Server (NTRS)

Sheng, Chunhua; Taylor, Lafayette K.; Chen, Jen-Ping; Jiang, Min-Yee; Whitfield, David L.

1996-01-01

This report presents multigrid methods for solving the 3-D incompressible viscous rotating flows in a NASA low-speed centrifugal compressor and a marine propeller 4119. Numerical formulations are given in both the rotating reference frame and the absolute frame. Comparisons are made for the accuracy, efficiency, and robustness between the steady-state scheme and the time-accurate scheme for simulating viscous rotating flows for complex internal and external flow applications. Prospects for further increase in efficiency and accuracy of unsteady time-accurate computations are discussed.

Simulation of the Dropping Mercury Electrode by Orthogonal Collocation.

DTIC Science & Technology

1982-08-18

Electro byOtoyI =111. - e 15,, "A’Al,.rt arp t2g? ____________ ;f f-1e of Navel Rehnar..h .905 Chemistry Program - Chemitry CO&e 41? Unkclass ified Pe . nI...transport to a dropping mercury electrode lomr.i. Accurate values for’ the concentration profiles and current are obtained with minimal computational effort...offered by COMPUTATIONAL ASP’ECTS KOutecky (14) which is corrected for spherical dittusion Results accurate to 0.4 0 of Koutecky’s calculated values I 08 n

Polymorphous Computing Architecture (PCA) Kernel Benchmark Measurements on the MIT Raw Microprocessor

DTIC Science & Technology

2006-06-14

Robert Graybill . A Raw hoard for the use of this project was provided by the Computer Architecture Croup at the Massachusetts Institute of Technology...simulator is presented by MIT as being an accurate model of the Raw chip, we have found that it does not accurately model the board. Our comparison...G4 processor, model 7410. with a 32 kbyte level-1 cache on-chip and a 2 Mbyte L2 cache connected through a 250 MH/ bus [12]. Each node has 256 Mbyte

Modeling of stress/strain behavior of fiber-reinforced ceramic matrix composites including stress redistribution

NASA Technical Reports Server (NTRS)

Mital, Subodh K.; Murthy, Pappu L. N.; Chamis, Christos C.

1994-01-01

A computational simulation procedure is presented for nonlinear analyses which incorporates microstress redistribution due to progressive fracture in ceramic matrix composites. This procedure facilitates an accurate simulation of the stress-strain behavior of ceramic matrix composites up to failure. The nonlinearity in the material behavior is accounted for at the constituent (fiber/matrix/interphase) level. This computational procedure is a part of recent upgrades to CEMCAN (Ceramic Matrix Composite Analyzer) computer code. The fiber substructuring technique in CEMCAN is used to monitor the damage initiation and progression as the load increases. The room-temperature tensile stress-strain curves for SiC fiber reinforced reaction-bonded silicon nitride (RBSN) matrix unidirectional and angle-ply laminates are simulated and compared with experimentally observed stress-strain behavior. Comparison between the predicted stress/strain behavior and experimental stress/strain curves is good. Collectively the results demonstrate that CEMCAN computer code provides the user with an effective computational tool to simulate the behavior of ceramic matrix composites.

Characterization of three-dimensional anisotropic heart valve tissue mechanical properties using inverse finite element analysis.

PubMed

Abbasi, Mostafa; Barakat, Mohammed S; Vahidkhah, Koohyar; Azadani, Ali N

2016-09-01

Computational modeling has an important role in design and assessment of medical devices. In computational simulations, considering accurate constitutive models is of the utmost importance to capture mechanical response of soft tissue and biomedical materials under physiological loading conditions. Lack of comprehensive three-dimensional constitutive models for soft tissue limits the effectiveness of computational modeling in research and development of medical devices. The aim of this study was to use inverse finite element (FE) analysis to determine three-dimensional mechanical properties of bovine pericardial leaflets of a surgical bioprosthesis under dynamic loading condition. Using inverse parameter estimation, 3D anisotropic Fung model parameters were estimated for the leaflets. The FE simulations were validated using experimental in-vitro measurements, and the impact of different constitutive material models was investigated on leaflet stress distribution. The results of this study showed that the anisotropic Fung model accurately simulated the leaflet deformation and coaptation during valve opening and closing. During systole, the peak stress reached to 3.17MPa at the leaflet boundary while during diastole high stress regions were primarily observed in the commissures with the peak stress of 1.17MPa. In addition, the Rayleigh damping coefficient that was introduced to FE simulations to simulate viscous damping effects of surrounding fluid was determined. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

Heath, Anna; Manolopoulou, Ioanna; Baio, Gianluca

2018-02-01

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

Assessment of electron propagator methods for the simulation of vibrationally-resolved valence and core photoionization spectra

PubMed Central

Baiardi, A.; Paoloni, L.; Barone, V.; Zakrzewski, V.G.; Ortiz, J.V.

2017-01-01

The analysis of photoelectron spectra is usually facilitated by quantum mechanical simulations. Due to the recent improvement of experimental techniques, the resolution of experimental spectra is rapidly increasing, and the inclusion of vibrational effects is usually mandatory to obtain a reliable reproduction of the spectra. With the aim of defining a robust computational protocol, a general time-independent formulation to compute different kinds of vibrationally-resolved electronic spectra has been generalized to support also photoelectron spectroscopy. The electronic structure data underlying the simulation are computed using different electron propagator approaches. In addition to the more standard approaches, a new and robust implementation of the second-order self-energy approximation of the electron propagator based on a transition operator reference (TOEP2) is presented. To validate our implementation, a series of molecules has been used as test cases. The result of the simulations shows that, for ultraviolet photoionization spectra, the more accurate non-diagonal approaches are needed to obtain a reliable reproduction of vertical ionization energies, but diagonal approaches are sufficient for energy gradients and pole strengths. For X-ray photoelectron spectroscopy, the TOEP2 approach, besides being more efficient, is also the most accurate in the reproduction of both vertical ionization energies and vibrationally-resolved bandshapes. PMID:28521087

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

PubMed

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

2008-02-01

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

Predicting Flows of Rarefied Gases

NASA Technical Reports Server (NTRS)

LeBeau, Gerald J.; Wilmoth, Richard G.

2005-01-01

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

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

NASA Astrophysics Data System (ADS)

Deiterding, Ralf; Wood, Stephen L.

2016-09-01

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

Numerical Prediction of Pitch Damping Stability Derivatives for Finned Projectiles

DTIC Science & Technology

2013-11-01

in part by a grant of high-performance computing time from the U.S. DOD High Performance Computing Modernization Program (HPCMP) at the Army...to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data...12 3.3.2 Time -Accurate Simulations

Multiscale Reactive Molecular Dynamics

DTIC Science & Technology

2012-08-15

biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system ...coupling to slower, cooperative motions of the system . These inherently multiscale problems require computationally efficient and accurate methods to...condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus

Direct differentiation of the quasi-incompressible fluid formulation of fluid-structure interaction using the PFEM

NASA Astrophysics Data System (ADS)

Zhu, Minjie; Scott, Michael H.

2017-07-01

Accurate and efficient response sensitivities for fluid-structure interaction (FSI) simulations are important for assessing the uncertain response of coastal and off-shore structures to hydrodynamic loading. To compute gradients efficiently via the direct differentiation method (DDM) for the fully incompressible fluid formulation, approximations of the sensitivity equations are necessary, leading to inaccuracies of the computed gradients when the geometry of the fluid mesh changes rapidly between successive time steps or the fluid viscosity is nonzero. To maintain accuracy of the sensitivity computations, a quasi-incompressible fluid is assumed for the response analysis of FSI using the particle finite element method and DDM is applied to this formulation, resulting in linearized equations for the response sensitivity that are consistent with those used to compute the response. Both the response and the response sensitivity can be solved using the same unified fractional step method. FSI simulations show that although the response using the quasi-incompressible and incompressible fluid formulations is similar, only the quasi-incompressible approach gives accurate response sensitivity for viscous, turbulent flows regardless of time step size.

Numerical simulation of steady and unsteady viscous flow in turbomachinery using pressure based algorithm

NASA Astrophysics Data System (ADS)

Lakshminarayana, B.; Ho, Y.; Basson, A.

1993-07-01

The objective of this research is to simulate steady and unsteady viscous flows, including rotor/stator interaction and tip clearance effects in turbomachinery. The numerical formulation for steady flow developed here includes an efficient grid generation scheme, particularly suited to computational grids for the analysis of turbulent turbomachinery flows and tip clearance flows, and a semi-implicit, pressure-based computational fluid dynamics scheme that directly includes artificial dissipation, and is applicable to both viscous and inviscid flows. The values of these artificial dissipation is optimized to achieve accuracy and convergency in the solution. The numerical model is used to investigate the structure of tip clearance flows in a turbine nozzle. The structure of leakage flow is captured accurately, including blade-to-blade variation of all three velocity components, pitch and yaw angles, losses and blade static pressures in the tip clearance region. The simulation also includes evaluation of such quantities of leakage mass flow, vortex strength, losses, dominant leakage flow regions and the spanwise extent affected by the leakage flow. It is demonstrated, through optimization of grid size and artificial dissipation, that the tip clearance flow field can be captured accurately. The above numerical formulation was modified to incorporate time accurate solutions. An inner loop iteration scheme is used at each time step to account for the non-linear effects. The computation of unsteady flow through a flat plate cascade subjected to a transverse gust reveals that the choice of grid spacing and the amount of artificial dissipation is critical for accurate prediction of unsteady phenomena. The rotor-stator interaction problem is simulated by starting the computation upstream of the stator, and the upstream rotor wake is specified from the experimental data. The results show that the stator potential effects have appreciable influence on the upstream rotor wake. The predicted unsteady wake profiles are compared with the available experimental data and the agreement is good. The numerical results are interpreted to draw conclusions on the unsteady wake transport mechanism in the blade passage.

Tetrahedral-Mesh Simulation of Turbulent Flows with the Space-Time Conservative Schemes

NASA Technical Reports Server (NTRS)

Chang, Chau-Lyan; Venkatachari, Balaji; Cheng, Gary C.

2015-01-01

Direct numerical simulations of turbulent flows are predominantly carried out using structured, hexahedral meshes despite decades of development in unstructured mesh methods. Tetrahedral meshes offer ease of mesh generation around complex geometries and the potential of an orientation free grid that would provide un-biased small-scale dissipation and more accurate intermediate scale solutions. However, due to the lack of consistent multi-dimensional numerical formulations in conventional schemes for triangular and tetrahedral meshes at the cell interfaces, numerical issues exist when flow discontinuities or stagnation regions are present. The space-time conservative conservation element solution element (CESE) method - due to its Riemann-solver-free shock capturing capabilities, non-dissipative baseline schemes, and flux conservation in time as well as space - has the potential to more accurately simulate turbulent flows using unstructured tetrahedral meshes. To pave the way towards accurate simulation of shock/turbulent boundary-layer interaction, a series of wave and shock interaction benchmark problems that increase in complexity, are computed in this paper with triangular/tetrahedral meshes. Preliminary computations for the normal shock/turbulence interactions are carried out with a relatively coarse mesh, by direct numerical simulations standards, in order to assess other effects such as boundary conditions and the necessity of a buffer domain. The results indicate that qualitative agreement with previous studies can be obtained for flows where, strong shocks co-exist along with unsteady waves that display a broad range of scales, with a relatively compact computational domain and less stringent requirements for grid clustering near the shock. With the space-time conservation properties, stable solutions without any spurious wave reflections can be obtained without a need for buffer domains near the outflow/farfield boundaries. Computational results for the isotropic turbulent flow decay, at a relatively high turbulent Mach number, show a nicely behaved spectral decay rate for medium to high wave numbers. The high-order CESE schemes offer very robust solutions even with the presence of strong shocks or widespread shocklets. The explicit formulation in conjunction with a close to unity theoretical upper Courant number bound has the potential to offer an efficient numerical framework for general compressible turbulent flow simulations with unstructured meshes.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

A flexible and accurate digital volume correlation method applicable to high-resolution volumetric images

NASA Astrophysics Data System (ADS)

Pan, Bing; Wang, Bo

2017-10-01

Digital volume correlation (DVC) is a powerful technique for quantifying interior deformation within solid opaque materials and biological tissues. In the last two decades, great efforts have been made to improve the accuracy and efficiency of the DVC algorithm. However, there is still a lack of a flexible, robust and accurate version that can be efficiently implemented in personal computers with limited RAM. This paper proposes an advanced DVC method that can realize accurate full-field internal deformation measurement applicable to high-resolution volume images with up to billions of voxels. Specifically, a novel layer-wise reliability-guided displacement tracking strategy combined with dynamic data management is presented to guide the DVC computation from slice to slice. The displacements at specified calculation points in each layer are computed using the advanced 3D inverse-compositional Gauss-Newton algorithm with the complete initial guess of the deformation vector accurately predicted from the computed calculation points. Since only limited slices of interest in the reference and deformed volume images rather than the whole volume images are required, the DVC calculation can thus be efficiently implemented on personal computers. The flexibility, accuracy and efficiency of the presented DVC approach are demonstrated by analyzing computer-simulated and experimentally obtained high-resolution volume images.

Enabling Predictive Simulation and UQ of Complex Multiphysics PDE Systems by the Development of Goal-Oriented Variational Sensitivity Analysis and a-Posteriori Error Estimation Methods

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

Estep, Donald

2015-11-30

This project addressed the challenge of predictive computational analysis of strongly coupled, highly nonlinear multiphysics systems characterized by multiple physical phenomena that span a large range of length- and time-scales. Specifically, the project was focused on computational estimation of numerical error and sensitivity analysis of computational solutions with respect to variations in parameters and data. In addition, the project investigated the use of accurate computational estimates to guide efficient adaptive discretization. The project developed, analyzed and evaluated new variational adjoint-based techniques for integration, model, and data error estimation/control and sensitivity analysis, in evolutionary multiphysics multiscale simulations.

Space Object Collision Probability via Monte Carlo on the Graphics Processing Unit

NASA Astrophysics Data System (ADS)

Vittaldev, Vivek; Russell, Ryan P.

2017-09-01

Fast and accurate collision probability computations are essential for protecting space assets. Monte Carlo (MC) simulation is the most accurate but computationally intensive method. A Graphics Processing Unit (GPU) is used to parallelize the computation and reduce the overall runtime. Using MC techniques to compute the collision probability is common in literature as the benchmark. An optimized implementation on the GPU, however, is a challenging problem and is the main focus of the current work. The MC simulation takes samples from the uncertainty distributions of the Resident Space Objects (RSOs) at any time during a time window of interest and outputs the separations at closest approach. Therefore, any uncertainty propagation method may be used and the collision probability is automatically computed as a function of RSO collision radii. Integration using a fixed time step and a quartic interpolation after every Runge Kutta step ensures that no close approaches are missed. Two orders of magnitude speedups over a serial CPU implementation are shown, and speedups improve moderately with higher fidelity dynamics. The tool makes the MC approach tractable on a single workstation, and can be used as a final product, or for verifying surrogate and analytical collision probability methods.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

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

PubMed

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

2017-06-07

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

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

PubMed

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

2017-06-26

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

Development of a fourth generation predictive capability maturity model.

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

Hills, Richard Guy; Witkowski, Walter R.; Urbina, Angel

2013-09-01

The Predictive Capability Maturity Model (PCMM) is an expert elicitation tool designed to characterize and communicate completeness of the approaches used for computational model definition, verification, validation, and uncertainty quantification associated for an intended application. The primary application of this tool at Sandia National Laboratories (SNL) has been for physics-based computational simulations in support of nuclear weapons applications. The two main goals of a PCMM evaluation are 1) the communication of computational simulation capability, accurately and transparently, and 2) the development of input for effective planning. As a result of the increasing importance of computational simulation to SNLs mission, themore » PCMM has evolved through multiple generations with the goal to provide more clarity, rigor, and completeness in its application. This report describes the approach used to develop the fourth generation of the PCMM.« less

Polynomial-time quantum algorithm for the simulation of chemical dynamics

PubMed Central

Kassal, Ivan; Jordan, Stephen P.; Love, Peter J.; Mohseni, Masoud; Aspuru-Guzik, Alán

2008-01-01

The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can be applied only to small systems. By contrast, we demonstrate that quantum computers could exactly simulate chemical reactions in polynomial time. Our algorithm uses the split-operator approach and explicitly simulates all electron-nuclear and interelectronic interactions in quadratic time. Surprisingly, this treatment is not only more accurate than the Born–Oppenheimer approximation but faster and more efficient as well, for all reactions with more than about four atoms. This is the case even though the entire electronic wave function is propagated on a grid with appropriately short time steps. Although the preparation and measurement of arbitrary states on a quantum computer is inefficient, here we demonstrate how to prepare states of chemical interest efficiently. We also show how to efficiently obtain chemically relevant observables, such as state-to-state transition probabilities and thermal reaction rates. Quantum computers using these techniques could outperform current classical computers with 100 qubits. PMID:19033207

Numerical simulation using vorticity-vector potential formulation

NASA Technical Reports Server (NTRS)

Tokunaga, Hiroshi

1993-01-01

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

Efficient Fourier-based algorithms for time-periodic unsteady problems

NASA Astrophysics Data System (ADS)

Gopinath, Arathi Kamath

2007-12-01

This dissertation work proposes two algorithms for the simulation of time-periodic unsteady problems via the solution of Unsteady Reynolds-Averaged Navier-Stokes (URANS) equations. These algorithms use a Fourier representation in time and hence solve for the periodic state directly without resolving transients (which consume most of the resources in a time-accurate scheme). In contrast to conventional Fourier-based techniques which solve the governing equations in frequency space, the new algorithms perform all the calculations in the time domain, and hence require minimal modifications to an existing solver. The complete space-time solution is obtained by iterating in a fifth pseudo-time dimension. Various time-periodic problems such as helicopter rotors, wind turbines, turbomachinery and flapping-wings can be simulated using the Time Spectral method. The algorithm is first validated using pitching airfoil/wing test cases. The method is further extended to turbomachinery problems, and computational results verified by comparison with a time-accurate calculation. The technique can be very memory intensive for large problems, since the solution is computed (and hence stored) simultaneously at all time levels. Often, the blade counts of a turbomachine are rescaled such that a periodic fraction of the annulus can be solved. This approximation enables the solution to be obtained at a fraction of the cost of a full-scale time-accurate solution. For a viscous computation over a three-dimensional single-stage rescaled compressor, an order of magnitude savings is achieved. The second algorithm, the reduced-order Harmonic Balance method is applicable only to turbomachinery flows, and offers even larger computational savings than the Time Spectral method. It simulates the true geometry of the turbomachine using only one blade passage per blade row as the computational domain. In each blade row of the turbomachine, only the dominant frequencies are resolved, namely, combinations of neighbor's blade passing. An appropriate set of frequencies can be chosen by the analyst/designer based on a trade-off between accuracy and computational resources available. A cost comparison with a time-accurate computation for an Euler calculation on a two-dimensional multi-stage compressor obtained an order of magnitude savings, and a RANS calculation on a three-dimensional single-stage compressor achieved two orders of magnitude savings, with comparable accuracy.

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

Incorporating contact angles in the surface tension force with the ACES interface curvature scheme

NASA Astrophysics Data System (ADS)

Owkes, Mark

2017-11-01

In simulations of gas-liquid flows interacting with solid boundaries, the contact line dynamics effect the interface motion and flow field through the surface tension force. The surface tension force is directly proportional to the interface curvature and the problem of accurately imposing a contact angle must be incorporated into the interface curvature calculation. Many commonly used algorithms to compute interface curvatures (e.g., height function method) require extrapolating the interface, with defined contact angle, into the solid to allow for the calculation of a curvature near a wall. Extrapolating can be an ill-posed problem, especially in three-dimensions or when multiple contact lines are near each other. We have developed an accurate methodology to compute interface curvatures that allows for contact angles to be easily incorporated while avoiding extrapolation and the associated challenges. The method, known as Adjustable Curvature Evaluation Scale (ACES), leverages a least squares fit of a polynomial to points computed on the volume-of-fluid (VOF) representation of the gas-liquid interface. The method is tested by simulating canonical test cases and then applied to simulate the injection and motion of water droplets in a channel (relevant to PEM fuel cells).

An effective absorbing layer for the boundary condition in acoustic seismic wave simulation

NASA Astrophysics Data System (ADS)

Yao, Gang; da Silva, Nuno V.; Wu, Di

2018-04-01

Efficient numerical simulation of seismic wavefields generally involves truncating the Earth model in order to keep computing time and memory requirements down. Absorbing boundary conditions, therefore, are applied to remove the boundary reflections caused by this truncation, thereby allowing for accurate modeling of wavefields. In this paper, we derive an effective absorbing boundary condition for both acoustic and elastic wave simulation, through the simplification of the damping term of the split perfectly matched layer (SPML) boundary condition. This new boundary condition is accurate, cost-effective, and easily implemented, especially for high-performance computing. Stability analysis shows that this boundary condition is effectively as stable as normal (non-absorbing) wave equations for explicit time-stepping finite differences. We found that for full-waveform inversion (FWI), the strengths of the effective absorbing layer—a reduction of the computational and memory cost coupled with a simplistic implementation—significantly outweighs the limitation of incomplete absorption of outgoing waves relative to the SPML. More importantly, we demonstrate that this limitation can easily be overcome through the use of two strategies in FWI, namely variable cell size and model extension thereby fully compensating for the imperfectness of the proposed absorbing boundary condition.

Analysis of the Characteristics of a Rotary Stepper Micromotor

NASA Astrophysics Data System (ADS)

Sone, Junji; Mizuma, Toshinari; Masunaga, Masakazu; Mochizuki, Shunsuke; Sarajic, Edin; Yamahata, Christophe; Fujita, Hiroyuki

A 3-phase electrostatic stepper micromotor was developed. To improve its performance for actual use, we have conducted numerical simulation to optimize the design. An improved simulation method is needed for calculation of various cases. To conduct circuit simulation of this micromotor, its structure is simplified, and a function for computing the force excited by the electrostatic field is added to the circuit simulator. We achieved a reasonably accurate simulation. We also considered an optimal drive waveform to achieve low-voltage operation.

A Comparative Study of Simulated and Measured Gear-Flap Flow Interaction

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Mineck, Raymond E.; Yao, Chungsheng; Jenkins, Luther N.; Fares, Ehab

2015-01-01

The ability of two CFD solvers to accurately characterize the transient, complex, interacting flowfield asso-ciated with a realistic gear-flap configuration is assessed via comparison of simulated flow with experimental measurements. The simulated results, obtained with NASA's FUN3D and Exa's PowerFLOW® for a high-fidelity, 18% scale semi-span model of a Gulfstream aircraft in landing configuration (39 deg flap deflection, main landing gear on and off) are compared to two-dimensional and stereo particle image velocimetry measurements taken within the gear-flap flow interaction region during wind tunnel tests of the model. As part of the bench-marking process, direct comparisons of the mean and fluctuating velocity fields are presented in the form of planar contour plots and extracted line profiles at measurement planes in various orientations stationed in the main gear wake. The measurement planes in the vicinity of the flap side edge and downstream of the flap trailing edge are used to highlight the effects of gear presence on tip vortex development and the ability of the computational tools to accurately capture such effects. The present study indicates that both computed datasets contain enough detail to construct a relatively accurate depiction of gear-flap flow interaction. Such a finding increases confidence in using the simulated volumetric flow solutions to examine the behavior of pertinent aer-odynamic mechanisms within the gear-flap interaction zone.

Dosimetry applications in GATE Monte Carlo toolkit.

PubMed

Papadimitroulas, Panagiotis

2017-09-01

Monte Carlo (MC) simulations are a well-established method for studying physical processes in medical physics. The purpose of this review is to present GATE dosimetry applications on diagnostic and therapeutic simulated protocols. There is a significant need for accurate quantification of the absorbed dose in several specific applications such as preclinical and pediatric studies. GATE is an open-source MC toolkit for simulating imaging, radiotherapy (RT) and dosimetry applications in a user-friendly environment, which is well validated and widely accepted by the scientific community. In RT applications, during treatment planning, it is essential to accurately assess the deposited energy and the absorbed dose per tissue/organ of interest, as well as the local statistical uncertainty. Several types of realistic dosimetric applications are described including: molecular imaging, radio-immunotherapy, radiotherapy and brachytherapy. GATE has been efficiently used in several applications, such as Dose Point Kernels, S-values, Brachytherapy parameters, and has been compared against various MC codes which are considered as standard tools for decades. Furthermore, the presented studies show reliable modeling of particle beams when comparing experimental with simulated data. Examples of different dosimetric protocols are reported for individualized dosimetry and simulations combining imaging and therapy dose monitoring, with the use of modern computational phantoms. Personalization of medical protocols can be achieved by combining GATE MC simulations with anthropomorphic computational models and clinical anatomical data. This is a review study, covering several dosimetric applications of GATE, and the different tools used for modeling realistic clinical acquisitions with accurate dose assessment. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Fast simulation of yttrium-90 bremsstrahlung photons with GATE.

PubMed

Rault, Erwann; Staelens, Steven; Van Holen, Roel; De Beenhouwer, Jan; Vandenberghe, Stefaan

2010-06-01

Multiple investigators have recently reported the use of yttrium-90 (90Y) bremsstrahlung single photon emission computed tomography (SPECT) imaging for the dosimetry of targeted radionuclide therapies. Because Monte Carlo (MC) simulations are useful for studying SPECT imaging, this study investigates the MC simulation of 90Y bremsstrahlung photons in SPECT. To overcome the computationally expensive simulation of electrons, the authors propose a fast way to simulate the emission of 90Y bremsstrahlung photons based on prerecorded bremsstrahlung photon probability density functions (PDFs). The accuracy of bremsstrahlung photon simulation is evaluated in two steps. First, the validity of the fast bremsstrahlung photon generator is checked. To that end, fast and analog simulations of photons emitted from a 90Y point source in a water phantom are compared. The same setup is then used to verify the accuracy of the bremsstrahlung photon simulations, comparing the results obtained with PDFs generated from both simulated and measured data to measurements. In both cases, the energy spectra and point spread functions of the photons detected in a scintillation camera are used. Results show that the fast simulation method is responsible for a 5% overestimation of the low-energy fluence (below 75 keV) of the bremsstrahlung photons detected using a scintillation camera. The spatial distribution of the detected photons is, however, accurately reproduced with the fast method and a computational acceleration of approximately 17-fold is achieved. When measured PDFs are used in the simulations, the simulated energy spectrum of photons emitted from a point source of 90Y in a water phantom and detected in a scintillation camera closely approximates the measured spectrum. The PSF of the photons imaged in the 50-300 keV energy window is also accurately estimated with a 12.4% underestimation of the full width at half maximum and 4.5% underestimation of the full width at tenth maximum. Despite its limited accuracy, the fast bremsstrahlung photon generator is well suited for the simulation of bremsstrahlung photons emitted in large homogeneous organs, such as the liver, and detected in a scintillation camera. The computational acceleration makes it very useful for future investigations of 90Y bremsstrahlung SPECT imaging.

The impact of 14-nm photomask uncertainties on computational lithography solutions

NASA Astrophysics Data System (ADS)

Sturtevant, John; Tejnil, Edita; Lin, Tim; Schultze, Steffen; Buck, Peter; Kalk, Franklin; Nakagawa, Kent; Ning, Guoxiang; Ackmann, Paul; Gans, Fritz; Buergel, Christian

2013-04-01

Computational lithography solutions rely upon accurate process models to faithfully represent the imaging system output for a defined set of process and design inputs. These models, which must balance accuracy demands with simulation runtime boundary conditions, rely upon the accurate representation of multiple parameters associated with the scanner and the photomask. While certain system input variables, such as scanner numerical aperture, can be empirically tuned to wafer CD data over a small range around the presumed set point, it can be dangerous to do so since CD errors can alias across multiple input variables. Therefore, many input variables for simulation are based upon designed or recipe-requested values or independent measurements. It is known, however, that certain measurement methodologies, while precise, can have significant inaccuracies. Additionally, there are known errors associated with the representation of certain system parameters. With shrinking total CD control budgets, appropriate accounting for all sources of error becomes more important, and the cumulative consequence of input errors to the computational lithography model can become significant. In this work, we examine with a simulation sensitivity study, the impact of errors in the representation of photomask properties including CD bias, corner rounding, refractive index, thickness, and sidewall angle. The factors that are most critical to be accurately represented in the model are cataloged. CD Bias values are based on state of the art mask manufacturing data and other variables changes are speculated, highlighting the need for improved metrology and awareness.

A computational workflow for designing silicon donor qubits

DOE PAGES

Humble, Travis S.; Ericson, M. Nance; Jakowski, Jacek; ...

2016-09-19

Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum chemistry calculations with electrostatic field solvers to performmore » detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. In conclusion, the resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices.« less

Multi-level emulation of a volcanic ash transport and dispersion model to quantify sensitivity to uncertain parameters

NASA Astrophysics Data System (ADS)

Harvey, Natalie J.; Huntley, Nathan; Dacre, Helen F.; Goldstein, Michael; Thomson, David; Webster, Helen

2018-01-01

Following the disruption to European airspace caused by the eruption of Eyjafjallajökull in 2010 there has been a move towards producing quantitative predictions of volcanic ash concentration using volcanic ash transport and dispersion simulators. However, there is no formal framework for determining the uncertainties of these predictions and performing many simulations using these complex models is computationally expensive. In this paper a Bayesian linear emulation approach is applied to the Numerical Atmospheric-dispersion Modelling Environment (NAME) to better understand the influence of source and internal model parameters on the simulator output. Emulation is a statistical method for predicting the output of a computer simulator at new parameter choices without actually running the simulator. A multi-level emulation approach is applied using two configurations of NAME with different numbers of model particles. Information from many evaluations of the computationally faster configuration is combined with results from relatively few evaluations of the slower, more accurate, configuration. This approach is effective when it is not possible to run the accurate simulator many times and when there is also little prior knowledge about the influence of parameters. The approach is applied to the mean ash column loading in 75 geographical regions on 14 May 2010. Through this analysis it has been found that the parameters that contribute the most to the output uncertainty are initial plume rise height, mass eruption rate, free tropospheric turbulence levels and precipitation threshold for wet deposition. This information can be used to inform future model development and observational campaigns and routine monitoring. The analysis presented here suggests the need for further observational and theoretical research into parameterisation of atmospheric turbulence. Furthermore it can also be used to inform the most important parameter perturbations for a small operational ensemble of simulations. The use of an emulator also identifies the input and internal parameters that do not contribute significantly to simulator uncertainty. Finally, the analysis highlights that the faster, less accurate, configuration of NAME can, on its own, provide useful information for the problem of predicting average column load over large areas.

Velocity field calculation for non-orthogonal numerical grids

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

Flach, G. P.

2015-03-01

Computational grids containing cell faces that do not align with an orthogonal (e.g. Cartesian, cylindrical) coordinate system are routinely encountered in porous-medium numerical simulations. Such grids are referred to in this study as non-orthogonal grids because some cell faces are not orthogonal to a coordinate system plane (e.g. xy, yz or xz plane in Cartesian coordinates). Non-orthogonal grids are routinely encountered at the Savannah River Site in porous-medium flow simulations for Performance Assessments and groundwater flow modeling. Examples include grid lines that conform to the sloping roof of a waste tank or disposal unit in a 2D Performance Assessment simulation,more » and grid surfaces that conform to undulating stratigraphic surfaces in a 3D groundwater flow model. Particle tracking is routinely performed after a porous-medium numerical flow simulation to better understand the dynamics of the flow field and/or as an approximate indication of the trajectory and timing of advective solute transport. Particle tracks are computed by integrating the velocity field from cell to cell starting from designated seed (starting) positions. An accurate velocity field is required to attain accurate particle tracks. However, many numerical simulation codes report only the volumetric flowrate (e.g. PORFLOW) and/or flux (flowrate divided by area) crossing cell faces. For an orthogonal grid, the normal flux at a cell face is a component of the Darcy velocity vector in the coordinate system, and the pore velocity for particle tracking is attained by dividing by water content. For a non-orthogonal grid, the flux normal to a cell face that lies outside a coordinate plane is not a true component of velocity with respect to the coordinate system. Nonetheless, normal fluxes are often taken as Darcy velocity components, either naively or with accepted approximation. To enable accurate particle tracking or otherwise present an accurate depiction of the velocity field for a non-orthogonal grid, Darcy velocity components are rigorously derived in this study from normal fluxes to cell faces, which are assumed to be provided by or readily computed from porous-medium simulation code output. The normal fluxes are presumed to satisfy mass balances for every computational cell, and if so, the derived velocity fields are consistent with these mass balances. Derivations are provided for general two-dimensional quadrilateral and three-dimensional hexagonal systems, and for the commonly encountered special cases of perfectly vertical side faces in 2D and 3D and a rectangular footprint in 3D.« less

Numerical Relativity, Black Hole Mergers, and Gravitational Waves: Part II

NASA Technical Reports Server (NTRS)

Centrella, Joan

2012-01-01

This series of 3 lectures will present recent developments in numerical relativity, and their applications to simulating black hole mergers and computing the resulting gravitational waveforms. In this second lecture, we focus on simulations of black hole binary mergers. We hig hlight the instabilities that plagued the codes for many years, the r ecent breakthroughs that led to the first accurate simulations, and the current state of the art.

Particle Hydrodynamics with Material Strength for Multi-Layer Orbital Debris Shield Design

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.

1999-01-01

Three dimensional simulation of oblique hypervelocity impact on orbital debris shielding places extreme demands on computer resources. Research to date has shown that particle models provide the most accurate and efficient means for computer simulation of shield design problems. In order to employ a particle based modeling approach to the wall plate impact portion of the shield design problem, it is essential that particle codes be augmented to represent strength effects. This report describes augmentation of a Lagrangian particle hydrodynamics code developed by the principal investigator, to include strength effects, allowing for the entire shield impact problem to be represented using a single computer code.

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

PubMed Central

2012-01-01

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

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

PubMed

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

2012-02-16

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

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

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

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

2016-04-15

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

Simplified Modeling of Oxidation of Hydrocarbons

NASA Technical Reports Server (NTRS)

Bellan, Josette; Harstad, Kenneth

2008-01-01

A method of simplified computational modeling of oxidation of hydrocarbons is undergoing development. This is one of several developments needed to enable accurate computational simulation of turbulent, chemically reacting flows. At present, accurate computational simulation of such flows is difficult or impossible in most cases because (1) the numbers of grid points needed for adequate spatial resolution of turbulent flows in realistically complex geometries are beyond the capabilities of typical supercomputers now in use and (2) the combustion of typical hydrocarbons proceeds through decomposition into hundreds of molecular species interacting through thousands of reactions. Hence, the combination of detailed reaction- rate models with the fundamental flow equations yields flow models that are computationally prohibitive. Hence, further, a reduction of at least an order of magnitude in the dimension of reaction kinetics is one of the prerequisites for feasibility of computational simulation of turbulent, chemically reacting flows. In the present method of simplified modeling, all molecular species involved in the oxidation of hydrocarbons are classified as either light or heavy; heavy molecules are those having 3 or more carbon atoms. The light molecules are not subject to meaningful decomposition, and the heavy molecules are considered to decompose into only 13 specified constituent radicals, a few of which are listed in the table. One constructs a reduced-order model, suitable for use in estimating the release of heat and the evolution of temperature in combustion, from a base comprising the 13 constituent radicals plus a total of 26 other species that include the light molecules and related light free radicals. Then rather than following all possible species through their reaction coordinates, one follows only the reduced set of reaction coordinates of the base. The behavior of the base was examined in test computational simulations of the combustion of heptane in a stirred reactor at various initial pressures ranging from 0.1 to 6 MPa. Most of the simulations were performed for stoichiometric mixtures; some were performed for fuel/oxygen mole ratios of 1/2 and 2.

Neural-Network Computer Transforms Coordinates

NASA Technical Reports Server (NTRS)

Josin, Gary M.

1990-01-01

Numerical simulation demonstrated ability of conceptual neural-network computer to generalize what it has "learned" from few examples. Ability to generalize achieved with even simple neural network (relatively few neurons) and after exposure of network to only few "training" examples. Ability to obtain fairly accurate mappings after only few training examples used to provide solutions to otherwise intractable mapping problems.

A high-order strong stability preserving Runge-Kutta method for three-dimensional full waveform modeling and inversion of anelastic models

NASA Astrophysics Data System (ADS)

Wang, N.; Shen, Y.; Yang, D.; Bao, X.; Li, J.; Zhang, W.

2017-12-01

Accurate and efficient forward modeling methods are important for high resolution full waveform inversion. Compared with the elastic case, solving anelastic wave equation requires more computational time, because of the need to compute additional material-independent anelastic functions. A numerical scheme with a large Courant-Friedrichs-Lewy (CFL) condition number enables us to use a large time step to simulate wave propagation, which improves computational efficiency. In this work, we apply the fourth-order strong stability preserving Runge-Kutta method with an optimal CFL coeffiecient to solve the anelastic wave equation. We use a fourth order DRP/opt MacCormack scheme for the spatial discretization, and we approximate the rheological behaviors of the Earth by using the generalized Maxwell body model. With a larger CFL condition number, we find that the computational efficient is significantly improved compared with the traditional fourth-order Runge-Kutta method. Then, we apply the scattering-integral method for calculating travel time and amplitude sensitivity kernels with respect to velocity and attenuation structures. For each source, we carry out one forward simulation and save the time-dependent strain tensor. For each station, we carry out three `backward' simulations for the three components and save the corresponding strain tensors. The sensitivity kernels at each point in the medium are the convolution of the two sets of the strain tensors. Finally, we show several synthetic tests to verify the effectiveness of the strong stability preserving Runge-Kutta method in generating accurate synthetics in full waveform modeling, and in generating accurate strain tensors for calculating sensitivity kernels at regional and global scales.

Experimental and numerical characterisation of the elasto-plastic properties of bovine trabecular bone and a trabecular bone analogue.

PubMed

Kelly, Nicola; McGarry, J Patrick

2012-05-01

The inelastic pressure dependent compressive behaviour of bovine trabecular bone is investigated through experimental and computational analysis. Two loading configurations are implemented, uniaxial and confined compression, providing two distinct loading paths in the von Mises-pressure stress plane. Experimental results reveal distinctive yielding followed by a constant nominal stress plateau for both uniaxial and confined compression. Computational simulation of the experimental tests using the Drucker-Prager and Mohr-Coulomb plasticity models fails to capture the confined compression behaviour of trabecular bone. The high pressure developed during confined compression does not result in plastic deformation using these formulations, and a near elastic response is computed. In contrast, the crushable foam plasticity models provide accurate simulation of the confined compression tests, with distinctive yield and plateau behaviour being predicted. The elliptical yield surfaces of the crushable foam formulations in the von Mises-pressure stress plane accurately characterise the plastic behaviour of trabecular bone. Results reveal that the hydrostatic yield stress is equal to the uniaxial yield stress for trabecular bone, demonstrating the importance of accurate characterisation and simulation of the pressure dependent plasticity. It is also demonstrated in this study that a commercially available trabecular bone analogue material, cellular rigid polyurethane foam, exhibits similar pressure dependent yield behaviour, despite having a lower stiffness and strength than trabecular bone. This study provides a novel insight into the pressure dependent yield behaviour of trabecular bone, demonstrating the inadequacy of uniaxial testing alone. For the first time, crushable foam plasticity formulations are implemented for trabecular bone. The enhanced understanding of the inelastic behaviour of trabecular bone established in this study will allow for more realistic simulation of orthopaedic device implantation and failure. Copyright © 2011 Elsevier Ltd. All rights reserved.

Numerical Simulations of Hypersonic Boundary Layer Transition

NASA Astrophysics Data System (ADS)

Bartkowicz, Matthew David

Numerical schemes for supersonic flows tend to use large amounts of artificial viscosity for stability. This tends to damp out the small scale structures in the flow. Recently some low-dissipation methods have been proposed which selectively eliminate the artificial viscosity in regions which do not require it. This work builds upon the low-dissipation method of Subbareddy and Candler which uses the flux vector splitting method of Steger and Warming but identifies the dissipation portion to eliminate it. Computing accurate fluxes typically relies on large grid stencils or coupled linear systems that become computationally expensive to solve. Unstructured grids allow for CFD solutions to be obtained on complex geometries, unfortunately, it then becomes difficult to create a large stencil or the coupled linear system. Accurate solutions require grids that quickly become too large to be feasible. In this thesis a method is proposed to obtain more accurate solutions using relatively local data, making it suitable for unstructured grids composed of hexahedral elements. Fluxes are reconstructed using local gradients to extend the range of data used. The method is then validated on several test problems. Simulations of boundary layer transition are then performed. An elliptic cone at Mach 8 is simulated based on an experiment at the Princeton Gasdynamics Laboratory. A simulated acoustic noise boundary condition is imposed to model the noisy conditions of the wind tunnel and the transitioning boundary layer observed. A computation of an isolated roughness element is done based on an experiment in Purdue's Mach 6 quiet wind tunnel. The mechanism for transition is identified as an instability in the upstream separation region and a comparison is made to experimental data. In the CFD a fully turbulent boundary layer is observed downstream.

Solid rocket booster internal flow analysis by highly accurate adaptive computational methods

NASA Technical Reports Server (NTRS)

Huang, C. Y.; Tworzydlo, W.; Oden, J. T.; Bass, J. M.; Cullen, C.; Vadaketh, S.

1991-01-01

The primary objective of this project was to develop an adaptive finite element flow solver for simulating internal flows in the solid rocket booster. Described here is a unique flow simulator code for analyzing highly complex flow phenomena in the solid rocket booster. New methodologies and features incorporated into this analysis tool are described.

Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations

NASA Astrophysics Data System (ADS)

Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.

2016-10-01

In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.

Adjoint-Based, Three-Dimensional Error Prediction and Grid Adaptation

NASA Technical Reports Server (NTRS)

Park, Michael A.

2002-01-01

Engineering computational fluid dynamics (CFD) analysis and design applications focus on output functions (e.g., lift, drag). Errors in these output functions are generally unknown and conservatively accurate solutions may be computed. Computable error estimates can offer the possibility to minimize computational work for a prescribed error tolerance. Such an estimate can be computed by solving the flow equations and the linear adjoint problem for the functional of interest. The computational mesh can be modified to minimize the uncertainty of a computed error estimate. This robust mesh-adaptation procedure automatically terminates when the simulation is within a user specified error tolerance. This procedure for estimating and adapting to error in a functional is demonstrated for three-dimensional Euler problems. An adaptive mesh procedure that links to a Computer Aided Design (CAD) surface representation is demonstrated for wing, wing-body, and extruded high lift airfoil configurations. The error estimation and adaptation procedure yielded corrected functions that are as accurate as functions calculated on uniformly refined grids with ten times as many grid points.

Simulating Scenes In Outer Space

NASA Technical Reports Server (NTRS)

Callahan, John D.

1989-01-01

Multimission Interactive Picture Planner, MIP, computer program for scientifically accurate and fast, three-dimensional animation of scenes in deep space. Versatile, reasonably comprehensive, and portable, and runs on microcomputers. New techniques developed to perform rapidly calculations and transformations necessary to animate scenes in scientifically accurate three-dimensional space. Written in FORTRAN 77 code. Primarily designed to handle Voyager, Galileo, and Space Telescope. Adapted to handle other missions.

Electrochemical carbon dioxide concentrator subsystem math model. [for manned space station

NASA Technical Reports Server (NTRS)

Marshall, R. D.; Carlson, J. N.; Schubert, F. H.

1974-01-01

A steady state computer simulation model has been developed to describe the performance of a total six man, self-contained electrochemical carbon dioxide concentrator subsystem built for the space station prototype. The math model combines expressions describing the performance of the electrochemical depolarized carbon dioxide concentrator cells and modules previously developed with expressions describing the performance of the other major CS-6 components. The model is capable of accurately predicting CS-6 performance over EDC operating ranges and the computer simulation results agree with experimental data obtained over the prediction range.

Design for progressive fracture in composite shell structures

NASA Technical Reports Server (NTRS)

Minnetyan, Levon; Murthy, Pappu L. N.

1992-01-01

The load carrying capability and structural behavior of composite shell structures and stiffened curved panels are investigated to provide accurate early design loads. An integrated computer code is utilized for the computational simulation of composite structural degradation under practical loading for realistic design. Damage initiation, growth, accumulation, and propagation to structural fracture are included in the simulation. Progressive fracture investigations providing design insight for several classes of composite shells are presented. Results demonstrate the significance of local defects, interfacial regions, and stress concentrations on the structural durability of composite shells.

Shock compression response of cold-rolled Ni/Al multilayer composites

DOE PAGES

Specht, Paul E.; Weihs, Timothy P.; Thadhani, Naresh N.

2017-01-06

Uniaxial strain, plate-on-plate impact experiments were performed on cold-rolled Ni/Al multilayer composites and the resulting Hugoniot was determined through time-resolved measurements combined with impedance matching. The experimental Hugoniot agreed with that previously predicted by two dimensional (2D) meso-scale calculations. Additional 2D meso-scale simulations were performed using the same computational method as the prior study to reproduce the experimentally measured free surface velocities and stress profiles. Finally, these simulations accurately replicated the experimental profiles, providing additional validation for the previous computational work.

WE-C-217BCD-08: Rapid Monte Carlo Simulations of DQE(f) of Scintillator-Based Detectors.

PubMed

Star-Lack, J; Abel, E; Constantin, D; Fahrig, R; Sun, M

2012-06-01

Monte Carlo simulations of DQE(f) can greatly aid in the design of scintillator-based detectors by helping optimize key parameters including scintillator material and thickness, pixel size, surface finish, and septa reflectivity. However, the additional optical transport significantly increases simulation times, necessitating a large number of parallel processors to adequately explore the parameter space. To address this limitation, we have optimized the DQE(f) algorithm, reducing simulation times per design iteration to 10 minutes on a single CPU. DQE(f) is proportional to the ratio, MTF(f)̂2 /NPS(f). The LSF-MTF simulation uses a slanted line source and is rapidly performed with relatively few gammas launched. However, the conventional NPS simulation for standard radiation exposure levels requires the acquisition of multiple flood fields (nRun), each requiring billions of input gamma photons (nGamma), many of which will scintillate, thereby producing thousands of optical photons (nOpt) per deposited MeV. The resulting execution time is proportional to the product nRun x nGamma x nOpt. In this investigation, we revisit the theoretical derivation of DQE(f), and reveal significant computation time savings through the optimization of nRun, nGamma, and nOpt. Using GEANT4, we determine optimal values for these three variables for a GOS scintillator-amorphous silicon portal imager. Both isotropic and Mie optical scattering processes were modeled. Simulation results were validated against the literature. We found that, depending on the radiative and optical attenuation properties of the scintillator, the NPS can be accurately computed using values for nGamma below 1000, and values for nOpt below 500/MeV. nRun should remain above 200. Using these parameters, typical computation times for a complete NPS ranged from 2-10 minutes on a single CPU. The number of launched particles and corresponding execution times for a DQE simulation can be dramatically reduced allowing for accurate computation with modest computer hardware. NIHRO1 CA138426. Several authors work for Varian Medical Systems. © 2012 American Association of Physicists in Medicine.

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

PubMed

Komeiji, Y; Yokoyama, H; Uebayasi, M; Taiji, M; Fukushige, T; Sugimoto, D; Takata, R; Shimizu, A; Itsukashi, K

1996-01-01

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH (Program for Energetic Analysis of bioCHemical molecules) was developed for molecular dynamics of biomolecules in combination with MD-GRAPE. Molecular dynamics simulation was performed for several protein-solvent systems with different sizes. Simulation of the largest system investigated (27,000 atoms) took only 5 sec/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulation of large biomolecules.

Improved computer simulation of the TCAS 3 circular array mounted on an aircraft

NASA Astrophysics Data System (ADS)

Rojas, R. G.; Chen, Y. C.; Burnside, Walter D.

1989-03-01

The Traffic advisory and Collision Avoidance System (TCAS) is being developed by the Federal Aviation Administration (FAA) to assist aircraft pilots in mid-air collision avoidance. This report concentrates on the computer simulation of the enchanced TCAS 2 systems mounted on a Boeing 727. First, the moment method is used to obtain an accurate model for the enhanced TCAS 2 antenna array. Then, the OSU Aircraft Code is used to generate theoretical radiation patterns of this model mounted on a simulated Boeing 727 model. Scattering error curves obtained from these patterns can be used to evaluate the performance of this system in determining the angular position of another aircraft with respect to the TCAS-equipped aircraft. Finally, the tracking of another aircraft is simulated when the TCAS-equipped aircraft follows a prescribed escape curve. In short, the computer models developed in this report have generality, completeness and yield reasonable results.

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Modeling of a Sequential Two-Stage Combustor

NASA Technical Reports Server (NTRS)

Hendricks, R. C.; Liu, N.-S.; Gallagher, J. R.; Ryder, R. C.; Brankovic, A.; Hendricks, J. A.

2005-01-01

A sequential two-stage, natural gas fueled power generation combustion system is modeled to examine the fundamental aerodynamic and combustion characteristics of the system. The modeling methodology includes CAD-based geometry definition, and combustion computational fluid dynamics analysis. Graphical analysis is used to examine the complex vortical patterns in each component, identifying sources of pressure loss. The simulations demonstrate the importance of including the rotating high-pressure turbine blades in the computation, as this results in direct computation of combustion within the first turbine stage, and accurate simulation of the flow in the second combustion stage. The direct computation of hot-streaks through the rotating high-pressure turbine stage leads to improved understanding of the aerodynamic relationships between the primary and secondary combustors and the turbomachinery.

REVEAL: An Extensible Reduced Order Model Builder for Simulation and Modeling

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

Agarwal, Khushbu; Sharma, Poorva; Ma, Jinliang

2013-04-30

Many science domains need to build computationally efficient and accurate representations of high fidelity, computationally expensive simulations. These computationally efficient versions are known as reduced-order models. This paper presents the design and implementation of a novel reduced-order model (ROM) builder, the REVEAL toolset. This toolset generates ROMs based on science- and engineering-domain specific simulations executed on high performance computing (HPC) platforms. The toolset encompasses a range of sampling and regression methods that can be used to generate a ROM, automatically quantifies the ROM accuracy, and provides support for an iterative approach to improve ROM accuracy. REVEAL is designed to bemore » extensible in order to utilize the core functionality with any simulator that has published input and output formats. It also defines programmatic interfaces to include new sampling and regression techniques so that users can ‘mix and match’ mathematical techniques to best suit the characteristics of their model. In this paper, we describe the architecture of REVEAL and demonstrate its usage with a computational fluid dynamics model used in carbon capture.« less

Computational modeling of cardiac hemodynamics: Current status and future outlook

NASA Astrophysics Data System (ADS)

Mittal, Rajat; Seo, Jung Hee; Vedula, Vijay; Choi, Young J.; Liu, Hang; Huang, H. Howie; Jain, Saurabh; Younes, Laurent; Abraham, Theodore; George, Richard T.

2016-01-01

The proliferation of four-dimensional imaging technologies, increasing computational speeds, improved simulation algorithms, and the widespread availability of powerful computing platforms is enabling simulations of cardiac hemodynamics with unprecedented speed and fidelity. Since cardiovascular disease is intimately linked to cardiovascular hemodynamics, accurate assessment of the patient's hemodynamic state is critical for the diagnosis and treatment of heart disease. Unfortunately, while a variety of invasive and non-invasive approaches for measuring cardiac hemodynamics are in widespread use, they still only provide an incomplete picture of the hemodynamic state of a patient. In this context, computational modeling of cardiac hemodynamics presents as a powerful non-invasive modality that can fill this information gap, and significantly impact the diagnosis as well as the treatment of cardiac disease. This article reviews the current status of this field as well as the emerging trends and challenges in cardiovascular health, computing, modeling and simulation and that are expected to play a key role in its future development. Some recent advances in modeling and simulations of cardiac flow are described by using examples from our own work as well as the research of other groups.

Unstructured mesh adaptivity for urban flooding modelling

NASA Astrophysics Data System (ADS)

Hu, R.; Fang, F.; Salinas, P.; Pain, C. C.

2018-05-01

Over the past few decades, urban floods have been gaining more attention due to their increase in frequency. To provide reliable flooding predictions in urban areas, various numerical models have been developed to perform high-resolution flood simulations. However, the use of high-resolution meshes across the whole computational domain causes a high computational burden. In this paper, a 2D control-volume and finite-element flood model using adaptive unstructured mesh technology has been developed. This adaptive unstructured mesh technique enables meshes to be adapted optimally in time and space in response to the evolving flow features, thus providing sufficient mesh resolution where and when it is required. It has the advantage of capturing the details of local flows and wetting and drying front while reducing the computational cost. Complex topographic features are represented accurately during the flooding process. For example, the high-resolution meshes around the buildings and steep regions are placed when the flooding water reaches these regions. In this work a flooding event that happened in 2002 in Glasgow, Scotland, United Kingdom has been simulated to demonstrate the capability of the adaptive unstructured mesh flooding model. The simulations have been performed using both fixed and adaptive unstructured meshes, and then results have been compared with those published 2D and 3D results. The presented method shows that the 2D adaptive mesh model provides accurate results while having a low computational cost.

A method for the computational modeling of the physics of heart murmurs

NASA Astrophysics Data System (ADS)

Seo, Jung Hee; Bakhshaee, Hani; Garreau, Guillaume; Zhu, Chi; Andreou, Andreas; Thompson, William R.; Mittal, Rajat

2017-05-01

A computational method for direct simulation of the generation and propagation of blood flow induced sounds is proposed. This computational hemoacoustic method is based on the immersed boundary approach and employs high-order finite difference methods to resolve wave propagation and scattering accurately. The current method employs a two-step, one-way coupled approach for the sound generation and its propagation through the tissue. The blood flow is simulated by solving the incompressible Navier-Stokes equations using the sharp-interface immersed boundary method, and the equations corresponding to the generation and propagation of the three-dimensional elastic wave corresponding to the murmur are resolved with a high-order, immersed boundary based, finite-difference methods in the time-domain. The proposed method is applied to a model problem of aortic stenosis murmur and the simulation results are verified and validated by comparing with known solutions as well as experimental measurements. The murmur propagation in a realistic model of a human thorax is also simulated by using the computational method. The roles of hemodynamics and elastic wave propagation on the murmur are discussed based on the simulation results.

A real-time digital computer program for the simulation of automatic spacecraft reentries

NASA Technical Reports Server (NTRS)

Kaylor, J. T.; Powell, L. F.; Powell, R. W.

1977-01-01

The automatic reentry flight dynamics simulator, a nonlinear, six-degree-of-freedom simulation, digital computer program, has been developed. The program includes a rotating, oblate earth model for accurate navigation calculations and contains adjustable gains on the aerodynamic stability and control parameters. This program uses a real-time simulation system and is designed to examine entries of vehicles which have constant mass properties whose attitudes are controlled by both aerodynamic surfaces and reaction control thrusters, and which have automatic guidance and control systems. The program has been used to study the space shuttle orbiter entry. This report includes descriptions of the equations of motion used, the control and guidance schemes that were implemented, the program flow and operation, and the hardware involved.

A methodological approach to a realistic evaluation of skin absorbed doses during manipulation of radioactive sources by means of GAMOS Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Italiano, Antonio; Amato, Ernesto; Auditore, Lucrezia; Baldari, Sergio

2018-05-01

The accurate evaluation of the radiation burden associated with radiation absorbed doses to the skin of the extremities during the manipulation of radioactive sources is a critical issue in operational radiological protection, deserving the most accurate calculation approaches available. Monte Carlo simulation of the radiation transport and interaction is the gold standard for the calculation of dose distributions in complex geometries and in presence of extended spectra of multi-radiation sources. We propose the use of Monte Carlo simulations in GAMOS, in order to accurately estimate the dose to the extremities during manipulation of radioactive sources. We report the results of these simulations for 90Y, 131I, 18F and 111In nuclides in water solutions enclosed in glass or plastic receptacles, such as vials or syringes. Skin equivalent doses at 70 μm of depth and dose-depth profiles are reported for different configurations, highlighting the importance of adopting a realistic geometrical configuration in order to get accurate dosimetric estimations. Due to the easiness of implementation of GAMOS simulations, case-specific geometries and nuclides can be adopted and results can be obtained in less than about ten minutes of computation time with a common workstation.

Discretization of the induced-charge boundary integral equation.

PubMed

Bardhan, Jaydeep P; Eisenberg, Robert S; Gillespie, Dirk

2009-07-01

Boundary-element methods (BEMs) for solving integral equations numerically have been used in many fields to compute the induced charges at dielectric boundaries. In this paper, we consider a more accurate implementation of BEM in the context of ions in aqueous solution near proteins, but our results are applicable more generally. The ions that modulate protein function are often within a few angstroms of the protein, which leads to the significant accumulation of polarization charge at the protein-solvent interface. Computing the induced charge accurately and quickly poses a numerical challenge in solving a popular integral equation using BEM. In particular, the accuracy of simulations can depend strongly on seemingly minor details of how the entries of the BEM matrix are calculated. We demonstrate that when the dielectric interface is discretized into flat tiles, the qualocation method of Tausch [IEEE Trans Comput.-Comput.-Aided Des. 20, 1398 (2001)] to compute the BEM matrix elements is always more accurate than the traditional centroid-collocation method. Qualocation is not more expensive to implement than collocation and can save significant computational time by reducing the number of boundary elements needed to discretize the dielectric interfaces.

Discretization of the induced-charge boundary integral equation

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.; Eisenberg, Robert S.; Gillespie, Dirk

2009-07-01

Boundary-element methods (BEMs) for solving integral equations numerically have been used in many fields to compute the induced charges at dielectric boundaries. In this paper, we consider a more accurate implementation of BEM in the context of ions in aqueous solution near proteins, but our results are applicable more generally. The ions that modulate protein function are often within a few angstroms of the protein, which leads to the significant accumulation of polarization charge at the protein-solvent interface. Computing the induced charge accurately and quickly poses a numerical challenge in solving a popular integral equation using BEM. In particular, the accuracy of simulations can depend strongly on seemingly minor details of how the entries of the BEM matrix are calculated. We demonstrate that when the dielectric interface is discretized into flat tiles, the qualocation method of Tausch [IEEE Trans Comput.-Comput.-Aided Des. 20, 1398 (2001)] to compute the BEM matrix elements is always more accurate than the traditional centroid-collocation method. Qualocation is not more expensive to implement than collocation and can save significant computational time by reducing the number of boundary elements needed to discretize the dielectric interfaces.

Learning Reverse Engineering and Simulation with Design Visualization

NASA Technical Reports Server (NTRS)

Hemsworth, Paul J.

2018-01-01

The Design Visualization (DV) group supports work at the Kennedy Space Center by utilizing metrology data with Computer-Aided Design (CAD) models and simulations to provide accurate visual representations that aid in decision-making. The capability to measure and simulate objects in real time helps to predict and avoid potential problems before they become expensive in addition to facilitating the planning of operations. I had the opportunity to work on existing and new models and simulations in support of DV and NASA’s Exploration Ground Systems (EGS).

Fast computation of high energy elastic collision scattering angle for electric propulsion plume simulation

NASA Astrophysics Data System (ADS)

Araki, Samuel J.

2016-11-01

In the plumes of Hall thrusters and ion thrusters, high energy ions experience elastic collisions with slow neutral atoms. These collisions involve a process of momentum exchange, altering the initial velocity vectors of the collision pair. In addition to the momentum exchange process, ions and atoms can exchange electrons, resulting in slow charge-exchange ions and fast atoms. In these simulations, it is particularly important to accurately perform computations of ion-atom elastic collisions in determining the plume current profile and assessing the integration of spacecraft components. The existing models are currently capable of accurate calculation but are not fast enough such that the calculation can be a bottleneck of plume simulations. This study investigates methods to accelerate an ion-atom elastic collision calculation that includes both momentum- and charge-exchange processes. The scattering angles are pre-computed through a classical approach with ab initio spin-orbit free potential and are stored in a two-dimensional array as functions of impact parameter and energy. When performing a collision calculation for an ion-atom pair, the scattering angle is computed by a table lookup and multiple linear interpolations, given the relative energy and randomly determined impact parameter. In order to further accelerate the calculations, the number of collision calculations is reduced by properly defining two cut-off cross-sections for the elastic scattering. In the MCC method, the target atom needs to be sampled; however, it is confirmed that initial target atom velocity does not play a significant role in typical electric propulsion plume simulations such that the sampling process is unnecessary. With these implementations, the computational run-time to perform a collision calculation is reduced significantly compared to previous methods, while retaining the accuracy of the high fidelity models.

Connecting Free Energy Surfaces in Implicit and Explicit Solvent: an Efficient Method to Compute Conformational and Solvation Free Energies

PubMed Central

Deng, Nanjie; Zhang, Bin W.; Levy, Ronald M.

2015-01-01

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions and protein-ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ~3 kcal/mol at only ~8 % of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the explicit/implicit thermodynamic cycle. PMID:26236174

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

PubMed

Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

2015-06-09

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

Accurate transport properties for H–CO and H–CO{sub 2}

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

Dagdigian, Paul J., E-mail: pjdagdigian@jhu.edu

2015-08-07

Transport properties for collisions of hydrogen atoms with CO and CO{sub 2} have been computed by means of quantum scattering calculations. The carbon oxides are important species in hydrocarbon combustion. The following potential energy surfaces (PES’s) for the interaction of the molecule fixed in its equilibrium geometry were employed: for H–CO, the PES was taken from the work of Song et al. [J. Phys. Chem. A 117, 7571 (2013)], while the PES for H–CO{sub 2} was computed in this study by a restricted coupled cluster method that included single, double, and (perturbatively) triple excitations. The computed transport properties were foundmore » to be significantly different from those computed by the conventional approach that employs isotropic Lennard-Jones (12-6) potentials. The effect of using the presently computed accurate transport properties in 1-dimensional combustion simulations of methane-air flames was investigated.« less

Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification

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

Reeve, Samuel Temple; Strachan, Alejandro, E-mail: strachan@purdue.edu

We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard–Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated undermore » three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential can be reasonably described to first order and does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.« less

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;

Fitting neuron models to spike trains.

PubMed

Rossant, Cyrille; Goodman, Dan F M; Fontaine, Bertrand; Platkiewicz, Jonathan; Magnusson, Anna K; Brette, Romain

2011-01-01

Computational modeling is increasingly used to understand the function of neural circuits in systems neuroscience. These studies require models of individual neurons with realistic input-output properties. Recently, it was found that spiking models can accurately predict the precisely timed spike trains produced by cortical neurons in response to somatically injected currents, if properly fitted. This requires fitting techniques that are efficient and flexible enough to easily test different candidate models. We present a generic solution, based on the Brian simulator (a neural network simulator in Python), which allows the user to define and fit arbitrary neuron models to electrophysiological recordings. It relies on vectorization and parallel computing techniques to achieve efficiency. We demonstrate its use on neural recordings in the barrel cortex and in the auditory brainstem, and confirm that simple adaptive spiking models can accurately predict the response of cortical neurons. Finally, we show how a complex multicompartmental model can be reduced to a simple effective spiking model.

The Space-Time Conservative Schemes for Large-Scale, Time-Accurate Flow Simulations with Tetrahedral Meshes

NASA Technical Reports Server (NTRS)

Venkatachari, Balaji Shankar; Streett, Craig L.; Chang, Chau-Lyan; Friedlander, David J.; Wang, Xiao-Yen; Chang, Sin-Chung

2016-01-01

Despite decades of development of unstructured mesh methods, high-fidelity time-accurate simulations are still predominantly carried out on structured, or unstructured hexahedral meshes by using high-order finite-difference, weighted essentially non-oscillatory (WENO), or hybrid schemes formed by their combinations. In this work, the space-time conservation element solution element (CESE) method is used to simulate several flow problems including supersonic jet/shock interaction and its impact on launch vehicle acoustics, and direct numerical simulations of turbulent flows using tetrahedral meshes. This paper provides a status report for the continuing development of the space-time conservation element solution element (CESE) numerical and software framework under the Revolutionary Computational Aerosciences (RCA) project. Solution accuracy and large-scale parallel performance of the numerical framework is assessed with the goal of providing a viable paradigm for future high-fidelity flow physics simulations.

MODFLOW equipped with a new method for the accurate simulation of axisymmetric flow

NASA Astrophysics Data System (ADS)

Samani, N.; Kompani-Zare, M.; Barry, D. A.

2004-01-01

Axisymmetric flow to a well is an important topic of groundwater hydraulics, the simulation of which depends on accurate computation of head gradients. Groundwater numerical models with conventional rectilinear grid geometry such as MODFLOW (in contrast to analytical models) generally have not been used to simulate aquifer test results at a pumping well because they are not designed or expected to closely simulate the head gradient near the well. A scaling method is proposed based on mapping the governing flow equation from cylindrical to Cartesian coordinates, and vice versa. A set of relationships and scales is derived to implement the conversion. The proposed scaling method is then embedded in MODFLOW 2000. To verify the accuracy of the method steady and unsteady flows in confined and unconfined aquifers with fully or partially penetrating pumping wells are simulated and compared with the corresponding analytical solutions. In all cases a high degree of accuracy is achieved.

Verification of sub-grid filtered drag models for gas-particle fluidized beds with immersed cylinder arrays

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

Sarkar, Avik; Sun, Xin; Sundaresan, Sankaran

2014-04-23

The accuracy of coarse-grid multiphase CFD simulations of fluidized beds may be improved via the inclusion of filtered constitutive models. In our previous study (Sarkar et al., Chem. Eng. Sci., 104, 399-412), we developed such a set of filtered drag relationships for beds with immersed arrays of cooling tubes. Verification of these filtered drag models is addressed in this work. Predictions from coarse-grid simulations with the sub-grid filtered corrections are compared against accurate, highly-resolved simulations of full-scale turbulent and bubbling fluidized beds. The filtered drag models offer a computationally efficient yet accurate alternative for obtaining macroscopic predictions, but the spatialmore » resolution of meso-scale clustering heterogeneities is sacrificed.« less

3D Staggered-Grid Finite-Difference Simulation of Acoustic Waves in Turbulent Moving Media

NASA Astrophysics Data System (ADS)

Symons, N. P.; Aldridge, D. F.; Marlin, D.; Wilson, D. K.; Sullivan, P.; Ostashev, V.

2003-12-01

Acoustic wave propagation in a three-dimensional heterogeneous moving atmosphere is accurately simulated with a numerical algorithm recently developed under the DOD Common High Performance Computing Software Support Initiative (CHSSI). Sound waves within such a dynamic environment are mathematically described by a set of four, coupled, first-order partial differential equations governing small-amplitude fluctuations in pressure and particle velocity. The system is rigorously derived from fundamental principles of continuum mechanics, ideal-fluid constitutive relations, and reasonable assumptions that the ambient atmospheric motion is adiabatic and divergence-free. An explicit, time-domain, finite-difference (FD) numerical scheme is used to solve the system for both pressure and particle velocity wavefields. The atmosphere is characterized by 3D gridded models of sound speed, mass density, and the three components of the wind velocity vector. Dependent variables are stored on staggered spatial and temporal grids, and centered FD operators possess 2nd-order and 4th-order space/time accuracy. Accurate sound wave simulation is achieved provided grid intervals are chosen appropriately. The gridding must be fine enough to reduce numerical dispersion artifacts to an acceptable level and maintain stability. The algorithm is designed to execute on parallel computational platforms by utilizing a spatial domain-decomposition strategy. Currently, the algorithm has been validated on four different computational platforms, and parallel scalability of approximately 85% has been demonstrated. Comparisons with analytic solutions for uniform and vertically stratified wind models indicate that the FD algorithm generates accurate results with either a vanishing pressure or vanishing vertical-particle velocity boundary condition. Simulations are performed using a kinematic turbulence wind profile developed with the quasi-wavelet method. In addition, preliminary results are presented using high-resolution 3D dynamic turbulent flowfields generated by a large-eddy simulation model of a stably stratified planetary boundary layer. Sandia National Laboratories is a operated by Sandia Corporation, a Lockheed Martin Company, for the USDOE under contract 94-AL85000.

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

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

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

2010-07-20

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

Efficient simulation of incompressible viscous flow over multi-element airfoils

NASA Technical Reports Server (NTRS)

Rogers, Stuart E.; Wiltberger, N. Lyn; Kwak, Dochan

1992-01-01

The incompressible, viscous, turbulent flow over single and multi-element airfoils is numerically simulated in an efficient manner by solving the incompressible Navier-Stokes equations. The computer code uses the method of pseudo-compressibility with an upwind-differencing scheme for the convective fluxes and an implicit line-relaxation solution algorithm. The motivation for this work includes interest in studying the high-lift take-off and landing configurations of various aircraft. In particular, accurate computation of lift and drag at various angles of attack, up to stall, is desired. Two different turbulence models are tested in computing the flow over an NACA 4412 airfoil; an accurate prediction of stall is obtained. The approach used for multi-element airfoils involves the use of multiple zones of structured grids fitted to each element. Two different approaches are compared: a patched system of grids, and an overlaid Chimera system of grids. Computational results are presented for two-element, three-element, and four-element airfoil configurations. Excellent agreement with experimental surface pressure coefficients is seen. The code converges in less than 200 iterations, requiring on the order of one minute of CPU time (on a CRAY YMP) per element in the airfoil configuration.

Soft tissue deformation estimation by spatio-temporal Kalman filter finite element method.

PubMed

Yarahmadian, Mehran; Zhong, Yongmin; Gu, Chengfan; Shin, Jaehyun

2018-01-01

Soft tissue modeling plays an important role in the development of surgical training simulators as well as in robot-assisted minimally invasive surgeries. It has been known that while the traditional Finite Element Method (FEM) promises the accurate modeling of soft tissue deformation, it still suffers from a slow computational process. This paper presents a Kalman filter finite element method to model soft tissue deformation in real time without sacrificing the traditional FEM accuracy. The proposed method employs the FEM equilibrium equation and formulates it as a filtering process to estimate soft tissue behavior using real-time measurement data. The model is temporally discretized using the Newmark method and further formulated as the system state equation. Simulation results demonstrate that the computational time of KF-FEM is approximately 10 times shorter than the traditional FEM and it is still as accurate as the traditional FEM. The normalized root-mean-square error of the proposed KF-FEM in reference to the traditional FEM is computed as 0.0116. It is concluded that the proposed method significantly improves the computational performance of the traditional FEM without sacrificing FEM accuracy. The proposed method also filters noises involved in system state and measurement data.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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

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

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

2015-03-28

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

Large Eddy Simulation of Turbulent Combustion

DTIC Science & Technology

2006-03-15

described accurately by the skeletal mechanism , usually the major reactants and products, NO and NO2 if we are interested in NOx formation, and any...LARGE EDDY SIMULATION OF TURBULENT COMBUSTION Principle Investigator: Heinz Pitsch Flow Physics and Computation Department of Mechanical Engineering ...are identified. These de- tailed mechanisms are reduced independently for various conditions and accuracy requirements. The skeletal mechanisms form

Direct numerical simulation of transition and turbulence in a spatially evolving boundary layer

NASA Technical Reports Server (NTRS)

Rai, Man M.; Moin, Parviz

1991-01-01

A high-order-accurate finite-difference approach to direct simulations of transition and turbulence in compressible flows is described. Attention is given to the high-free-stream disturbance case in which transition to turbulence occurs close to the leading edge. In effect, computation requirements are reduced. A method for numerically generating free-stream disturbances is presented.

BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations

PubMed Central

Ghaffarizadeh, Ahmadreza; Friedman, Samuel H.; Macklin, Paul

2016-01-01

Motivation: Computational models of multicellular systems require solving systems of PDEs for release, uptake, decay and diffusion of multiple substrates in 3D, particularly when incorporating the impact of drugs, growth substrates and signaling factors on cell receptors and subcellular systems biology. Results: We introduce BioFVM, a diffusive transport solver tailored to biological problems. BioFVM can simulate release and uptake of many substrates by cell and bulk sources, diffusion and decay in large 3D domains. It has been parallelized with OpenMP, allowing efficient simulations on desktop workstations or single supercomputer nodes. The code is stable even for large time steps, with linear computational cost scalings. Solutions are first-order accurate in time and second-order accurate in space. The code can be run by itself or as part of a larger simulator. Availability and implementation: BioFVM is written in C ++ with parallelization in OpenMP. It is maintained and available for download at http://BioFVM.MathCancer.org and http://BioFVM.sf.net under the Apache License (v2.0). Contact: paul.macklin@usc.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26656933

A parallel implementation of an off-lattice individual-based model of multicellular populations

NASA Astrophysics Data System (ADS)

Harvey, Daniel G.; Fletcher, Alexander G.; Osborne, James M.; Pitt-Francis, Joe

2015-07-01

As computational models of multicellular populations include ever more detailed descriptions of biophysical and biochemical processes, the computational cost of simulating such models limits their ability to generate novel scientific hypotheses and testable predictions. While developments in microchip technology continue to increase the power of individual processors, parallel computing offers an immediate increase in available processing power. To make full use of parallel computing technology, it is necessary to develop specialised algorithms. To this end, we present a parallel algorithm for a class of off-lattice individual-based models of multicellular populations. The algorithm divides the spatial domain between computing processes and comprises communication routines that ensure the model is correctly simulated on multiple processors. The parallel algorithm is shown to accurately reproduce the results of a deterministic simulation performed using a pre-existing serial implementation. We test the scaling of computation time, memory use and load balancing as more processes are used to simulate a cell population of fixed size. We find approximate linear scaling of both speed-up and memory consumption on up to 32 processor cores. Dynamic load balancing is shown to provide speed-up for non-regular spatial distributions of cells in the case of a growing population.

Explicit and implicit calculations of turbulent cavity flows with and without yaw angle

NASA Astrophysics Data System (ADS)

Yen, Guan-Wei

1989-08-01

Computations were performed to simulate turbulent supersonic flows past three-dimensional deep cavities with and without yaw. Simulation of these self-sustained oscillatory flows were generated through time accurate solutions of the Reynolds averaged complete Navier-Stokes equations using two different schemes: (1) MacCormack, finite-difference; and (2) implicit, upwind, finite-volume schemes. The second scheme, which is approximately 30 percent faster, is found to produce better time accurate results. The Reynolds stresses were modeled, using the Baldwin-Lomax algebraic turbulence model with certain modifications. The computational results include instantaneous and time averaged flow properties everywhere in the computational domain. Time series analyses were performed for the instantaneous pressure values on the cavity floor. The time averaged computational results show good agreement with the experimental data along the cavity floor and walls. When the yaw angle is nonzero, there is no longer a single length scale (length-to-depth ratio) for the flow, as is the case for zero yaw angle flow. The dominant directions and inclinations of the vortices are dramatically different for this nonsymmetric flow. The vortex shedding from the cavity into the mainstream flow is captured computationally. This phenomenon, which is due to the oscillation of the shear layer, is confirmed by the solutions of both schemes.

Explicit and implicit calculations of turbulent cavity flows with and without yaw angle. M.S. Thesis

NASA Technical Reports Server (NTRS)

Yen, Guan-Wei

1989-01-01

Computations were performed to simulate turbulent supersonic flows past three-dimensional deep cavities with and without yaw. Simulation of these self-sustained oscillatory flows were generated through time accurate solutions of the Reynolds averaged complete Navier-Stokes equations using two different schemes: (1) MacCormack, finite-difference; and (2) implicit, upwind, finite-volume schemes. The second scheme, which is approximately 30 percent faster, is found to produce better time accurate results. The Reynolds stresses were modeled, using the Baldwin-Lomax algebraic turbulence model with certain modifications. The computational results include instantaneous and time averaged flow properties everywhere in the computational domain. Time series analyses were performed for the instantaneous pressure values on the cavity floor. The time averaged computational results show good agreement with the experimental data along the cavity floor and walls. When the yaw angle is nonzero, there is no longer a single length scale (length-to-depth ratio) for the flow, as is the case for zero yaw angle flow. The dominant directions and inclinations of the vortices are dramatically different for this nonsymmetric flow. The vortex shedding from the cavity into the mainstream flow is captured computationally. This phenomenon, which is due to the oscillation of the shear layer, is confirmed by the solutions of both schemes.

Dimension reduction method for SPH equations

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

Tartakovsky, Alexandre M.; Scheibe, Timothy D.

2011-08-26

Smoothed Particle Hydrodynamics model of a complex multiscale processe often results in a system of ODEs with an enormous number of unknowns. Furthermore, a time integration of the SPH equations usually requires time steps that are smaller than the observation time by many orders of magnitude. A direct solution of these ODEs can be extremely expensive. Here we propose a novel dimension reduction method that gives an approximate solution of the SPH ODEs and provides an accurate prediction of the average behavior of the modeled system. The method consists of two main elements. First, effective equationss for evolution of averagemore » variables (e.g. average velocity, concentration and mass of a mineral precipitate) are obtained by averaging the SPH ODEs over the entire computational domain. These effective ODEs contain non-local terms in the form of volume integrals of functions of the SPH variables. Second, a computational closure is used to close the system of the effective equations. The computational closure is achieved via short bursts of the SPH model. The dimension reduction model is used to simulate flow and transport with mixing controlled reactions and mineral precipitation. An SPH model is used model transport at the porescale. Good agreement between direct solutions of the SPH equations and solutions obtained with the dimension reduction method for different boundary conditions confirms the accuracy and computational efficiency of the dimension reduction model. The method significantly accelerates SPH simulations, while providing accurate approximation of the solution and accurate prediction of the average behavior of the system.« less

Modelling and simulation of complex sociotechnical systems: envisioning and analysing work environments

PubMed Central

Hettinger, Lawrence J.; Kirlik, Alex; Goh, Yang Miang; Buckle, Peter

2015-01-01

Accurate comprehension and analysis of complex sociotechnical systems is a daunting task. Empirically examining, or simply envisioning the structure and behaviour of such systems challenges traditional analytic and experimental approaches as well as our everyday cognitive capabilities. Computer-based models and simulations afford potentially useful means of accomplishing sociotechnical system design and analysis objectives. From a design perspective, they can provide a basis for a common mental model among stakeholders, thereby facilitating accurate comprehension of factors impacting system performance and potential effects of system modifications. From a research perspective, models and simulations afford the means to study aspects of sociotechnical system design and operation, including the potential impact of modifications to structural and dynamic system properties, in ways not feasible with traditional experimental approaches. This paper describes issues involved in the design and use of such models and simulations and describes a proposed path forward to their development and implementation. Practitioner Summary: The size and complexity of real-world sociotechnical systems can present significant barriers to their design, comprehension and empirical analysis. This article describes the potential advantages of computer-based models and simulations for understanding factors that impact sociotechnical system design and operation, particularly with respect to process and occupational safety. PMID:25761227

Reservoir simulation with the cubic plus (cross-) association equation of state for water, CO2, hydrocarbons, and tracers

NASA Astrophysics Data System (ADS)

Moortgat, Joachim

2018-04-01

This work presents an efficient reservoir simulation framework for multicomponent, multiphase, compressible flow, based on the cubic-plus-association (CPA) equation of state (EOS). CPA is an accurate EOS for mixtures that contain non-polar hydrocarbons, self-associating polar water, and cross-associating molecules like methane, ethane, unsaturated hydrocarbons, CO2, and H2S. While CPA is accurate, its mathematical formulation is highly non-linear, resulting in excessive computational costs that have made the EOS unfeasible for large scale reservoir simulations. This work presents algorithms that overcome these bottlenecks and achieve an efficiency comparable to the much simpler cubic EOS approach. The main applications that require such accurate phase behavior modeling are 1) the study of methane leakage from high-pressure production wells and its potential impact on groundwater resources, 2) modeling of geological CO2 sequestration in brine aquifers when one is interested in more than the CO2 and H2O components, e.g. methane, other light hydrocarbons, and various tracers, and 3) enhanced oil recovery by CO2 injection in reservoirs that have previously been waterflooded or contain connate water. We present numerical examples of all those scenarios, extensive validation of the CPA EOS with experimental data, and analyses of the efficiency of our proposed numerical schemes. The accuracy, efficiency, and robustness of the presented phase split computations pave the way to more widespread adoption of CPA in reservoir simulators.

Time-Spectral Rotorcraft Simulations on Overset Grids

NASA Technical Reports Server (NTRS)

Leffell, Joshua I.; Murman, Scott M.; Pulliam, Thomas H.

2014-01-01

The Time-Spectral method is derived as a Fourier collocation scheme and applied to NASA's overset Reynolds-averaged Navier-Stokes (RANS) solver OVERFLOW. The paper outlines the Time-Spectral OVERFLOWimplementation. Successful low-speed laminar plunging NACA 0012 airfoil simulations demonstrate the capability of the Time-Spectral method to resolve the highly-vortical wakes typical of more expensive three-dimensional rotorcraft configurations. Dealiasing, in the form of spectral vanishing viscosity (SVV), facilitates the convergence of Time-Spectral calculations of high-frequency flows. Finally, simulations of the isolated V-22 Osprey tiltrotor for both hover and forward (edgewise) flight validate the three-dimensional Time-Spectral OVERFLOW implementation. The Time-Spectral hover simulation matches the time-accurate calculation using a single harmonic. Significantly more temporal modes and SVV are required to accurately compute the forward flight case because of its more active, high-frequency wake.

Simulations of string vibrations with boundary conditions of third kind using the functional transformation method

NASA Astrophysics Data System (ADS)

Trautmann, L.; Petrausch, S.; Bauer, M.

2005-09-01

The functional transformation method (FTM) is an established mathematical method for accurate simulation of multidimensional physical systems from various fields of science, including optics, heat and mass transfer, electrical engineering, and acoustics. It is a frequency-domain method based on the decomposition into eigenvectors and eigenfrequencies of the underlying physical problem. In this article, the FTM is applied to real-time simulations of vibrating strings which are ideally fixed at one end while the fixing at the other end is modeled by a frequency-dependent input impedance. Thus, boundary conditions of third kind are applied to the model at the end fixed with the input impedance. It is shown that accurate and stable simulations are achieved with nearly the same computational cost as with strings ideally fixed at both ends.

Time-Accurate Numerical Prediction of Free Flight Aerodynamics of a Finned Projectile

DTIC Science & Technology

2005-09-01

develop (with fewer dollars) more lethal and effective munitions. The munitions must stay abreast of the latest technology available to our...consuming. Computer simulations can and have provided an effective means of determining the unsteady aerodynamics and flight mechanics of guided projectile...Recently, the time-accurate technique was used to obtain improved results for Magnus moment and roll damping moment of a spinning projectile at transonic

First principles modeling of the metal-electrolyte interface: A novel approach to the study of the electrochemical interface

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

Fernandez-Serra, Maria Victoria

2016-09-12

The research objective of this proposal is the computational modeling of the metal-electrolyte interface purely from first principles. The accurate calculation of the electrostatic potential at electrically biased metal-electrolyte interfaces is a current challenge for periodic “ab-initio” simulations. It is also an essential requisite for predicting the correspondence between the macroscopic voltage and the microscopic interfacial charge distribution in electrochemical fuel cells. This interfacial charge distribution is the result of the chemical bonding between solute and metal atoms, and therefore cannot be accurately calculated with the use of semi-empirical classical force fields. The project aims to study in detail themore » structure and dynamics of aqueous electrolytes at metallic interfaces taking into account the effect of the electrode potential. Another side of the project is to produce an accurate method to simulate the water/metal interface. While both experimental and theoretical surface scientists have made a lot of progress on the understanding and characterization of both atomistic structures and reactions at the solid/vacuum interface, the theoretical description of electrochemical interfaces is still lacking behind. A reason for this is that a complete and accurate first principles description of both the liquid and the metal interfaces is still computationally too expensive and complex, since their characteristics are governed by the explicit atomic and electronic structure built at the interface as a response to environmental conditions. This project will characterize in detail how different theoretical levels of modeling describer the metal/water interface. In particular the role of van der Waals interactions will be carefully analyzed and prescriptions to perform accurate simulations will be produced.« less

Modelling terahertz radiation absorption and reflection with computational phantoms of skin and associated appendages

NASA Astrophysics Data System (ADS)

Vilagosh, Zoltan; Lajevardipour, Alireza; Wood, Andrew

2018-01-01

Finite-difference time-domain (FDTD) computational phantoms aid the analysis of THz radiation interaction with human skin. The presented computational phantoms have accurate anatomical layering and electromagnetic properties. A novel "large sheet" simulation technique is used allowing for a realistic representation of lateral absorption and reflection of in-vivo measurements. Simulations carried out to date have indicated that hair follicles act as THz propagation channels and confirms the possible role of melanin, both in nevi and skin pigmentation, to act as a significant absorber of THz radiation. A novel freezing technique has promise in increasing the depth of skin penetration of THz radiation to aid diagnostic imaging.

Development of a Aerothermoelastic-Acoustics Simulation Capability of Flight Vehicles

NASA Technical Reports Server (NTRS)

Gupta, K. K.; Choi, S. B.; Ibrahim, A.

2010-01-01

A novel numerical, finite element based analysis methodology is presented in this paper suitable for accurate and efficient simulation of practical, complex flight vehicles. An associated computer code, developed in this connection, is also described in some detail. Thermal effects of high speed flow obtained from a heat conduction analysis are incorporated in the modal analysis which in turn affects the unsteady flow arising out of interaction of elastic structures with the air. Numerical examples pertaining to representative problems are given in much detail testifying to the efficacy of the advocated techniques. This is a unique implementation of temperature effects in a finite element CFD based multidisciplinary simulation analysis capability involving large scale computations.

SIVEH: numerical computing simulation of wireless energy-harvesting sensor nodes.

PubMed

Sanchez, Antonio; Blanc, Sara; Climent, Salvador; Yuste, Pedro; Ors, Rafael

2013-09-04

The paper presents a numerical energy harvesting model for sensor nodes, SIVEH (Simulator I-V for EH), based on I-V hardware tracking. I-V tracking is demonstrated to be more accurate than traditional energy modeling techniques when some of the components present different power dissipation at either different operating voltages or drawn currents. SIVEH numerical computing allows fast simulation of long periods of time-days, weeks, months or years-using real solar radiation curves. Moreover, SIVEH modeling has been enhanced with sleep time rate dynamic adjustment, while seeking energy-neutral operation. This paper presents the model description, a functional verification and a critical comparison with the classic energy approach.

Numerical experiments in homogeneous turbulence

NASA Technical Reports Server (NTRS)

Rogallo, R. S.

1981-01-01

The direct simulation methods developed by Orszag and Patternson (1972) for isotropic turbulence were extended to homogeneous turbulence in an incompressible fluid subjected to uniform deformation or rotation. The results of simulations for irrotational strain (plane and axisymmetric), shear, rotation, and relaxation toward isotropy following axisymmetric strain are compared with linear theory and experimental data. Emphasis is placed on the shear flow because of its importance and because of the availability of accurate and detailed experimental data. The computed results are used to assess the accuracy of two popular models used in the closure of the Reynolds-stress equations. Data from a variety of the computed fields and the details of the numerical methods used in the simulation are also presented.

SIVEH: Numerical Computing Simulation of Wireless Energy-Harvesting Sensor Nodes

PubMed Central

Sanchez, Antonio; Blanc, Sara; Climent, Salvador; Yuste, Pedro; Ors, Rafael

2013-01-01

The paper presents a numerical energy harvesting model for sensor nodes, SIVEH (Simulator I–V for EH), based on I–V hardware tracking. I–V tracking is demonstrated to be more accurate than traditional energy modeling techniques when some of the components present different power dissipation at either different operating voltages or drawn currents. SIVEH numerical computing allows fast simulation of long periods of time—days, weeks, months or years—using real solar radiation curves. Moreover, SIVEH modeling has been enhanced with sleep time rate dynamic adjustment, while seeking energy-neutral operation. This paper presents the model description, a functional verification and a critical comparison with the classic energy approach. PMID:24008287

Numerical investigations in three-dimensional internal flows

NASA Astrophysics Data System (ADS)

Rose, William C.

1988-08-01

An investigation into the use of computational fluid dynamics (CFD) was performed to examine the expected heat transfer rates that will occur within the NASA-Ames 100 megawatt arc heater nozzle. This nozzle was tentatively designed and identified to provide research for a directly connected combustion experiment specifically related to the National Aerospace Plane Program (NASP) aircraft, and is expected to simulate the flow field entering the combustor section. It was found that extremely fine grids, that is very small mesh spacing near the wall, are required to accurately model the heat transfer process and, in fact, must contain a point within the laminar sublayer if results are to be taken directly from a numerical simulation code. In the present study, an alternative to this very fine mesh and its attendant increase in computational time was invoked and is based on a wall-function method. It was shown that solutions could be obtained that give accurate indications of surface heat transfer rate throughout the nozzle in approximately 1/100 of the computer time required to do the simulation directly without the use of the wall-function implementation. Finally, a maximum heating value in the throat region of the proposed slit nozzle for the 100 megawatt arc heater was shown to be approximately 6 MW per square meter.

Monte Carlo Simulation for Polychromatic X-Ray Fluorescence Computed Tomography with Sheet-Beam Geometry

PubMed Central

Jiang, Shanghai

2017-01-01

X-ray fluorescence computed tomography (XFCT) based on sheet beam can save a huge amount of time to obtain a whole set of projections using synchrotron. However, it is clearly unpractical for most biomedical research laboratories. In this paper, polychromatic X-ray fluorescence computed tomography with sheet-beam geometry is tested by Monte Carlo simulation. First, two phantoms (A and B) filled with PMMA are used to simulate imaging process through GEANT 4. Phantom A contains several GNP-loaded regions with the same size (10 mm) in height and diameter but different Au weight concentration ranging from 0.3% to 1.8%. Phantom B contains twelve GNP-loaded regions with the same Au weight concentration (1.6%) but different diameter ranging from 1 mm to 9 mm. Second, discretized presentation of imaging model is established to reconstruct more accurate XFCT images. Third, XFCT images of phantoms A and B are reconstructed by filter back-projection (FBP) and maximum likelihood expectation maximization (MLEM) with and without correction, respectively. Contrast-to-noise ratio (CNR) is calculated to evaluate all the reconstructed images. Our results show that it is feasible for sheet-beam XFCT system based on polychromatic X-ray source and the discretized imaging model can be used to reconstruct more accurate images. PMID:28567054

Fast CPU-based Monte Carlo simulation for radiotherapy dose calculation.

PubMed

Ziegenhein, Peter; Pirner, Sven; Ph Kamerling, Cornelis; Oelfke, Uwe

2015-08-07

Monte-Carlo (MC) simulations are considered to be the most accurate method for calculating dose distributions in radiotherapy. Its clinical application, however, still is limited by the long runtimes conventional implementations of MC algorithms require to deliver sufficiently accurate results on high resolution imaging data. In order to overcome this obstacle we developed the software-package PhiMC, which is capable of computing precise dose distributions in a sub-minute time-frame by leveraging the potential of modern many- and multi-core CPU-based computers. PhiMC is based on the well verified dose planning method (DPM). We could demonstrate that PhiMC delivers dose distributions which are in excellent agreement to DPM. The multi-core implementation of PhiMC scales well between different computer architectures and achieves a speed-up of up to 37[Formula: see text] compared to the original DPM code executed on a modern system. Furthermore, we could show that our CPU-based implementation on a modern workstation is between 1.25[Formula: see text] and 1.95[Formula: see text] faster than a well-known GPU implementation of the same simulation method on a NVIDIA Tesla C2050. Since CPUs work on several hundreds of GB RAM the typical GPU memory limitation does not apply for our implementation and high resolution clinical plans can be calculated.

Development of an aeroelastic methodology for surface morphing rotors

NASA Astrophysics Data System (ADS)

Cook, James R.

Helicopter performance capabilities are limited by maximum lift characteristics and vibratory loading. In high speed forward flight, dynamic stall and transonic flow greatly increase the amplitude of vibratory loads. Experiments and computational simulations alike have indicated that a variety of active rotor control devices are capable of reducing vibratory loads. For example, periodic blade twist and flap excitation have been optimized to reduce vibratory loads in various rotors. Airfoil geometry can also be modified in order to increase lift coefficient, delay stall, or weaken transonic effects. To explore the potential benefits of active controls, computational methods are being developed for aeroelastic rotor evaluation, including coupling between computational fluid dynamics (CFD) and computational structural dynamics (CSD) solvers. In many contemporary CFD/CSD coupling methods it is assumed that the airfoil is rigid to reduce the interface by single dimension. Some methods retain the conventional one-dimensional beam model while prescribing an airfoil shape to simulate active chord deformation. However, to simulate the actual response of a compliant airfoil it is necessary to include deformations that originate not only from control devices (such as piezoelectric actuators), but also inertial forces, elastic stresses, and aerodynamic pressures. An accurate representation of the physics requires an interaction with a more complete representation of loads and geometry. A CFD/CSD coupling methodology capable of communicating three-dimensional structural deformations and a distribution of aerodynamic forces over the wetted blade surface has not yet been developed. In this research an interface is created within the Fully Unstructured Navier-Stokes (FUN3D) solver that communicates aerodynamic forces on the blade surface to University of Michigan's Nonlinear Active Beam Solver (UM/NLABS -- referred to as NLABS in this thesis). Interface routines are developed for transmission of force and deflection information to achieve an aeroelastic coupling updated at each time step. The method is validated first by comparing the integrated aerodynamic work at CFD and CSD nodes to verify work conservation across the interface. Second, the method is verified by comparing the sectional blade loads and deflections of a rotor in hover and in forward flight with experimental data. Finally, stability analyses for pitch/plunge flutter and camber flutter are performed with comprehensive CSD/low-order-aerodynamics and tightly coupled CFD/CSD simulations and compared to analytical solutions of Peters' thin airfoil theory to verify proper aeroelastic behavior. The effects of simple harmonic camber actuation are examined and compared to the response predicted by Peters' finite-state (F-S) theory. In anticipation of active rotor experiments inside enclosed facilities, computational simulations are performed to evaluate the capability of CFD for accurately simulating flow inside enclosed volumes. A computational methodology for accurately simulating a rotor inside a test chamber is developed to determine the influence of test facility components and turbulence modeling and performance predictions. A number of factors that influence the physical accuracy of the simulation, such as temporal resolution, grid resolution, and aeroelasticity are also evaluated.

Utility of a novel error-stepping method to improve gradient-based parameter identification by increasing the smoothness of the local objective surface: a case-study of pulmonary mechanics.

PubMed

Docherty, Paul D; Schranz, Christoph; Chase, J Geoffrey; Chiew, Yeong Shiong; Möller, Knut

2014-05-01

Accurate model parameter identification relies on accurate forward model simulations to guide convergence. However, some forward simulation methodologies lack the precision required to properly define the local objective surface and can cause failed parameter identification. The role of objective surface smoothness in identification of a pulmonary mechanics model was assessed using forward simulation from a novel error-stepping method and a proprietary Runge-Kutta method. The objective surfaces were compared via the identified parameter discrepancy generated in a Monte Carlo simulation and the local smoothness of the objective surfaces they generate. The error-stepping method generated significantly smoother error surfaces in each of the cases tested (p<0.0001) and more accurate model parameter estimates than the Runge-Kutta method in three of the four cases tested (p<0.0001) despite a 75% reduction in computational cost. Of note, parameter discrepancy in most cases was limited to a particular oblique plane, indicating a non-intuitive multi-parameter trade-off was occurring. The error-stepping method consistently improved or equalled the outcomes of the Runge-Kutta time-integration method for forward simulations of the pulmonary mechanics model. This study indicates that accurate parameter identification relies on accurate definition of the local objective function, and that parameter trade-off can occur on oblique planes resulting prematurely halted parameter convergence. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Utilizing Direct Numerical Simulations of Transition and Turbulence in Design Optimization

NASA Technical Reports Server (NTRS)

Rai, Man M.

2015-01-01

Design optimization methods that use the Reynolds-averaged Navier-Stokes equations with the associated turbulence and transition models, or other model-based forms of the governing equations, may result in aerodynamic designs with actual performance levels that are noticeably different from the expected values because of the complexity of modeling turbulence/transition accurately in certain flows. Flow phenomena such as wake-blade interaction and trailing edge vortex shedding in turbines and compressors (examples of such flows) may require a computational approach that is free of transition/turbulence models, such as direct numerical simulations (DNS), for the underlying physics to be computed accurately. Here we explore the possibility of utilizing DNS data in designing a turbine blade section. The ultimate objective is to substantially reduce differences between predicted performance metrics and those obtained in reality. The redesign of a typical low-pressure turbine blade section with the goal of reducing total pressure loss in the row is provided as an example. The basic ideas presented here are of course just as applicable elsewhere in aerodynamic shape optimization as long as the computational costs are not excessive.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Project Integration Architecture (PIA) and Computational Analysis Programming Interface (CAPRI) for Accessing Geometry Data from CAD Files

NASA Technical Reports Server (NTRS)

Benyo, Theresa L.

2002-01-01

Integration of a supersonic inlet simulation with a computer aided design (CAD) system is demonstrated. The integration is performed using the Project Integration Architecture (PIA). PIA provides a common environment for wrapping many types of applications. Accessing geometry data from CAD files is accomplished by incorporating appropriate function calls from the Computational Analysis Programming Interface (CAPRI). CAPRI is a CAD vendor neutral programming interface that aids in acquiring geometry data directly from CAD files. The benefits of wrapping a supersonic inlet simulation into PIA using CAPRI are; direct access of geometry data, accurate capture of geometry data, automatic conversion of data units, CAD vendor neutral operation, and on-line interactive history capture. This paper describes the PIA and the CAPRI wrapper and details the supersonic inlet simulation demonstration.

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

NASA Technical Reports Server (NTRS)

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

2015-01-01

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

Advances in Numerical Boundary Conditions for Computational Aeroacoustics

NASA Technical Reports Server (NTRS)

Tam, Christopher K. W.

1997-01-01

Advances in Computational Aeroacoustics (CAA) depend critically on the availability of accurate, nondispersive, least dissipative computation algorithm as well as high quality numerical boundary treatments. This paper focuses on the recent developments of numerical boundary conditions. In a typical CAA problem, one often encounters two types of boundaries. Because a finite computation domain is used, there are external boundaries. On the external boundaries, boundary conditions simulating the solution outside the computation domain are to be imposed. Inside the computation domain, there may be internal boundaries. On these internal boundaries, boundary conditions simulating the presence of an object or surface with specific acoustic characteristics are to be applied. Numerical boundary conditions, both external or internal, developed for simple model problems are reviewed and examined. Numerical boundary conditions for real aeroacoustic problems are also discussed through specific examples. The paper concludes with a description of some much needed research in numerical boundary conditions for CAA.

Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A., Jr.

1997-01-01

Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

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

PubMed

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

2014-12-18

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

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

PubMed Central

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

2014-01-01

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

Computer Models Simulate Fine Particle Dispersion

NASA Technical Reports Server (NTRS)

2010-01-01

Through a NASA Seed Fund partnership with DEM Solutions Inc., of Lebanon, New Hampshire, scientists at Kennedy Space Center refined existing software to study the electrostatic phenomena of granular and bulk materials as they apply to planetary surfaces. The software, EDEM, allows users to import particles and obtain accurate representations of their shapes for modeling purposes, such as simulating bulk solids behavior, and was enhanced to be able to more accurately model fine, abrasive, cohesive particles. These new EDEM capabilities can be applied in many industries unrelated to space exploration and have been adopted by several prominent U.S. companies, including John Deere, Pfizer, and Procter & Gamble.

Quantitative comparison of hemodynamics in simulated and 3D angiography models of cerebral aneurysms by use of computational fluid dynamics.

PubMed

Saho, Tatsunori; Onishi, Hideo

2015-07-01

In this study, we evaluated hemodynamics using simulated models and determined how cerebral aneurysms develop in simulated and patient-specific models based on medical images. Computational fluid dynamics (CFD) was analyzed by use of OpenFOAM software. Flow velocity, stream line, and wall shear stress (WSS) were evaluated in a simulated model aneurysm with known geometry and in a three-dimensional angiographic model. The ratio of WSS at the aneurysm compared with that at the basilar artery was 1:10 in simulated model aneurysms with a diameter of 10 mm and 1:18 in the angiographic model, indicating similar tendencies. Vortex flow occurred in both model aneurysms, and the WSS decreased in larger model aneurysms. The angiographic model provided accurate CFD information, and the tendencies of simulated and angiographic models were similar. These findings indicate that hemodynamic effects are involved in the development of aneurysms.

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.

Massively-parallel FDTD simulations to address mask electromagnetic effects in hyper-NA immersion lithography

NASA Astrophysics Data System (ADS)

Tirapu Azpiroz, Jaione; Burr, Geoffrey W.; Rosenbluth, Alan E.; Hibbs, Michael

2008-03-01

In the Hyper-NA immersion lithography regime, the electromagnetic response of the reticle is known to deviate in a complicated manner from the idealized Thin-Mask-like behavior. Already, this is driving certain RET choices, such as the use of polarized illumination and the customization of reticle film stacks. Unfortunately, full 3-D electromagnetic mask simulations are computationally intensive. And while OPC-compatible mask electromagnetic field (EMF) models can offer a reasonable tradeoff between speed and accuracy for full-chip OPC applications, full understanding of these complex physical effects demands higher accuracy. Our paper describes recent advances in leveraging High Performance Computing as a critical step towards lithographic modeling of the full manufacturing process. In this paper, highly accurate full 3-D electromagnetic simulation of very large mask layouts are conducted in parallel with reasonable turnaround time, using a Blue- Gene/L supercomputer and a Finite-Difference Time-Domain (FDTD) code developed internally within IBM. A 3-D simulation of a large 2-D layout spanning 5μm×5μm at the wafer plane (and thus (20μm×20μm×0.5μm at the mask) results in a simulation with roughly 12.5GB of memory (grid size of 10nm at the mask, single-precision computation, about 30 bytes/grid point). FDTD is flexible and easily parallelizable to enable full simulations of such large layout in approximately an hour using one BlueGene/L "midplane" containing 512 dual-processor nodes with 256MB of memory per processor. Our scaling studies on BlueGene/L demonstrate that simulations up to 100μm × 100μm at the mask can be computed in a few hours. Finally, we will show that the use of a subcell technique permits accurate simulation of features smaller than the grid discretization, thus improving on the tradeoff between computational complexity and simulation accuracy. We demonstrate the correlation of the real and quadrature components that comprise the Boundary Layer representation of the EMF behavior of a mask blank to intensity measurements of the mask diffraction patterns by an Aerial Image Measurement System (AIMS) with polarized illumination. We also discuss how this model can become a powerful tool for the assessment of the impact to the lithographic process of a mask blank.

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

PubMed

Badal, Andreu; Badano, Aldo

2009-11-01

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

Multiscale Modeling of Damage Processes in Aluminum Alloys: Grain-Scale Mechanisms

NASA Technical Reports Server (NTRS)

Hochhalter, J. D.; Veilleux, M. G.; Bozek, J. E.; Glaessgen, E. H.; Ingraffea, A. R.

2008-01-01

This paper has two goals related to the development of a physically-grounded methodology for modeling the initial stages of fatigue crack growth in an aluminum alloy. The aluminum alloy, AA 7075-T651, is susceptible to fatigue cracking that nucleates from cracked second phase iron-bearing particles. Thus, the first goal of the paper is to validate an existing framework for the prediction of the conditions under which the particles crack. The observed statistics of particle cracking (defined as incubation for this alloy) must be accurately predicted to simulate the stochastic nature of microstructurally small fatigue crack (MSFC) formation. Also, only by simulating incubation of damage in a statistically accurate manner can subsequent stages of crack growth be accurately predicted. To maintain fidelity and computational efficiency, a filtering procedure was developed to eliminate particles that were unlikely to crack. The particle filter considers the distributions of particle sizes and shapes, grain texture, and the configuration of the surrounding grains. This filter helps substantially reduce the number of particles that need to be included in the microstructural models and forms the basis of the future work on the subsequent stages of MSFC, crack nucleation and microstructurally small crack propagation. A physics-based approach to simulating fracture should ultimately begin at nanometer length scale, in which atomistic simulation is used to predict the fundamental damage mechanisms of MSFC. These mechanisms include dislocation formation and interaction, interstitial void formation, and atomic diffusion. However, atomistic simulations quickly become computationally intractable as the system size increases, especially when directly linking to the already large microstructural models. Therefore, the second goal of this paper is to propose a method that will incorporate atomistic simulation and small-scale experimental characterization into the existing multiscale framework. At the microscale, the nanoscale mechanics are represented within cohesive zones where appropriate, i.e. where the mechanics observed at the nanoscale can be represented as occurring on a plane such as at grain boundaries or slip planes at a crack front. Important advancements that are yet to be made include: 1. an increased fidelity in cohesive zone modeling; 2. a means to understand how atomistic simulation scales with time; 3. a new experimental methodology for generating empirical models for CZMs and emerging materials; and 4. a validation of simulations of the damage processes at the nano-micro scale. With ever-increasing computer power, the long-term ability to employ atomistic simulation for the prognosis of structural components will not be limited by computation power, but by our lack of knowledge in incorporating atomistic models into simulations of MSFC into a multiscale framework.

Shock compression response of cold-rolled Ni/Al multilayer composites

NASA Astrophysics Data System (ADS)

Specht, Paul E.; Weihs, Timothy P.; Thadhani, Naresh N.

2017-01-01

Uniaxial strain, plate-on-plate impact experiments were performed on cold-rolled Ni/Al multilayer composites and the resulting Hugoniot was determined through time-resolved measurements combined with impedance matching. The experimental Hugoniot agreed with that previously predicted by two dimensional (2D) meso-scale calculations [Specht et al., J. Appl. Phys. 111, 073527 (2012)]. Additional 2D meso-scale simulations were performed using the same computational method as the prior study to reproduce the experimentally measured free surface velocities and stress profiles. These simulations accurately replicated the experimental profiles, providing additional validation for the previous computational work.

Efficient Parallel Algorithm For Direct Numerical Simulation of Turbulent Flows

NASA Technical Reports Server (NTRS)

Moitra, Stuti; Gatski, Thomas B.

1997-01-01

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

Efficient Parallel Kernel Solvers for Computational Fluid Dynamics Applications

NASA Technical Reports Server (NTRS)

Sun, Xian-He

1997-01-01

Distributed-memory parallel computers dominate today's parallel computing arena. These machines, such as Intel Paragon, IBM SP2, and Cray Origin2OO, have successfully delivered high performance computing power for solving some of the so-called "grand-challenge" problems. Despite initial success, parallel machines have not been widely accepted in production engineering environments due to the complexity of parallel programming. On a parallel computing system, a task has to be partitioned and distributed appropriately among processors to reduce communication cost and to attain load balance. More importantly, even with careful partitioning and mapping, the performance of an algorithm may still be unsatisfactory, since conventional sequential algorithms may be serial in nature and may not be implemented efficiently on parallel machines. In many cases, new algorithms have to be introduced to increase parallel performance. In order to achieve optimal performance, in addition to partitioning and mapping, a careful performance study should be conducted for a given application to find a good algorithm-machine combination. This process, however, is usually painful and elusive. The goal of this project is to design and develop efficient parallel algorithms for highly accurate Computational Fluid Dynamics (CFD) simulations and other engineering applications. The work plan is 1) developing highly accurate parallel numerical algorithms, 2) conduct preliminary testing to verify the effectiveness and potential of these algorithms, 3) incorporate newly developed algorithms into actual simulation packages. The work plan has well achieved. Two highly accurate, efficient Poisson solvers have been developed and tested based on two different approaches: (1) Adopting a mathematical geometry which has a better capacity to describe the fluid, (2) Using compact scheme to gain high order accuracy in numerical discretization. The previously developed Parallel Diagonal Dominant (PDD) algorithm and Reduced Parallel Diagonal Dominant (RPDD) algorithm have been carefully studied on different parallel platforms for different applications, and a NASA simulation code developed by Man M. Rai and his colleagues has been parallelized and implemented based on data dependency analysis. These achievements are addressed in detail in the paper.

Permeability Sensitivity Functions and Rapid Simulation of Hydraulic-Testing Measurements Using Perturbation Theory

NASA Astrophysics Data System (ADS)

Escobar Gómez, J. D.; Torres-Verdín, C.

2018-03-01

Single-well pressure-diffusion simulators enable improved quantitative understanding of hydraulic-testing measurements in the presence of arbitrary spatial variations of rock properties. Simulators of this type implement robust numerical algorithms which are often computationally expensive, thereby making the solution of the forward modeling problem onerous and inefficient. We introduce a time-domain perturbation theory for anisotropic permeable media to efficiently and accurately approximate the transient pressure response of spatially complex aquifers. Although theoretically valid for any spatially dependent rock/fluid property, our single-phase flow study emphasizes arbitrary spatial variations of permeability and anisotropy, which constitute key objectives of hydraulic-testing operations. Contrary to time-honored techniques, the perturbation method invokes pressure-flow deconvolution to compute the background medium's permeability sensitivity function (PSF) with a single numerical simulation run. Subsequently, the first-order term of the perturbed solution is obtained by solving an integral equation that weighs the spatial variations of permeability with the spatial-dependent and time-dependent PSF. Finally, discrete convolution transforms the constant-flow approximation to arbitrary multirate conditions. Multidimensional numerical simulation studies for a wide range of single-well field conditions indicate that perturbed solutions can be computed in less than a few CPU seconds with relative errors in pressure of <5%, corresponding to perturbations in background permeability of up to two orders of magnitude. Our work confirms that the proposed joint perturbation-convolution (JPC) method is an efficient alternative to analytical and numerical solutions for accurate modeling of pressure-diffusion phenomena induced by Neumann or Dirichlet boundary conditions.

Quantum chemical calculations of interatomic potentials for computer simulation of solids

NASA Technical Reports Server (NTRS)

1977-01-01

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

Design and Implementation of a Motor Incremental Shaft Encoder

DTIC Science & Technology

2008-09-01

SDC Student Design Center VHDL Verilog Hardware Description Language VSC Voltage Source Converters ZCE Zero Crossing Event xiii EXECUTIVE...student to make accurate predictions of voltage source converters ( VSC ) behavior via software simulation; these simulated results could also be... VSC ), and several other off-the-shelf components, a circuit board interface between FPGA and the power source, and a desktop computer [1]. Now, the

Sharp Interface Tracking in Rotating Microflows of Solvent Extraction

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

Glimm, James; Almeida, Valmor de; Jiao, Xiangmin

2013-01-08

The objective of this project is to develop a specialized sharp interface tracking simulation capability for predicting interaction of micron-sized drops and bubbles in rotating flows relevant to optimized design of contactor devices used in solvent extraction processes of spent nuclear fuel reprocessing. The primary outcomes of this project include the capability to resolve drops and bubbles micro-hydrodynamics in solvent extraction contactors, determining from first principles continuum fluid mechanics how micro-drops and bubbles interact with each other and the surrounding shearing fluid for realistic flows. In the near term, this effort will play a central role in providing parameters andmore » insight into the flow dynamics of models that average over coarser scales, say at the millimeter unit length. In the longer term, it will prove to be the platform to conduct full-device, detailed simulations as parallel computing power reaches the exaflop level. The team will develop an accurate simulation tool for flows containing interacting droplets and bubbles with sharp interfaces under conditions that mimic those found in realistic contactor operations. The main objective is to create an off-line simulation capability to model drop and bubble interactions in a domain representative of the averaged length scale. The technical approach is to combine robust interface tracking software, subgrid modeling, validation quality experiments, powerful computational hardware, and a team with simulation modeling, physical modeling and technology integration experience. Simulations will then fully resolve the microflow of drops and bubbles at the microsecond time scale. This approach is computationally intensive but very accurate in treating important coupled physical phenomena in the vicinity of interfaces. The method makes it possible to resolve spatial scales smaller than the typical distance between bubbles and to model some non-equilibrium thermodynamic features such as finite critical tension in cavitating liquids« less

Validation of Bayesian analysis of compartmental kinetic models in medical imaging.

PubMed

Sitek, Arkadiusz; Li, Quanzheng; El Fakhri, Georges; Alpert, Nathaniel M

2016-10-01

Kinetic compartmental analysis is frequently used to compute physiologically relevant quantitative values from time series of images. In this paper, a new approach based on Bayesian analysis to obtain information about these parameters is presented and validated. The closed-form of the posterior distribution of kinetic parameters is derived with a hierarchical prior to model the standard deviation of normally distributed noise. Markov chain Monte Carlo methods are used for numerical estimation of the posterior distribution. Computer simulations of the kinetics of F18-fluorodeoxyglucose (FDG) are used to demonstrate drawing statistical inferences about kinetic parameters and to validate the theory and implementation. Additionally, point estimates of kinetic parameters and covariance of those estimates are determined using the classical non-linear least squares approach. Posteriors obtained using methods proposed in this work are accurate as no significant deviation from the expected shape of the posterior was found (one-sided P>0.08). It is demonstrated that the results obtained by the standard non-linear least-square methods fail to provide accurate estimation of uncertainty for the same data set (P<0.0001). The results of this work validate new methods for a computer simulations of FDG kinetics. Results show that in situations where the classical approach fails in accurate estimation of uncertainty, Bayesian estimation provides an accurate information about the uncertainties in the parameters. Although a particular example of FDG kinetics was used in the paper, the methods can be extended for different pharmaceuticals and imaging modalities. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Sensitivity Analysis and Optimization of Enclosure Radiation with Applications to Crystal Growth

NASA Technical Reports Server (NTRS)

Tiller, Michael M.

1995-01-01

In engineering, simulation software is often used as a convenient means for carrying out experiments to evaluate physical systems. The benefit of using simulations as 'numerical' experiments is that the experimental conditions can be easily modified and repeated at much lower cost than the comparable physical experiment. The goal of these experiments is to 'improve' the process or result of the experiment. In most cases, the computational experiments employ the same trial and error approach as their physical counterparts. When using this approach for complex systems, the cause and effect relationship of the system may never be fully understood and efficient strategies for improvement never utilized. However, it is possible when running simulations to accurately and efficiently determine the sensitivity of the system results with respect to simulation to accurately and efficiently determine the sensitivity of the system results with respect to simulation parameters (e.g., initial conditions, boundary conditions, and material properties) by manipulating the underlying computations. This results in a better understanding of the system dynamics and gives us efficient means to improve processing conditions. We begin by discussing the steps involved in performing simulations. Then we consider how sensitivity information about simulation results can be obtained and ways this information may be used to improve the process or result of the experiment. Next, we discuss optimization and the efficient algorithms which use sensitivity information. We draw on all this information to propose a generalized approach for integrating simulation and optimization, with an emphasis on software programming issues. After discussing our approach to simulation and optimization we consider an application involving crystal growth. This application is interesting because it includes radiative heat transfer. We discuss the computation of radiative new factors and the impact this mode of heat transfer has on our approach. Finally, we will demonstrate the results of our optimization.

A New Algorithm with Plane Waves and Wavelets for Random Velocity Fields with Many Spatial Scales

NASA Astrophysics Data System (ADS)

Elliott, Frank W.; Majda, Andrew J.

1995-03-01

A new Monte Carlo algorithm for constructing and sampling stationary isotropic Gaussian random fields with power-law energy spectrum, infrared divergence, and fractal self-similar scaling is developed here. The theoretical basis for this algorithm involves the fact that such a random field is well approximated by a superposition of random one-dimensional plane waves involving a fixed finite number of directions. In general each one-dimensional plane wave is the sum of a random shear layer and a random acoustical wave. These one-dimensional random plane waves are then simulated by a wavelet Monte Carlo method for a single space variable developed recently by the authors. The computational results reported in this paper demonstrate remarkable low variance and economical representation of such Gaussian random fields through this new algorithm. In particular, the velocity structure function for an imcorepressible isotropic Gaussian random field in two space dimensions with the Kolmogoroff spectrum can be simulated accurately over 12 decades with only 100 realizations of the algorithm with the scaling exponent accurate to 1.1% and the constant prefactor accurate to 6%; in fact, the exponent of the velocity structure function can be computed over 12 decades within 3.3% with only 10 realizations. Furthermore, only 46,592 active computational elements are utilized in each realization to achieve these results for 12 decades of scaling behavior.

Examining ion channel properties using free-energy methods.

PubMed

Domene, Carmen; Furini, Simone

2009-01-01

Recent advances in structural biology have revealed the architecture of a number of transmembrane channels, allowing for these complex biological systems to be understood in atomistic detail. Computational simulations are a powerful tool by which the dynamic and energetic properties, and thereby the function of these protein architectures, can be investigated. The experimentally observable properties of a system are often determined more by energetic than dynamics, and therefore understanding the underlying free energy (FE) of biophysical processes is of crucial importance. Critical to the accurate evaluation of FE values are the problems of obtaining accurate sampling of complex biological energy landscapes, and of obtaining accurate representations of the potential energy of a system, this latter problem having been addressed through the development of molecular force fields. While these challenges are common to all FE methods, depending on the system under study, and the questions being asked of it, one technique for FE calculation may be preferable to another, the choice of method and simulation protocol being crucial to achieve efficiency. Applied in a correct manner, FE calculations represent a predictive and affordable computational tool with which to make relevant contact with experiments. This chapter, therefore, aims to give an overview of the most widely implemented computational methods used to calculate the FE associated with particular biochemical or biophysical events, and to highlight their recent applications to ion channels. Copyright © 2009 Elsevier Inc. All rights reserved.

An efficient two-stage approach for image-based FSI analysis of atherosclerotic arteries

PubMed Central

Rayz, Vitaliy L.; Mofrad, Mohammad R. K.; Saloner, David

2010-01-01

Patient-specific biomechanical modeling of atherosclerotic arteries has the potential to aid clinicians in characterizing lesions and determining optimal treatment plans. To attain high levels of accuracy, recent models use medical imaging data to determine plaque component boundaries in three dimensions, and fluid–structure interaction is used to capture mechanical loading of the diseased vessel. As the plaque components and vessel wall are often highly complex in shape, constructing a suitable structured computational mesh is very challenging and can require a great deal of time. Models based on unstructured computational meshes require relatively less time to construct and are capable of accurately representing plaque components in three dimensions. These models unfortunately require additional computational resources and computing time for accurate and meaningful results. A two-stage modeling strategy based on unstructured computational meshes is proposed to achieve a reasonable balance between meshing difficulty and computational resource and time demand. In this method, a coarsegrained simulation of the full arterial domain is used to guide and constrain a fine-scale simulation of a smaller region of interest within the full domain. Results for a patient-specific carotid bifurcation model demonstrate that the two-stage approach can afford a large savings in both time for mesh generation and time and resources needed for computation. The effects of solid and fluid domain truncation were explored, and were shown to minimally affect accuracy of the stress fields predicted with the two-stage approach. PMID:19756798

Control surface hinge moment prediction using computational fluid dynamics

NASA Astrophysics Data System (ADS)

Simpson, Christopher David

The following research determines the feasibility of predicting control surface hinge moments using various computational methods. A detailed analysis is conducted using a 2D GA(W)-1 airfoil with a 20% plain flap. Simple hinge moment prediction methods are tested, including empirical Datcom relations and XFOIL. Steady-state and time-accurate turbulent, viscous, Navier-Stokes solutions are computed using Fun3D. Hinge moment coefficients are computed. Mesh construction techniques are discussed. An adjoint-based mesh adaptation case is also evaluated. An NACA 0012 45-degree swept horizontal stabilizer with a 25% elevator is also evaluated using Fun3D. Results are compared with experimental wind-tunnel data obtained from references. Finally, the costs of various solution methods are estimated. Results indicate that while a steady-state Navier-Stokes solution can accurately predict control surface hinge moments for small angles of attack and deflection angles, a time-accurate solution is necessary to accurately predict hinge moments in the presence of flow separation. The ability to capture the unsteady vortex shedding behavior present in moderate to large control surface deflections is found to be critical to hinge moment prediction accuracy. Adjoint-based mesh adaptation is shown to give hinge moment predictions similar to a globally-refined mesh for a steady-state 2D simulation.

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

PubMed

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

2016-12-01

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

A Simple and Accurate Rate-Driven Infiltration Model

NASA Astrophysics Data System (ADS)

Cui, G.; Zhu, J.

2017-12-01

In this study, we develop a novel Rate-Driven Infiltration Model (RDIMOD) for simulating infiltration into soils. Unlike traditional methods, RDIMOD avoids numerically solving the highly non-linear Richards equation or simply modeling with empirical parameters. RDIMOD employs infiltration rate as model input to simulate one-dimensional infiltration process by solving an ordinary differential equation. The model can simulate the evolutions of wetting front, infiltration rate, and cumulative infiltration on any surface slope including vertical and horizontal directions. Comparing to the results from the Richards equation for both vertical infiltration and horizontal infiltration, RDIMOD simply and accurately predicts infiltration processes for any type of soils and soil hydraulic models without numerical difficulty. Taking into account the accuracy, capability, and computational effectiveness and stability, RDIMOD can be used in large-scale hydrologic and land-atmosphere modeling.

Improved haptic interface for colonoscopy simulation.

PubMed

Woo, Hyun Soo; Kim, Woo Seok; Ahn, Woojin; Lee, Doo Yong; Yi, Sun Young

2007-01-01

This paper presents an improved haptic interface of the KAIST-Ewha colonoscopy simulator II. The haptic interface enables the distal portion of the colonoscope to be freely bent while guaranteeing enough workspace and reflective forces for colonoscopy simulation. Its force-torque sensor measures profiles of the user. Manipulation of the colonoscope tip is monitored by four deflection sensors, and triggers computation to render accurate graphic images corresponding to the angle knob rotation. Tack switches are attached on the valve-actuation buttons of the colonoscope to simulate air-injection or suction, and the corresponding deformation of the colon.

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

PubMed Central

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

2012-01-01

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

Parametric Study of a YAV-8B Harrier in Ground Effect Using Time-Dependent Navier-Stokes Computations

NASA Technical Reports Server (NTRS)

Shishir, Pandya; Chaderjian, Neal; Ahmad, Jsaim; Kwak, Dochan (Technical Monitor)

2001-01-01

Flow simulations using the time-dependent Navier-Stokes equations remain a challenge for several reasons. Principal among them are the difficulty to accurately model complex flows, and the time needed to perform the computations. A parametric study of such complex problems is not considered practical due to the large cost associated with computing many time-dependent solutions. The computation time for each solution must be reduced in order to make a parametric study possible. With successful reduction of computation time, the issue of accuracy, and appropriateness of turbulence models will become more tractable.

Complex Osteotomies of Tibial Plateau Malunions Using Computer-Assisted Planning and Patient-Specific Surgical Guides.

PubMed

Fürnstahl, Philipp; Vlachopoulos, Lazaros; Schweizer, Andreas; Fucentese, Sandro F; Koch, Peter P

2015-08-01

The accurate reduction of tibial plateau malunions can be challenging without guidance. In this work, we report on a novel technique that combines 3-dimensional computer-assisted planning with patient-specific surgical guides for improving reliability and accuracy of complex intraarticular corrective osteotomies. Preoperative planning based on 3-dimensional bone models was performed to simulate fragment mobilization and reduction in 3 cases. Surgical implementation of the preoperative plan using patient-specific cutting and reduction guides was evaluated; benefits and limitations of the approach were identified and discussed. The preliminary results are encouraging and show that complex, intraarticular corrective osteotomies can be accurately performed with this technique. For selective patients with complex malunions around the tibia plateau, this method might be an attractive option, with the potential to facilitate achieving the most accurate correction possible.

Comparison of alternative designs for reducing complex neurons to equivalent cables.

PubMed

Burke, R E

2000-01-01

Reduction of the morphological complexity of actual neurons into accurate, computationally efficient surrogate models is an important problem in computational neuroscience. The present work explores the use of two morphoelectrotonic transformations, somatofugal voltage attenuation (AT cables) and signal propagation delay (DL cables), as bases for construction of electrotonically equivalent cable models of neurons. In theory, the AT and DL cables should provide more accurate lumping of membrane regions that have the same transmembrane potential than the familiar equivalent cables that are based only on somatofugal electrotonic distance (LM cables). In practice, AT and DL cables indeed provided more accurate simulations of the somatic transient responses produced by fully branched neuron models than LM cables. This was the case in the presence of a somatic shunt as well as when membrane resistivity was uniform.

Simulation of Inviscid Compressible Multi-Phase Flow with Condensation

NASA Technical Reports Server (NTRS)

Kelleners, Philip

2003-01-01

Condensation of vapours in rapid expansions of compressible gases is investigated. In the case of high temperature gradients the condensation will start at conditions well away from thermodynamic equilibrium of the fluid. In those cases homogeneous condensation is dominant over heterogeneous condensation. The present work is concerned with development of a simulation tool for computation of high speed compressible flows with homogeneous condensation. The resulting ow solver should preferably be accurate and robust to be used for simulation of industrial flows in general geometries.

Computational considerations for the simulation of shock-induced sound

NASA Technical Reports Server (NTRS)

Casper, Jay; Carpenter, Mark H.

1996-01-01

The numerical study of aeroacoustic problems places stringent demands on the choice of a computational algorithm, because it requires the ability to propagate disturbances of small amplitude and short wavelength. The demands are particularly high when shock waves are involved, because the chosen algorithm must also resolve discontinuities in the solution. The extent to which a high-order-accurate shock-capturing method can be relied upon for aeroacoustics applications that involve the interaction of shocks with other waves has not been previously quantified. Such a study is initiated in this work. A fourth-order-accurate essentially nonoscillatory (ENO) method is used to investigate the solutions of inviscid, compressible flows with shocks in a quasi-one-dimensional nozzle flow. The design order of accuracy is achieved in the smooth regions of a steady-state test case. However, in an unsteady test case, only first-order results are obtained downstream of a sound-shock interaction. The difficulty in obtaining a globally high-order-accurate solution in such a case with a shock-capturing method is demonstrated through the study of a simplified, linear model problem. Some of the difficult issues and ramifications for aeroacoustics simulations of flows with shocks that are raised by these results are discussed.

Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design.

PubMed

Sinko, William; Lindert, Steffen; McCammon, J Andrew

2013-01-01

Protein flexibility plays a major role in biomolecular recognition. In many cases, it is not obvious how molecular structure will change upon association with other molecules. In proteins, these changes can be major, with large deviations in overall backbone structure, or they can be more subtle as in a side-chain rotation. Either way the algorithms that predict the favorability of biomolecular association require relatively accurate predictions of the bound structure to give an accurate assessment of the energy involved in association. Here, we review a number of techniques that have been proposed to accommodate receptor flexibility in the simulation of small molecules binding to protein receptors. We investigate modifications to standard rigid receptor docking algorithms and also explore enhanced sampling techniques, and the combination of free energy calculations and enhanced sampling techniques. The understanding and allowance for receptor flexibility are helping to make computer simulations of ligand protein binding more accurate. These developments may help improve the efficiency of drug discovery and development. Efficiency will be essential as we begin to see personalized medicine tailored to individual patients, which means specific drugs are needed for each patient's genetic makeup. © 2012 John Wiley & Sons A/S.

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

PubMed

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

2017-10-01

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

Virtual reality neurosurgery: a simulator blueprint.

PubMed

Spicer, Mark A; van Velsen, Martin; Caffrey, John P; Apuzzo, Michael L J

2004-04-01

This article details preliminary studies undertaken to integrate the most relevant advancements across multiple disciplines in an effort to construct a highly realistic neurosurgical simulator based on a distributed computer architecture. Techniques based on modified computational modeling paradigms incorporating finite element analysis are presented, as are current and projected efforts directed toward the implementation of a novel bidirectional haptic device. Patient-specific data derived from noninvasive magnetic resonance imaging sequences are used to construct a computational model of the surgical region of interest. Magnetic resonance images of the brain may be coregistered with those obtained from magnetic resonance angiography, magnetic resonance venography, and diffusion tensor imaging to formulate models of varying anatomic complexity. The majority of the computational burden is encountered in the presimulation reduction of the computational model and allows realization of the required threshold rates for the accurate and realistic representation of real-time visual animations. Intracranial neurosurgical procedures offer an ideal testing site for the development of a totally immersive virtual reality surgical simulator when compared with the simulations required in other surgical subspecialties. The material properties of the brain as well as the typically small volumes of tissue exposed in the surgical field, coupled with techniques and strategies to minimize computational demands, provide unique opportunities for the development of such a simulator. Incorporation of real-time haptic and visual feedback is approached here and likely will be accomplished soon.

In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway

NASA Astrophysics Data System (ADS)

Ning, Jiying; Erdemci-Tandogan, Gonca; Yufenyuy, Ernest L.; Wagner, Jef; Himes, Benjamin A.; Zhao, Gongpu; Aiken, Christopher; Zandi, Roya; Zhang, Peijun

2016-12-01

HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation.

Higher-order methods for simulations on quantum computers

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

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

1999-09-01

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

Near-realtime simulations of biolelectric activity in small mammalian hearts using graphical processing units

PubMed Central

Vigmond, Edward J.; Boyle, Patrick M.; Leon, L. Joshua; Plank, Gernot

2014-01-01

Simulations of cardiac bioelectric phenomena remain a significant challenge despite continual advancements in computational machinery. Spanning large temporal and spatial ranges demands millions of nodes to accurately depict geometry, and a comparable number of timesteps to capture dynamics. This study explores a new hardware computing paradigm, the graphics processing unit (GPU), to accelerate cardiac models, and analyzes results in the context of simulating a small mammalian heart in real time. The ODEs associated with membrane ionic flow were computed on traditional CPU and compared to GPU performance, for one to four parallel processing units. The scalability of solving the PDE responsible for tissue coupling was examined on a cluster using up to 128 cores. Results indicate that the GPU implementation was between 9 and 17 times faster than the CPU implementation and scaled similarly. Solving the PDE was still 160 times slower than real time. PMID:19964295

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

PubMed

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

2018-04-05

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

Numerical Simulations of Single Flow Element in a Nuclear Thermal Thrust Chamber

NASA Technical Reports Server (NTRS)

Cheng, Gary; Ito, Yasushi; Ross, Doug; Chen, Yen-Sen; Wang, Ten-See

2007-01-01

The objective of this effort is to develop an efficient and accurate computational methodology to predict both detailed and global thermo-fluid environments of a single now element in a hypothetical solid-core nuclear thermal thrust chamber assembly, Several numerical and multi-physics thermo-fluid models, such as chemical reactions, turbulence, conjugate heat transfer, porosity, and power generation, were incorporated into an unstructured-grid, pressure-based computational fluid dynamics solver. The numerical simulations of a single now element provide a detailed thermo-fluid environment for thermal stress estimation and insight for possible occurrence of mid-section corrosion. In addition, detailed conjugate heat transfer simulations were employed to develop the porosity models for efficient pressure drop and thermal load calculations.

3D nozzle flow simulations including state-to-state kinetics calculation

NASA Astrophysics Data System (ADS)

Cutrone, L.; Tuttafesta, M.; Capitelli, M.; Schettino, A.; Pascazio, G.; Colonna, G.

2014-12-01

In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma. In this paper, we present an optimized methodology to approach plasma numerical simulation by state-to-state kinetics calculations in a fully 3D Navier-Stokes CFD solver. Numerical simulations of an expanding flow are presented aimed at comparing the behavior of state-to-state chemical kinetics models with respect to the macroscopic thermochemical non-equilibrium models that are usually used in the numerical computation of high temperature hypersonic flows. The comparison is focused both on the differences in the numerical results and on the computational effort associated with each approach.

Simulation of reactive polydisperse sprays strongly coupled to unsteady flows in solid rocket motors: Efficient strategy using Eulerian Multi-Fluid methods

NASA Astrophysics Data System (ADS)

Sibra, A.; Dupays, J.; Murrone, A.; Laurent, F.; Massot, M.

2017-06-01

In this paper, we tackle the issue of the accurate simulation of evaporating and reactive polydisperse sprays strongly coupled to unsteady gaseous flows. In solid propulsion, aluminum particles are included in the propellant to improve the global performances but the distributed combustion of these droplets in the chamber is suspected to be a driving mechanism of hydrodynamic and acoustic instabilities. The faithful prediction of two-phase interactions is a determining step for future solid rocket motor optimization. When looking at saving computational ressources as required for industrial applications, performing reliable simulations of two-phase flow instabilities appears as a challenge for both modeling and scientific computing. The size polydispersity, which conditions the droplet dynamics, is a key parameter that has to be accounted for. For moderately dense sprays, a kinetic approach based on a statistical point of view is particularly appropriate. The spray is described by a number density function and its evolution follows a Williams-Boltzmann transport equation. To solve it, we use Eulerian Multi-Fluid methods, based on a continuous discretization of the size phase space into sections, which offer an accurate treatment of the polydispersion. The objective of this paper is threefold: first to derive a new Two Size Moment Multi-Fluid model that is able to tackle evaporating polydisperse sprays at low cost while accurately describing the main driving mechanisms, second to develop a dedicated evaporation scheme to treat simultaneously mass, moment and energy exchanges with the gas and between the sections. Finally, to design a time splitting operator strategy respecting both reactive two-phase flow physics and cost/accuracy ratio required for industrial computations. Using a research code, we provide 0D validations of the new scheme before assessing the splitting technique's ability on a reference two-phase flow acoustic case. Implemented in the industrial-oriented CEDRE code, all developments allow to simulate realistic solid rocket motor configurations featuring the first polydisperse reactive computations with a fully Eulerian method.

Real-Time Hardware-in-the-Loop Simulation of Ares I Launch Vehicle

NASA Technical Reports Server (NTRS)

Tobbe, Patrick; Matras, Alex; Walker, David; Wilson, Heath; Fulton, Chris; Alday, Nathan; Betts, Kevin; Hughes, Ryan; Turbe, Michael

2009-01-01

The Ares Real-Time Environment for Modeling, Integration, and Simulation (ARTEMIS) has been developed for use by the Ares I launch vehicle System Integration Laboratory at the Marshall Space Flight Center. The primary purpose of the Ares System Integration Laboratory is to test the vehicle avionics hardware and software in a hardware - in-the-loop environment to certify that the integrated system is prepared for flight. ARTEMIS has been designed to be the real-time simulation backbone to stimulate all required Ares components for verification testing. ARTE_VIIS provides high -fidelity dynamics, actuator, and sensor models to simulate an accurate flight trajectory in order to ensure realistic test conditions. ARTEMIS has been designed to take advantage of the advances in underlying computational power now available to support hardware-in-the-loop testing to achieve real-time simulation with unprecedented model fidelity. A modular realtime design relying on a fully distributed computing architecture has been implemented.

Control of joint motion simulators for biomechanical research

NASA Technical Reports Server (NTRS)

Colbaugh, R.; Glass, K.

1992-01-01

The authors present a hierarchical adaptive algorithm for controlling upper extremity human joint motion simulators. A joint motion simulator is a computer-controlled, electromechanical system which permits the application of forces to the tendons of a human cadaver specimen in such a way that the cadaver joint under study achieves a desired motion in a physiologic manner. The proposed control scheme does not require knowledge of the cadaver specimen dynamic model, and solves on-line the indeterminate problem which arises because human joints typically possess more actuators than degrees of freedom. Computer simulation results are given for an elbow/forearm system and wrist/hand system under hierarchical control. The results demonstrate that any desired normal joint motion can be accurately tracked with the proposed algorithm. These simulation results indicate that the controller resolved the indeterminate problem redundancy in a physiologic manner, and show that the control scheme was robust to parameter uncertainty and to sensor noise.

Creation of an idealized nasopharynx geometry for accurate computational fluid dynamics simulations of nasal airflow in patient-specific models lacking the nasopharynx anatomy

PubMed Central

Borojeni, Azadeh A.T.; Frank-Ito, Dennis O.; Kimbell, Julia S.; Rhee, John S.; Garcia, Guilherme J. M.

2016-01-01

Virtual surgery planning based on computational fluid dynamics (CFD) simulations has the potential to improve surgical outcomes for nasal airway obstruction (NAO) patients, but the benefits of virtual surgery planning must outweigh the risks of radiation exposure. Cone beam computed tomography (CBCT) scans represent an attractive imaging modality for virtual surgery planning due to lower costs and lower radiation exposures compared with conventional CT scans. However, to minimize the radiation exposure, the CBCT sinusitis protocol sometimes images only the nasal cavity, excluding the nasopharynx. The goal of this study was to develop an idealized nasopharynx geometry for accurate representation of outlet boundary conditions when the nasopharynx geometry is unavailable. Anatomically-accurate models of the nasopharynx created from thirty CT scans were intersected with planes rotated at different angles to obtain an average geometry. Cross sections of the idealized nasopharynx were approximated as ellipses with cross-sectional areas and aspect ratios equal to the average in the actual patient-specific models. CFD simulations were performed to investigate whether nasal airflow patterns were affected when the CT-based nasopharynx was replaced by the idealized nasopharynx in 10 NAO patients. Despite the simple form of the idealized geometry, all biophysical variables (nasal resistance, airflow rate, and heat fluxes) were very similar in the idealized vs. patient-specific models. The results confirmed the expectation that the nasopharynx geometry has a minimal effect in the nasal airflow patterns during inspiration. The idealized nasopharynx geometry will be useful in future CFD studies of nasal airflow based on medical images that exclude the nasopharynx. PMID:27525807

Numerical sensitivity analysis of a variational data assimilation procedure for cardiac conductivities

NASA Astrophysics Data System (ADS)

Barone, Alessandro; Fenton, Flavio; Veneziani, Alessandro

2017-09-01

An accurate estimation of cardiac conductivities is critical in computational electro-cardiology, yet experimental results in the literature significantly disagree on the values and ratios between longitudinal and tangential coefficients. These are known to have a strong impact on the propagation of potential particularly during defibrillation shocks. Data assimilation is a procedure for merging experimental data and numerical simulations in a rigorous way. In particular, variational data assimilation relies on the least-square minimization of the misfit between simulations and experiments, constrained by the underlying mathematical model, which in this study is represented by the classical Bidomain system, or its common simplification given by the Monodomain problem. Operating on the conductivity tensors as control variables of the minimization, we obtain a parameter estimation procedure. As the theory of this approach currently provides only an existence proof and it is not informative for practical experiments, we present here an extensive numerical simulation campaign to assess practical critical issues such as the size and the location of the measurement sites needed for in silico test cases of potential experimental and realistic settings. This will be finalized with a real validation of the variational data assimilation procedure. Results indicate the presence of lower and upper bounds for the number of sites which guarantee an accurate and minimally redundant parameter estimation, the location of sites being generally non critical for properly designed experiments. An effective combination of parameter estimation based on the Monodomain and Bidomain models is tested for the sake of computational efficiency. Parameter estimation based on the Monodomain equation potentially leads to the accurate computation of the transmembrane potential in real settings.

Dynamic Load Predictions for Launchers Using Extra-Large Eddy Simulations X-Les

NASA Astrophysics Data System (ADS)

Maseland, J. E. J.; Soemarwoto, B. I.; Kok, J. C.

2005-02-01

Flow-induced unsteady loads can have a strong impact on performance and flight characteristics of aerospace vehicles and therefore play a crucial role in their design and operation. Complementary to costly flight tests and delicate wind-tunnel experiments, unsteady loads can be calculated using time-accurate Computational Fluid Dynamics. A capability to accurately predict the dynamic loads on aerospace structures at flight Reynolds numbers can be of great value for the design and analysis of aerospace vehicles. Advanced space launchers are subject to dynamic loads in the base region during the ascent to space. In particular the engine and nozzle experience aerodynamic pressure fluctuations resulting from massive flow separations. Understanding these phenomena is essential for performance enhancements for future launchers which operate a larger nozzle. A new hybrid RANS-LES turbulence modelling approach termed eXtra-Large Eddy Simulations (X-LES) holds the promise to capture the flow structures associated with massive separations and enables the prediction of the broad-band spectrum of dynamic loads. This type of method has become a focal point, reducing the cost of full LES, driven by the demand for their applicability in an industrial environment. The industrial feasibility of X-LES simulations is demonstrated by computing the unsteady aerodynamic loads on the main-engine nozzle of a generic space launcher configuration. The potential to calculate the dynamic loads is qualitatively assessed for transonic flow conditions in a comparison to wind-tunnel experiments. In terms of turn-around-times, X-LES computations are already feasible within the time-frames of the development process to support the structural design. Key words: massive separated flows; buffet loads; nozzle vibrations; space launchers; time-accurate CFD; composite RANS-LES formulation.

Department of Defense High Performance Computing Modernization Program. 2007 Annual Report

DTIC Science & Technology

2008-03-01

Directorate, Kirtland AFB, NM Applications of Time-Accurate CFD in Order to Account for Blade -Row Interactions and Distortion Transfer in the Design of...Patterson AFB, OH Direct Numerical Simulations of Active Control for Low- Pressure Turbine Blades Herman Fasel, University of Arizona, Tucson, AZ (Air Force...interactions with the rotor wake . These HI-ARMS computations compare favorably with available wind tunnel test measurements of surface and flowfield

Color appearance for photorealistic image synthesis

NASA Astrophysics Data System (ADS)

Marini, Daniele; Rizzi, Alessandro; Rossi, Maurizio

2000-12-01

Photorealistic Image Synthesis is a relevant research and application field in computer graphics, whose aim is to produce synthetic images that are undistinguishable from real ones. Photorealism is based upon accurate computational models of light material interaction, that allow us to compute the spectral intensity light field of a geometrically described scene. The fundamental methods are ray tracing and radiosity. While radiosity allows us to compute the diffuse component of the emitted and reflected light, applying ray tracing in a two pass solution we can also cope with non diffuse properties of the model surfaces. Both methods can be implemented to generate an accurate photometric distribution of light of the simulated environment. A still open problem is the visualization phase, whose purpose is to display the final result of the simulated mode on a monitor screen or on a printed paper. The tone reproduction problem consists of finding the best solution to compress the extended dynamic range of the computed light field into the limited range of the displayable colors. Recently some scholars have addressed this problem considering the perception stage of image formation, so including a model of the human visual system in the visualization process. In this paper we present a working hypothesis to solve the tone reproduction problem of synthetic image generation, integrating Retinex perception model into the photo realistic image synthesis context.

A computer program for the simulation of heat and moisture flow in soils

NASA Technical Reports Server (NTRS)

Camillo, P.; Schmugge, T. J.

1981-01-01

A computer program that simulates the flow of heat and moisture in soils is described. The space-time dependence of temperature and moisture content is described by a set of diffusion-type partial differential equations. The simulator uses a predictor/corrector to numerically integrate them, giving wetness and temperature profiles as a function of time. The simulator was used to generate solutions to diffusion-type partial differential equations for which analytical solutions are known. These equations include both constant and variable diffusivities, and both flux and constant concentration boundary conditions. In all cases, the simulated and analytic solutions agreed to within the error bounds which were imposed on the integrator. Simulations of heat and moisture flow under actual field conditions were also performed. Ground truth data were used for the boundary conditions and soil transport properties. The qualitative agreement between simulated and measured profiles is an indication that the model equations are reasonably accurate representations of the physical processes involved.

Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces.

PubMed

Bardhan, Jaydeep P; Altman, Michael D; Willis, David J; Lippow, Shaun M; Tidor, Bruce; White, Jacob K

2007-07-07

Surface formulations of biophysical modeling problems offer attractive theoretical and computational properties. Numerical simulations based on these formulations usually begin with discretization of the surface under consideration; often, the surface is curved, possessing complicated structure and possibly singularities. Numerical simulations commonly are based on approximate, rather than exact, discretizations of these surfaces. To assess the strength of the dependence of simulation accuracy on the fidelity of surface representation, here methods were developed to model several important surface formulations using exact surface discretizations. Following and refining Zauhar's work [J. Comput.-Aided Mol. Des. 9, 149 (1995)], two classes of curved elements were defined that can exactly discretize the van der Waals, solvent-accessible, and solvent-excluded (molecular) surfaces. Numerical integration techniques are presented that can accurately evaluate nonsingular and singular integrals over these curved surfaces. After validating the exactness of the surface discretizations and demonstrating the correctness of the presented integration methods, a set of calculations are presented that compare the accuracy of approximate, planar-triangle-based discretizations and exact, curved-element-based simulations of surface-generalized-Born (sGB), surface-continuum van der Waals (scvdW), and boundary-element method (BEM) electrostatics problems. Results demonstrate that continuum electrostatic calculations with BEM using curved elements, piecewise-constant basis functions, and centroid collocation are nearly ten times more accurate than planar-triangle BEM for basis sets of comparable size. The sGB and scvdW calculations give exceptional accuracy even for the coarsest obtainable discretized surfaces. The extra accuracy is attributed to the exact representation of the solute-solvent interface; in contrast, commonly used planar-triangle discretizations can only offer improved approximations with increasing discretization and associated increases in computational resources. The results clearly demonstrate that the methods for approximate integration on an exact geometry are far more accurate than exact integration on an approximate geometry. A MATLAB implementation of the presented integration methods and sample data files containing curved-element discretizations of several small molecules are available online as supplemental material.

Electrochemical carbon dioxide concentrator: Math model

NASA Technical Reports Server (NTRS)

Marshall, R. D.; Schubert, F. H.; Carlson, J. N.

1973-01-01

A steady state computer simulation model of an Electrochemical Depolarized Carbon Dioxide Concentrator (EDC) has been developed. The mathematical model combines EDC heat and mass balance equations with empirical correlations derived from experimental data to describe EDC performance as a function of the operating parameters involved. The model is capable of accurately predicting performance over EDC operating ranges. Model simulation results agree with the experimental data obtained over the prediction range.

Simulation-Based Airframe Noise Prediction of a Full-Scale, Full Aircraft

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Fares, Ehab

2016-01-01

A previously validated computational approach applied to an 18%-scale, semi-span Gulfstream aircraft model was extended to the full-scale, full-span aircraft in the present investigation. The full-scale flap and main landing gear geometries used in the simulations are nearly identical to those flown on the actual aircraft. The lattice Boltzmann solver PowerFLOW® was used to perform time-accurate predictions of the flow field associated with this aircraft. The simulations were performed at a Mach number of 0.2 with the flap deflected 39 deg. and main landing gear deployed (landing configuration). Special attention was paid to the accurate prediction of major sources of flap tip and main landing gear noise. Computed farfield noise spectra for three selected baseline configurations (flap deflected 39 deg. with and without main gear extended, and flap deflected 0 deg. with gear deployed) are presented. The flap brackets are shown to be important contributors to the farfield noise spectra in the mid- to high-frequency range. Simulated farfield noise spectra for the baseline configurations, obtained using a Ffowcs Williams and Hawkings acoustic analogy approach, were found to be in close agreement with acoustic measurements acquired during the 2006 NASA-Gulfstream joint flight test of the same aircraft.

Bond breaking in epoxy systems: A combined QM/MM approach

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

Barr, Stephen A.; Ecker, Allison M.; Berry, Rajiv J., E-mail: Rajiv.Berry@us.af.mil

2016-06-28

A novel method to combine quantum mechanics (QM) and molecular mechanics has been developed to accurately and efficiently account for covalent bond breaking in polymer systems under high strain without the use of predetermined break locations. Use of this method will provide a better fundamental understanding of the mechano-chemical origins of fracture in thermosets. Since classical force fields cannot accurately account for bond breaking, and QM is too demanding to simulate large systems, a hybrid approach is required. In the method presented here, strain is applied to the system using a classical force field, and all bond lengths are monitored.more » When a bond is stretched past a threshold value, a zone surrounding the bond is used in a QM energy minimization to determine which, if any, bonds break. The QM results are then used to reconstitute the system to continue the classical simulation at progressively larger strain until another QM calculation is triggered. In this way, a QM calculation is only computed when and where needed, allowing for efficient simulations. A robust QM method for energy minimization has been determined, as well as appropriate values for the QM zone size and the threshold bond length. Compute times do not differ dramatically from classical molecular mechanical simulations.« less

Transient Vibration Prediction for Rotors on Ball Bearings Using Load-dependent Non-linear Bearing Stiffness

NASA Technical Reports Server (NTRS)

Fleming, David P.; Poplawski, J. V.

2002-01-01

Rolling-element bearing forces vary nonlinearly with bearing deflection. Thus an accurate rotordynamic transient analysis requires bearing forces to be determined at each step of the transient solution. Analyses have been carried out to show the effect of accurate bearing transient forces (accounting for non-linear speed and load dependent bearing stiffness) as compared to conventional use of average rolling-element bearing stiffness. Bearing forces were calculated by COBRA-AHS (Computer Optimized Ball and Roller Bearing Analysis - Advanced High Speed) and supplied to the rotordynamics code ARDS (Analysis of Rotor Dynamic Systems) for accurate simulation of rotor transient behavior. COBRA-AHS is a fast-running 5 degree-of-freedom computer code able to calculate high speed rolling-element bearing load-displacement data for radial and angular contact ball bearings and also for cylindrical and tapered roller beatings. Results show that use of nonlinear bearing characteristics is essential for accurate prediction of rotordynamic behavior.

Numerical modeling of the SNS H{sup −} ion source

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

Veitzer, Seth A.; Beckwith, Kristian R. C.; Kundrapu, Madhusudhan

Ion source rf antennas that produce H- ions can fail when plasma heating causes ablation of the insulating coating due to small structural defects such as cracks. Reducing antenna failures that reduce the operating capabilities of the Spallation Neutron Source (SNS) accelerator is one of the top priorities of the SNS H- Source Program at ORNL. Numerical modeling of ion sources can provide techniques for optimizing design in order to reduce antenna failures. There are a number of difficulties in developing accurate models of rf inductive plasmas. First, a large range of spatial and temporal scales must be resolved inmore » order to accurately capture the physics of plasma motion, including the Debye length, rf frequencies on the order of tens of MHz, simulation time scales of many hundreds of rf periods, large device sizes on tens of cm, and ion motions that are thousands of times slower than electrons. This results in large simulation domains with many computational cells for solving plasma and electromagnetic equations, short time steps, and long-duration simulations. In order to reduce the computational requirements, one can develop implicit models for both fields and particle motions (e.g. divergence-preserving ADI methods), various electrostatic models, or magnetohydrodynamic models. We have performed simulations using all three of these methods and have found that fluid models have the greatest potential for giving accurate solutions while still being fast enough to perform long timescale simulations in a reasonable amount of time. We have implemented a number of fluid models with electromagnetics using the simulation tool USim and applied them to modeling the SNS H- ion source. We found that a reduced, single-fluid MHD model with an imposed magnetic field due to the rf antenna current and the confining multi-cusp field generated increased bulk plasma velocities of > 200 m/s in the region of the antenna where ablation is often observed in the SNS source. We report here on comparisons of simulated plasma parameters and code performance using more accurate physical models, such as two-temperature extended MHD models, for both a related benchmark system describing a inductively coupled plasma reactor, and for the SNS ion source. We also present results from scaling studies for mesh generation and solvers in the USim simulation code.« less

Computing the total atmospheric refraction for real-time optical imaging sensor simulation

NASA Astrophysics Data System (ADS)

Olson, Richard F.

2015-05-01

Fast and accurate computation of light path deviation due to atmospheric refraction is an important requirement for real-time simulation of optical imaging sensor systems. A large body of existing literature covers various methods for application of Snell's Law to the light path ray tracing problem. This paper provides a discussion of the adaptation to real time simulation of atmospheric refraction ray tracing techniques used in mid-1980's LOWTRAN releases. The refraction ray trace algorithm published in a LOWTRAN-6 technical report by Kneizys (et. al.) has been coded in MATLAB for development, and in C-language for simulation use. To this published algorithm we have added tuning parameters for variable path segment lengths, and extensions for Earth grazing and exoatmospheric "near Earth" ray paths. Model atmosphere properties used to exercise the refraction algorithm were obtained from tables published in another LOWTRAN-6 related report. The LOWTRAN-6 based refraction model is applicable to atmospheric propagation at wavelengths in the IR and visible bands of the electromagnetic spectrum. It has been used during the past two years by engineers at the U.S. Army Aviation and Missile Research, Development and Engineering Center (AMRDEC) in support of several advanced imaging sensor simulations. Recently, a faster (but sufficiently accurate) method using Gauss-Chebyshev Quadrature integration for evaluating the refraction integral was adopted.

Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters.

PubMed

Tieleman, D Peter

2006-10-01

A key function of biological membranes is to provide mechanisms for the controlled transport of ions, nutrients, metabolites, peptides and proteins between a cell and its environment. We are using computer simulations to study several processes involved in transport. In model membranes, the distribution of small molecules can be accurately calculated; we are making progress towards understanding the factors that determine the partitioning behaviour in the inhomogeneous lipid environment, with implications for drug distribution, membrane protein folding and the energetics of voltage gating. Lipid bilayers can be simulated at a scale that is sufficiently large to study significant defects, such as those caused by electroporation. Computer simulations of complex membrane proteins, such as potassium channels and ATP-binding cassette (ABC) transporters, can give detailed information about the atomistic dynamics that form the basis of ion transport, selectivity, conformational change and the molecular mechanism of ATP-driven transport. This is illustrated in the present review with recent simulation studies of the voltage-gated potassium channel KvAP and the ABC transporter BtuCD.

Challenges and solutions for realistic room simulation

NASA Astrophysics Data System (ADS)

Begault, Durand R.

2002-05-01

Virtual room acoustic simulation (auralization) techniques have traditionally focused on answering questions related to speech intelligibility or musical quality, typically in large volumetric spaces. More recently, auralization techniques have been found to be important for the externalization of headphone-reproduced virtual acoustic images. Although externalization can be accomplished using a minimal simulation, data indicate that realistic auralizations need to be responsive to head motion cues for accurate localization. Computational demands increase when providing for the simulation of coupled spaces, small rooms lacking meaningful reverberant decays, or reflective surfaces in outdoor environments. Auditory threshold data for both early reflections and late reverberant energy levels indicate that much of the information captured in acoustical measurements is inaudible, minimizing the intensive computational requirements of real-time auralization systems. Results are presented for early reflection thresholds as a function of azimuth angle, arrival time, and sound-source type, and reverberation thresholds as a function of reverberation time and level within 250-Hz-2-kHz octave bands. Good agreement is found between data obtained in virtual room simulations and those obtained in real rooms, allowing a strategy for minimizing computational requirements of real-time auralization systems.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Process Simulation of Gas Metal Arc Welding Software

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

Murray, Paul E.

2005-09-06

ARCWELDER is a Windows-based application that simulates gas metal arc welding (GMAW) of steel and aluminum. The software simulates the welding process in an accurate and efficient manner, provides menu items for process parameter selection, and includes a graphical user interface with the option to animate the process. The user enters the base and electrode material, open circuit voltage, wire diameter, wire feed speed, welding speed, and standoff distance. The program computes the size and shape of a square-groove or V-groove weld in the flat position. The program also computes the current, arc voltage, arc length, electrode extension, transfer ofmore » droplets, heat input, filler metal deposition, base metal dilution, and centerline cooling rate, in English or SI units. The simulation may be used to select welding parameters that lead to desired operation conditions.« less

Parameter Estimation for a Turbulent Buoyant Jet Using Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Christopher, Jason D.; Wimer, Nicholas T.; Hayden, Torrey R. S.; Lapointe, Caelan; Grooms, Ian; Rieker, Gregory B.; Hamlington, Peter E.

2016-11-01

Approximate Bayesian Computation (ABC) is a powerful tool that allows sparse experimental or other "truth" data to be used for the prediction of unknown model parameters in numerical simulations of real-world engineering systems. In this presentation, we introduce the ABC approach and then use ABC to predict unknown inflow conditions in simulations of a two-dimensional (2D) turbulent, high-temperature buoyant jet. For this test case, truth data are obtained from a simulation with known boundary conditions and problem parameters. Using spatially-sparse temperature statistics from the 2D buoyant jet truth simulation, we show that the ABC method provides accurate predictions of the true jet inflow temperature. The success of the ABC approach in the present test suggests that ABC is a useful and versatile tool for engineering fluid dynamics research.

Successes and Challenges of Incompressible Flow Simulation

NASA Technical Reports Server (NTRS)

Kwak, Dochan; Kiris, Cetin

2003-01-01

During the past thirty years, numerical methods and simulation tools for incompressible flows have been advanced as a subset of CFD discipline. Even though incompressible flows are encountered in many areas of engineering, simulation of compressible flow has been the major driver for developing computational algorithms and tools. This is probably due to rather stringent requirements for predicting aerodynamic performance characteristics of flight vehicles, while flow devices involving low speed or incompressible flow could be reasonably well designed without resorting to accurate numerical simulations. As flow devices are required to be more sophisticated and highly efficient, CFD tools become indispensable in fluid engineering for incompressible and low speed flow. This paper is intended to review some of the successes made possible by advances in computational technologies during the same period, and discuss some of the current challenges.

Accuracy evaluation of fluoroscopy-based 2D and 3D pose reconstruction with unicompartmental knee arthroplasty.

PubMed

Van Duren, B H; Pandit, H; Beard, D J; Murray, D W; Gill, H S

2009-04-01

The recent development in Oxford lateral unicompartmental knee arthroplasty (UKA) design requires a valid method of assessing its kinematics. In particular, the use of single plane fluoroscopy to reconstruct the 3D kinematics of the implanted knee. The method has been used previously to investigate the kinematics of UKA, but mostly it has been used in conjunction with total knee arthroplasty (TKA). However, no accuracy assessment of the method when used for UKA has previously been reported. In this study we performed computer simulation tests to investigate the effect of the different geometry of the unicompartmental implant has on the accuracy of the method in comparison to the total knee implants. A phantom was built to perform in vitro tests to determine the accuracy of the method for UKA. The computer simulations suggested that the use of the method for UKA would prove less accurate than for TKA's. The rotational degrees of freedom for the femur showed greatest disparity between the UKA and TKA. The phantom tests showed that the in-plane translations were accurate to <0.5mm RMS and the out-of-plane translations were less accurate with 4.1mm RMS. The rotational accuracies were between 0.6 degrees and 2.3 degrees which are less accurate than those reported in the literature for TKA, however, the method is sufficient for studying overall knee kinematics.

Oxygen transport properties estimation by DSMC-CT simulations

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

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

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

Optimization of tissue physical parameters for accurate temperature estimation from finite-element simulation of radiofrequency ablation.

PubMed

Subramanian, Swetha; Mast, T Douglas

2015-10-07

Computational finite element models are commonly used for the simulation of radiofrequency ablation (RFA) treatments. However, the accuracy of these simulations is limited by the lack of precise knowledge of tissue parameters. In this technical note, an inverse solver based on the unscented Kalman filter (UKF) is proposed to optimize values for specific heat, thermal conductivity, and electrical conductivity resulting in accurately simulated temperature elevations. A total of 15 RFA treatments were performed on ex vivo bovine liver tissue. For each RFA treatment, 15 finite-element simulations were performed using a set of deterministically chosen tissue parameters to estimate the mean and variance of the resulting tissue ablation. The UKF was implemented as an inverse solver to recover the specific heat, thermal conductivity, and electrical conductivity corresponding to the measured area of the ablated tissue region, as determined from gross tissue histology. These tissue parameters were then employed in the finite element model to simulate the position- and time-dependent tissue temperature. Results show good agreement between simulated and measured temperature.

A polynomial chaos approach to the analysis of vehicle dynamics under uncertainty

NASA Astrophysics Data System (ADS)

Kewlani, Gaurav; Crawford, Justin; Iagnemma, Karl

2012-05-01

The ability of ground vehicles to quickly and accurately analyse their dynamic response to a given input is critical to their safety and efficient autonomous operation. In field conditions, significant uncertainty is associated with terrain and/or vehicle parameter estimates, and this uncertainty must be considered in the analysis of vehicle motion dynamics. Here, polynomial chaos approaches that explicitly consider parametric uncertainty during modelling of vehicle dynamics are presented. They are shown to be computationally more efficient than the standard Monte Carlo scheme, and experimental results compared with the simulation results performed on ANVEL (a vehicle simulator) indicate that the method can be utilised for efficient and accurate prediction of vehicle motion in realistic scenarios.

Chemical vapor deposition fluid flow simulation modelling tool

NASA Technical Reports Server (NTRS)

Bullister, Edward T.

1992-01-01

Accurate numerical simulation of chemical vapor deposition (CVD) processes requires a general purpose computational fluid dynamics package combined with specialized capabilities for high temperature chemistry. In this report, we describe the implementation of these specialized capabilities in the spectral element code NEKTON. The thermal expansion of the gases involved is shown to be accurately approximated by the low Mach number perturbation expansion of the incompressible Navier-Stokes equations. The radiative heat transfer between multiple interacting radiating surfaces is shown to be tractable using the method of Gebhart. The disparate rates of reaction and diffusion in CVD processes are calculated via a point-implicit time integration scheme. We demonstrate the use above capabilities on prototypical CVD applications.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

A semi-analytical bearing model considering outer race flexibility for model based bearing load monitoring

NASA Astrophysics Data System (ADS)

Kerst, Stijn; Shyrokau, Barys; Holweg, Edward

2018-05-01

This paper proposes a novel semi-analytical bearing model addressing flexibility of the bearing outer race structure. It furthermore presents the application of this model in a bearing load condition monitoring approach. The bearing model is developed as current computational low cost bearing models fail to provide an accurate description of the more and more common flexible size and weight optimized bearing designs due to their assumptions of rigidity. In the proposed bearing model raceway flexibility is described by the use of static deformation shapes. The excitation of the deformation shapes is calculated based on the modelled rolling element loads and a Fourier series based compliance approximation. The resulting model is computational low cost and provides an accurate description of the rolling element loads for flexible outer raceway structures. The latter is validated by a simulation-based comparison study with a well-established bearing simulation software tool. An experimental study finally shows the potential of the proposed model in a bearing load monitoring approach.

Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids

NASA Astrophysics Data System (ADS)

Cheng, Bingqing; Ceriotti, Michele

2018-02-01

The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures.

Surface wind accuracy for modeling mineral dust emissions: Comparing two regional models in a Bodélé case study

NASA Astrophysics Data System (ADS)

Laurent, B.; Heinold, B.; Tegen, I.; Bouet, C.; Cautenet, G.

2008-05-01

After a decade of research on improving the description of surface and soil features in desert regions to accurately model mineral dust emissions, we now emphasize the need for deeper evaluating the accuracy of modeled 10-m surface wind speeds U 10 . Two mesoscale models, the Lokal-Modell (LM) and the Regional Atmospheric Modeling System (RAMS), coupled with an explicit dust emission model have previously been used to simulate mineral dust events in the Bodélé region. We compare LM and RAMS U 10 , together with measurements at the Chicha site (BoDEx campaign) and Faya-Largeau meteorological station. Surface features and soil schemes are investigated to correctly simulate U 10 intensity and diurnal variability. The uncertainties in dust emissions computed with LM and RAMS U 10 and different soil databases are estimated. This sensitivity study shows the importance of accurate computation of surface winds to improve the quantification of regional dust emissions from the Bodélé

Fitting Neuron Models to Spike Trains

PubMed Central

Rossant, Cyrille; Goodman, Dan F. M.; Fontaine, Bertrand; Platkiewicz, Jonathan; Magnusson, Anna K.; Brette, Romain

2011-01-01

Computational modeling is increasingly used to understand the function of neural circuits in systems neuroscience. These studies require models of individual neurons with realistic input–output properties. Recently, it was found that spiking models can accurately predict the precisely timed spike trains produced by cortical neurons in response to somatically injected currents, if properly fitted. This requires fitting techniques that are efficient and flexible enough to easily test different candidate models. We present a generic solution, based on the Brian simulator (a neural network simulator in Python), which allows the user to define and fit arbitrary neuron models to electrophysiological recordings. It relies on vectorization and parallel computing techniques to achieve efficiency. We demonstrate its use on neural recordings in the barrel cortex and in the auditory brainstem, and confirm that simple adaptive spiking models can accurately predict the response of cortical neurons. Finally, we show how a complex multicompartmental model can be reduced to a simple effective spiking model. PMID:21415925

The role of computer-aided 3D surgery and stereolithographic modelling for vector orientation in premaxillary and trans-sinusoidal maxillary distraction osteogenesis.

PubMed

Varol, Altan; Basa, Selçuk

2009-06-01

Maxillary distraction osteogenesis is a challenging procedure when it is performed with internal submerged distractors due to obligation of setting accurate distraction vectors. Five patients with severe maxillary retrognathy were planned with Mimics 10.01 CMF and Simplant 10.01 software. Distraction vectors and rods of distractors were arranged in 3D environment and on STL models. All patients were operated under general anaesthesia and complete Le Fort I downfracture was performed. All distractions were performed according to orientated vectors. All patients achieved stable occlusion and satisfactory aesthetic outcome at the end of the treatment period. Preoperative bending of internal maxillary distractors prevents significant loss of operation time. 3D computer-aided surgical simulation and model surgery provide accurate orientation of distraction vectors for premaxillary and internal trans-sinusoidal maxillary distraction. Combination of virtual surgical simulation and stereolithographic models surgery can be validated as an effective method of preoperative planning for complicated maxillofacial surgery cases.

Efficient Simulation of Wing Modal Response: Application of 2nd Order Shape Sensitivities and Neural Networks

NASA Technical Reports Server (NTRS)

Kapania, Rakesh K.; Liu, Youhua

2000-01-01

At the preliminary design stage of a wing structure, an efficient simulation, one needing little computation but yielding adequately accurate results for various response quantities, is essential in the search of optimal design in a vast design space. In the present paper, methods of using sensitivities up to 2nd order, and direct application of neural networks are explored. The example problem is how to decide the natural frequencies of a wing given the shape variables of the structure. It is shown that when sensitivities cannot be obtained analytically, the finite difference approach is usually more reliable than a semi-analytical approach provided an appropriate step size is used. The use of second order sensitivities is proved of being able to yield much better results than the case where only the first order sensitivities are used. When neural networks are trained to relate the wing natural frequencies to the shape variables, a negligible computation effort is needed to accurately determine the natural frequencies of a new design.

Hyperfine excitation of C2H in collisions with ortho- and para-H2

NASA Astrophysics Data System (ADS)

Dagdigian, Paul J.

2018-06-01

Accurate estimation of the abundance of the ethynyl (C2H) radical requires accurate radiative and collisional rate coefficients. Hyperfine-resolved rate coefficients for (de-)excitation of C2H in collisions with ortho- and para-H2 are presented in this work. These rate coefficients were computed in time-independent close-coupling quantum scattering calculations that employed a potential energy surface recently computed at the coupled-clusters level of theory that describes the interaction of C2H with H2. Rate coefficients for temperatures from 10 to 300 K were computed for all transitions among the first 40 hyperfine energy levels of C2H in collisions with ortho- and para-H2. These rate coefficients were employed in simple radiative transfer calculations to simulate the excitation of C2H in typical molecular clouds.

Computation of Transonic Nozzle Sound Transmission and Rotor Problems by the Dispersion-Relation-Preserving Scheme

NASA Technical Reports Server (NTRS)

Tam, Christopher K. W.; Aganin, Alexei

2000-01-01

The transonic nozzle transmission problem and the open rotor noise radiation problem are solved computationally. Both are multiple length scales problems. For efficient and accurate numerical simulation, the multiple-size-mesh multiple-time-step Dispersion-Relation-Preserving scheme is used to calculate the time periodic solution. To ensure an accurate solution, high quality numerical boundary conditions are also needed. For the nozzle problem, a set of nonhomogeneous, outflow boundary conditions are required. The nonhomogeneous boundary conditions not only generate the incoming sound waves but also, at the same time, allow the reflected acoustic waves and entropy waves, if present, to exit the computation domain without reflection. For the open rotor problem, there is an apparent singularity at the axis of rotation. An analytic extension approach is developed to provide a high quality axis boundary treatment.

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

PubMed

Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

2015-04-21

Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

Modeling of Radiotherapy Linac Source Terms Using ARCHER Monte Carlo Code: Performance Comparison for GPU and MIC Parallel Computing Devices

NASA Astrophysics Data System (ADS)

Lin, Hui; Liu, Tianyu; Su, Lin; Bednarz, Bryan; Caracappa, Peter; Xu, X. George

2017-09-01

Monte Carlo (MC) simulation is well recognized as the most accurate method for radiation dose calculations. For radiotherapy applications, accurate modelling of the source term, i.e. the clinical linear accelerator is critical to the simulation. The purpose of this paper is to perform source modelling and examine the accuracy and performance of the models on Intel Many Integrated Core coprocessors (aka Xeon Phi) and Nvidia GPU using ARCHER and explore the potential optimization methods. Phase Space-based source modelling for has been implemented. Good agreements were found in a tomotherapy prostate patient case and a TrueBeam breast case. From the aspect of performance, the whole simulation for prostate plan and breast plan cost about 173s and 73s with 1% statistical error.

Efficient simulation of incompressible viscous flow over multi-element airfoils

NASA Technical Reports Server (NTRS)

Rogers, Stuart E.; Wiltberger, N. Lyn; Kwak, Dochan

1993-01-01

The incompressible, viscous, turbulent flow over single and multi-element airfoils is numerically simulated in an efficient manner by solving the incompressible Navier-Stokes equations. The solution algorithm employs the method of pseudo compressibility and utilizes an upwind differencing scheme for the convective fluxes, and an implicit line-relaxation scheme. The motivation for this work includes interest in studying high-lift take-off and landing configurations of various aircraft. In particular, accurate computation of lift and drag at various angles of attack up to stall is desired. Two different turbulence models are tested in computing the flow over an NACA 4412 airfoil; an accurate prediction of stall is obtained. The approach used for multi-element airfoils involves the use of multiple zones of structured grids fitted to each element. Two different approaches are compared; a patched system of grids, and an overlaid Chimera system of grids. Computational results are presented for two-element, three-element, and four-element airfoil configurations. Excellent agreement with experimental surface pressure coefficients is seen. The code converges in less than 200 iterations, requiring on the order of one minute of CPU time on a CRAY YMP per element in the airfoil configuration.

Parallel Higher-order Finite Element Method for Accurate Field Computations in Wakefield and PIC Simulations

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

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

Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell)more » approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.« less

Towards Full Aircraft Airframe Noise Prediction: Lattice Boltzmann Simulations

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Fares, Ehab; Casalino, Damiano

2014-01-01

Computational results for an 18%-scale, semi-span Gulfstream aircraft model are presented. Exa Corporation's lattice Boltzmann PowerFLOW(trademark) solver was used to perform time-dependent simulations of the flow field associated with this high-fidelity aircraft model. The simulations were obtained for free-air at a Mach number of 0.2 with the flap deflected at 39 deg (landing configuration). We focused on accurately predicting the prominent noise sources at the flap tips and main landing gear for the two baseline configurations, namely, landing flap setting without and with gear deployed. Capitalizing on the inherently transient nature of the lattice Boltzmann formulation, the complex time-dependent flow features associated with the flap were resolved very accurately and efficiently. To properly simulate the noise sources over a broad frequency range, the tailored grid was very dense near the flap inboard and outboard tips. Extensive comparison of the computed time-averaged and unsteady surface pressures with wind tunnel measurements showed excellent agreement for the global aerodynamic characteristics and the local flow field at the flap inboard and outboard tips and the main landing gear. In particular, the computed fluctuating surface pressure field for the flap agreed well with the measurements in both amplitude and frequency content, indicating that the prominent airframe noise sources at the tips were captured successfully. Gear-flap interaction effects were remarkably well predicted and were shown to affect only the inboard flap tip, altering the steady and unsteady pressure fields in that region. The simulated farfield noise spectra for both baseline configurations, obtained using a Ffowcs-Williams and Hawkings acoustic analogy approach, were shown to be in close agreement with measured values.

Comparison of three-dimensional poisson solution methods for particle-based simulation and inhomogeneous dielectrics.

PubMed

Berti, Claudio; Gillespie, Dirk; Bardhan, Jaydeep P; Eisenberg, Robert S; Fiegna, Claudio

2012-07-01

Particle-based simulation represents a powerful approach to modeling physical systems in electronics, molecular biology, and chemical physics. Accounting for the interactions occurring among charged particles requires an accurate and efficient solution of Poisson's equation. For a system of discrete charges with inhomogeneous dielectrics, i.e., a system with discontinuities in the permittivity, the boundary element method (BEM) is frequently adopted. It provides the solution of Poisson's equation, accounting for polarization effects due to the discontinuity in the permittivity by computing the induced charges at the dielectric boundaries. In this framework, the total electrostatic potential is then found by superimposing the elemental contributions from both source and induced charges. In this paper, we present a comparison between two BEMs to solve a boundary-integral formulation of Poisson's equation, with emphasis on the BEMs' suitability for particle-based simulations in terms of solution accuracy and computation speed. The two approaches are the collocation and qualocation methods. Collocation is implemented following the induced-charge computation method of D. Boda et al. [J. Chem. Phys. 125, 034901 (2006)]. The qualocation method is described by J. Tausch et al. [IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 20, 1398 (2001)]. These approaches are studied using both flat and curved surface elements to discretize the dielectric boundary, using two challenging test cases: a dielectric sphere embedded in a different dielectric medium and a toy model of an ion channel. Earlier comparisons of the two BEM approaches did not address curved surface elements or semiatomistic models of ion channels. Our results support the earlier findings that for flat-element calculations, qualocation is always significantly more accurate than collocation. On the other hand, when the dielectric boundary is discretized with curved surface elements, the two methods are essentially equivalent; i.e., they have comparable accuracies for the same number of elements. We find that ions in water--charges embedded in a high-dielectric medium--are harder to compute accurately than charges in a low-dielectric medium.

Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency

NASA Astrophysics Data System (ADS)

Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao

2008-05-01

Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.

Insights into the deactivation of 5-bromouracil after ultraviolet excitation

NASA Astrophysics Data System (ADS)

Peccati, Francesca; Mai, Sebastian; González, Leticia

2017-03-01

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Insights into the deactivation of 5-bromouracil after ultraviolet excitation

PubMed Central

2017-01-01

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C–Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320905

Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)

NASA Astrophysics Data System (ADS)

Haigis, Volker; Belkhodja, Yacine; Coudert, François-Xavier; Vuilleumier, Rodolphe; Boutin, Anne

2014-08-01

Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material.

FASTSIM2: a second-order accurate frictional rolling contact algorithm

NASA Astrophysics Data System (ADS)

Vollebregt, E. A. H.; Wilders, P.

2011-01-01

In this paper we consider the frictional (tangential) steady rolling contact problem. We confine ourselves to the simplified theory, instead of using full elastostatic theory, in order to be able to compute results fast, as needed for on-line application in vehicle system dynamics simulation packages. The FASTSIM algorithm is the leading technology in this field and is employed in all dominant railway vehicle system dynamics packages (VSD) in the world. The main contribution of this paper is a new version "FASTSIM2" of the FASTSIM algorithm, which is second-order accurate. This is relevant for VSD, because with the new algorithm 16 times less grid points are required for sufficiently accurate computations of the contact forces. The approach is based on new insights in the characteristics of the rolling contact problem when using the simplified theory, and on taking precise care of the contact conditions in the numerical integration scheme employed.

ACCURATE CHEMICAL MASTER EQUATION SOLUTION USING MULTI-FINITE BUFFERS

PubMed Central

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-01-01

The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the Accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multi-finite buffers for reducing the state space by O(n!), exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes, and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be pre-computed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multi-scale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks. PMID:27761104

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

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

Badal, Andreu; Badano, Aldo

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

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

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.

Realistic Analytical Polyhedral MRI Phantoms

PubMed Central

Ngo, Tri M.; Fung, George S. K.; Han, Shuo; Chen, Min; Prince, Jerry L.; Tsui, Benjamin M. W.; McVeigh, Elliot R.; Herzka, Daniel A.

2015-01-01

Purpose Analytical phantoms have closed form Fourier transform expressions and are used to simulate MRI acquisitions. Existing 3D analytical phantoms are unable to accurately model shapes of biomedical interest. It is demonstrated that polyhedral analytical phantoms have closed form Fourier transform expressions and can accurately represent 3D biomedical shapes. Theory The derivations of the Fourier transform of a polygon and polyhedron are presented. Methods The Fourier transform of a polyhedron was implemented and its accuracy in representing faceted and smooth surfaces was characterized. Realistic anthropomorphic polyhedral brain and torso phantoms were constructed and their use in simulated 3D/2D MRI acquisitions was described. Results Using polyhedra, the Fourier transform of faceted shapes can be computed to within machine precision. Smooth surfaces can be approximated with increasing accuracy by increasing the number of facets in the polyhedron; the additional accumulated numerical imprecision of the Fourier transform of polyhedra with many faces remained small. Simulations of 3D/2D brain and 2D torso cine acquisitions produced realistic reconstructions free of high frequency edge aliasing as compared to equivalent voxelized/rasterized phantoms. Conclusion Analytical polyhedral phantoms are easy to construct and can accurately simulate shapes of biomedical interest. PMID:26479724

AN INTEGRAL EQUATION REPRESENTATION OF WIDE-BAND ELECTROMAGNETIC SCATTERING BY THIN SHEETS

EPA Science Inventory

An efficient, accurate numerical modeling scheme has been developed, based on the integral equation solution to compute electromagnetic (EM) responses of thin sheets over a wide frequency band. The thin-sheet approach is useful for simulating the EM response of a fracture system ...

Evaporation kinetics of Mg2SiO4 crystals and melts from molecular dynamics simulations

NASA Technical Reports Server (NTRS)

Kubicki, J. D.; Stolper, E. M.

1993-01-01

Computer simulations based on the molecular dynamics (MD) technique were used to study the mechanisms and kinetics of free evaporation from crystalline and molten forsterite (i.e., Mg2SiO4) on an atomic level. The interatomic potential employed for these simulations reproduces the energetics of bonding in forsterite and in gas-phase MgO and SiO2 reasonably accurately. Results of the simulation include predicted evaporation rates, diffusion rates, and reaction mechanisms for Mg2SiO4(s or l) yields 2Mg(g) + 20(g) + SiO2(g).

Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics.

PubMed

Lin, Yen Ting; Chylek, Lily A; Lemons, Nathan W; Hlavacek, William S

2018-06-21

The chemical kinetics of many complex systems can be concisely represented by reaction rules, which can be used to generate reaction events via a kinetic Monte Carlo method that has been termed network-free simulation. Here, we demonstrate accelerated network-free simulation through a novel approach to equation-free computation. In this process, variables are introduced that approximately capture system state. Derivatives of these variables are estimated using short bursts of exact stochastic simulation and finite differencing. The variables are then projected forward in time via a numerical integration scheme, after which a new exact stochastic simulation is initialized and the whole process repeats. The projection step increases efficiency by bypassing the firing of numerous individual reaction events. As we show, the projected variables may be defined as populations of building blocks of chemical species. The maximal number of connected molecules included in these building blocks determines the degree of approximation. Equation-free acceleration of network-free simulation is found to be both accurate and efficient.

GEMINI-TITAN (GT)-9- TRAINING - AEROSPACE FLIGHT SIMULATOR - PILOT - TX

NASA Image and Video Library

1966-03-01

S66-27990 (March 1966) --- Astronaut Eugene A. Cernan, pilot for the Gemini-9 spaceflight, works out procedures for his historic space excursion in a unique manned Aerospace Flight Simulator at LTV Corp. at Dallas, Texas. The LTV simulator is used frequently by NASA astronauts for a variety of space programs maneuvers to provide many of the sensations and visual scenes of actual spaceflight. Controlled through a complex of computers, the device makes it possible for the astronauts to work out procedures, solve problems and simulate missions in real time with great accuracy. The astronaut rides in a spacecraft-like gondola which moves in roll, pitch and yaw in response to his controls and accurate computer inputs. The simulator's usual spacecraft displays and canopy have been removed and AMU backpack complete with control electronics installed. The astronaut makes his simulated flight in an inflated pressure suit and with the NASA-developed Extravehicular Life Support system chest pack which will be used in the Gemini flight. Photo credit: NASA

An approach for accurate simulation of liquid mixing in a T-shaped micromixer.

PubMed

Matsunaga, Takuya; Lee, Ho-Joon; Nishino, Koichi

2013-04-21

In this paper, we propose a new computational method for efficient evaluation of the fluid mixing behaviour in a T-shaped micromixer with a rectangular cross section at high Schmidt number under steady state conditions. Our approach enables a low-cost high-quality simulation based on tracking of fluid particles for convective fluid mixing and posterior solving of a model of the species equation for molecular diffusion. The examined parameter range is Re = 1.33 × 10(-2) to 240 at Sc = 3600. The proposed method is shown to simulate well the mixing quality even in the engulfment regime, where the ordinary grid-based simulation is not able to obtain accurate solutions with affordable mesh sizes due to the numerical diffusion at high Sc. The obtained results agree well with a backward random-walk Monte Carlo simulation, by which the accuracy of the proposed method is verified. For further investigation of the characteristics of the proposed method, the Sc dependency is examined in a wide range of Sc from 10 to 3600 at Re = 200. The study reveals that the model discrepancy error emerges more significantly in the concentration distribution at lower Sc, while the resulting mixing quality is accurate over the entire range.

Stochastic simulation of enzyme-catalyzed reactions with disparate timescales.

PubMed

Barik, Debashis; Paul, Mark R; Baumann, William T; Cao, Yang; Tyson, John J

2008-10-01

Many physiological characteristics of living cells are regulated by protein interaction networks. Because the total numbers of these protein species can be small, molecular noise can have significant effects on the dynamical properties of a regulatory network. Computing these stochastic effects is made difficult by the large timescale separations typical of protein interactions (e.g., complex formation may occur in fractions of a second, whereas catalytic conversions may take minutes). Exact stochastic simulation may be very inefficient under these circumstances, and methods for speeding up the simulation without sacrificing accuracy have been widely studied. We show that the "total quasi-steady-state approximation" for enzyme-catalyzed reactions provides a useful framework for efficient and accurate stochastic simulations. The method is applied to three examples: a simple enzyme-catalyzed reaction where enzyme and substrate have comparable abundances, a Goldbeter-Koshland switch, where a kinase and phosphatase regulate the phosphorylation state of a common substrate, and coupled Goldbeter-Koshland switches that exhibit bistability. Simulations based on the total quasi-steady-state approximation accurately capture the steady-state probability distributions of all components of these reaction networks. In many respects, the approximation also faithfully reproduces time-dependent aspects of the fluctuations. The method is accurate even under conditions of poor timescale separation.

Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.

PubMed

Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L

2016-01-01

Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples. © 2016 Elsevier Inc. All rights reserved.

Time-Accurate Local Time Stepping and High-Order Time CESE Methods for Multi-Dimensional Flows Using Unstructured Meshes

NASA Technical Reports Server (NTRS)

Chang, Chau-Lyan; Venkatachari, Balaji Shankar; Cheng, Gary

2013-01-01

With the wide availability of affordable multiple-core parallel supercomputers, next generation numerical simulations of flow physics are being focused on unsteady computations for problems involving multiple time scales and multiple physics. These simulations require higher solution accuracy than most algorithms and computational fluid dynamics codes currently available. This paper focuses on the developmental effort for high-fidelity multi-dimensional, unstructured-mesh flow solvers using the space-time conservation element, solution element (CESE) framework. Two approaches have been investigated in this research in order to provide high-accuracy, cross-cutting numerical simulations for a variety of flow regimes: 1) time-accurate local time stepping and 2) highorder CESE method. The first approach utilizes consistent numerical formulations in the space-time flux integration to preserve temporal conservation across the cells with different marching time steps. Such approach relieves the stringent time step constraint associated with the smallest time step in the computational domain while preserving temporal accuracy for all the cells. For flows involving multiple scales, both numerical accuracy and efficiency can be significantly enhanced. The second approach extends the current CESE solver to higher-order accuracy. Unlike other existing explicit high-order methods for unstructured meshes, the CESE framework maintains a CFL condition of one for arbitrarily high-order formulations while retaining the same compact stencil as its second-order counterpart. For large-scale unsteady computations, this feature substantially enhances numerical efficiency. Numerical formulations and validations using benchmark problems are discussed in this paper along with realistic examples.

A performance evaluation postprocessor for computer-aided design and analysis of communication systems

NASA Technical Reports Server (NTRS)

Tranter, W. H.

1979-01-01

A technique for estimating the signal-to-noise ratio at a point in a digital simulation of a communication system is described; the technique is essentially a digital realization of a technique proposed by Shepertycki (1964) for the evaluation of analog communication systems. Signals having lowpass or bandpass spectra may be used. Simulation results show the technique to be accurate over a wide range of signal-to-noise ratios.

Multi-disciplinary coupling effects for integrated design of propulsion systems

NASA Technical Reports Server (NTRS)

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

1993-01-01

Effective computational simulation procedures are described for modeling the inherent multi-disciplinary interactions which govern the accurate response of propulsion systems. Results are presented for propulsion system responses including multi-disciplinary coupling effects using coupled multi-discipline thermal, structural, and acoustic tailoring; an integrated system of multi-disciplinary simulators; coupled material behavior/fabrication process tailoring; sensitivities using a probabilistic simulator; and coupled materials, structures, fracture, and probabilistic behavior simulator. The results demonstrate that superior designs can be achieved if the analysis/tailoring methods account for the multi-disciplinary coupling effects. The coupling across disciplines can be used to develop an integrated coupled multi-discipline numerical propulsion system simulator.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Validity of the Born approximation for beyond Gaussian weak lensing observables

DOE PAGES

Petri, Andrea; Haiman, Zoltan; May, Morgan

2017-06-06

Accurate forward modeling of weak lensing (WL) observables from cosmological parameters is necessary for upcoming galaxy surveys. Because WL probes structures in the nonlinear regime, analytical forward modeling is very challenging, if not impossible. Numerical simulations of WL features rely on ray tracing through the outputs of N-body simulations, which requires knowledge of the gravitational potential and accurate solvers for light ray trajectories. A less accurate procedure, based on the Born approximation, only requires knowledge of the density field, and can be implemented more efficiently and at a lower computational cost. In this work, we use simulations to show thatmore » deviations of the Born-approximated convergence power spectrum, skewness and kurtosis from their fully ray-traced counterparts are consistent with the smallest nontrivial O(Φ 3) post-Born corrections (so-called geodesic and lens-lens terms). Our results imply a cancellation among the larger O(Φ 4) (and higher order) terms, consistent with previous analytic work. We also find that cosmological parameter bias induced by the Born-approximated power spectrum is negligible even for a LSST-like survey, once galaxy shape noise is considered. When considering higher order statistics such as the κ skewness and kurtosis, however, we find significant bias of up to 2.5σ. Using the LensTools software suite, we show that the Born approximation saves a factor of 4 in computing time with respect to the full ray tracing in reconstructing the convergence.« less

Validity of the Born approximation for beyond Gaussian weak lensing observables

NASA Astrophysics Data System (ADS)

Petri, Andrea; Haiman, Zoltán; May, Morgan

2017-06-01

Accurate forward modeling of weak lensing (WL) observables from cosmological parameters is necessary for upcoming galaxy surveys. Because WL probes structures in the nonlinear regime, analytical forward modeling is very challenging, if not impossible. Numerical simulations of WL features rely on ray tracing through the outputs of N -body simulations, which requires knowledge of the gravitational potential and accurate solvers for light ray trajectories. A less accurate procedure, based on the Born approximation, only requires knowledge of the density field, and can be implemented more efficiently and at a lower computational cost. In this work, we use simulations to show that deviations of the Born-approximated convergence power spectrum, skewness and kurtosis from their fully ray-traced counterparts are consistent with the smallest nontrivial O (Φ3) post-Born corrections (so-called geodesic and lens-lens terms). Our results imply a cancellation among the larger O (Φ4) (and higher order) terms, consistent with previous analytic work. We also find that cosmological parameter bias induced by the Born-approximated power spectrum is negligible even for a LSST-like survey, once galaxy shape noise is considered. When considering higher order statistics such as the κ skewness and kurtosis, however, we find significant bias of up to 2.5 σ . Using the LensTools software suite, we show that the Born approximation saves a factor of 4 in computing time with respect to the full ray tracing in reconstructing the convergence.

High Performance Computing Modeling Advances Accelerator Science for High-Energy Physics

DOE PAGES

Amundson, James; Macridin, Alexandru; Spentzouris, Panagiotis

2014-07-28

The development and optimization of particle accelerators are essential for advancing our understanding of the properties of matter, energy, space, and time. Particle accelerators are complex devices whose behavior involves many physical effects on multiple scales. Therefore, advanced computational tools utilizing high-performance computing are essential for accurately modeling them. In the past decade, the US Department of Energy's SciDAC program has produced accelerator-modeling tools that have been employed to tackle some of the most difficult accelerator science problems. The authors discuss the Synergia framework and its applications to high-intensity particle accelerator physics. Synergia is an accelerator simulation package capable ofmore » handling the entire spectrum of beam dynamics simulations. Our authors present Synergia's design principles and its performance on HPC platforms.« less

Realistic simulated MRI and SPECT databases. Application to SPECT/MRI registration evaluation.

PubMed

Aubert-Broche, Berengere; Grova, Christophe; Reilhac, Anthonin; Evans, Alan C; Collins, D Louis

2006-01-01

This paper describes the construction of simulated SPECT and MRI databases that account for realistic anatomical and functional variability. The data is used as a gold-standard to evaluate four SPECT/MRI similarity-based registration methods. Simulation realism was accounted for using accurate physical models of data generation and acquisition. MRI and SPECT simulations were generated from three subjects to take into account inter-subject anatomical variability. Functional SPECT data were computed from six functional models of brain perfusion. Previous models of normal perfusion and ictal perfusion observed in Mesial Temporal Lobe Epilepsy (MTLE) were considered to generate functional variability. We studied the impact noise and intensity non-uniformity in MRI simulations and SPECT scatter correction may have on registration accuracy. We quantified the amount of registration error caused by anatomical and functional variability. Registration involving ictal data was less accurate than registration involving normal data. MR intensity nonuniformity was the main factor decreasing registration accuracy. The proposed simulated database is promising to evaluate many functional neuroimaging methods, involving MRI and SPECT data.

Advanced Methodology for Simulation of Complex Flows Using Structured Grid Systems

NASA Technical Reports Server (NTRS)

Steinthorsson, Erlendur; Modiano, David

1995-01-01

Detailed simulations of viscous flows in complicated geometries pose a significant challenge to current capabilities of Computational Fluid Dynamics (CFD). To enable routine application of CFD to this class of problems, advanced methodologies are required that employ (a) automated grid generation, (b) adaptivity, (c) accurate discretizations and efficient solvers, and (d) advanced software techniques. Each of these ingredients contributes to increased accuracy, efficiency (in terms of human effort and computer time), and/or reliability of CFD software. In the long run, methodologies employing structured grid systems will remain a viable choice for routine simulation of flows in complex geometries only if genuinely automatic grid generation techniques for structured grids can be developed and if adaptivity is employed more routinely. More research in both these areas is urgently needed.

Alternative Modal Basis Selection Procedures for Nonlinear Random Response Simulation

NASA Technical Reports Server (NTRS)

Przekop, Adam; Guo, Xinyun; Rizzi, Stephen A.

2010-01-01

Three procedures to guide selection of an efficient modal basis in a nonlinear random response analysis are examined. One method is based only on proper orthogonal decomposition, while the other two additionally involve smooth orthogonal decomposition. Acoustic random response problems are employed to assess the performance of the three modal basis selection approaches. A thermally post-buckled beam exhibiting snap-through behavior, a shallowly curved arch in the auto-parametric response regime and a plate structure are used as numerical test articles. The results of the three reduced-order analyses are compared with the results of the computationally taxing simulation in the physical degrees of freedom. For the cases considered, all three methods are shown to produce modal bases resulting in accurate and computationally efficient reduced-order nonlinear simulations.

Effectiveness of “Thin-Layer” and “Effective Medium” Approximations in Numerical Simulation of Dielectric Spectra of Biological Cell Suspensions

NASA Astrophysics Data System (ADS)

Asami, Koji

2010-12-01

There are a few concerns in dielectric modeling of biological cells by the finite-element method (FEM) to simulate their dielectric spectra. Cells possess thin plasma membranes and membrane-bound intracellular organelles, requiring extra fine meshes and considerable computational tasks in the simulation. To solve the problems, the “thin-layer” approximation (TLA) and the “effective medium” approximation (EMA) were adopted. TLA deals with the membrane as an interface of the specific membrane impedance, and therefore it is not necessary to divide the membrane region. EMA regards the composite cytoplasm as an effective homogeneous phase whose dielectric properties are calculated separately. It was proved that TLA and EMA were both useful for greatly reducing computational tasks while accurately coinciding with analytical solutions.

High order discretization techniques for real-space ab initio simulations

NASA Astrophysics Data System (ADS)

Anderson, Christopher R.

2018-03-01

In this paper, we present discretization techniques to address numerical problems that arise when constructing ab initio approximations that use real-space computational grids. We present techniques to accommodate the singular nature of idealized nuclear and idealized electronic potentials, and we demonstrate the utility of using high order accurate grid based approximations to Poisson's equation in unbounded domains. To demonstrate the accuracy of these techniques, we present results for a Full Configuration Interaction computation of the dissociation of H2 using a computed, configuration dependent, orbital basis set.

Doppler measurements of the ionosphere on the occasion of the Apollo-Soyuz test project. Part 1: Computer simulation of ionospheric-induced Doppler shifts

NASA Technical Reports Server (NTRS)

Grossi, M. D.; Gay, R. H.

1975-01-01

A computer simulation of the ionospheric experiment of the Apollo-Soyuz Test Project (ASTP) was performed. ASTP is the first example of USA/USSR cooperation in space and is scheduled for summer 1975. The experiment consists of performing dual-frequency Doppler measurements (at 162 and 324 MHz) between the Apollo Command Service Module (CSM) and the ASTP Docking Module (DM), both orbiting at 221-km height and at a relative distance of 300 km. The computer simulation showed that, with the Doppler measurement resolution of approximately 3 mHz provided by the instrumentation (in 10-sec integration time), ionospheric-induced Doppler shifts will be measurable accurately at all times, with some rare exceptions occurring when the radio path crosses regions of minimum ionospheric density. The computer simulation evaluated the ability of the experiment to measure changes of columnar electron content between CSM and DM (from which horizontal gradients of electron density at 221-km height can be obtained) and to measure variations in DM-to-ground columnar content (from which an averaged columnar content and the electron density at the DM can be deduced, under some simplifying assumptions).

A new paradigm for atomically detailed simulations of kinetics in biophysical systems.

PubMed

Elber, Ron

2017-01-01

The kinetics of biochemical and biophysical events determined the course of life processes and attracted considerable interest and research. For example, modeling of biological networks and cellular responses relies on the availability of information on rate coefficients. Atomically detailed simulations hold the promise of supplementing experimental data to obtain a more complete kinetic picture. However, simulations at biological time scales are challenging. Typical computer resources are insufficient to provide the ensemble of trajectories at the correct length that is required for straightforward calculations of time scales. In the last years, new technologies emerged that make atomically detailed simulations of rate coefficients possible. Instead of computing complete trajectories from reactants to products, these approaches launch a large number of short trajectories at different positions. Since the trajectories are short, they are computed trivially in parallel on modern computer architecture. The starting and termination positions of the short trajectories are chosen, following statistical mechanics theory, to enhance efficiency. These trajectories are analyzed. The analysis produces accurate estimates of time scales as long as hours. The theory of Milestoning that exploits the use of short trajectories is discussed, and several applications are described.

Transmitted wavefront testing with large dynamic range based on computer-aided deflectometry

NASA Astrophysics Data System (ADS)

Wang, Daodang; Xu, Ping; Gong, Zhidong; Xie, Zhongmin; Liang, Rongguang; Xu, Xinke; Kong, Ming; Zhao, Jun

2018-06-01

The transmitted wavefront testing technique is demanded for the performance evaluation of transmission optics and transparent glass, in which the achievable dynamic range is a key issue. A computer-aided deflectometric testing method with fringe projection is proposed for the accurate testing of transmitted wavefronts with a large dynamic range. Ray tracing of the modeled testing system is carried out to achieve the virtual ‘null’ testing of transmitted wavefront aberrations. The ray aberration is obtained from the ray tracing result and measured slope, with which the test wavefront aberration can be reconstructed. To eliminate testing system modeling errors, a system geometry calibration based on computer-aided reverse optimization is applied to realize accurate testing. Both numerical simulation and experiments have been carried out to demonstrate the feasibility and high accuracy of the proposed testing method. The proposed testing method can achieve a large dynamic range compared with the interferometric method, providing a simple, low-cost and accurate way for the testing of transmitted wavefronts from various kinds of optics and a large amount of industrial transmission elements.

An Efficient Finite Element Framework to Assess Flexibility Performances of SMA Self-Expandable Carotid Artery Stents

PubMed Central

Ferraro, Mauro; Auricchio, Ferdinando; Boatti, Elisa; Scalet, Giulia; Conti, Michele; Morganti, Simone; Reali, Alessandro

2015-01-01

Computer-based simulations are nowadays widely exploited for the prediction of the mechanical behavior of different biomedical devices. In this aspect, structural finite element analyses (FEA) are currently the preferred computational tool to evaluate the stent response under bending. This work aims at developing a computational framework based on linear and higher order FEA to evaluate the flexibility of self-expandable carotid artery stents. In particular, numerical simulations involving large deformations and inelastic shape memory alloy constitutive modeling are performed, and the results suggest that the employment of higher order FEA allows accurately representing the computational domain and getting a better approximation of the solution with a widely-reduced number of degrees of freedom with respect to linear FEA. Moreover, when buckling phenomena occur, higher order FEA presents a superior capability of reproducing the nonlinear local effects related to buckling phenomena. PMID:26184329

Anisotropic Stochastic Vortex Structure Method for Simulating Particle Collision in Turbulent Shear Flows

NASA Astrophysics Data System (ADS)

Dizaji, Farzad; Marshall, Jeffrey; Grant, John; Jin, Xing

2017-11-01

Accounting for the effect of subgrid-scale turbulence on interacting particles remains a challenge when using Reynolds-Averaged Navier Stokes (RANS) or Large Eddy Simulation (LES) approaches for simulation of turbulent particulate flows. The standard stochastic Lagrangian method for introducing turbulence into particulate flow computations is not effective when the particles interact via collisions, contact electrification, etc., since this method is not intended to accurately model relative motion between particles. We have recently developed the stochastic vortex structure (SVS) method and demonstrated its use for accurate simulation of particle collision in homogeneous turbulence; the current work presents an extension of the SVS method to turbulent shear flows. The SVS method simulates subgrid-scale turbulence using a set of randomly-positioned, finite-length vortices to generate a synthetic fluctuating velocity field. It has been shown to accurately reproduce the turbulence inertial-range spectrum and the probability density functions for the velocity and acceleration fields. In order to extend SVS to turbulent shear flows, a new inversion method has been developed to orient the vortices in order to generate a specified Reynolds stress field. The extended SVS method is validated in the present study with comparison to direct numerical simulations for a planar turbulent jet flow. This research was supported by the U.S. National Science Foundation under Grant CBET-1332472.

Computational study of noise in a large signal transduction network.

PubMed

Intosalmi, Jukka; Manninen, Tiina; Ruohonen, Keijo; Linne, Marja-Leena

2011-06-21

Biochemical systems are inherently noisy due to the discrete reaction events that occur in a random manner. Although noise is often perceived as a disturbing factor, the system might actually benefit from it. In order to understand the role of noise better, its quality must be studied in a quantitative manner. Computational analysis and modeling play an essential role in this demanding endeavor. We implemented a large nonlinear signal transduction network combining protein kinase C, mitogen-activated protein kinase, phospholipase A2, and β isoform of phospholipase C networks. We simulated the network in 300 different cellular volumes using the exact Gillespie stochastic simulation algorithm and analyzed the results in both the time and frequency domain. In order to perform simulations in a reasonable time, we used modern parallel computing techniques. The analysis revealed that time and frequency domain characteristics depend on the system volume. The simulation results also indicated that there are several kinds of noise processes in the network, all of them representing different kinds of low-frequency fluctuations. In the simulations, the power of noise decreased on all frequencies when the system volume was increased. We concluded that basic frequency domain techniques can be applied to the analysis of simulation results produced by the Gillespie stochastic simulation algorithm. This approach is suited not only to the study of fluctuations but also to the study of pure noise processes. Noise seems to have an important role in biochemical systems and its properties can be numerically studied by simulating the reacting system in different cellular volumes. Parallel computing techniques make it possible to run massive simulations in hundreds of volumes and, as a result, accurate statistics can be obtained from computational studies. © 2011 Intosalmi et al; licensee BioMed Central Ltd.

High temperature phonon dispersion in graphene using classical molecular dynamics

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

Anees, P., E-mail: anees@igcar.gov.in; Panigrahi, B. K.; Valsakumar, M. C., E-mail: anees@igcar.gov.in

2014-04-24

Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 Kmore » the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.« less

A new lumped-parameter approach to simulating flow processes in unsaturated dual-porosity media

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

Zimmerman, R.W.; Hadgu, T.; Bodvarsson, G.S.

We have developed a new lumped-parameter dual-porosity approach to simulating unsaturated flow processes in fractured rocks. Fluid flow between the fracture network and the matrix blocks is described by a nonlinear equation that relates the imbibition rate to the local difference in liquid-phase pressure between the fractures and the matrix blocks. This equation is a generalization of the Warren-Root equation, but unlike the Warren-Root equation, is accurate in both the early and late time regimes. The fracture/matrix interflow equation has been incorporated into a computational module, compatible with the TOUGH simulator, to serve as a source/sink term for fracture elements.more » The new approach achieves accuracy comparable to simulations in which the matrix blocks are discretized, but typically requires an order of magnitude less computational time.« less

Large-eddy simulation of a boundary layer with concave streamwise curvature

NASA Technical Reports Server (NTRS)

Lund, Thomas S.

1994-01-01

Turbulence modeling continues to be one of the most difficult problems in fluid mechanics. Existing prediction methods are well developed for certain classes of simple equilibrium flows, but are still not entirely satisfactory for a large category of complex non-equilibrium flows found in engineering practice. Direct and large-eddy simulation (LES) approaches have long been believed to have great potential for the accurate prediction of difficult turbulent flows, but the associated computational cost has been prohibitive for practical problems. This remains true for direct simulation but is no longer clear for large-eddy simulation. Advances in computer hardware, numerical methods, and subgrid-scale modeling have made it possible to conduct LES for flows or practical interest at Reynolds numbers in the range of laboratory experiments. The objective of this work is to apply ES and the dynamic subgrid-scale model to the flow of a boundary layer over a concave surface.

CFD Simulation of Liquid Rocket Engine Injectors

NASA Technical Reports Server (NTRS)

Farmer, Richard; Cheng, Gary; Chen, Yen-Sen; Garcia, Roberto (Technical Monitor)

2001-01-01

Detailed design issues associated with liquid rocket engine injectors and combustion chamber operation require CFD methodology which simulates highly three-dimensional, turbulent, vaporizing, and combusting flows. The primary utility of such simulations involves predicting multi-dimensional effects caused by specific injector configurations. SECA, Inc. and Engineering Sciences, Inc. have been developing appropriate computational methodology for NASA/MSFC for the past decade. CFD tools and computers have improved dramatically during this time period; however, the physical submodels used in these analyses must still remain relatively simple in order to produce useful results. Simulations of clustered coaxial and impinger injector elements for hydrogen and hydrocarbon fuels, which account for real fluid properties, is the immediate goal of this research. The spray combustion codes are based on the FDNS CFD code' and are structured to represent homogeneous and heterogeneous spray combustion. The homogeneous spray model treats the flow as a continuum of multi-phase, multicomponent fluids which move without thermal or velocity lags between the phases. Two heterogeneous models were developed: (1) a volume-of-fluid (VOF) model which represents the liquid core of coaxial or impinger jets and their atomization and vaporization, and (2) a Blob model which represents the injected streams as a cloud of droplets the size of the injector orifice which subsequently exhibit particle interaction, vaporization, and combustion. All of these spray models are computationally intensive, but this is unavoidable to accurately account for the complex physics and combustion which is to be predicted, Work is currently in progress to parallelize these codes to improve their computational efficiency. These spray combustion codes were used to simulate the three test cases which are the subject of the 2nd International Workshop on-Rocket Combustion Modeling. Such test cases are considered by these investigators to be very valuable for code validation because combustion kinetics, turbulence models and atomization models based on low pressure experiments of hydrogen air combustion do not adequately verify analytical or CFD submodels which are necessary to simulate rocket engine combustion. We wish to emphasize that the simulations which we prepared for this meeting are meant to test the accuracy of the approximations used in our general purpose spray combustion models, rather than represent a definitive analysis of each of the experiments which were conducted. Our goal is to accurately predict local temperatures and mixture ratios in rocket engines; hence predicting individual experiments is used only for code validation. To replace the conventional JANNAF standard axisymmetric finite-rate (TDK) computer code 2 for performance prediction with CFD cases, such codes must posses two features. Firstly, they must be as easy to use and of comparable run times for conventional performance predictions. Secondly, they must provide more detailed predictions of the flowfields near the injector face. Specifically, they must accurately predict the convective mixing of injected liquid propellants in terms of the injector element configurations.

A Mass Spectrometer Simulator in Your Computer

ERIC Educational Resources Information Center

Gagnon, Michel

2012-01-01

Introduced to study components of ionized gas, the mass spectrometer has evolved into a highly accurate device now used in many undergraduate and research laboratories. Unfortunately, despite their importance in the formation of future scientists, mass spectrometers remain beyond the financial reach of many high schools and colleges. As a result,…

Computerized technique for recording board defect data

Treesearch

R. Bruce Anderson; R. Edward Thomas; Charles J. Gatchell; Neal D. Bennett; Neal D. Bennett

1993-01-01

A computerized technique for recording board defect data has been developed that is faster and more accurate than manual techniques. The lumber database generated by this technique is a necessary input to computer simulation models that estimate potential cutting yields from various lumber breakdown sequences. The technique allows collection of detailed information...

Just Click Here: New Technology and Testing.

ERIC Educational Resources Information Center

Cutshall, Sandy

2001-01-01

With increasing emphasis on accurate assessment and accountability, computer-based testing and simulation may signify the future for teachers wishing to keep current on technology in the classroom. If career and technical education is to use new testing technology, features such as authentic assessment and criterion-based testing must be…

Speedup computation of HD-sEMG signals using a motor unit-specific electrical source model.

PubMed

Carriou, Vincent; Boudaoud, Sofiane; Laforet, Jeremy

2018-01-23

Nowadays, bio-reliable modeling of muscle contraction is becoming more accurate and complex. This increasing complexity induces a significant increase in computation time which prevents the possibility of using this model in certain applications and studies. Accordingly, the aim of this work is to significantly reduce the computation time of high-density surface electromyogram (HD-sEMG) generation. This will be done through a new model of motor unit (MU)-specific electrical source based on the fibers composing the MU. In order to assess the efficiency of this approach, we computed the normalized root mean square error (NRMSE) between several simulations on single generated MU action potential (MUAP) using the usual fiber electrical sources and the MU-specific electrical source. This NRMSE was computed for five different simulation sets wherein hundreds of MUAPs are generated and summed into HD-sEMG signals. The obtained results display less than 2% error on the generated signals compared to the same signals generated with fiber electrical sources. Moreover, the computation time of the HD-sEMG signal generation model is reduced to about 90% compared to the fiber electrical source model. Using this model with MU electrical sources, we can simulate HD-sEMG signals of a physiological muscle (hundreds of MU) in less than an hour on a classical workstation. Graphical Abstract Overview of the simulation of HD-sEMG signals using the fiber scale and the MU scale. Upscaling the electrical source to the MU scale reduces the computation time by 90% inducing only small deviation of the same simulated HD-sEMG signals.

Decision rules for unbiased inventory estimates

NASA Technical Reports Server (NTRS)

Argentiero, P. D.; Koch, D.

1979-01-01

An efficient and accurate procedure for estimating inventories from remote sensing scenes is presented. In place of the conventional and expensive full dimensional Bayes decision rule, a one-dimensional feature extraction and classification technique was employed. It is shown that this efficient decision rule can be used to develop unbiased inventory estimates and that for large sample sizes typical of satellite derived remote sensing scenes, resulting accuracies are comparable or superior to more expensive alternative procedures. Mathematical details of the procedure are provided in the body of the report and in the appendix. Results of a numerical simulation of the technique using statistics obtained from an observed LANDSAT scene are included. The simulation demonstrates the effectiveness of the technique in computing accurate inventory estimates.

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

Nutaro, James; Kuruganti, Teja

Numerical simulations of the wave equation that are intended to provide accurate time domain solutions require a computational mesh with grid points separated by a distance less than the wavelength of the source term and initial data. However, calculations of radio signal pathloss generally do not require accurate time domain solutions. This paper describes an approach for calculating pathloss by using the finite difference time domain and transmission line matrix models of wave propagation on a grid with points separated by distances much greater than the signal wavelength. The calculated pathloss can be kept close to the true value formore » freespace propagation with an appropriate selection of initial conditions. This method can also simulate diffraction with an error governed by the ratio of the signal wavelength to the grid spacing.« less

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

Kim, K.; Petersson, N. A.; Rodgers, A.

Acoustic waveform modeling is a computationally intensive task and full three-dimensional simulations are often impractical for some geophysical applications such as long-range wave propagation and high-frequency sound simulation. In this study, we develop a two-dimensional high-order accurate finite-difference code for acoustic wave modeling. We solve the linearized Euler equations by discretizing them with the sixth order accurate finite difference stencils away from the boundary and the third order summation-by-parts (SBP) closure near the boundary. Non-planar topographic boundary is resolved by formulating the governing equation in curvilinear coordinates following the interface. We verify the implementation of the algorithm by numerical examplesmore » and demonstrate the capability of the proposed method for practical acoustic wave propagation problems in the atmosphere.« less

An accurate and efficient laser-envelope solver for the modeling of laser-plasma accelerators

DOE PAGES

Benedetti, C.; Schroeder, C. B.; Geddes, C. G. R.; ...

2017-10-17

Detailed and reliable numerical modeling of laser-plasma accelerators (LPAs), where a short and intense laser pulse interacts with an underdense plasma over distances of up to a meter, is a formidably challenging task. This is due to the great disparity among the length scales involved in the modeling, ranging from the micron scale of the laser wavelength to the meter scale of the total laser-plasma interaction length. The use of the time-averaged ponderomotive force approximation, where the laser pulse is described by means of its envelope, enables efficient modeling of LPAs by removing the need to model the details ofmore » electron motion at the laser wavelength scale. Furthermore, it allows simulations in cylindrical geometry which captures relevant 3D physics at 2D computational cost. A key element of any code based on the time-averaged ponderomotive force approximation is the laser envelope solver. In this paper we present the accurate and efficient envelope solver used in the code INF & RNO (INtegrated Fluid & paRticle simulatioN cOde). The features of the INF & RNO laser solver enable an accurate description of the laser pulse evolution deep into depletion even at a reasonably low resolution, resulting in significant computational speed-ups.« less

An accurate and efficient laser-envelope solver for the modeling of laser-plasma accelerators

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

Benedetti, C.; Schroeder, C. B.; Geddes, C. G. R.

Detailed and reliable numerical modeling of laser-plasma accelerators (LPAs), where a short and intense laser pulse interacts with an underdense plasma over distances of up to a meter, is a formidably challenging task. This is due to the great disparity among the length scales involved in the modeling, ranging from the micron scale of the laser wavelength to the meter scale of the total laser-plasma interaction length. The use of the time-averaged ponderomotive force approximation, where the laser pulse is described by means of its envelope, enables efficient modeling of LPAs by removing the need to model the details ofmore » electron motion at the laser wavelength scale. Furthermore, it allows simulations in cylindrical geometry which captures relevant 3D physics at 2D computational cost. A key element of any code based on the time-averaged ponderomotive force approximation is the laser envelope solver. In this paper we present the accurate and efficient envelope solver used in the code INF & RNO (INtegrated Fluid & paRticle simulatioN cOde). The features of the INF & RNO laser solver enable an accurate description of the laser pulse evolution deep into depletion even at a reasonably low resolution, resulting in significant computational speed-ups.« less

An accurate and efficient laser-envelope solver for the modeling of laser-plasma accelerators

NASA Astrophysics Data System (ADS)

Benedetti, C.; Schroeder, C. B.; Geddes, C. G. R.; Esarey, E.; Leemans, W. P.

2018-01-01

Detailed and reliable numerical modeling of laser-plasma accelerators (LPAs), where a short and intense laser pulse interacts with an underdense plasma over distances of up to a meter, is a formidably challenging task. This is due to the great disparity among the length scales involved in the modeling, ranging from the micron scale of the laser wavelength to the meter scale of the total laser-plasma interaction length. The use of the time-averaged ponderomotive force approximation, where the laser pulse is described by means of its envelope, enables efficient modeling of LPAs by removing the need to model the details of electron motion at the laser wavelength scale. Furthermore, it allows simulations in cylindrical geometry which captures relevant 3D physics at 2D computational cost. A key element of any code based on the time-averaged ponderomotive force approximation is the laser envelope solver. In this paper we present the accurate and efficient envelope solver used in the code INF&RNO (INtegrated Fluid & paRticle simulatioN cOde). The features of the INF&RNO laser solver enable an accurate description of the laser pulse evolution deep into depletion even at a reasonably low resolution, resulting in significant computational speed-ups.

A discontinuous Galerkin conservative level set scheme for interface capturing in multiphase flows

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

Owkes, Mark, E-mail: mfc86@cornell.edu; Desjardins, Olivier

2013-09-15

The accurate conservative level set (ACLS) method of Desjardins et al. [O. Desjardins, V. Moureau, H. Pitsch, An accurate conservative level set/ghost fluid method for simulating turbulent atomization, J. Comput. Phys. 227 (18) (2008) 8395–8416] is extended by using a discontinuous Galerkin (DG) discretization. DG allows for the scheme to have an arbitrarily high order of accuracy with the smallest possible computational stencil resulting in an accurate method with good parallel scaling. This work includes a DG implementation of the level set transport equation, which moves the level set with the flow field velocity, and a DG implementation of themore » reinitialization equation, which is used to maintain the shape of the level set profile to promote good mass conservation. A near second order converging interface curvature is obtained by following a height function methodology (common amongst volume of fluid schemes) in the context of the conservative level set. Various numerical experiments are conducted to test the properties of the method and show excellent results, even on coarse meshes. The tests include Zalesak’s disk, two-dimensional deformation of a circle, time evolution of a standing wave, and a study of the Kelvin–Helmholtz instability. Finally, this novel methodology is employed to simulate the break-up of a turbulent liquid jet.« less

Lithographic image simulation for the 21st century with 19th-century tools

NASA Astrophysics Data System (ADS)

Gordon, Ronald L.; Rosenbluth, Alan E.

2004-01-01

Simulation of lithographic processes in semiconductor manufacturing has gone from a crude learning tool 20 years ago to a critical part of yield enhancement strategy today. Although many disparate models, championed by equally disparate communities, exist to describe various photoresist development phenomena, these communities would all agree that the one piece of the simulation picture that can, and must, be computed accurately is the image intensity in the photoresist. The imaging of a photomask onto a thin-film stack is one of the only phenomena in the lithographic process that is described fully by well-known, definitive physical laws. Although many approximations are made in the derivation of the Fourier transform relations between the mask object, the pupil, and the image, these and their impacts are well-understood and need little further investigation. The imaging process in optical lithography is modeled as a partially-coherent, Kohler illumination system. As Hopkins has shown, we can separate the computation into 2 pieces: one that takes information about the illumination source, the projection lens pupil, the resist stack, and the mask size or pitch, and the other that only needs the details of the mask structure. As the latter piece of the calculation can be expressed as a fast Fourier transform, it is the first piece that dominates. This piece involves computation of a potentially large number of numbers called Transmission Cross-Coefficients (TCCs), which are correlations of the pupil function weighted with the illumination intensity distribution. The advantage of performing the image calculations this way is that the computation of these TCCs represents an up-front cost, not to be repeated if one is only interested in changing the mask features, which is the case in Model-Based Optical Proximity Correction (MBOPC). The down side, however, is that the number of these expensive double integrals that must be performed increases as the square of the mask unit cell area; this number can cause even the fastest computers to balk if one needs to study medium- or long-range effects. One can reduce this computational burden by approximating with a smaller area, but accuracy is usually a concern, especially when building a model that will purportedly represent a manufacturing process. This work will review the current methodologies used to simulate the intensity distribution in air above the resist and address the above problems. More to the point, a methodology has been developed to eliminate the expensive numerical integrations in the TCC calculations, as the resulting integrals in many cases of interest can be either evaluated analytically, or replaced by analytical functions accurate to within machine precision. With the burden of computing these numbers lightened, more accurate representations of the image field can be realized, and better overall models are then possible.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

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

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

The applicability of a computer model for predicting head injury incurred during actual motor vehicle collisions.

PubMed

Moran, Stephan G; Key, Jason S; McGwin, Gerald; Keeley, Jason W; Davidson, James S; Rue, Loring W

2004-07-01

Head injury is a significant cause of both morbidity and mortality. Motor vehicle collisions (MVCs) are the most common source of head injury in the United States. No studies have conclusively determined the applicability of computer models for accurate prediction of head injuries sustained in actual MVCs. This study sought to determine the applicability of such models for predicting head injuries sustained by MVC occupants. The Crash Injury Research and Engineering Network (CIREN) database was queried for restrained drivers who sustained a head injury. These collisions were modeled using occupant dynamic modeling (MADYMO) software, and head injury scores were generated. The computer-generated head injury scores then were evaluated with respect to the actual head injuries sustained by the occupants to determine the applicability of MADYMO computer modeling for predicting head injury. Five occupants meeting the selection criteria for the study were selected from the CIREN database. The head injury scores generated by MADYMO were lower than expected given the actual injuries sustained. In only one case did the computer analysis predict a head injury of a severity similar to that actually sustained by the occupant. Although computer modeling accurately simulates experimental crash tests, it may not be applicable for predicting head injury in actual MVCs. Many complicating factors surrounding actual MVCs make accurate computer modeling difficult. Future modeling efforts should consider variables such as age of the occupant and should account for a wider variety of crash scenarios.

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

NASA Technical Reports Server (NTRS)

DeBonis, James R.

2013-01-01

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

Analyzing Spacecraft Telecommunication Systems

NASA Technical Reports Server (NTRS)

Kordon, Mark; Hanks, David; Gladden, Roy; Wood, Eric

2004-01-01

Multi-Mission Telecom Analysis Tool (MMTAT) is a C-language computer program for analyzing proposed spacecraft telecommunication systems. MMTAT utilizes parameterized input and computational models that can be run on standard desktop computers to perform fast and accurate analyses of telecommunication links. MMTAT is easy to use and can easily be integrated with other software applications and run as part of almost any computational simulation. It is distributed as either a stand-alone application program with a graphical user interface or a linkable library with a well-defined set of application programming interface (API) calls. As a stand-alone program, MMTAT provides both textual and graphical output. The graphs make it possible to understand, quickly and easily, how telecommunication performance varies with variations in input parameters. A delimited text file that can be read by any spreadsheet program is generated at the end of each run. The API in the linkable-library form of MMTAT enables the user to control simulation software and to change parameters during a simulation run. Results can be retrieved either at the end of a run or by use of a function call at any time step.

Computational Modeling of Ultrafast Pulse Propagation in Nonlinear Optical Materials

NASA Technical Reports Server (NTRS)

Goorjian, Peter M.; Agrawal, Govind P.; Kwak, Dochan (Technical Monitor)

1996-01-01

There is an emerging technology of photonic (or optoelectronic) integrated circuits (PICs or OEICs). In PICs, optical and electronic components are grown together on the same chip. rib build such devices and subsystems, one needs to model the entire chip. Accurate computer modeling of electromagnetic wave propagation in semiconductors is necessary for the successful development of PICs. More specifically, these computer codes would enable the modeling of such devices, including their subsystems, such as semiconductor lasers and semiconductor amplifiers in which there is femtosecond pulse propagation. Here, the computer simulations are made by solving the full vector, nonlinear, Maxwell's equations, coupled with the semiconductor Bloch equations, without any approximations. The carrier is retained in the description of the optical pulse, (i.e. the envelope approximation is not made in the Maxwell's equations), and the rotating wave approximation is not made in the Bloch equations. These coupled equations are solved to simulate the propagation of femtosecond optical pulses in semiconductor materials. The simulations describe the dynamics of the optical pulses, as well as the interband and intraband.

Cyclic injection, storage, and withdrawal of heated water in a sandstone aquifer at St. Paul, Minnesota: Analysis of thermal data and nonisothermal modeling of short-term test cycles

USGS Publications Warehouse

Miller, Robert T.; Delin, G.N.

1994-01-01

A three-dimensional, anisotropic, nonisothermal, ground-water-flow, and thermal-energy-transport model was constructed to simulate the four short-term test cycles. The model was used to simulate the entire short-term testing period of approximately 400 days. The only model properties varied during model calibration were longitudinal and transverse thermal dispersivities, which, for final calibration, were simulated as 3.3 and 0.33 meters, respectively. The model was calibrated by comparing model-computed results to (1) measured temperatures at selected altitudes in four observation wells, (2) measured temperatures at the production well, and (3) calculated thermal efficiencies of the aquifer. Model-computed withdrawal-water temperatures were within an average of about 3 percent of measured values and model-computed aquifer-thermal efficiencies were within an average of about 5 percent of calculated values for the short-term test cycles. These data indicate that the model accurately simulated thermal-energy storage within the Franconia-Ironton-Galesville aquifer.

Supersonic propulsion simulation by incorporating component models in the large perturbation inlet (LAPIN) computer code

NASA Technical Reports Server (NTRS)

Cole, Gary L.; Richard, Jacques C.

1991-01-01

An approach to simulating the internal flows of supersonic propulsion systems is presented. The approach is based on a fairly simple modification of the Large Perturbation Inlet (LAPIN) computer code. LAPIN uses a quasi-one dimensional, inviscid, unsteady formulation of the continuity, momentum, and energy equations. The equations are solved using a shock capturing, finite difference algorithm. The original code, developed for simulating supersonic inlets, includes engineering models of unstart/restart, bleed, bypass, and variable duct geometry, by means of source terms in the equations. The source terms also provide a mechanism for incorporating, with the inlet, propulsion system components such as compressor stages, combustors, and turbine stages. This requires each component to be distributed axially over a number of grid points. Because of the distributed nature of such components, this representation should be more accurate than a lumped parameter model. Components can be modeled by performance map(s), which in turn are used to compute the source terms. The general approach is described. Then, simulation of a compressor/fan stage is discussed to show the approach in detail.

Simulation of Stagnation Region Heating in Hypersonic Flow on Tetrahedral Grids

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.

2007-01-01

Hypersonic flow simulations using the node based, unstructured grid code FUN3D are presented. Applications include simple (cylinder) and complex (towed ballute) configurations. Emphasis throughout is on computation of stagnation region heating in hypersonic flow on tetrahedral grids. Hypersonic flow over a cylinder provides a simple test problem for exposing any flaws in a simulation algorithm with regard to its ability to compute accurate heating on such grids. Such flaws predominantly derive from the quality of the captured shock. The importance of pure tetrahedral formulations are discussed. Algorithm adjustments for the baseline Roe / Symmetric, Total-Variation-Diminishing (STVD) formulation to deal with simulation accuracy are presented. Formulations of surface normal gradients to compute heating and diffusion to the surface as needed for a radiative equilibrium wall boundary condition and finite catalytic wall boundary in the node-based unstructured environment are developed. A satisfactory resolution of the heating problem on tetrahedral grids is not realized here; however, a definition of a test problem, and discussion of observed algorithm behaviors to date are presented in order to promote further research on this important problem.

ANOPP/VMS HSCT ground contour system

NASA Technical Reports Server (NTRS)

Rawls, John, Jr.; Glaab, Lou

1992-01-01

This viewgraph shows the integration of the Visual Motion Simulator with ANOPP. ANOPP is an acronym for the Aircraft NOise Prediction Program. It is a computer code consisting of dedicated noise prediction modules for jet, propeller, and rotor powered aircraft along with flight support and noise propagation modules, all executed under the control of an executive system. The Visual Motion Simulator (VMS) is a ground based motion simulator with six degrees of freedom. The transport-type cockpit is equipped with conventional flight and engine-thrust controls and with flight instrument displays. Control forces on the wheel, column, and rudder pedals are provided by a hydraulic system coupled with an analog computer. The simulator provides variable-feel characteristics of stiffness, damping, coulomb friction, breakout forces, and inertia. The VMS provides a wide range of realistic flight trajectories necessary for computing accurate ground contours. The NASA VMS will be discussed in detail later in this presentation. An equally important part of the system for both ANOPP and VMS is the engine performance. This will also be discussed in the presentation.

Multiscale Methods for Accurate, Efficient, and Scale-Aware Models of the Earth System

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

Goldhaber, Steve; Holland, Marika

The major goal of this project was to contribute improvements to the infrastructure of an Earth System Model in order to support research in the Multiscale Methods for Accurate, Efficient, and Scale-Aware models of the Earth System project. In support of this, the NCAR team accomplished two main tasks: improving input/output performance of the model and improving atmospheric model simulation quality. Improvement of the performance and scalability of data input and diagnostic output within the model required a new infrastructure which can efficiently handle the unstructured grids common in multiscale simulations. This allows for a more computationally efficient model, enablingmore » more years of Earth System simulation. The quality of the model simulations was improved by reducing grid-point noise in the spectral element version of the Community Atmosphere Model (CAM-SE). This was achieved by running the physics of the model using grid-cell data on a finite-volume grid.« less

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

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

Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.

Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

DOE PAGES

Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.; ...

2015-04-21

Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

Evaluation of a Computational Model of Situational Awareness

NASA Technical Reports Server (NTRS)

Burdick, Mark D.; Shively, R. Jay; Rutkewski, Michael (Technical Monitor)

2000-01-01

Although the use of the psychological construct of situational awareness (SA) assists researchers in creating a flight environment that is safer and more predictable, its true potential remains untapped until a valid means of predicting SA a priori becomes available. Previous work proposed a computational model of SA (CSA) that sought to Fill that void. The current line of research is aimed at validating that model. The results show that the model accurately predicted SA in a piloted simulation.

Can a numerically stable subgrid-scale model for turbulent flow computation be ideally accurate?: a preliminary theoretical study for the Gaussian filtered Navier-Stokes equations.

PubMed

Ida, Masato; Taniguchi, Nobuyuki

2003-09-01

This paper introduces a candidate for the origin of the numerical instabilities in large eddy simulation repeatedly observed in academic and practical industrial flow computations. Without resorting to any subgrid-scale modeling, but based on a simple assumption regarding the streamwise component of flow velocity, it is shown theoretically that in a channel-flow computation, the application of the Gaussian filtering to the incompressible Navier-Stokes equations yields a numerically unstable term, a cross-derivative term, which is similar to one appearing in the Gaussian filtered Vlasov equation derived by Klimas [J. Comput. Phys. 68, 202 (1987)] and also to one derived recently by Kobayashi and Shimomura [Phys. Fluids 15, L29 (2003)] from the tensor-diffusivity subgrid-scale term in a dynamic mixed model. The present result predicts that not only the numerical methods and the subgrid-scale models employed but also only the applied filtering process can be a seed of this numerical instability. An investigation concerning the relationship between the turbulent energy scattering and the unstable term shows that the instability of the term does not necessarily represent the backscatter of kinetic energy which has been considered a possible origin of numerical instabilities in large eddy simulation. The present findings raise the question whether a numerically stable subgrid-scale model can be ideally accurate.

Direct numerical simulation of particulate flows with an overset grid method

NASA Astrophysics Data System (ADS)

Koblitz, A. R.; Lovett, S.; Nikiforakis, N.; Henshaw, W. D.

2017-08-01

We evaluate an efficient overset grid method for two-dimensional and three-dimensional particulate flows for small numbers of particles at finite Reynolds number. The rigid particles are discretised using moving overset grids overlaid on a Cartesian background grid. This allows for strongly-enforced boundary conditions and local grid refinement at particle surfaces, thereby accurately capturing the viscous boundary layer at modest computational cost. The incompressible Navier-Stokes equations are solved with a fractional-step scheme which is second-order-accurate in space and time, while the fluid-solid coupling is achieved with a partitioned approach including multiple sub-iterations to increase stability for light, rigid bodies. Through a series of benchmark studies we demonstrate the accuracy and efficiency of this approach compared to other boundary conformal and static grid methods in the literature. In particular, we find that fully resolving boundary layers at particle surfaces is crucial to obtain accurate solutions to many common test cases. With our approach we are able to compute accurate solutions using as little as one third the number of grid points as uniform grid computations in the literature. A detailed convergence study shows a 13-fold decrease in CPU time over a uniform grid test case whilst maintaining comparable solution accuracy.

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

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

Hoang, Tuan L.; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, CA 94550; Marian, Jaime, E-mail: jmarian@ucla.edu

2015-11-01

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a proceduremore » for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe{sup 3+}, He{sup +} and H{sup +}) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.« less

Reconstructing Solvent Density of Myoglobin Unit Cell from Proximal Radial Distribution Functions of Amino Acids

NASA Astrophysics Data System (ADS)

Galbraith, Madeline; Lynch, Gc; Pettitt, Bm

Understanding the solvent density around a protein crystal structure is an important step for refining accurate crystal structures for use in dynamics simulations or in free energy calculations. The free energy of solvation has typically been approximated using an implicit continuum solvent model or an all atom MD simulation, with a trade-off between accuracy and computation time. For proteins, using precomputed proximal radial distribution functions (pRDFs) of the solvent to reconstruct solvent density on a grid is much faster than all atom MD simulations and more accurate than using implicit solvent models. MD simulations were run for the 20 common amino acids and pRDFs were calculated for several atom type data sets with and without hydrogens, using atom types representative of amino acid side chain atoms. Preliminary results from reconstructions suggest using a data set with 15 heavy atoms and 3 hydrogen yields results with the lowest error without a tradeoff on time. The results of using precomputed pRDFs to reconstruct the solvent density of water for the myoglobin (pdb ID 2mgk) unit cell quantifies the accuracy of the method in comparison with the crystallographic data. Funding Acknowledgement: This research was funded by the CPRIT Summer Undergraduate Program in Computational Cancer Biology, training Grant award RP 140113 from the Cancer Prevention & Research Institute of Texas (CPRIT).

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

NASA Astrophysics Data System (ADS)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

NASA Astrophysics Data System (ADS)

Hoang, Tuan L.; Marian, Jaime; Bulatov, Vasily V.; Hosemann, Peter

2015-11-01

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a procedure for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe3+, He+ and H+) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.

Ku-Band rendezvous radar performance computer simulation model

NASA Technical Reports Server (NTRS)

Magnusson, H. G.; Goff, M. F.

1984-01-01

All work performed on the Ku-band rendezvous radar performance computer simulation model program since the release of the preliminary final report is summarized. Developments on the program fall into three distinct categories: (1) modifications to the existing Ku-band radar tracking performance computer model; (2) the addition of a highly accurate, nonrealtime search and acquisition performance computer model to the total software package developed on this program; and (3) development of radar cross section (RCS) computation models for three additional satellites. All changes in the tracking model involved improvements in the automatic gain control (AGC) and the radar signal strength (RSS) computer models. Although the search and acquisition computer models were developed under the auspices of the Hughes Aircraft Company Ku-Band Integrated Radar and Communications Subsystem program office, they have been supplied to NASA as part of the Ku-band radar performance comuter model package. Their purpose is to predict Ku-band acquisition performance for specific satellite targets on specific missions. The RCS models were developed for three satellites: the Long Duration Exposure Facility (LDEF) spacecraft, the Solar Maximum Mission (SMM) spacecraft, and the Space Telescopes.

Ku-Band rendezvous radar performance computer simulation model

NASA Astrophysics Data System (ADS)

Magnusson, H. G.; Goff, M. F.

1984-06-01

All work performed on the Ku-band rendezvous radar performance computer simulation model program since the release of the preliminary final report is summarized. Developments on the program fall into three distinct categories: (1) modifications to the existing Ku-band radar tracking performance computer model; (2) the addition of a highly accurate, nonrealtime search and acquisition performance computer model to the total software package developed on this program; and (3) development of radar cross section (RCS) computation models for three additional satellites. All changes in the tracking model involved improvements in the automatic gain control (AGC) and the radar signal strength (RSS) computer models. Although the search and acquisition computer models were developed under the auspices of the Hughes Aircraft Company Ku-Band Integrated Radar and Communications Subsystem program office, they have been supplied to NASA as part of the Ku-band radar performance comuter model package. Their purpose is to predict Ku-band acquisition performance for specific satellite targets on specific missions. The RCS models were developed for three satellites: the Long Duration Exposure Facility (LDEF) spacecraft, the Solar Maximum Mission (SMM) spacecraft, and the Space Telescopes.

A computer simulation model to compute the radiation transfer of mountainous regions

NASA Astrophysics Data System (ADS)

Li, Yuguang; Zhao, Feng; Song, Rui

2011-11-01

In mountainous regions, the radiometric signal recorded at the sensor depends on a number of factors such as sun angle, atmospheric conditions, surface cover type, and topography. In this paper, a computer simulation model of radiation transfer is designed and evaluated. This model implements the Monte Carlo ray-tracing techniques and is specifically dedicated to the study of light propagation in mountainous regions. The radiative processes between sun light and the objects within the mountainous region are realized by using forward Monte Carlo ray-tracing methods. The performance of the model is evaluated through detailed comparisons with the well-established 3D computer simulation model: RGM (Radiosity-Graphics combined Model) based on the same scenes and identical spectral parameters, which shows good agreements between these two models' results. By using the newly developed computer model, series of typical mountainous scenes are generated to analyze the physical mechanism of mountainous radiation transfer. The results show that the effects of the adjacent slopes are important for deep valleys and they particularly affect shadowed pixels, and the topographic effect needs to be considered in mountainous terrain before accurate inferences from remotely sensed data can be made.

Parallel Implementation of Triangular Cellular Automata for Computing Two-Dimensional Elastodynamic Response on Arbitrary Domains

NASA Astrophysics Data System (ADS)

Leamy, Michael J.; Springer, Adam C.

In this research we report parallel implementation of a Cellular Automata-based simulation tool for computing elastodynamic response on complex, two-dimensional domains. Elastodynamic simulation using Cellular Automata (CA) has recently been presented as an alternative, inherently object-oriented technique for accurately and efficiently computing linear and nonlinear wave propagation in arbitrarily-shaped geometries. The local, autonomous nature of the method should lead to straight-forward and efficient parallelization. We address this notion on symmetric multiprocessor (SMP) hardware using a Java-based object-oriented CA code implementing triangular state machines (i.e., automata) and the MPI bindings written in Java (MPJ Express). We use MPJ Express to reconfigure our existing CA code to distribute a domain's automata to cores present on a dual quad-core shared-memory system (eight total processors). We note that this message passing parallelization strategy is directly applicable to computer clustered computing, which will be the focus of follow-on research. Results on the shared memory platform indicate nearly-ideal, linear speed-up. We conclude that the CA-based elastodynamic simulator is easily configured to run in parallel, and yields excellent speed-up on SMP hardware.

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Benchmarking of Heavy Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in designing and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

SYSTID - A flexible tool for the analysis of communication systems.

NASA Technical Reports Server (NTRS)

Dawson, C. T.; Tranter, W. H.

1972-01-01

Description of the System Time Domain Simulation (SYSTID) computer-aided analysis program which is specifically structured for communication systems analysis. The SYSTID program is user oriented so that very little knowledge of computer techniques and very little programming ability are required for proper application. The program is designed so that the user can go from a system block diagram to an accurate simulation by simply programming a single English language statement for each block in the system. The mathematical and functional models available in the SYSTID library are presented. An example problem is given which illustrates the ease of modeling communication systems. Examples of the outputs available are presented, and proposed improvements are summarized.

Efficient Voronoi volume estimation for DEM simulations of granular materials under confined conditions

PubMed Central

Frenning, Göran

2015-01-01

When the discrete element method (DEM) is used to simulate confined compression of granular materials, the need arises to estimate the void space surrounding each particle with Voronoi polyhedra. This entails recurring Voronoi tessellation with small changes in the geometry, resulting in a considerable computational overhead. To overcome this limitation, we propose a method with the following features:•A local determination of the polyhedron volume is used, which considerably simplifies implementation of the method.•A linear approximation of the polyhedron volume is utilised, with intermittent exact volume calculations when needed.•The method allows highly accurate volume estimates to be obtained at a considerably reduced computational cost. PMID:26150975

The Mathematical Modeling and Computer Simulation of Electrochemical Micromachining Using Ultrashort Pulses

NASA Astrophysics Data System (ADS)

Kozak, J.; Gulbinowicz, D.; Gulbinowicz, Z.

2009-05-01

The need for complex and accurate three dimensional (3-D) microcomponents is increasing rapidly for many industrial and consumer products. Electrochemical machining process (ECM) has the potential of generating desired crack-free and stress-free surfaces of microcomponents. This paper reports a study of pulse electrochemical micromachining (PECMM) using ultrashort (nanoseconds) pulses for generating complex 3-D microstructures of high accuracy. A mathematical model of the microshaping process with taking into consideration unsteady phenomena in electrical double layer has been developed. The software for computer simulation of PECM has been developed and the effects of machining parameters on anodic localization and final shape of machined surface are presented.

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

DOE PAGES

Engelmann, Christian; Naughton, III, Thomas J.

2016-03-22

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

Unsteady 3D flow simulations in cranial arterial tree

NASA Astrophysics Data System (ADS)

Grinberg, Leopold; Anor, Tomer; Madsen, Joseph; Karniadakis, George

2008-11-01

High resolution unsteady 3D flow simulations in major cranial arteries have been performed. Two cases were considered: 1) a healthy volunteer with a complete Circle of Willis (CoW); and 2) a patient with hydrocephalus and an incomplete CoW. Computation was performed on 3344 processors of the new half petaflop supercomputer in TACC. Two new numerical approaches were developed and implemented: 1) a new two-level domain decomposition method, which couples continuous and discontinuous Galerkin discretization of the computational domain; and 2) a new type of outflow boundary conditions, which imposes, in an accurate and computationally efficient manner, clinically measured flow rates. In the first simulation, a geometric model of 65 cranial arteries was reconstructed. Our simulation reveals a high degree of asymmetry in the flow at the left and right parts of the CoW and the presence of swirling flow in most of the CoW arteries. In the second simulation, one of the main findings was a high pressure drop at the right anterior communicating artery (PCA). Due to the incompleteness of the CoW and the pressure drop at the PCA, the right internal carotid artery supplies blood to most regions of the brain.

Rotor Airloads Prediction Using Unstructured Meshes and Loose CFD/CSD Coupling

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Lee-Rausch, Elizabeth M.

2008-01-01

The FUN3D unsteady Reynolds-averaged Navier-Stokes solver for unstructured grids has been modified to allow prediction of trimmed rotorcraft airloads. The trim of the rotorcraft and the aeroelastic deformation of the rotor blades are accounted for via loose coupling with the CAMRAD II rotorcraft computational structural dynamics code. The set of codes is used to analyze the HART-II Baseline, Minimum Noise and Minimum Vibration test conditions. The loose coupling approach is found to be stable and convergent for the cases considered. Comparison of the resulting airloads and structural deformations with experimentally measured data is presented. The effect of grid resolution and temporal accuracy is examined. Rotorcraft airloads prediction presents a very substantial challenge for Computational Fluid Dynamics (CFD). Not only must the unsteady nature of the flow be accurately modeled, but since most rotorcraft blades are not structurally stiff, an accurate simulation must account for the blade structural dynamics. In addition, trim of the rotorcraft to desired thrust and moment targets depends on both aerodynamic loads and structural deformation, and vice versa. Further, interaction of the fuselage with the rotor flow field can be important, so that relative motion between the blades and the fuselage must be accommodated. Thus a complete simulation requires coupled aerodynamics, structures and trim, with the ability to model geometrically complex configurations. NASA has recently initiated a Subsonic Rotary Wing (SRW) Project under the overall Fundamental Aeronautics Program. Within the context of SRW are efforts aimed at furthering the state of the art of high-fidelity rotorcraft flow simulations, using both structured and unstructured meshes. Structured-mesh solvers have an advantage in computation speed, but even though remarkably complex configurations may be accommodated using the overset grid approach, generation of complex structured-mesh systems can require months to set up. As a result, many rotorcraft simulations using structured-grid CFD neglect the fuselage. On the other hand, unstructured-mesh solvers are easily able to handle complex geometries, but suffer from slower execution speed. However, advances in both computer hardware and CFD algorithms have made previously state-of-the-art computations routine for unstructured-mesh solvers, so that rotorcraft simulations using unstructured grids are now viable. The aim of the present work is to develop a first principles rotorcraft simulation tool based on an unstructured CFD solver.

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

PubMed

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

2018-01-18

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

Atomistic and coarse-grained computer simulations of raft-like lipid mixtures.

PubMed

Pandit, Sagar A; Scott, H Larry

2007-01-01

Computer modeling can provide insights into the existence, structure, size, and thermodynamic stability of localized raft-like regions in membranes. However, the challenges in the construction and simulation of accurate models of heterogeneous membranes are great. The primary obstacle in modeling the lateral organization within a membrane is the relatively slow lateral diffusion rate for lipid molecules. Microsecond or longer time-scales are needed to fully model the formation and stability of a raft in a membra ne. Atomistic simulations currently are not able to reach this scale, but they do provide quantitative information on the intermolecular forces and correlations that are involved in lateral organization. In this chapter, the steps needed to carry out and analyze atomistic simulations of hydrated lipid bilayers having heterogeneous composition are outlined. It is then shown how the data from a molecular dynamics simulation can be used to construct a coarse-grained model for the heterogeneous bilayer that can predict the lateral organization and stability of rafts at up to millisecond time-scales.

LES-based filter-matrix lattice Boltzmann model for simulating fully developed turbulent channel flow

NASA Astrophysics Data System (ADS)

Zhuo, Congshan; Zhong, Chengwen

2016-11-01

In this paper, a three-dimensional filter-matrix lattice Boltzmann (FMLB) model based on large eddy simulation (LES) was verified for simulating wall-bounded turbulent flows. The Vreman subgrid-scale model was employed in the present FMLB-LES framework, which had been proved to be capable of predicting turbulent near-wall region accurately. The fully developed turbulent channel flows were performed at a friction Reynolds number Reτ of 180. The turbulence statistics computed from the present FMLB-LES simulations, including mean stream velocity profile, Reynolds stress profile and root-mean-square velocity fluctuations greed well with the LES results of multiple-relaxation-time (MRT) LB model, and some discrepancies in comparison with those direct numerical simulation (DNS) data of Kim et al. was also observed due to the relatively low grid resolution. Moreover, to investigate the influence of grid resolution on the present LES simulation, a DNS simulation on a finer gird was also implemented by present FMLB-D3Q19 model. Comparisons of detailed computed various turbulence statistics with available benchmark data of DNS showed quite well agreement.

SRS Computer Animation and Drive Train System

NASA Technical Reports Server (NTRS)

Arthun, Daniel; Schachner, Christian

2001-01-01

The spinning rocket simulator (SRS) is an ongoing project at Oral Roberts University. The goal of the SRS is to gather crucial data concerning a spinning rocket under thrust for the purpose of analysis and correction of the coning motion experienced by this type of spacecraft maneuver. The computer animation simulates a virtual, scale model of the component of the SRS that represents the spacecraft itself. This component is known as the (VSM), or virtual spacecraft model. During actual physical simulation, this component of the SRS will experience a coning. The goal of the animation is to cone the VSM within that range to accurately represent the motion of the actual simulator. The drive system of the SRS is the apparatus that turns the actual simulator. It consists of a drive motor, motor mount and chain to power the simulator into motion. The motor mount is adjustable and rigid for high torque application. A digital stepper motor controller actuates the main drive motor for linear acceleration. The chain transfers power from the motor to the simulator via sprockets on both ends.

Development of an Efficient CFD Model for Nuclear Thermal Thrust Chamber Assembly Design

NASA Technical Reports Server (NTRS)

Cheng, Gary; Ito, Yasushi; Ross, Doug; Chen, Yen-Sen; Wang, Ten-See

2007-01-01

The objective of this effort is to develop an efficient and accurate computational methodology to predict both detailed thermo-fluid environments and global characteristics of the internal ballistics for a hypothetical solid-core nuclear thermal thrust chamber assembly (NTTCA). Several numerical and multi-physics thermo-fluid models, such as real fluid, chemically reacting, turbulence, conjugate heat transfer, porosity, and power generation, were incorporated into an unstructured-grid, pressure-based computational fluid dynamics solver as the underlying computational methodology. The numerical simulations of detailed thermo-fluid environment of a single flow element provide a mechanism to estimate the thermal stress and possible occurrence of the mid-section corrosion of the solid core. In addition, the numerical results of the detailed simulation were employed to fine tune the porosity model mimic the pressure drop and thermal load of the coolant flow through a single flow element. The use of the tuned porosity model enables an efficient simulation of the entire NTTCA system, and evaluating its performance during the design cycle.

Modelling NOX concentrations through CFD-RANS in an urban hot-spot using high resolution traffic emissions and meteorology from a mesoscale model

NASA Astrophysics Data System (ADS)

Sanchez, Beatriz; Santiago, Jose Luis; Martilli, Alberto; Martin, Fernando; Borge, Rafael; Quaassdorff, Christina; de la Paz, David

2017-08-01

Air quality management requires more detailed studies about air pollution at urban and local scale over long periods of time. This work focuses on obtaining the spatial distribution of NOx concentration averaged over several days in a heavily trafficked urban area in Madrid (Spain) using a computational fluid dynamics (CFD) model. A methodology based on weighted average of CFD simulations is applied computing the time evolution of NOx dispersion as a sequence of steady-state scenarios taking into account the actual atmospheric conditions. The inputs of emissions are estimated from the traffic emission model and the meteorological information used is derived from a mesoscale model. Finally, the computed concentration map correlates well with 72 passive samplers deployed in the research area. This work reveals the potential of using urban mesoscale simulations together with detailed traffic emissions so as to provide accurate maps of pollutant concentration at microscale using CFD simulations.

Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design.

PubMed

Loeffler, Johannes R; Ehmki, Emanuel S R; Fuchs, Julian E; Liedl, Klaus R

2016-05-01

Urea derivatives are ubiquitously found in many chemical disciplines. N,N'-substituted ureas may show different conformational preferences depending on their substitution pattern. The high energetic barrier for isomerization of the cis and trans state poses additional challenges on computational simulation techniques aiming at a reproduction of the biological properties of urea derivatives. Herein, we investigate energetics of urea conformations and their interconversion using a broad spectrum of methodologies ranging from data mining, via quantum chemistry to molecular dynamics simulation and free energy calculations. We find that the inversion of urea conformations is inherently slow and beyond the time scale of typical simulation protocols. Therefore, extra care needs to be taken by computational chemists to work with appropriate model systems. We find that both knowledge-driven approaches as well as physics-based methods may guide molecular modelers towards accurate starting structures for expensive calculations to ensure that conformations of urea derivatives are modeled as adequately as possible.

Molecular-Level Simulations of the Turbulent Taylor-Green Flow

NASA Astrophysics Data System (ADS)

Gallis, M. A.; Bitter, N. P.; Koehler, T. P.; Plimpton, S. J.; Torczynski, J. R.; Papadakis, G.

2017-11-01

The Direct Simulation Monte Carlo (DSMC) method, a statistical, molecular-level technique that provides accurate solutions to the Boltzmann equation, is applied to the turbulent Taylor-Green vortex flow. The goal of this work is to investigate whether DSMC can accurately simulate energy decay in a turbulent flow. If so, then simulating turbulent flows at the molecular level can provide new insights because the energy decay can be examined in detail from molecular to macroscopic length scales, thereby directly linking molecular relaxation processes to macroscopic transport processes. The DSMC simulations are performed on half a million cores of Sequoia, the 17 Pflop platform at Lawrence Livermore National Laboratory, and the kinetic-energy dissipation rate and the energy spectrum are computed directly from the molecular velocities. The DSMC simulations are found to reproduce the Kolmogorov -5/3 law and to agree with corresponding Navier-Stokes simulations obtained using a spectral method. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Implementation and evaluation of the Level Set method: Towards efficient and accurate simulation of wet etching for microengineering applications

NASA Astrophysics Data System (ADS)

Montoliu, C.; Ferrando, N.; Gosálvez, M. A.; Cerdá, J.; Colom, R. J.

2013-10-01

The use of atomistic methods, such as the Continuous Cellular Automaton (CCA), is currently regarded as a computationally efficient and experimentally accurate approach for the simulation of anisotropic etching of various substrates in the manufacture of Micro-electro-mechanical Systems (MEMS). However, when the features of the chemical process are modified, a time-consuming calibration process needs to be used to transform the new macroscopic etch rates into a corresponding set of atomistic rates. Furthermore, changing the substrate requires a labor-intensive effort to reclassify most atomistic neighborhoods. In this context, the Level Set (LS) method provides an alternative approach where the macroscopic forces affecting the front evolution are directly applied at the discrete level, thus avoiding the need for reclassification and/or calibration. Correspondingly, we present a fully-operational Sparse Field Method (SFM) implementation of the LS approach, discussing in detail the algorithm and providing a thorough characterization of the computational cost and simulation accuracy, including a comparison to the performance by the most recent CCA model. We conclude that the SFM implementation achieves similar accuracy as the CCA method with less fluctuations in the etch front and requiring roughly 4 times less memory. Although SFM can be up to 2 times slower than CCA for the simulation of anisotropic etchants, it can also be up to 10 times faster than CCA for isotropic etchants. In addition, we present a parallel, GPU-based implementation (gSFM) and compare it to an optimized, multicore CPU version (cSFM), demonstrating that the SFM algorithm can be successfully parallelized and the simulation times consequently reduced, while keeping the accuracy of the simulations. Although modern multicore CPUs provide an acceptable option, the massively parallel architecture of modern GPUs is more suitable, as reflected by computational times for gSFM up to 7.4 times faster than for cSFM.

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

Papadimitroulas, P; Kagadis, GC; Loudos, G

Purpose: Our purpose is to evaluate the administered absorbed dose in pediatric, nuclear imaging studies. Monte Carlo simulations with the incorporation of pediatric computational models can serve as reference for the accurate determination of absorbed dose. The procedure of the calculated dosimetric factors is described, while a dataset of reference doses is created. Methods: Realistic simulations were executed using the GATE toolkit and a series of pediatric computational models, developed by the “IT'IS Foundation”. The series of the phantoms used in our work includes 6 models in the range of 5–14 years old (3 boys and 3 girls). Pre-processing techniquesmore » were applied to the images, to incorporate the phantoms in GATE simulations. The resolution of the phantoms was set to 2 mm3. The most important organ densities were simulated according to the GATE “Materials Database”. Several used radiopharmaceuticals in SPECT and PET applications are being tested, following the EANM pediatric dosage protocol. The biodistributions of the several isotopes used as activity maps in the simulations, were derived by the literature. Results: Initial results of absorbed dose per organ (mGy) are presented in a 5 years old girl from the whole body exposure to 99mTc - SestaMIBI, 30 minutes after administration. Heart, kidney, liver, ovary, pancreas and brain are the most critical organs, in which the S-factors are calculated. The statistical uncertainty in the simulation procedure was kept lower than 5%. The Sfactors for each target organ are calculated in Gy/(MBq*sec) with highest dose being absorbed in kidneys and pancreas (9.29*10{sup 10} and 0.15*10{sup 10} respectively). Conclusion: An approach for the accurate dosimetry on pediatric models is presented, creating a reference dosage dataset for several radionuclides in children computational models with the advantages of MC techniques. Our study is ongoing, extending our investigation to other reference models and evaluating the results with clinical estimated doses.« less

SU-C-BRC-06: OpenCL-Based Cross-Platform Monte Carlo Simulation Package for Carbon Ion Therapy

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

Qin, N; Tian, Z; Pompos, A

2016-06-15

Purpose: Monte Carlo (MC) simulation is considered to be the most accurate method for calculation of absorbed dose and fundamental physical quantities related to biological effects in carbon ion therapy. Its long computation time impedes clinical and research applications. We have developed an MC package, goCMC, on parallel processing platforms, aiming at achieving accurate and efficient simulations for carbon therapy. Methods: goCMC was developed under OpenCL framework. It supported transport simulation in voxelized geometry with kinetic energy up to 450 MeV/u. Class II condensed history algorithm was employed for charged particle transport with stopping power computed via Bethe-Bloch equation. Secondarymore » electrons were not transported with their energy locally deposited. Energy straggling and multiple scattering were modeled. Production of secondary charged particles from nuclear interactions was implemented based on cross section and yield data from Geant4. They were transported via the condensed history scheme. goCMC supported scoring various quantities of interest e.g. physical dose, particle fluence, spectrum, linear energy transfer, and positron emitting nuclei. Results: goCMC has been benchmarked against Geant4 with different phantoms and beam energies. For 100 MeV/u, 250 MeV/u and 400 MeV/u beams impinging to a water phantom, range difference was 0.03 mm, 0.20 mm and 0.53 mm, and mean dose difference was 0.47%, 0.72% and 0.79%, respectively. goCMC can run on various computing devices. Depending on the beam energy and voxel size, it took 20∼100 seconds to simulate 10{sup 7} carbons on an AMD Radeon GPU card. The corresponding CPU time for Geant4 with the same setup was 60∼100 hours. Conclusion: We have developed an OpenCL-based cross-platform carbon MC simulation package, goCMC. Its accuracy, efficiency and portability make goCMC attractive for research and clinical applications in carbon therapy.« less

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

PubMed

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

1996-02-01

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

Laplace Transform Based Radiative Transfer Studies

NASA Astrophysics Data System (ADS)

Hu, Y.; Lin, B.; Ng, T.; Yang, P.; Wiscombe, W.; Herath, J.; Duffy, D.

2006-12-01

Multiple scattering is the major uncertainty for data analysis of space-based lidar measurements. Until now, accurate quantitative lidar data analysis has been limited to very thin objects that are dominated by single scattering, where photons from the laser beam only scatter a single time with particles in the atmosphere before reaching the receiver, and simple linear relationship between physical property and lidar signal exists. In reality, multiple scattering is always a factor in space-based lidar measurement and it dominates space- based lidar returns from clouds, dust aerosols, vegetation canopy and phytoplankton. While multiple scattering are clear signals, the lack of a fast-enough lidar multiple scattering computation tool forces us to treat the signal as unwanted "noise" and use simple multiple scattering correction scheme to remove them. Such multiple scattering treatments waste the multiple scattering signals and may cause orders of magnitude errors in retrieved physical properties. Thus the lack of fast and accurate time-dependent radiative transfer tools significantly limits lidar remote sensing capabilities. Analyzing lidar multiple scattering signals requires fast and accurate time-dependent radiative transfer computations. Currently, multiple scattering is done with Monte Carlo simulations. Monte Carlo simulations take minutes to hours and are too slow for interactive satellite data analysis processes and can only be used to help system / algorithm design and error assessment. We present an innovative physics approach to solve the time-dependent radiative transfer problem. The technique utilizes FPGA based reconfigurable computing hardware. The approach is as following, 1. Physics solution: Perform Laplace transform on the time and spatial dimensions and Fourier transform on the viewing azimuth dimension, and convert the radiative transfer differential equation solving into a fast matrix inversion problem. The majority of the radiative transfer computation goes to matrix inversion processes, FFT and inverse Laplace transforms. 2. Hardware solutions: Perform the well-defined matrix inversion, FFT and Laplace transforms on highly parallel, reconfigurable computing hardware. This physics-based computational tool leads to accurate quantitative analysis of space-based lidar signals and improves data quality of current lidar mission such as CALIPSO. This presentation will introduce the basic idea of this approach, preliminary results based on SRC's FPGA-based Mapstation, and how we may apply it to CALIPSO data analysis.

CFD - Mature Technology?

NASA Technical Reports Server (NTRS)

Kwak, Dochan

2005-01-01

Over the past 30 years, numerical methods and simulation tools for fluid dynamic problems have advanced as a new discipline, namely, computational fluid dynamics (CFD). Although a wide spectrum of flow regimes are encountered in many areas of science and engineering, simulation of compressible flow has been the major driver for developing computational algorithms and tools. This is probably due to a large demand for predicting the aerodynamic performance characteristics of flight vehicles, such as commercial, military, and space vehicles. As flow analysis is required to be more accurate and computationally efficient for both commercial and mission-oriented applications (such as those encountered in meteorology, aerospace vehicle development, general fluid engineering and biofluid analysis) CFD tools for engineering become increasingly important for predicting safety, performance and cost. This paper presents the author's perspective on the maturity of CFD, especially from an aerospace engineering point of view.

TRIM—3D: a three-dimensional model for accurate simulation of shallow water flow

USGS Publications Warehouse

Casulli, Vincenzo; Bertolazzi, Enrico; Cheng, Ralph T.

1993-01-01

A semi-implicit finite difference formulation for the numerical solution of three-dimensional tidal circulation is discussed. The governing equations are the three-dimensional Reynolds equations in which the pressure is assumed to be hydrostatic. A minimal degree of implicitness has been introduced in the finite difference formula so that the resulting algorithm permits the use of large time steps at a minimal computational cost. This formulation includes the simulation of flooding and drying of tidal flats, and is fully vectorizable for an efficient implementation on modern vector computers. The high computational efficiency of this method has made it possible to provide the fine details of circulation structure in complex regions that previous studies were unable to obtain. For proper interpretation of the model results suitable interactive graphics is also an essential tool.

Least Squares Shadowing Sensitivity Analysis of Chaotic Flow Around a Two-Dimensional Airfoil

NASA Technical Reports Server (NTRS)

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

2016-01-01

Gradient-based sensitivity analysis has proven to be an enabling technology for many applications, including design of aerospace vehicles. However, conventional sensitivity analysis methods break down when applied to long-time averages of chaotic systems. This breakdown is a serious limitation because many aerospace applications involve physical phenomena that exhibit chaotic dynamics, most notably high-resolution large-eddy and direct numerical simulations of turbulent aerodynamic flows. A recently proposed methodology, Least Squares Shadowing (LSS), avoids this breakdown and advances the state of the art in sensitivity analysis for chaotic flows. The first application of LSS to a chaotic flow simulated with a large-scale computational fluid dynamics solver is presented. The LSS sensitivity computed for this chaotic flow is verified and shown to be accurate, but the computational cost of the current LSS implementation is high.

Simulation software: engineer processes before reengineering.

PubMed

Lepley, C J

2001-01-01

People make decisions all the time using intuition. But what happens when you are asked: "Are you sure your predictions are accurate? How much will a mistake cost? What are the risks associated with this change?" Once a new process is engineered, it is difficult to analyze what would have been different if other options had been chosen. Simulating a process can help senior clinical officers solve complex patient flow problems and avoid wasted efforts. Simulation software can give you the data you need to make decisions. The author introduces concepts, methodologies, and applications of computer aided simulation to illustrate their use in making decisions to improve workflow design.

Optical laboratory solution and error model simulation of a linear time-varying finite element equation

NASA Technical Reports Server (NTRS)

Taylor, B. K.; Casasent, D. P.

1989-01-01

The use of simplified error models to accurately simulate and evaluate the performance of an optical linear-algebra processor is described. The optical architecture used to perform banded matrix-vector products is reviewed, along with a linear dynamic finite-element case study. The laboratory hardware and ac-modulation technique used are presented. The individual processor error-source models and their simulator implementation are detailed. Several significant simplifications are introduced to ease the computational requirements and complexity of the simulations. The error models are verified with a laboratory implementation of the processor, and are used to evaluate its potential performance.

Simulating the interaction of the heliosphere with the local interstellar medium: MHD results from a finite volume approach, first bidimensional results

NASA Technical Reports Server (NTRS)

Chanteur, G.; Khanfir, R.

1995-01-01

We have designed a full compressible MHD code working on unstructured meshes in order to be able to compute accurately sharp structures embedded in large scale simulations. The code is based on a finite volume method making use of a kinetic flux splitting. A bidimensional version of the code has been used to simulate the interaction of a moving interstellar medium, magnetized or unmagnetized with a rotating and magnetized heliopspheric plasma source. Being aware that these computations are not realistic due to the restriction to two dimensions, we present it to demonstrate the ability of this new code to handle this problem. An axisymetric version, now under development, will be operational in a few months. Ultimately we plan to run a full 3d version.

Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores.

PubMed

Wells, David B; Bhattacharya, Swati; Carr, Rogan; Maffeo, Christopher; Ho, Anthony; Comer, Jeffrey; Aksimentiev, Aleksei

2012-01-01

Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.

An Experimental and Numerical Study of a Supersonic Burner for CFD Model Development

NASA Technical Reports Server (NTRS)

Magnotti, G.; Cutler, A. D.

2008-01-01

A laboratory scale supersonic burner has been developed for validation of computational fluid dynamics models. Detailed numerical simulations were performed for the flow inside the combustor, and coupled with finite element thermal analysis to obtain more accurate outflow conditions. A database of nozzle exit profiles for a wide range of conditions of interest was generated to be used as boundary conditions for simulation of the external jet, or for validation of non-intrusive measurement techniques. A set of experiments was performed to validate the numerical results. In particular, temperature measurements obtained by using an infrared camera show that the computed heat transfer was larger than the measured value. Relaminarization in the convergent part of the nozzle was found to be responsible for this discrepancy, and further numerical simulations sustained this conclusion.

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.

Particle kinetic simulation of high altitude hypervelocity flight

NASA Technical Reports Server (NTRS)

Boyd, Iain; Haas, Brian L.

1994-01-01

Rarefied flows about hypersonic vehicles entering the upper atmosphere or through nozzles expanding into a near vacuum may only be simulated accurately with a direct simulation Monte Carlo (DSMC) method. Under this grant, researchers enhanced the models employed in the DSMC method and performed simulations in support of existing NASA projects or missions. DSMC models were developed and validated for simulating rotational, vibrational, and chemical relaxation in high-temperature flows, including effects of quantized anharmonic oscillators and temperature-dependent relaxation rates. State-of-the-art advancements were made in simulating coupled vibration-dissociation recombination for post-shock flows. Models were also developed to compute vehicle surface temperatures directly in the code rather than requiring isothermal estimates. These codes were instrumental in simulating aerobraking of NASA's Magellan spacecraft during orbital maneuvers to assess heat transfer and aerodynamic properties of the delicate satellite. NASA also depended upon simulations of entry of the Galileo probe into the atmosphere of Jupiter to provide drag and flow field information essential for accurate interpretation of an onboard experiment. Finally, the codes have been used extensively to simulate expanding nozzle flows in low-power thrusters in support of propulsion activities at NASA-Lewis. Detailed comparisons between continuum calculations and DSMC results helped to quantify the limitations of continuum CFD codes in rarefied applications.

Investigation of prescribed movement in fluid–structure interaction simulation for the human phonation process☆

PubMed Central

Zörner, S.; Kaltenbacher, M.; Döllinger, M.

2013-01-01

In a partitioned approach for computational fluid–structure interaction (FSI) the coupling between fluid and structure causes substantial computational resources. Therefore, a convenient alternative is to reduce the problem to a pure flow simulation with preset movement and applying appropriate boundary conditions. This work investigates the impact of replacing the fully-coupled interface condition with a one-way coupling. To continue to capture structural movement and its effect onto the flow field, prescribed wall movements from separate simulations and/or measurements are used. As an appropriate test case, we apply the different coupling strategies to the human phonation process, which is a highly complex interaction of airflow through the larynx and structural vibration of the vocal folds (VF). We obtain vocal fold vibrations from a fully-coupled simulation and use them as input data for the simplified simulation, i.e. just solving the fluid flow. All computations are performed with our research code CFS++, which is based on the finite element (FE) method. The presented results show that a pure fluid simulation with prescribed structural movement can substitute the fully-coupled approach. However, caution must be used to ensure accurate boundary conditions on the interface, and we found that only a pressure driven flow correctly responds to the physical effects when using specified motion. PMID:24204083

Fast ray-tracing of human eye optics on Graphics Processing Units.

PubMed

Wei, Qi; Patkar, Saket; Pai, Dinesh K

2014-05-01

We present a new technique for simulating retinal image formation by tracing a large number of rays from objects in three dimensions as they pass through the optic apparatus of the eye to objects. Simulating human optics is useful for understanding basic questions of vision science and for studying vision defects and their corrections. Because of the complexity of computing such simulations accurately, most previous efforts used simplified analytical models of the normal eye. This makes them less effective in modeling vision disorders associated with abnormal shapes of the ocular structures which are hard to be precisely represented by analytical surfaces. We have developed a computer simulator that can simulate ocular structures of arbitrary shapes, for instance represented by polygon meshes. Topographic and geometric measurements of the cornea, lens, and retina from keratometer or medical imaging data can be integrated for individualized examination. We utilize parallel processing using modern Graphics Processing Units (GPUs) to efficiently compute retinal images by tracing millions of rays. A stable retinal image can be generated within minutes. We simulated depth-of-field, accommodation, chromatic aberrations, as well as astigmatism and correction. We also show application of the technique in patient specific vision correction by incorporating geometric models of the orbit reconstructed from clinical medical images. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Simulation of Satellite, Airborne and Terrestrial LiDAR with DART (I):Waveform Simulation with Quasi-Monte Carlo Ray Tracing

NASA Technical Reports Server (NTRS)

Gastellu-Etchegorry, Jean-Philippe; Yin, Tiangang; Lauret, Nicolas; Grau, Eloi; Rubio, Jeremy; Cook, Bruce D.; Morton, Douglas C.; Sun, Guoqing

2016-01-01

Light Detection And Ranging (LiDAR) provides unique data on the 3-D structure of atmosphere constituents and the Earth's surface. Simulating LiDAR returns for different laser technologies and Earth scenes is fundamental for evaluating and interpreting signal and noise in LiDAR data. Different types of models are capable of simulating LiDAR waveforms of Earth surfaces. Semi-empirical and geometric models can be imprecise because they rely on simplified simulations of Earth surfaces and light interaction mechanisms. On the other hand, Monte Carlo ray tracing (MCRT) models are potentially accurate but require long computational time. Here, we present a new LiDAR waveform simulation tool that is based on the introduction of a quasi-Monte Carlo ray tracing approach in the Discrete Anisotropic Radiative Transfer (DART) model. Two new approaches, the so-called "box method" and "Ray Carlo method", are implemented to provide robust and accurate simulations of LiDAR waveforms for any landscape, atmosphere and LiDAR sensor configuration (view direction, footprint size, pulse characteristics, etc.). The box method accelerates the selection of the scattering direction of a photon in the presence of scatterers with non-invertible phase function. The Ray Carlo method brings traditional ray-tracking into MCRT simulation, which makes computational time independent of LiDAR field of view (FOV) and reception solid angle. Both methods are fast enough for simulating multi-pulse acquisition. Sensitivity studies with various landscapes and atmosphere constituents are presented, and the simulated LiDAR signals compare favorably with their associated reflectance images and Laser Vegetation Imaging Sensor (LVIS) waveforms. The LiDAR module is fully integrated into DART, enabling more detailed simulations of LiDAR sensitivity to specific scene elements (e.g., atmospheric aerosols, leaf area, branches, or topography) and sensor configuration for airborne or satellite LiDAR sensors.

Dosimetry of nasal uptake of soluble and reactive gases: A first study of inter-human variability (Journal Article)

EPA Science Inventory

Anatomically accurate human child and adult nasal tract models will be used in concert with computationally simulated air flow information to investigate the influence of age-related differences in anatomy on inhalation dosimetry in the upper and lower airways. The findings of t...

Computational modeling and analysis of the hydrodynamics of human swimming

NASA Astrophysics Data System (ADS)

von Loebbecke, Alfred

Computational modeling and simulations are used to investigate the hydrodynamics of competitive human swimming. The simulations employ an immersed boundary (IB) solver that allows us to simulate viscous, incompressible, unsteady flow past complex, moving/deforming three-dimensional bodies on stationary Cartesian grids. This study focuses on the hydrodynamics of the "dolphin kick". Three female and two male Olympic level swimmers are used to develop kinematically accurate models of this stroke for the simulations. A simulation of a dolphin undergoing its natural swimming motion is also presented for comparison. CFD enables the calculation of flow variables throughout the domain and over the swimmer's body surface during the entire kick cycle. The feet are responsible for all thrust generation in the dolphin kick. Moreover, it is found that the down-kick (ventral position) produces more thrust than the up-kick. A quantity of interest to the swimming community is the drag of a swimmer in motion (active drag). Accurate estimates of this quantity have been difficult to obtain in experiments but are easily calculated with CFD simulations. Propulsive efficiencies of the human swimmers are found to be in the range of 11% to 30%. The dolphin simulation case has a much higher efficiency of 55%. Investigation of vortex structures in the wake indicate that the down-kick can produce a vortex ring with a jet of accelerated fluid flowing through its center. This vortex ring and the accompanying jet are the primary thrust generating mechanisms in the human dolphin kick. In an attempt to understand the propulsive mechanisms of surface strokes, we have also conducted a computational analysis of two different styles of arm-pulls in the backstroke and the front crawl. These simulations involve only the arm and no air-water interface is included. Two of the four strokes are specifically designed to take advantage of lift-based propulsion by undergoing lateral motions of the hand (sculling) and by orienting the palm obliquely to the flow. The focus of the current study is on quantifying the relative contributions of drag and lift to thrust production and use this as a basis for determining the relative effectiveness the stroke styles.

Virtual ellipsometry on layered micro-facet surfaces.

PubMed

Wang, Chi; Wilkie, Alexander; Harcuba, Petr; Novosad, Lukas

2017-09-18

Microfacet-based BRDF models are a common tool to describe light scattering from glossy surfaces. Apart from their wide-ranging applications in optics, such models also play a significant role in computer graphics for photorealistic rendering purposes. In this paper, we mainly investigate the computer graphics aspect of this technology, and present a polarisation-aware brute force simulation of light interaction with both single and multiple layered micro-facet surfaces. Such surface models are commonly used in computer graphics, but the resulting BRDF is ultimately often only approximated. Recently, there has been work to try to make these approximations more accurate, and to better understand the behaviour of existing analytical models. However, these brute force verification attempts still emitted the polarisation state of light and, as we found out, this renders them prone to mis-estimating the shape of the resulting BRDF lobe for some particular material types, such as smooth layered dielectric surfaces. For these materials, non-polarising computations can mis-estimate some areas of the resulting BRDF shape by up to 23%. But we also identified some other material types, such as dielectric layers over rough conductors, for which the difference turned out to be almost negligible. The main contribution of our work is to clearly demonstrate that the effect of polarisation is important for accurate simulation of certain material types, and that there are also other common materials for which it can apparently be ignored. As this required a BRDF simulator that we could rely on, a secondary contribution is that we went to considerable lengths to validate our software. We compare it against a state-of-art model from graphics, a library from optics, and also against ellipsometric measurements of real surface samples.

Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates.

PubMed

Hikiri, Simon; Yoshidome, Takashi; Ikeguchi, Mitsunori

2016-12-13

The configurational entropy of solute molecules is a crucially important quantity to study various biophysical processes. Consequently, it is necessary to establish an efficient quantitative computational method to calculate configurational entropy as accurately as possible. In the present paper, we investigate the quantitative performance of the quasi-harmonic and related computational methods, including widely used methods implemented in popular molecular dynamics (MD) software packages, compared with the Clausius method, which is capable of accurately computing the change of the configurational entropy upon temperature change. Notably, we focused on the choice of the coordinate systems (i.e., internal or Cartesian coordinates). The Boltzmann-quasi-harmonic (BQH) method using internal coordinates outperformed all the six methods examined here. The introduction of improper torsions in the BQH method improves its performance, and anharmonicity of proper torsions in proteins is identified to be the origin of the superior performance of the BQH method. In contrast, widely used methods implemented in MD packages show rather poor performance. In addition, the enhanced sampling of replica-exchange MD simulations was found to be efficient for the convergent behavior of entropy calculations. Also in folding/unfolding transitions of a small protein, Chignolin, the BQH method was reasonably accurate. However, the independent term without the correlation term in the BQH method was most accurate for the folding entropy among the methods considered in this study, because the QH approximation of the correlation term in the BQH method was no longer valid for the divergent unfolded structures.

Tapering the sky response for angular power spectrum estimation from low-frequency radio-interferometric data.

PubMed

Choudhuri, Samir; Bharadwaj, Somnath; Roy, Nirupam; Ghosh, Abhik; Ali, Sk Saiyad

2016-06-11

It is important to correctly subtract point sources from radio-interferometric data in order to measure the power spectrum of diffuse radiation like the Galactic synchrotron or the Epoch of Reionization 21-cm signal. It is computationally very expensive and challenging to image a very large area and accurately subtract all the point sources from the image. The problem is particularly severe at the sidelobes and the outer parts of the main lobe where the antenna response is highly frequency dependent and the calibration also differs from that of the phase centre. Here, we show that it is possible to overcome this problem by tapering the sky response. Using simulated 150 MHz observations, we demonstrate that it is possible to suppress the contribution due to point sources from the outer parts by using the Tapered Gridded Estimator to measure the angular power spectrum C ℓ of the sky signal. We also show from the simulation that this method can self-consistently compute the noise bias and accurately subtract it to provide an unbiased estimation of C ℓ .

Computation of Steady and Unsteady Laminar Flames: Theory

NASA Technical Reports Server (NTRS)

Hagstrom, Thomas; Radhakrishnan, Krishnan; Zhou, Ruhai

1999-01-01

In this paper we describe the numerical analysis underlying our efforts to develop an accurate and reliable code for simulating flame propagation using complex physical and chemical models. We discuss our spatial and temporal discretization schemes, which in our current implementations range in order from two to six. In space we use staggered meshes to define discrete divergence and gradient operators, allowing us to approximate complex diffusion operators while maintaining ellipticity. Our temporal discretization is based on the use of preconditioning to produce a highly efficient linearly implicit method with good stability properties. High order for time accurate simulations is obtained through the use of extrapolation or deferred correction procedures. We also discuss our techniques for computing stationary flames. The primary issue here is the automatic generation of initial approximations for the application of Newton's method. We use a novel time-stepping procedure, which allows the dynamic updating of the flame speed and forces the flame front towards a specified location. Numerical experiments are presented, primarily for the stationary flame problem. These illustrate the reliability of our techniques, and the dependence of the results on various code parameters.

Algorithms for Stellar Perturbation Computations on Oort Cloud Comets

NASA Astrophysics Data System (ADS)

Rickman, Hans; Fouchard, Marc; Valsecchi, Giovanni B.; Froeschlé, Christiane

2005-12-01

We investigate different approximate methods of computing the perturbations on the orbits of Oort cloud comets caused by passing stars, by checking them against an accurate numerical integration using Everhart’s RA15 code. The scenario under study is the one relevant for long-term simulations of the cloud’s response to a predefined set of stellar passages. Our sample of stellar encounters simulates those experienced by the Solar System currently, but extrapolated over a time of 1010 years. We measure the errors of perihelion distance perturbations for high-eccentricity orbits introduced by several estimators including the classical impulse approximation and Dybczyński’s (1994, Celest. Mech. Dynam. Astron. 58, 1330 1338) method and we study how they depend on the encounter parameters (approach distance and relative velocity). We introduce a sequential variant of Dybczyński’s approach, cutting the encounter into several steps whereby the heliocentric motion of the comet is taken into account. For the scenario at hand this is found to offer an efficient means to obtain accurate results for practically any domain of the parameter space.

Large calculation of the flow over a hypersonic vehicle using a GPU

NASA Astrophysics Data System (ADS)

Elsen, Erich; LeGresley, Patrick; Darve, Eric

2008-12-01

Graphics processing units are capable of impressive computing performance up to 518 Gflops peak performance. Various groups have been using these processors for general purpose computing; most efforts have focussed on demonstrating relatively basic calculations, e.g. numerical linear algebra, or physical simulations for visualization purposes with limited accuracy. This paper describes the simulation of a hypersonic vehicle configuration with detailed geometry and accurate boundary conditions using the compressible Euler equations. To the authors' knowledge, this is the most sophisticated calculation of this kind in terms of complexity of the geometry, the physical model, the numerical methods employed, and the accuracy of the solution. The Navier-Stokes Stanford University Solver (NSSUS) was used for this purpose. NSSUS is a multi-block structured code with a provably stable and accurate numerical discretization which uses a vertex-based finite-difference method. A multi-grid scheme is used to accelerate the solution of the system. Based on a comparison of the Intel Core 2 Duo and NVIDIA 8800GTX, speed-ups of over 40× were demonstrated for simple test geometries and 20× for complex geometries.

Computer graphics testbed to simulate and test vision systems for space applications

NASA Technical Reports Server (NTRS)

Cheatham, John B.; Wu, Chris K.; Lin, Y. H.

1991-01-01

A system was developed for displaying computer graphics images of space objects and the use of the system was demonstrated as a testbed for evaluating vision systems for space applications. In order to evaluate vision systems, it is desirable to be able to control all factors involved in creating the images used for processing by the vision system. Considerable time and expense is involved in building accurate physical models of space objects. Also, precise location of the model relative to the viewer and accurate location of the light source require additional effort. As part of this project, graphics models of space objects such as the Solarmax satellite are created that the user can control the light direction and the relative position of the object and the viewer. The work is also aimed at providing control of hue, shading, noise and shadows for use in demonstrating and testing imaging processing techniques. The simulated camera data can provide XYZ coordinates, pitch, yaw, and roll for the models. A physical model is also being used to provide comparison of camera images with the graphics images.

The Effective-One-Body Approach to the General Relativistic Two Body Problem

NASA Astrophysics Data System (ADS)

Damour, Thibault; Nagar, Alessandro

The two-body problem in General Relativity has been the subject of many analytical investigations. After reviewing some of the methods used to tackle this problem (and, more generally, the N-body problem), we focus on a new, recently introduced approach to the motion and radiation of (comparable mass) binary systems: the Effective One Body (EOB) formalism. We review the basic elements of this formalism, and discuss some of its recent developments. Several recent comparisons between EOB predictions and Numerical Relativity (NR) simulations have shown the aptitude of the EOB formalism to provide accurate descriptions of the dynamics and radiation of various binary systems (comprising black holes or neutron stars) in regimes that are inaccessible to other analytical approaches (such as the last orbits and the merger of comparable mass black holes). In synergy with NR simulations, post-Newtonian (PN) theory and Gravitational Self-Force (GSF) computations, the EOB formalism is likely to provide an efficient way of computing the very many accurate template waveforms that are needed for Gravitational Wave (GW) data analysis purposes.

Teaching physiology and the World Wide Web: electrochemistry and electrophysiology on the Internet.

PubMed

Dwyer, T M; Fleming, J; Randall, J E; Coleman, T G

1997-12-01

Students seek active learning experiences that can rapidly impart relevant information in the most convenient way possible. Computer-assisted education can now use the resources of the World Wide Web to convey the important characteristics of events as elemental as the physical properties of osmotically active particles in the cell and as complex as the nerve action potential or the integrative behavior of the intact organism. We have designed laboratory exercises that introduce first-year medical students to membrane and action potentials, as well as the more complex example of integrative physiology, using the dynamic properties of computer simulations. Two specific examples are presented. The first presents the physical laws that apply to osmotic, chemical, and electrical gradients, leading to the development of the concept of membrane potentials; this module concludes with the simulation of the ability of the sodium-potassium pump to establish chemical gradients and maintain cell volume. The second module simulates the action potential according to the Hodgkin-Huxley model, illustrating the concepts of threshold, inactivation, refractory period, and accommodation. Students can access these resources during the scheduled laboratories or on their own time via our Web site on the Internet (http./(/)phys-main.umsmed.edu) by using the World Wide Web protocol. Accurate version control is possible because one valid, but easily edited, copy of the labs exists at the Web site. A common graphical interface is possible through the use of the Hypertext mark-up language. Platform independence is possible through the logical and arithmetic calculations inherent to graphical browsers and the Javascript computer language. The initial success of this program indicates that medical education can be very effective both by the use of accurate simulations and by the existence of a universally accessible Internet resource.

A computationally fast, reduced model for simulating landslide dynamics and tsunamis generated by landslides in natural terrains

NASA Astrophysics Data System (ADS)

Mohammed, F.

2016-12-01

Landslide hazards such as fast-moving debris flows, slow-moving landslides, and other mass flows cause numerous fatalities, injuries, and damage. Landslide occurrences in fjords, bays, and lakes can additionally generate tsunamis with locally extremely high wave heights and runups. Two-dimensional depth-averaged models can successfully simulate the entire lifecycle of the three-dimensional landslide dynamics and tsunami propagation efficiently and accurately with the appropriate assumptions. Landslide rheology is defined using viscous fluids, visco-plastic fluids, and granular material to account for the possible landslide source materials. Saturated and unsaturated rheologies are further included to simulate debris flow, debris avalanches, mudflows, and rockslides respectively. The models are obtained by reducing the fully three-dimensional Navier-Stokes equations with the internal rheological definition of the landslide material, the water body, and appropriate scaling assumptions to obtain the depth-averaged two-dimensional models. The landslide and tsunami models are coupled to include the interaction between the landslide and the water body for tsunami generation. The reduced models are solved numerically with a fast semi-implicit finite-volume, shock-capturing based algorithm. The well-balanced, positivity preserving algorithm accurately accounts for wet-dry interface transition for the landslide runout, landslide-water body interface, and the tsunami wave flooding on land. The models are implemented as a General-Purpose computing on Graphics Processing Unit-based (GPGPU) suite of models, either coupled or run independently within the suite. The GPGPU implementation provides up to 1000 times speedup over a CPU-based serial computation. This enables simulations of multiple scenarios of hazard realizations that provides a basis for a probabilistic hazard assessment. The models have been successfully validated against experiments, past studies, and field data for landslides and tsunamis.

Corruption of accuracy and efficiency of Markov chain Monte Carlo simulation by inaccurate numerical implementation of conceptual hydrologic models

NASA Astrophysics Data System (ADS)

Schoups, G.; Vrugt, J. A.; Fenicia, F.; van de Giesen, N. C.

2010-10-01

Conceptual rainfall-runoff models have traditionally been applied without paying much attention to numerical errors induced by temporal integration of water balance dynamics. Reliance on first-order, explicit, fixed-step integration methods leads to computationally cheap simulation models that are easy to implement. Computational speed is especially desirable for estimating parameter and predictive uncertainty using Markov chain Monte Carlo (MCMC) methods. Confirming earlier work of Kavetski et al. (2003), we show here that the computational speed of first-order, explicit, fixed-step integration methods comes at a cost: for a case study with a spatially lumped conceptual rainfall-runoff model, it introduces artificial bimodality in the marginal posterior parameter distributions, which is not present in numerically accurate implementations of the same model. The resulting effects on MCMC simulation include (1) inconsistent estimates of posterior parameter and predictive distributions, (2) poor performance and slow convergence of the MCMC algorithm, and (3) unreliable convergence diagnosis using the Gelman-Rubin statistic. We studied several alternative numerical implementations to remedy these problems, including various adaptive-step finite difference schemes and an operator splitting method. Our results show that adaptive-step, second-order methods, based on either explicit finite differencing or operator splitting with analytical integration, provide the best alternative for accurate and efficient MCMC simulation. Fixed-step or adaptive-step implicit methods may also be used for increased accuracy, but they cannot match the efficiency of adaptive-step explicit finite differencing or operator splitting. Of the latter two, explicit finite differencing is more generally applicable and is preferred if the individual hydrologic flux laws cannot be integrated analytically, as the splitting method then loses its advantage.

Development of the Glenn-HT Computer Code to Enable Time-Filtered Navier-Stokes (TFNS) Simulations and Application to Film Cooling on a Flat Plate Through Long Cooling Tubes

NASA Technical Reports Server (NTRS)

Ameri, Ali; Shyam, Vikram; Rigby, David; Poinsatte, Philip; Thurman, Douglas; Steinthorsson, Erlendur

2014-01-01

Computational fluid dynamics (CFD) analysis using Reynolds-averaged Navier-Stokes (RANS) formulation for turbomachinery-related flows has enabled improved engine component designs. RANS methodology has limitations which are related to its inability to accurately describe the spectrum of flow phenomena encountered in engines. Examples of flows that are difficult to compute accurately with RANS include phenomena such as laminarturbulent transition, turbulent mixing due to mixing of streams, and separated flows. Large eddy simulation (LES) can improve accuracy but at a considerably higher cost. In recent years, hybrid schemes which take advantage of both unsteady RANS and LES have been proposed. This study investigated an alternative scheme, the time-filtered Navier-Stokes (TFNS) method applied to compressible flows. The method developed by Shih and Liu was implemented in the Glenn-HT code and applied to film cooling flows. In this report the method and its implementation is briefly described. The film effectiveness results obtained for film cooling from a row of 30 holes with a pitch of 3.0 diameters emitting air at a nominal density ratio of unity and four blowing ratios of 0.5, 1.0, 1.5 and 2.0 are shown. Flow features under those conditions are also described.

Fast Particle Methods for Multiscale Phenomena Simulations

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

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

NASA Astrophysics Data System (ADS)

Castellucci, Paul

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

Contributions of the ARM Program to Radiative Transfer Modeling for Climate and Weather Applications

NASA Technical Reports Server (NTRS)

Mlawer, Eli J.; Iacono, Michael J.; Pincus, Robert; Barker, Howard W.; Oreopoulos, Lazaros; Mitchell, David L.

2016-01-01

Accurate climate and weather simulations must account for all relevant physical processes and their complex interactions. Each of these atmospheric, ocean, and land processes must be considered on an appropriate spatial and temporal scale, which leads these simulations to require a substantial computational burden. One especially critical physical process is the flow of solar and thermal radiant energy through the atmosphere, which controls planetary heating and cooling and drives the large-scale dynamics that moves energy from the tropics toward the poles. Radiation calculations are therefore essential for climate and weather simulations, but are themselves quite complex even without considering the effects of variable and inhomogeneous clouds. Clear-sky radiative transfer calculations have to account for thousands of absorption lines due to water vapor, carbon dioxide, and other gases, which are irregularly distributed across the spectrum and have shapes dependent on pressure and temperature. The line-by-line (LBL) codes that treat these details have a far greater computational cost than can be afforded by global models. Therefore, the crucial requirement for accurate radiation calculations in climate and weather prediction models must be satisfied by fast solar and thermal radiation parameterizations with a high level of accuracy that has been demonstrated through extensive comparisons with LBL codes. See attachment for continuation.

AccuRT: A versatile tool for radiative transfer simulations in the coupled atmosphere-ocean system

NASA Astrophysics Data System (ADS)

Hamre, Børge; Stamnes, Snorre; Stamnes, Knut; Stamnes, Jakob

2017-02-01

Reliable, accurate, and efficient modeling of the transport of electromagnetic radiation in turbid media has important applications in the study of the Earth's climate by remote sensing. For example, such modeling is needed to develop forward-inverse methods used to quantify types and concentrations of aerosol and cloud particles in the atmosphere, the dissolved organic and particulate biogeochemical matter in lakes, rivers, coastal, and open-ocean waters. It is also needed to simulate the performance of remote sensing detectors deployed on aircraft, balloons, and satellites as well as radiometric detectors deployed on buoys, gliders and other aquatic observing systems. Accurate radiative transfer modeling is also required to compute irradiances and scalar irradiances that are used to compute warming/cooling and photolysis rates in the atmosphere and primary production and warming/cooling rates in the water column. AccuRT is a radiative transfer model for the coupled atmosphere-water system that is designed to be a versatile tool for researchers in the ocean optics and remote sensing communities. It addresses the needs of researchers interested in analyzing irradiance and radiance measurements in the field and laboratory as well as those interested in making simulations of the top-of-the-atmosphere radiance in support of remote sensing algorithm development.

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly.

PubMed

Kumar, M Senthil; Schwartz, Russell

2010-12-09

Virus capsid assembly has been a key model system for studies of complex self-assembly but it does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or deduce them from the relatively indirect experimental measures available. In this work, we develop a computational strategy to deduce coat-coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can provide rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions.

Simulation of floods caused by overloaded sewer systems: extensions of shallow-water equations

NASA Astrophysics Data System (ADS)

Hilden, Michael

2005-03-01

The outflow of water from a manhole onto a street is a typical flow problem within the simulation of floods in urban areas that are caused by overloaded sewer systems in the event of heavy rains. The reliable assessment of the flood risk for the connected houses requires accurate simulations of the water flow processes in the sewer system and in the street.The Navier-Stokes equations (NSEs) describe the free surface flow of the fluid water accurately, but since their numerical solution requires high CPU times and much memory, their application is not practical. However, their solutions for selected flow problems are applied as reference states to assess the results of other model approaches.The classical shallow-water equations (SWEs) require only fractions (factor 1/100) of the NSEs' computational effort. They assume hydrostatic pressure distribution, depth-averaged horizontal velocities and neglect vertical velocities. These shallow-water assumptions are not fulfilled for the outflow of water from a manhole onto the street. Accordingly, calculations show differences between NSEs and SWEs solutions.The SWEs are extended in order to assess the flood risks in urban areas reliably within applicable computational efforts. Separating vortex regions from the main flow and approximating vertical velocities to involve their contributions into a pressure correction yield suitable results.

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly

NASA Astrophysics Data System (ADS)

Senthil Kumar, M.; Schwartz, Russell

2010-12-01

Virus capsid assembly has been a key model system for studies of complex self-assembly but it does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or deduce them from the relatively indirect experimental measures available. In this work, we develop a computational strategy to deduce coat-coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can provide rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions.

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

van Rij, Jennifer A; Yu, Yi-Hsiang; Guo, Yi

This study explores and verifies the generalized body-modes method for evaluating the structural loads on a wave energy converter (WEC). Historically, WEC design methodologies have focused primarily on accurately evaluating hydrodynamic loads, while methodologies for evaluating structural loads have yet to be fully considered and incorporated into the WEC design process. As wave energy technologies continue to advance, however, it has become increasingly evident that an accurate evaluation of the structural loads will enable an optimized structural design, as well as the potential utilization of composites and flexible materials, and hence reduce WEC costs. Although there are many computational fluidmore » dynamics, structural analyses and fluid-structure-interaction (FSI) codes available, the application of these codes is typically too computationally intensive to be practical in the early stages of the WEC design process. The generalized body-modes method, however, is a reduced order, linearized, frequency-domain FSI approach, performed in conjunction with the linear hydrodynamic analysis, with computation times that could realistically be incorporated into the WEC design process. The objective of this study is to verify the generalized body-modes approach in comparison to high-fidelity FSI simulations to accurately predict structural deflections and stress loads in a WEC. Two verification cases are considered, a free-floating barge and a fixed-bottom column. Details for both the generalized body-modes models and FSI models are first provided. Results for each of the models are then compared and discussed. Finally, based on the verification results obtained, future plans for incorporating the generalized body-modes method into the WEC simulation tool, WEC-Sim, and the overall WEC design process are discussed.« less

Computation of transmitted and received B1 fields in magnetic resonance imaging.

PubMed

Milles, Julien; Zhu, Yue Min; Chen, Nan-Kuei; Panych, Lawrence P; Gimenez, Gérard; Guttmann, Charles R G

2006-05-01

Computation of B1 fields is a key issue for determination and correction of intensity nonuniformity in magnetic resonance images. This paper presents a new method for computing transmitted and received B1 fields. Our method combines a modified MRI acquisition protocol and an estimation technique based on the Levenberg-Marquardt algorithm and spatial filtering. It enables accurate estimation of transmitted and received B1 fields for both homogeneous and heterogeneous objects. The method is validated using numerical simulations and experimental data from phantom and human scans. The experimental results are in agreement with theoretical expectations.

Three-dimensional multigrid Navier-Stokes computations for turbomachinery applications

NASA Astrophysics Data System (ADS)

Subramanian, S. V.

1989-07-01

The fully three-dimensional, time-dependent compressible Navier-Stokes equations in cylindrical coordinates are presently used, in conjunction with the multistage Runge-Kutta numerical integration scheme for solution of the governing flow equations, to simulate complex flowfields within turbomechanical components whose pertinent effects encompass those of viscosity, compressibility, blade rotation, and tip clearance. Computed results are presented for selected cascades, emphasizing the code's capabilities in the accurate prediction of such features as airfoil loadings, exit flow angles, shocks, and secondary flows. Computations for several test cases have been performed on a Cray-YMP, using nearly 90,000 grid points.

RANS computations of tip vortex cavitation

NASA Astrophysics Data System (ADS)

Decaix, Jean; Balarac, Guillaume; Dreyer, Matthieu; Farhat, Mohamed; Münch, Cécile

2015-12-01

The present study is related to the development of the tip vortex cavitation in Kaplan turbines. The investigation is carried out on a simplified test case consisting of a NACA0009 blade with a gap between the blade tip and the side wall. Computations with and without cavitation are performed using a R ANS modelling and a transport equation for the liquid volume fraction. Compared with experimental data, the R ANS computations turn out to be able to capture accurately the development of the tip vortex. The simulations have also highlighted the influence of cavitation on the tip vortex trajectory.

Computer-aided-engineering system for modeling and analysis of ECLSS integration testing

NASA Technical Reports Server (NTRS)

Sepahban, Sonbol

1987-01-01

The accurate modeling and analysis of two-phase fluid networks found in environmental control and life support systems is presently undertaken by computer-aided engineering (CAE) techniques whose generalized fluid dynamics package can solve arbitrary flow networks. The CAE system for integrated test bed modeling and analysis will also furnish interfaces and subsystem/test-article mathematical models. Three-dimensional diagrams of the test bed are generated by the system after performing the requisite simulation and analysis.

Eddylicious: A Python package for turbulent inflow generation

NASA Astrophysics Data System (ADS)

Mukha, Timofey; Liefvendahl, Mattias

2018-01-01

A Python package for generating inflow for scale-resolving computer simulations of turbulent flow is presented. The purpose of the package is to unite existing inflow generation methods in a single code-base and make them accessible to users of various Computational Fluid Dynamics (CFD) solvers. The currently existing functionality consists of an accurate inflow generation method suitable for flows with a turbulent boundary layer inflow and input/output routines for coupling with the open-source CFD solver OpenFOAM.

LES-ODT Simulations of Turbulent Reacting Shear Layers

NASA Astrophysics Data System (ADS)

Hoffie, Andreas; Echekki, Tarek

2012-11-01

Large-eddy simulations (LES) combined with the one-dimensional turbulence (ODT) simulations of a spatially developing turbulent reacting shear layer with heat release and high Reynolds numbers were conducted and compared to results from direct numerical simulations (DNS) of the same configuration. The LES-ODT approach is based on LES solutions for momentum on a coarse grid and solutions for momentum and reactive scalars on a fine ODT grid, which is embedded in the LES computational domain. The shear layer is simulated with a single-step, second-order reaction with an Arrhenius reaction rate. The transport equations are solved using a low Mach number approximation. The LES-ODT simulations yield reasonably accurate predictions of turbulence and passive/reactive scalars' statistics compared to DNS results.

Nonequilibrium diffusive gas dynamics: Poiseuille microflow

NASA Astrophysics Data System (ADS)

Abramov, Rafail V.; Otto, Jasmine T.

2018-05-01

We test the recently developed hierarchy of diffusive moment closures for gas dynamics together with the near-wall viscosity scaling on the Poiseuille flow of argon and nitrogen in a one micrometer wide channel, and compare it against the corresponding Direct Simulation Monte Carlo computations. We find that the diffusive regularized Grad equations with viscosity scaling provide the most accurate approximation to the benchmark DSMC results. At the same time, the conventional Navier-Stokes equations without the near-wall viscosity scaling are found to be the least accurate among the tested closures.

Accelerated path-integral simulations using ring-polymer interpolation

NASA Astrophysics Data System (ADS)

Buxton, Samuel J.; Habershon, Scott

2017-12-01

Imaginary-time path-integral (PI) molecular simulations can be used to calculate exact quantum statistical mechanical properties for complex systems containing many interacting atoms and molecules. The limiting computational factor in a PI simulation is typically the evaluation of the potential energy surface (PES) and forces at each ring-polymer "bead"; for an n-bead ring-polymer, a PI simulation is typically n times greater than the corresponding classical simulation. To address the increased computational effort of PI simulations, several approaches have been developed recently, most notably based on the idea of ring-polymer contraction which exploits either the separation of the PES into short-range and long-range contributions or the availability of a computationally inexpensive PES which can be incorporated to effectively smooth the ring-polymer PES; neither approach is satisfactory in applications to systems modeled by PESs given by on-the-fly ab initio calculations. In this article, we describe a new method, ring-polymer interpolation (RPI), which can be used to accelerate PI simulations without any prior assumptions about the PES. In simulations of liquid water modeled by an empirical PES (or force field) under ambient conditions, where quantum effects are known to play a subtle role in influencing experimental observables such as radial distribution functions, we find that RPI can accurately reproduce the results of fully-converged PI simulations, albeit with far fewer PES evaluations. This approach therefore opens the possibility of large-scale PI simulations using ab initio PESs evaluated on-the-fly without the drawbacks of current methods.

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

PubMed

Schwenke, Michael; Georgii, Joachim; Preusser, Tobias

2017-07-01

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

NASA and CFD - Making investments for the future

NASA Technical Reports Server (NTRS)

Hessenius, Kristin A.; Richardson, P. F.

1992-01-01

From a NASA perspective, CFD is a new tool for fluid flow simulation and prediction with virtually none of the inherent limitations of other ground-based simulation techniques. A primary goal of NASA's CFD research program is to develop efficient and accurate computational techniques for utilization in the design and analysis of aerospace vehicles. The program in algorithm development has systematically progressed through the hierarchy of engineering simplifications of the Navier-Stokes equations, starting with the inviscid formulations such as transonic small disturbance, full potential, and Euler.

Scramjet Combustor Simulations Using Reduced Chemical Kinetics for Practical Fuels

DTIC Science & Technology

2003-12-01

the aerospace industry in reducing prototype and testing costs and the time needed to bring products to market . Accurate simulation of chemical...JP-8 kinetics and soot models into the UNICORN CFD code (Montgomery et al., 2003a) NSF Phase I and II SBIRs for development of a computer-assisted...divided by diameter QSS quasi-steady state REI Reaction Engineering International UNICORN UNsteady Ignition and COmbustion with ReactioNs VULCAN Viscous Upwind aLgorithm for Complex flow ANalysis

3D liver volume reconstructed for palpation training.

PubMed

Tibamoso, Gerardo; Perez-Gutierrez, Byron; Uribe-Quevedo, Alvaro

2013-01-01

Virtual Reality systems for medical procedures such as the palpation of different organs, requires fast, robust, accurate and reliable computational methods for providing realism during interaction with the 3D biological models. This paper presents the segmentation, reconstruction and palpation simulation of a healthy liver volume as a tool for training. The chosen method considers the mechanical characteristics and liver properties for correctly simulating palpation interactions, which results appropriate as a complementary tool for training medical students in familiarizing with the liver anatomy.

Proton Straggling in Thick Silicon Detectors

NASA Technical Reports Server (NTRS)

Selesnick, R. S.; Baker, D. N.; Kanekal, S. G.

2017-01-01

Straggling functions for protons in thick silicon radiation detectors are computed by Monte Carlo simulation. Mean energy loss is constrained by the silicon stopping power, providing higher straggling at low energy and probabilities for stopping within the detector volume. By matching the first four moments of simulated energy-loss distributions, straggling functions are approximated by a log-normal distribution that is accurate for Vavilov k is greater than or equal to 0:3. They are verified by comparison to experimental proton data from a charged particle telescope.

Probabilistic Approach to Enable Extreme-Scale Simulations under Uncertainty and System Faults. Final Technical Report

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

Knio, Omar

2017-05-05

The current project develops a novel approach that uses a probabilistic description to capture the current state of knowledge about the computational solution. To effectively spread the computational effort over multiple nodes, the global computational domain is split into many subdomains. Computational uncertainty in the solution translates into uncertain boundary conditions for the equation system to be solved on those subdomains, and many independent, concurrent subdomain simulations are used to account for this bound- ary condition uncertainty. By relying on the fact that solutions on neighboring subdomains must agree with each other, a more accurate estimate for the global solutionmore » can be achieved. Statistical approaches in this update process make it possible to account for the effect of system faults in the probabilistic description of the computational solution, and the associated uncertainty is reduced through successive iterations. By combining all of these elements, the probabilistic reformulation allows splitting the computational work over very many independent tasks for good scalability, while being robust to system faults.« less

Loci-STREAM Version 0.9

NASA Technical Reports Server (NTRS)

Wright, Jeffrey; Thakur, Siddharth

2006-01-01

Loci-STREAM is an evolving computational fluid dynamics (CFD) software tool for simulating possibly chemically reacting, possibly unsteady flows in diverse settings, including rocket engines, turbomachines, oil refineries, etc. Loci-STREAM implements a pressure- based flow-solving algorithm that utilizes unstructured grids. (The benefit of low memory usage by pressure-based algorithms is well recognized by experts in the field.) The algorithm is robust for flows at all speeds from zero to hypersonic. The flexibility of arbitrary polyhedral grids enables accurate, efficient simulation of flows in complex geometries, including those of plume-impingement problems. The present version - Loci-STREAM version 0.9 - includes an interface with the Portable, Extensible Toolkit for Scientific Computation (PETSc) library for access to enhanced linear-equation-solving programs therein that accelerate convergence toward a solution. The name "Loci" reflects the creation of this software within the Loci computational framework, which was developed at Mississippi State University for the primary purpose of simplifying the writing of complex multidisciplinary application programs to run in distributed-memory computing environments including clusters of personal computers. Loci has been designed to relieve application programmers of the details of programming for distributed-memory computers.

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.

Coupling MD Simulations and X-ray Absorption Spectroscopy to Study Ions in Solution

NASA Astrophysics Data System (ADS)

Marcos, E. Sánchez; Beret, E. C.; Martínez, J. M.; Pappalardo, R. R.; Ayala, R.; Muñoz-Páez, A.

2007-12-01

The structure of ionic solutions is a key-point in understanding physicochemical properties of electrolyte solutions. Among the reduced number of experimental techniques which can supply direct information on the ion environment, X-ray Absorption techniques (XAS) have gained importance during the last decades although they are not free of difficulties associated to the data analysis leading to provide reliable structures. Computer simulations of ions in solution is a theoretical alternative to provide information on the solvation structure. Thus, the use of computational chemistry can increase the understanding of these systems although an accurate description of ionic solvation phenomena represents nowadays a significant challenge to theoretical chemistry. We present: (a) the assignment of features in the XANES spectrum to well defined structural motif in the ion environment, (b) MD-based evaluation of EXAFS parameters used in the fitting procedure to make easier the structural resolution, and (c) the use of the agreement between experimental and simulated XANES spectra to help in the choice of a given intermolecular potential for Computer Simulations. Chemical problems examined are: (a) the identification of the second hydration shell in dilute aqueous solutions of highly-charged cations, such as Cr3+, Rh3+, Ir3+, (b) the invisibility by XAS of certain structures characterized by Computer Simulations but exhibiting high dynamical behavior and (c) the solvation of Br- in acetonitrile.

Coupling MD Simulations and X-ray Absorption Spectroscopy to Study Ions in Solution

NASA Astrophysics Data System (ADS)

Marcos, E. Sánchez; Beret, E. C.; Martínez, J. M.; Pappalardo, R. R.; Ayala, R.; Muñoz-Páez, A.

2007-11-01

The structure of ionic solutions is a key-point in understanding physicochemical properties of electrolyte solutions. Among the reduced number of experimental techniques which can supply direct information on the ion environment, X-ray Absorption techniques (XAS) have gained importance during the last decades although they are not free of difficulties associated to the data analysis leading to provide reliable structures. Computer simulations of ions in solution is a theoretical alternative to provide information on the solvation structure. Thus, the use of computational chemistry can increase the understanding of these systems although an accurate description of ionic solvation phenomena represents nowadays a significant challenge to theoretical chemistry. We present: (a) the assignment of features in the XANES spectrum to well defined structural motif in the ion environment, (b) MD-based evaluation of EXAFS parameters used in the fitting procedure to make easier the structural resolution, and (c) the use of the agreement between experimental and simulated XANES spectra to help in the choice of a given intermolecular potential for Computer Simulations. Chemical problems examined are: (a) the identification of the second hydration shell in dilute aqueous solutions of highly-charged cations, such as Cr3+, Rh3+, Ir3+, (b) the invisibility by XAS of certain structures characterized by Computer Simulations but exhibiting high dynamical behavior and (c) the solvation of Br- in acetonitrile.

Accelerating Sequential Gaussian Simulation with a constant path

NASA Astrophysics Data System (ADS)

Nussbaumer, Raphaël; Mariethoz, Grégoire; Gravey, Mathieu; Gloaguen, Erwan; Holliger, Klaus

2018-03-01

Sequential Gaussian Simulation (SGS) is a stochastic simulation technique commonly employed for generating realizations of Gaussian random fields. Arguably, the main limitation of this technique is the high computational cost associated with determining the kriging weights. This problem is compounded by the fact that often many realizations are required to allow for an adequate uncertainty assessment. A seemingly simple way to address this problem is to keep the same simulation path for all realizations. This results in identical neighbourhood configurations and hence the kriging weights only need to be determined once and can then be re-used in all subsequent realizations. This approach is generally not recommended because it is expected to result in correlation between the realizations. Here, we challenge this common preconception and make the case for the use of a constant path approach in SGS by systematically evaluating the associated benefits and limitations. We present a detailed implementation, particularly regarding parallelization and memory requirements. Extensive numerical tests demonstrate that using a constant path allows for substantial computational gains with very limited loss of simulation accuracy. This is especially the case for a constant multi-grid path. The computational savings can be used to increase the neighbourhood size, thus allowing for a better reproduction of the spatial statistics. The outcome of this study is a recommendation for an optimal implementation of SGS that maximizes accurate reproduction of the covariance structure as well as computational efficiency.

Bioprosthetic heart valve heterograft biomaterials: structure, mechanical behavior and computational simulation.

PubMed

Sacks, Michael S; Mirnajafi, Ali; Sun, Wei; Schmidt, Paul

2006-11-01

The present review surveys significant developments in the biomechanical characterization and computational simulation of biologically derived chemically cross-linked soft tissues, or 'heterograft' biomaterials, used in replacement bioprosthetic heart valve (BHV). A survey of mechanical characterization techniques, relevant mechanical properties and computational simulation approaches is presented for both the source tissues and cross-linked biomaterials. Since durability remains the critical problem with current bioprostheses, changes with the mechanical behavior with fatigue are also presented. Moreover, given the complex nature of the mechanical properties of heterograft biomaterials it is not surprising that most constitutive (stress-strain) models, historically used to characterize their behavior, were oversimplified. Simulations of BHV function utilizing these models have inevitably been inaccurate. Thus, more recent finite element simulations utilizing nonlinear constitutive models, which achieve greater model fidelity, are reviewed. An important conclusion of this review is the need for accurate constitutive models, rigorously validated with appropriate experimental data, in order that the design benefits of computational models can be realized. Finally, for at least the coming 20 years, BHVs fabricated from heterograft biomaterials will continue to be extensively used, and will probably remain as the dominant valve design. We should thus recognize that rational, scientifically based approaches to BHV biomaterial development and design can lead to significantly improved BHV, over the coming decades, which can potentially impact millions of patients worldwide with heart valve disease.

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

NASA Astrophysics Data System (ADS)

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

2013-07-01

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

On simulating flow with multiple time scales using a method of averages

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

Margolin, L.G.

1997-12-31

The author presents a new computational method based on averaging to efficiently simulate certain systems with multiple time scales. He first develops the method in a simple one-dimensional setting and employs linear stability analysis to demonstrate numerical stability. He then extends the method to multidimensional fluid flow. His method of averages does not depend on explicit splitting of the equations nor on modal decomposition. Rather he combines low order and high order algorithms in a generalized predictor-corrector framework. He illustrates the methodology in the context of a shallow fluid approximation to an ocean basin circulation. He finds that his newmore » method reproduces the accuracy of a fully explicit second-order accurate scheme, while costing less than a first-order accurate scheme.« less

Parallel methodology to capture cyclic variability in motored engines

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

Ameen, Muhsin M.; Yang, Xiaofeng; Kuo, Tang-Wei

2016-07-28

Numerical prediction of of cycle-to-cycle variability (CCV) in SI engines is extremely challenging for two key reasons: (i) high-fidelity methods such as large eddy simulation (LES) are require to accurately capture the in-cylinder turbulent flowfield, and (ii) CCV is experienced over long timescales and hence the simulations need to be performed for hundreds of consecutive cycles. In this study, a new methodology is proposed to dissociate this long time-scale problem into several shorter time-scale problems, which can considerably reduce the computational time without sacrificing the fidelity of the simulations. The strategy is to perform multiple single-cycle simulations in parallel bymore » effectively perturbing the simulation parameters such as the initial and boundary conditions. It is shown that by perturbing the initial velocity field effectively based on the intensity of the in-cylinder turbulence, the mean and variance of the in-cylinder flowfield is captured reasonably well. Adding perturbations in the initial pressure field and the boundary pressure improves the predictions. It is shown that this new approach is able to give accurate predictions of the flowfield statistics in less than one-tenth of time required for the conventional approach of simulating consecutive engine cycles.« less

Airframe Icing Research Gaps: NASA Perspective

NASA Technical Reports Server (NTRS)

Potapczuk, Mark

2009-01-01

qCurrent Airframe Icing Technology Gaps: Development of a full 3D ice accretion simulation model. Development of an improved simulation model for SLD conditions. CFD modeling of stall behavior for ice-contaminated wings/tails. Computational methods for simulation of stability and control parameters. Analysis of thermal ice protection system performance. Quantification of 3D ice shape geometric characteristics Development of accurate ground-based simulation of SLD conditions. Development of scaling methods for SLD conditions. Development of advanced diagnostic techniques for assessment of tunnel cloud conditions. Identification of critical ice shapes for aerodynamic performance degradation. Aerodynamic scaling issues associated with testing scale model ice shape geometries. Development of altitude scaling methods for thermal ice protections systems. Development of accurate parameter identification methods. Measurement of stability and control parameters for an ice-contaminated swept wing aircraft. Creation of control law modifications to prevent loss of control during icing encounters. 3D ice shape geometries. Collection efficiency data for ice shape geometries. SLD ice shape data, in-flight and ground-based, for simulation verification. Aerodynamic performance data for 3D geometries and various icing conditions. Stability and control parameter data for iced aircraft configurations. Thermal ice protection system data for simulation validation.

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

NASA Astrophysics Data System (ADS)

Kumar, M.; Duffy, C.

2006-05-01

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

Efficient coarse simulation of a growing avascular tumor

PubMed Central

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

2013-01-01

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

Accurate artificial boundary conditions for the semi-discretized linear Schrödinger and heat equations on rectangular domains

NASA Astrophysics Data System (ADS)

Ji, Songsong; Yang, Yibo; Pang, Gang; Antoine, Xavier

2018-01-01

The aim of this paper is to design some accurate artificial boundary conditions for the semi-discretized linear Schrödinger and heat equations in rectangular domains. The Laplace transform in time and discrete Fourier transform in space are applied to get Green's functions of the semi-discretized equations in unbounded domains with single-source. An algorithm is given to compute these Green's functions accurately through some recurrence relations. Furthermore, the finite-difference method is used to discretize the reduced problem with accurate boundary conditions. Numerical simulations are presented to illustrate the accuracy of our method in the case of the linear Schrödinger and heat equations. It is shown that the reflection at the corners is correctly eliminated.

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

NASA Astrophysics Data System (ADS)

Doblack, Benjamin N.

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

Advancing Drug Discovery through Enhanced Free Energy Calculations.

PubMed

Abel, Robert; Wang, Lingle; Harder, Edward D; Berne, B J; Friesner, Richard A

2017-07-18

A principal goal of drug discovery project is to design molecules that can tightly and selectively bind to the target protein receptor. Accurate prediction of protein-ligand binding free energies is therefore of central importance in computational chemistry and computer aided drug design. Multiple recent improvements in computing power, classical force field accuracy, enhanced sampling methods, and simulation setup have enabled accurate and reliable calculations of protein-ligands binding free energies, and position free energy calculations to play a guiding role in small molecule drug discovery. In this Account, we outline the relevant methodological advances, including the REST2 (Replica Exchange with Solute Temperting) enhanced sampling, the incorporation of REST2 sampling with convential FEP (Free Energy Perturbation) through FEP/REST, the OPLS3 force field, and the advanced simulation setup that constitute our FEP+ approach, followed by the presentation of extensive comparisons with experiment, demonstrating sufficient accuracy in potency prediction (better than 1 kcal/mol) to substantially impact lead optimization campaigns. The limitations of the current FEP+ implementation and best practices in drug discovery applications are also discussed followed by the future methodology development plans to address those limitations. We then report results from a recent drug discovery project, in which several thousand FEP+ calculations were successfully deployed to simultaneously optimize potency, selectivity, and solubility, illustrating the power of the approach to solve challenging drug design problems. The capabilities of free energy calculations to accurately predict potency and selectivity have led to the advance of ongoing drug discovery projects, in challenging situations where alternative approaches would have great difficulties. The ability to effectively carry out projects evaluating tens of thousands, or hundreds of thousands, of proposed drug candidates, is potentially transformative in enabling hard to drug targets to be attacked, and in facilitating the development of superior compounds, in various dimensions, for a wide range of targets. More effective integration of FEP+ calculations into the drug discovery process will ensure that the results are deployed in an optimal fashion for yielding the best possible compounds entering the clinic; this is where the greatest payoff is in the exploitation of computer driven design capabilities. A key conclusion from the work described is the surprisingly robust and accurate results that are attainable within the conventional classical simulation, fixed charge paradigm. No doubt there are individual cases that would benefit from a more sophisticated energy model or dynamical treatment, and properties other than protein-ligand binding energies may be more sensitive to these approximations. We conclude that an inflection point in the ability of MD simulations to impact drug discovery has now been attained, due to the confluence of hardware and software development along with the formulation of "good enough" theoretical methods and models.

Simulation-based Mastery Learning Improves Cardiac Auscultation Skills in Medical Students

PubMed Central

McGaghie, William C.; Cohen, Elaine R.; Kaye, Marsha; Wayne, Diane B.

2010-01-01

Background Cardiac auscultation is a core clinical skill. However, prior studies show that trainee skills are often deficient and that clinical experience is not a proxy for competence. Objective To describe a mastery model of cardiac auscultation education and evaluate its effectiveness in improving bedside cardiac auscultation skills. Design Untreated control group design with pretest and posttest. Participants Third-year students who received a cardiac auscultation curriculum and fourth year students who did not. Intervention A cardiac auscultation curriculum consisting of a computer tutorial and a cardiac patient simulator. All third-year students were required to meet or exceed a minimum passing score (MPS) set by an expert panel at posttest. Measurements Diagnostic accuracy with simulated heart sounds and actual patients. Results Trained third-year students (n = 77) demonstrated significantly higher cardiac auscultation accuracy compared to untrained fourth year students (n = 31) in assessment of simulated heart sounds (93.8% vs. 73.9%, p < 0.001) and with real patients (81.8% vs. 75.1%, p = 0.003). USMLE scores correlated modestly with a computer-based multiple choice assessment using simulated heart sounds but not with bedside skills on real patients. Conclusions A cardiac auscultation curriculum consisting of deliberate practice with a computer-based tutorial and a cardiac patient simulator resulted in improved assessment of simulated heart sounds and more accurate examination of actual patients. PMID:20339952

Novel Method for Incorporating Model Uncertainties into Gravitational Wave Parameter Estimates

NASA Astrophysics Data System (ADS)

Moore, Christopher J.; Gair, Jonathan R.

2014-12-01

Posterior distributions on parameters computed from experimental data using Bayesian techniques are only as accurate as the models used to construct them. In many applications, these models are incomplete, which both reduces the prospects of detection and leads to a systematic error in the parameter estimates. In the analysis of data from gravitational wave detectors, for example, accurate waveform templates can be computed using numerical methods, but the prohibitive cost of these simulations means this can only be done for a small handful of parameters. In this Letter, a novel method to fold model uncertainties into data analysis is proposed; the waveform uncertainty is analytically marginalized over using with a prior distribution constructed by using Gaussian process regression to interpolate the waveform difference from a small training set of accurate templates. The method is well motivated, easy to implement, and no more computationally expensive than standard techniques. The new method is shown to perform extremely well when applied to a toy problem. While we use the application to gravitational wave data analysis to motivate and illustrate the technique, it can be applied in any context where model uncertainties exist.

Three Dimensional Simulations of Multiphase Flows Using a Lattice Boltzmann Method Suitable for High Density Ratios - 12126

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

Gokaltun, Seckin; McDaniel, Dwayne; Roelant, David

2012-07-01

Multiphase flows involving gas and liquid phases can be observed in engineering operations at various Department of Energy sites, such as mixing of slurries using pulsed-air mixers and hydrogen gas generation in liquid waste tanks etc. The dynamics of the gas phase in the liquid domain play an important role in the mixing effectiveness of the pulsed-air mixers or in the level of gas pressure build-up in waste tanks. To understand such effects, computational fluid dynamics methods (CFD) can be utilized by developing a three-dimensional computerized multiphase flow model that can predict accurately the behavior of gas motion inside liquid-filledmore » tanks by solving the governing mathematical equations that represent the physics of the phenomena. In this paper, such a CFD method, lattice Boltzmann method (LBM), is presented that can model multiphase flows accurately and efficiently. LBM is favored over traditional Navier-Stokes based computational models since interfacial forces are handled more effectively in LBM. The LBM is easier to program, more efficient to solve on parallel computers, and has the ability to capture the interface between different fluid phases intrinsically. The LBM used in this paper can solve for the incompressible and viscous flow field in three dimensions, while at the same time, solve the Cahn-Hillard equation to track the position of the gas-liquid interface specifically when the density and viscosity ratios between the two fluids are high. This feature is of primary importance since the previous LBM models proposed for multiphase flows become unstable when the density ratio is larger than 10. The ability to provide stable and accurate simulations at large density ratios becomes important when the simulation case involves fluids such as air and water with a density ratio around 1000 that are common to many engineering problems. In order to demonstrate the capability of the 3D LBM method at high density ratios, a static bubble simulation is conducted to solve for the pressure difference between the inside and outside of a gas bubble in a liquid domain. Once the results show that the method is in agreement with the Laplace law, buoyant bubble simulations are conducted. The initial results obtained for bubble shape during the rising process was found to be in agreement with the theoretical expectations. (authors)« less

Computational aspects in high intensity ultrasonic surgery planning.

PubMed

Pulkkinen, A; Hynynen, K

2010-01-01

Therapeutic ultrasound treatment planning is discussed and computational aspects regarding it are reviewed. Nonlinear ultrasound simulations were solved with a combined frequency domain Rayleigh and KZK model. Ultrasonic simulations were combined with thermal simulations and were used to compute heating of muscle tissue in vivo for four different focused ultrasound transducers. The simulations were compared with measurements and good agreement was found for large F-number transducers. However, at F# 1.9 the simulated rate of temperature rise was approximately a factor of 2 higher than the measured ones. The power levels used with the F# 1 transducer were too low to show any nonlinearity. The simulations were used to investigate the importance of nonlinarities generated in the coupling water, and also the importance of including skin in the simulations. Ignoring either of these in the model would lead to larger errors. Most notably, the nonlinearities generated in the water can enhance the focal temperature by more than 100%. The simulations also demonstrated that pulsed high power sonications may provide an opportunity to significantly (up to a factor of 3) reduce the treatment time. In conclusion, nonlinear propagation can play an important role in shaping the energy distribution during a focused ultrasound treatment and it should not be ignored in planning. However, the current simulation methods are accurate only with relatively large F-numbers and better models need to be developed for sharply focused transducers. Copyright 2009 Elsevier Ltd. All rights reserved.

A method to incorporate the effect of beam quality on image noise in a digitally reconstructed radiograph (DRR) based computer simulation for optimisation of digital radiography

NASA Astrophysics Data System (ADS)

Moore, Craig S.; Wood, Tim J.; Saunderson, John R.; Beavis, Andrew W.

2017-09-01

The use of computer simulated digital x-radiographs for optimisation purposes has become widespread in recent years. To make these optimisation investigations effective, it is vital simulated radiographs contain accurate anatomical and system noise. Computer algorithms that simulate radiographs based solely on the incident detector x-ray intensity (‘dose’) have been reported extensively in the literature. However, while it has been established for digital mammography that x-ray beam quality is an important factor when modelling noise in simulated images there are no such studies for diagnostic imaging of the chest, abdomen and pelvis. This study investigates the influence of beam quality on image noise in a digital radiography (DR) imaging system, and incorporates these effects into a digitally reconstructed radiograph (DRR) computer simulator. Image noise was measured on a real DR imaging system as a function of dose (absorbed energy) over a range of clinically relevant beam qualities. Simulated ‘absorbed energy’ and ‘beam quality’ DRRs were then created for each patient and tube voltage under investigation. Simulated noise images, corrected for dose and beam quality, were subsequently produced from the absorbed energy and beam quality DRRs, using the measured noise, absorbed energy and beam quality relationships. The noise images were superimposed onto the noiseless absorbed energy DRRs to create the final images. Signal-to-noise measurements in simulated chest, abdomen and spine images were within 10% of the corresponding measurements in real images. This compares favourably to our previous algorithm where images corrected for dose only were all within 20%.

Consistent Large-Eddy Simulation of a Temporal Mixing Layer Laden with Evaporating Drops. Part 2; A Posteriori Modelling

NASA Technical Reports Server (NTRS)

Leboissertier, Anthony; Okong'O, Nora; Bellan, Josette

2005-01-01

Large-eddy simulation (LES) is conducted of a three-dimensional temporal mixing layer whose lower stream is initially laden with liquid drops which may evaporate during the simulation. The gas-phase equations are written in an Eulerian frame for two perfect gas species (carrier gas and vapour emanating from the drops), while the liquid-phase equations are written in a Lagrangian frame. The effect of drop evaporation on the gas phase is considered through mass, species, momentum and energy source terms. The drop evolution is modelled using physical drops, or using computational drops to represent the physical drops. Simulations are performed using various LES models previously assessed on a database obtained from direct numerical simulations (DNS). These LES models are for: (i) the subgrid-scale (SGS) fluxes and (ii) the filtered source terms (FSTs) based on computational drops. The LES, which are compared to filtered-and-coarsened (FC) DNS results at the coarser LES grid, are conducted with 64 times fewer grid points than the DNS, and up to 64 times fewer computational than physical drops. It is found that both constant-coefficient and dynamic Smagorinsky SGS-flux models, though numerically stable, are overly dissipative and damp generated small-resolved-scale (SRS) turbulent structures. Although the global growth and mixing predictions of LES using Smagorinsky models are in good agreement with the FC-DNS, the spatial distributions of the drops differ significantly. In contrast, the constant-coefficient scale-similarity model and the dynamic gradient model perform well in predicting most flow features, with the latter model having the advantage of not requiring a priori calibration of the model coefficient. The ability of the dynamic models to determine the model coefficient during LES is found to be essential since the constant-coefficient gradient model, although more accurate than the Smagorinsky model, is not consistently numerically stable despite using DNS-calibrated coefficients. With accurate SGS-flux models, namely scale-similarity and dynamic gradient, the FST model allows up to a 32-fold reduction in computational drops compared to the number of physical drops, without degradation of accuracy; a 64-fold reduction leads to a slight decrease in accuracy.

Learning-based stochastic object models for use in optimizing imaging systems

NASA Astrophysics Data System (ADS)

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

2017-03-01

It is widely known that the optimization of imaging systems based on objective, or task-based, measures of image quality via computer-simulation requires use of a stochastic object model (SOM). However, the development of computationally tractable SOMs that can accurately model the statistical variations in anatomy within a specified ensemble of patients remains a challenging task. Because they are established by use of image data corresponding a single patient, previously reported numerical anatomical models lack of the ability to accurately model inter- patient variations in anatomy. In certain applications, however, databases of high-quality volumetric images are available that can facilitate this task. In this work, a novel and tractable methodology for learning a SOM from a set of volumetric training images is developed. The proposed method is based upon geometric attribute distribution (GAD) models, which characterize the inter-structural centroid variations and the intra-structural shape variations of each individual anatomical structure. The GAD models are scalable and deformable, and constrained by their respective principal attribute variations learned from training data. By use of the GAD models, random organ shapes and positions can be generated and integrated to form an anatomical phantom. The randomness in organ shape and position will reflect the variability of anatomy present in the training data. To demonstrate the methodology, a SOM corresponding to the pelvis of an adult male was computed and a corresponding ensemble of phantoms was created. Additionally, computer-simulated X-ray projection images corresponding to the phantoms were computed, from which tomographic images were reconstructed.

Theory and computer simulation of hard-core Yukawa mixtures: thermodynamical, structural and phase coexistence properties.

PubMed

Mkanya, Anele; Pellicane, Giuseppe; Pini, Davide; Caccamo, Carlo

2017-09-13

We report extensive calculations, based on the modified hypernetted chain (MHNC) theory, on the hierarchical reference theory (HRT), and on Monte Carlo simulations, of thermodynamical, structural and phase coexistence properties of symmetric binary hard-core Yukawa mixtures (HCYM) with attractive interactions at equal species concentration. The obtained results are throughout compared with those available in the literature for the same systems. It turns out that the MHNC predictions for thermodynamic and structural quantities are quite accurate in comparison with the MC data. The HRT is equally accurate for thermodynamics, and slightly less accurate for structure. Liquid-vapor (LV) and liquid-liquid (LL) consolute coexistence conditions as emerging from simulations, are also highly satisfactorily reproduced by both the MHNC and HRT for relatively long ranged potentials. When the potential range reduces, the MHNC faces problems in determining the LV binodal line; however, the LL consolute line and the critical end point (CEP) temperature and density turn out to be still satisfactorily predicted within this theory. The HRT also predicts with good accuracy the CEP position. The possibility of employing liquid state theories HCYM for the purpose of reliably determining phase equilibria in multicomponent colloidal fluids of current technological interest, is discussed.

Theory and computer simulation of hard-core Yukawa mixtures: thermodynamical, structural and phase coexistence properties

NASA Astrophysics Data System (ADS)

Mkanya, Anele; Pellicane, Giuseppe; Pini, Davide; Caccamo, Carlo

2017-09-01

We report extensive calculations, based on the modified hypernetted chain (MHNC) theory, on the hierarchical reference theory (HRT), and on Monte Carlo simulations, of thermodynamical, structural and phase coexistence properties of symmetric binary hard-core Yukawa mixtures (HCYM) with attractive interactions at equal species concentration. The obtained results are throughout compared with those available in the literature for the same systems. It turns out that the MHNC predictions for thermodynamic and structural quantities are quite accurate in comparison with the MC data. The HRT is equally accurate for thermodynamics, and slightly less accurate for structure. Liquid-vapor (LV) and liquid-liquid (LL) consolute coexistence conditions as emerging from simulations, are also highly satisfactorily reproduced by both the MHNC and HRT for relatively long ranged potentials. When the potential range reduces, the MHNC faces problems in determining the LV binodal line; however, the LL consolute line and the critical end point (CEP) temperature and density turn out to be still satisfactorily predicted within this theory. The HRT also predicts with good accuracy the CEP position. The possibility of employing liquid state theories HCYM for the purpose of reliably determining phase equilibria in multicomponent colloidal fluids of current technological interest, is discussed.

Potential pitfalls of strain rate imaging: angle dependency

NASA Technical Reports Server (NTRS)

Castro, P. L.; Greenberg, N. L.; Drinko, J.; Garcia, M. J.; Thomas, J. D.

2000-01-01

Strain Rate Imaging (SRI) is a new echocardiographic technique that allows for the real-time determination of myocardial SR, which may be used for the early and accurate detection of coronary artery disease. We sought to study whether SR is affected by scan line alignment in a computer simulation and an in vivo experiment. Through the computer simulation and the in vivo experiment we generated and validated safe scanning sectors within the ultrasound scan sector and showed that while SRI will be an extremely valuable tool in detecting coronary artery disease there are potential pitfalls for the unwary clinician. Only after accounting for these affects due to angle dependency, can clinicians utilize SRI's potential as a valuable tool in detecting coronary artery disease.

Computer Simulation Results for the Two-Point Probability Function of Composite Media

NASA Astrophysics Data System (ADS)

Smith, P.; Torquato, S.

1988-05-01

Computer simulation results are reported for the two-point matrix probability function S2 of two-phase random media composed of disks distributed with an arbitrary degree of impenetrability λ. The novel technique employed to sample S2( r) (which gives the probability of finding the endpoints of a line segment of length r in the matrix) is very accurate and has a fast execution time. Results for the limiting cases λ = 0 (fully penetrable disks) and λ = 1 (hard disks), respectively, compare very favorably with theoretical predictions made by Torquato and Beasley and by Torquato and Lado. Results are also reported for several values of λ. that lie between these two extremes: cases which heretofore have not been examined.

Benchmarking of neutron production of heavy-ion transport codes

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

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

Physics-based subsurface visualization of human tissue.

PubMed

Sharp, Richard; Adams, Jacob; Machiraju, Raghu; Lee, Robert; Crane, Robert

2007-01-01

In this paper, we present a framework for simulating light transport in three-dimensional tissue with inhomogeneous scattering properties. Our approach employs a computational model to simulate light scattering in tissue through the finite element solution of the diffusion equation. Although our model handles both visible and nonvisible wavelengths, we especially focus on the interaction of near infrared (NIR) light with tissue. Since most human tissue is permeable to NIR light, tools to noninvasively image tumors, blood vasculature, and monitor blood oxygenation levels are being constructed. We apply this model to a numerical phantom to visually reproduce the images generated by these real-world tools. Therefore, in addition to enabling inverse design of detector instruments, our computational tools produce physically-accurate visualizations of subsurface structures.

Cloud computing approaches for prediction of ligand binding poses and pathways.

PubMed

Lawrenz, Morgan; Shukla, Diwakar; Pande, Vijay S

2015-01-22

We describe an innovative protocol for ab initio prediction of ligand crystallographic binding poses and highly effective analysis of large datasets generated for protein-ligand dynamics. We include a procedure for setup and performance of distributed molecular dynamics simulations on cloud computing architectures, a model for efficient analysis of simulation data, and a metric for evaluation of model convergence. We give accurate binding pose predictions for five ligands ranging in affinity from 7 nM to > 200 μM for the immunophilin protein FKBP12, for expedited results in cases where experimental structures are difficult to produce. Our approach goes beyond single, low energy ligand poses to give quantitative kinetic information that can inform protein engineering and ligand design.

Algorithm for planning a double-jaw orthognathic surgery using a computer-aided surgical simulation (CASS) protocol. Part 1: planning sequence

PubMed Central

Xia, J. J.; Gateno, J.; Teichgraeber, J. F.; Yuan, P.; Chen, K.-C.; Li, J.; Zhang, X.; Tang, Z.; Alfi, D. M.

2015-01-01

The success of craniomaxillofacial (CMF) surgery depends not only on the surgical techniques, but also on an accurate surgical plan. The adoption of computer-aided surgical simulation (CASS) has created a paradigm shift in surgical planning. However, planning an orthognathic operation using CASS differs fundamentally from planning using traditional methods. With this in mind, the Surgical Planning Laboratory of Houston Methodist Research Institute has developed a CASS protocol designed specifically for orthognathic surgery. The purpose of this article is to present an algorithm using virtual tools for planning a double-jaw orthognathic operation. This paper will serve as an operation manual for surgeons wanting to incorporate CASS into their clinical practice. PMID:26573562

Microcanonical-ensemble computer simulation of the high-temperature expansion coefficients of the Helmholtz free energy of a square-well fluid

NASA Astrophysics Data System (ADS)

Sastre, Francisco; Moreno-Hilario, Elizabeth; Sotelo-Serna, Maria Guadalupe; Gil-Villegas, Alejandro

2018-02-01

The microcanonical-ensemble computer simulation method (MCE) is used to evaluate the perturbation terms Ai of the Helmholtz free energy of a square-well (SW) fluid. The MCE method offers a very efficient and accurate procedure for the determination of perturbation terms of discrete-potential systems such as the SW fluid and surpass the standard NVT canonical ensemble Monte Carlo method, allowing the calculation of the first six expansion terms. Results are presented for the case of a SW potential with attractive ranges 1.1 ≤ λ ≤ 1.8. Using semi-empirical representation of the MCE values for Ai, we also discuss the accuracy in the determination of the phase diagram of this system.

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

NASA Technical Reports Server (NTRS)

Slater, John W.; Saunders, John D.

2010-01-01

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

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

PubMed

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

2011-12-15

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

A streamline splitting pore-network approach for computationally inexpensive and accurate simulation of transport in porous media

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

Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew

2014-03-20

Several approaches have been developed in the literature for solving flow and transport at the pore-scale. Some authors use a direct modeling approach where the fundamental flow and transport equations are solved on the actual pore-space geometry. Such direct modeling, while very accurate, comes at a great computational cost. Network models are computationally more efficient because the pore-space morphology is approximated. Typically, a mixed cell method (MCM) is employed for solving the flow and transport system which assumes pore-level perfect mixing. This assumption is invalid at moderate to high Peclet regimes. In this work, a novel Eulerian perspective on modelingmore » flow and transport at the pore-scale is developed. The new streamline splitting method (SSM) allows for circumventing the pore-level perfect mixing assumption, while maintaining the computational efficiency of pore-network models. SSM was verified with direct simulations and excellent matches were obtained against micromodel experiments across a wide range of pore-structure and fluid-flow parameters. The increase in the computational cost from MCM to SSM is shown to be minimal, while the accuracy of SSM is much higher than that of MCM and comparable to direct modeling approaches. Therefore, SSM can be regarded as an appropriate balance between incorporating detailed physics and controlling computational cost. The truly predictive capability of the model allows for the study of pore-level interactions of fluid flow and transport in different porous materials. In this paper, we apply SSM and MCM to study the effects of pore-level mixing on transverse dispersion in 3D disordered granular media.« less

Model Reduction of Computational Aerothermodynamics for Multi-Discipline Analysis in High Speed Flows

NASA Astrophysics Data System (ADS)

Crowell, Andrew Rippetoe

This dissertation describes model reduction techniques for the computation of aerodynamic heat flux and pressure loads for multi-disciplinary analysis of hypersonic vehicles. NASA and the Department of Defense have expressed renewed interest in the development of responsive, reusable hypersonic cruise vehicles capable of sustained high-speed flight and access to space. However, an extensive set of technical challenges have obstructed the development of such vehicles. These technical challenges are partially due to both the inability to accurately test scaled vehicles in wind tunnels and to the time intensive nature of high-fidelity computational modeling, particularly for the fluid using Computational Fluid Dynamics (CFD). The aim of this dissertation is to develop efficient and accurate models for the aerodynamic heat flux and pressure loads to replace the need for computationally expensive, high-fidelity CFD during coupled analysis. Furthermore, aerodynamic heating and pressure loads are systematically evaluated for a number of different operating conditions, including: simple two-dimensional flow over flat surfaces up to three-dimensional flows over deformed surfaces with shock-shock interaction and shock-boundary layer interaction. An additional focus of this dissertation is on the implementation and computation of results using the developed aerodynamic heating and pressure models in complex fluid-thermal-structural simulations. Model reduction is achieved using a two-pronged approach. One prong focuses on developing analytical corrections to isothermal, steady-state CFD flow solutions in order to capture flow effects associated with transient spatially-varying surface temperatures and surface pressures (e.g., surface deformation, surface vibration, shock impingements, etc.). The second prong is focused on minimizing the computational expense of computing the steady-state CFD solutions by developing an efficient surrogate CFD model. The developed two-pronged approach is found to exhibit balanced performance in terms of accuracy and computational expense, relative to several existing approaches. This approach enables CFD-based loads to be implemented into long duration fluid-thermal-structural simulations.

Algorithms for Hyperspectral Endmember Extraction and Signature Classification with Morphological Dendritic Networks

NASA Astrophysics Data System (ADS)

Schmalz, M.; Ritter, G.

Accurate multispectral or hyperspectral signature classification is key to the nonimaging detection and recognition of space objects. Additionally, signature classification accuracy depends on accurate spectral endmember determination [1]. Previous approaches to endmember computation and signature classification were based on linear operators or neural networks (NNs) expressed in terms of the algebra (R, +, x) [1,2]. Unfortunately, class separation in these methods tends to be suboptimal, and the number of signatures that can be accurately classified often depends linearly on the number of NN inputs. This can lead to poor endmember distinction, as well as potentially significant classification errors in the presence of noise or densely interleaved signatures. In contrast to traditional CNNs, autoassociative morphological memories (AMM) are a construct similar to Hopfield autoassociatived memories defined on the (R, +, ?,?) lattice algebra [3]. Unlimited storage and perfect recall of noiseless real valued patterns has been proven for AMMs [4]. However, AMMs suffer from sensitivity to specific noise models, that can be characterized as erosive and dilative noise. On the other hand, the prior definition of a set of endmembers corresponds to material spectra lying on vertices of the minimum convex region covering the image data. These vertices can be characterized as morphologically independent patterns. It has further been shown that AMMs can be based on dendritic computation [3,6]. These techniques yield improved accuracy and class segmentation/separation ability in the presence of highly interleaved signature data. In this paper, we present a procedure for endmember determination based on AMM noise sensitivity, which employs morphological dendritic computation. We show that detected endmembers can be exploited by AMM based classification techniques, to achieve accurate signature classification in the presence of noise, closely spaced or interleaved signatures, and simulated camera optical distortions. In particular, we examine two critical cases: (1) classification of multiple closely spaced signatures that are difficult to separate using distance measures, and (2) classification of materials in simulated hyperspectral images of spaceborne satellites. In each case, test data are derived from a NASA database of space material signatures. Additional analysis pertains to computational complexity and noise sensitivity, which are superior to classical NN based techniques.

CFD analysis of a Darrieus wind turbine

NASA Astrophysics Data System (ADS)

Niculescu, M. L.; Cojocaru, M. G.; Pricop, M. V.; Pepelea, D.; Dumitrache, A.; Crunteanu, D. E.

2017-07-01

The Darrieus wind turbine has some advantages over the horizontal-axis wind turbine. Firstly, its tip speed ratio is lower than that of the horizontal-axis wind turbine and, therefore, its noise is smaller, privileging their placement near populated areas. Secondly, the Darrieus wind turbine does needs no orientation mechanism with respect to wind direction in contrast to the horizontal-axis wind turbine. However, the efficiency of the Darrieus wind turbine is lower than that of the horizontal-axis wind turbine since its aerodynamics is much more complex. With the advances in computational fluids and computers, it is possible to simulate the Darrieus wind turbine more accurately to understand better its aerodynamics. For these reasons, the present papers deals with the computational aerodynamics of a Darrieus wind turbine applying the state of the art of CFD methods (anisotropic turbulence models, transition from laminar to turbulent, scale adaptive simulation) to better understand its unsteady behavior.

Equation-free multiscale computation: algorithms and applications.

PubMed

Kevrekidis, Ioannis G; Samaey, Giovanni

2009-01-01

In traditional physicochemical modeling, one derives evolution equations at the (macroscopic, coarse) scale of interest; these are used to perform a variety of tasks (simulation, bifurcation analysis, optimization) using an arsenal of analytical and numerical techniques. For many complex systems, however, although one observes evolution at a macroscopic scale of interest, accurate models are only given at a more detailed (fine-scale, microscopic) level of description (e.g., lattice Boltzmann, kinetic Monte Carlo, molecular dynamics). Here, we review a framework for computer-aided multiscale analysis, which enables macroscopic computational tasks (over extended spatiotemporal scales) using only appropriately initialized microscopic simulation on short time and length scales. The methodology bypasses the derivation of macroscopic evolution equations when these equations conceptually exist but are not available in closed form-hence the term equation-free. We selectively discuss basic algorithms and underlying principles and illustrate the approach through representative applications. We also discuss potential difficulties and outline areas for future research.

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.