Wijma, Hein J; Marrink, Siewert J; Janssen, Dick B
2014-07-28
Computational approaches could decrease the need for the laborious high-throughput experimental screening that is often required to improve enzymes by mutagenesis. Here, we report that using multiple short molecular dynamics (MD) simulations makes it possible to accurately model enantioselectivity for large numbers of enzyme-substrate combinations at low computational costs. We chose four different haloalkane dehalogenases as model systems because of the availability of a large set of experimental data on the enantioselective conversion of 45 different substrates. To model the enantioselectivity, we quantified the frequency of occurrence of catalytically productive conformations (near attack conformations) for pairs of enantiomers during MD simulations. We found that the angle of nucleophilic attack that leads to carbon-halogen bond cleavage was a critical variable that limited the occurrence of productive conformations; enantiomers for which this angle reached values close to 180° were preferentially converted. A cluster of 20-40 very short (10 ps) MD simulations allowed adequate conformational sampling and resulted in much better agreement to experimental enantioselectivities than single long MD simulations (22 ns), while the computational costs were 50-100 fold lower. With single long MD simulations, the dynamics of enzyme-substrate complexes remained confined to a conformational subspace that rarely changed significantly, whereas with multiple short MD simulations a larger diversity of conformations of enzyme-substrate complexes was observed. PMID:24916632
Joldes, Grand Roman; Wittek, Adam; Miller, Karol
2008-01-01
Real time computation of soft tissue deformation is important for the use of augmented reality devices and for providing haptic feedback during operation or surgeon training. This requires algorithms that are fast, accurate and can handle material nonlinearities and large deformations. A set of such algorithms is presented in this paper, starting with the finite element formulation and the integration scheme used and addressing common problems such as hourglass control and locking. The computation examples presented prove that by using these algorithms, real time computations become possible without sacrificing the accuracy of the results. For a brain model having more than 7000 degrees of freedom, we computed the reaction forces due to indentation with frequency of around 1000 Hz using a standard dual core PC. Similarly, we conducted simulation of brain shift using a model with more than 50 000 degrees of freedom in less than a minute. The speed benefits of our models results from combining the Total Lagrangian formulation with explicit time integration and low order finite elements. PMID:19152791
Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Prudencio, E.; Schussman, G.; Uplenchwar, R.; Ko, K.; /SLAC
2009-06-19
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) 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.
Time-Accurate Computational Fluid Dynamics Simulation of a Pair of Moving Solid Rocket Boosters
NASA Technical Reports Server (NTRS)
Strutzenberg, Louise L.; Williams, Brandon R.
2011-01-01
Since the Columbia accident, the threat to the Shuttle launch vehicle from debris during the liftoff timeframe has been assessed by the Liftoff Debris Team at NASA/MSFC. In addition to engineering methods of analysis, CFD-generated flow fields during the liftoff timeframe have been used in conjunction with 3-DOF debris transport methods to predict the motion of liftoff debris. Early models made use of a quasi-steady flow field approximation with the vehicle positioned at a fixed location relative to the ground; however, a moving overset mesh capability has recently been developed for the Loci/CHEM CFD software which enables higher-fidelity simulation of the Shuttle transient plume startup and liftoff environment. The present work details the simulation of the launch pad and mobile launch platform (MLP) with truncated solid rocket boosters (SRBs) moving in a prescribed liftoff trajectory derived from Shuttle flight measurements. Using Loci/CHEM, time-accurate RANS and hybrid RANS/LES simulations were performed for the timeframe T0+0 to T0+3.5 seconds, which consists of SRB startup to a vehicle altitude of approximately 90 feet above the MLP. Analysis of the transient flowfield focuses on the evolution of the SRB plumes in the MLP plume holes and the flame trench, impingement on the flame deflector, and especially impingment on the MLP deck resulting in upward flow which is a transport mechanism for debris. The results show excellent qualitative agreement with the visual record from past Shuttle flights, and comparisons to pressure measurements in the flame trench and on the MLP provide confidence in these simulation capabilities.
NASA Astrophysics Data System (ADS)
Yi, Sha-Sha; Pan, Cong; Hu, Zhong-Han
2015-12-01
Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waals interaction in classical molecular dynamics simulations, it has been a long-lasting issue to develop accurate methods for the longranged Coulomb interaction. In this short review, we discuss three types of methodologies for the accurate treatment of electrostatics in simulations of explicit molecules: truncation-type methods, Ewald-type methods, and mean-field-type methods. Throughout the discussion, we brief the formulations and developments of these methods, emphasize the intrinsic connections among the three types of methods, and focus on the existing problems which are often associated with the boundary conditions of electrostatics. This brief survey is summarized with a short perspective on future trends along the method developments and applications in the field of biological simulations. Project supported by the National Natural Science Foundation of China (Grant Nos. 91127015 and 21522304) and the Open Project from the State Key Laboratory of Theoretical Physics, and the Innovation Project from the State Key Laboratory of Supramolecular Structure and Materials.
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. PMID:25615870
NASA Astrophysics Data System (ADS)
Farah, A.
The Ionospheric delay is still one of the largest sources of error that affects the positioning accuracy of any satellite positioning system. This problem could be solved due to the dispersive nature of the Ionosphere by combining simultaneous measurements of signals at two different frequencies but it is still there for single- frequency users. Much effort has been made in establishing models for single- frequency users to make this effect as small as possible. These models vary in accuracy, input data and computational complexity, so the choice between the different models depends on the individual circumstances of the user. From the simulation point of view, the model needed should be accurate with a global coverage and good description to the Ionosphere's variable nature with both time and location. The author reviews some of these established models, starting with the BENT model, the Klobuchar model and the IRI (International Reference Ionosphere) model. Since quiet a long time, Klobuchar model considers the most widely used model ever in this field, due to its simplicity and time saving. Any GPS user could find Klobuchar model's coefficients in the broadcast navigation message. CODE, Centre for Orbit Determination in Europe provides a new set of coefficients for Klobuchar model, which gives more accurate results for the Ionospheric delay computation. IGS (International GPS Service) services include providing GPS community with a global Ionospheric maps in IONEX-format (IONosphere Map Exchange format) which enables the computation of the Ionospheric delay at the desired location and time. The study was undertaken from GPS-data simulation point of view. The aim was to select a model for the simulation of GPS data that gives a good description of the Ionosphere's nature with a high degree of accuracy in computing the Ionospheric delay that yields to better-simulated data. A new model developed by the author based on IGS global Ionospheric maps. A comparison
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
The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. 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.
NASA Astrophysics Data System (ADS)
Mehmani, Yashar; Oostrom, Mart; Balhoff, Matthew T.
2014-03-01
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 modeling 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 validated against micromodel experiments; excellent matches were obtained 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 3-D disordered granular media.
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 modeling 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.
Gritzo, L.A.; Koski, J.A.; Suo-Anttila, A.J.
1999-03-16
The Container Analysis Fire Environment computer code (CAFE) is intended to provide Type B package designers with an enhanced engulfing fire boundary condition when combined with the PATRAN/P-Thermal commercial code. Historically an engulfing fire boundary condition has been modeled as {sigma}T{sup 4} where {sigma} is the Stefan-Boltzman constant, and T is the fire temperature. The CAFE code includes the necessary chemistry, thermal radiation, and fluid mechanics to model an engulfing fire. Effects included are the local cooling of gases that form a protective boundary layer that reduces the incoming radiant heat flux to values lower than expected from a simple {sigma}T{sup 4} model. In addition, the effect of object shape on mixing that may increase the local fire temperature is included. Both high and low temperature regions that depend upon the local availability of oxygen are also calculated. Thus the competing effects that can both increase and decrease the local values of radiant heat flux are included in a reamer that is not predictable a-priori. The CAFE package consists of a group of computer subroutines that can be linked to workstation-based thermal analysis codes in order to predict package performance during regulatory and other accident fire scenarios.
Accurate modeling of parallel scientific computations
NASA Technical Reports Server (NTRS)
Nicol, David M.; Townsend, James C.
1988-01-01
Scientific codes are usually parallelized by partitioning a grid among processors. To achieve top performance it is necessary to partition the grid so as to balance workload and minimize communication/synchronization costs. This problem is particularly acute when the grid is irregular, changes over the course of the computation, and is not known until load time. Critical mapping and remapping decisions rest on the ability to accurately predict performance, given a description of a grid and its partition. This paper discusses one approach to this problem, and illustrates its use on a one-dimensional fluids code. The models constructed are shown to be accurate, and are used to find optimal remapping schedules.
Progress in fast, accurate multi-scale climate simulations
Collins, W. D.; Johansen, H.; Evans, K. J.; Woodward, C. S.; Caldwell, P. M.
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
Progress in fast, accurate multi-scale climate simulations
Collins, W. D.; Johansen, H.; Evans, K. J.; Woodward, C. S.; Caldwell, P. M.
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 enabling 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.
Progress in Fast, Accurate Multi-scale Climate Simulations
Collins, William D; Johansen, Hans; Evans, Katherine J; Woodward, Carol S.; Caldwell, Peter
2015-01-01
We present a survey of physical and computational techniques that have the potential to con- tribute to the next generation of high-fidelity, multi-scale climate simulations. Examples of the climate science problems that can be investigated with more depth 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 enabling improved accuracy and fidelity in simulation of dynamics and allow more complete representations of climate features at the global scale. At the same time, part- nerships with computer science teams have focused on taking advantage of evolving computer architectures, such as many-core processors and GPUs, so that these 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.
Software simulator for multiple computer simulation system
NASA Technical Reports Server (NTRS)
Ogrady, E. P.
1983-01-01
A description is given of the structure and use of a computer program that simulates the operation of a parallel processor simulation system. The program is part of an investigation to determine algorithms that are suitable for simulating continous systems on a parallel processor configuration. The simulator is designed to accurately simulate the problem-solving phase of a simulation study. Care has been taken to ensure the integrity and correctness of data exchanges and to correctly sequence periods of computation and periods of data exchange. It is pointed out that the functions performed during a problem-setup phase or a reset phase are not simulated. In particular, there is no attempt to simulate the downloading process that loads object code into the local, transfer, and mapping memories of processing elements or the memories of the run control processor and the system control processor. The main program of the simulator carries out some problem-setup functions of the system control processor in that it requests the user to enter values for simulation system parameters and problem parameters. The method by which these values are transferred to the other processors, however, is not simulated.
Time accurate simulations of compressible shear flows
NASA Technical Reports Server (NTRS)
Givi, Peyman; Steinberger, Craig J.; Vidoni, Thomas J.; Madnia, Cyrus K.
1993-01-01
The objectives of this research are to employ direct numerical simulation (DNS) to study the phenomenon of mixing (or lack thereof) in compressible free shear flows and to suggest new means of enhancing mixing in such flows. The shear flow configurations under investigation are those of parallel mixing layers and planar jets under both non-reacting and reacting nonpremixed conditions. During the three-years of this research program, several important issues regarding mixing and chemical reactions in compressible shear flows were investigated.
Accurate Langevin approaches to simulate Markovian channel dynamics
NASA Astrophysics Data System (ADS)
Huang, Yandong; Rüdiger, Sten; Shuai, Jianwei
2015-12-01
The stochasticity of ion-channels dynamic is significant for physiological processes on neuronal cell membranes. Microscopic simulations of the ion-channel gating with Markov chains can be considered to be an accurate standard. However, such Markovian simulations are computationally demanding for membrane areas of physiologically relevant sizes, which makes the noise-approximating or Langevin equation methods advantageous in many cases. In this review, we discuss the Langevin-like approaches, including the channel-based and simplified subunit-based stochastic differential equations proposed by Fox and Lu, and the effective Langevin approaches in which colored noise is added to deterministic differential equations. In the framework of Fox and Lu’s classical models, several variants of numerical algorithms, which have been recently developed to improve accuracy as well as efficiency, are also discussed. Through the comparison of different simulation algorithms of ion-channel noise with the standard Markovian simulation, we aim to reveal the extent to which the existing Langevin-like methods approximate results using Markovian methods. Open questions for future studies are also discussed.
Accurate simulation of optical properties in dyes.
Jacquemin, Denis; Perpète, Eric A; Ciofini, Ilaria; Adamo, Carlo
2009-02-17
Since Antiquity, humans have produced and commercialized dyes. To this day, extraction of natural dyes often requires lengthy and costly procedures. In the 19th century, global markets and new industrial products drove a significant effort to synthesize artificial dyes, characterized by low production costs, huge quantities, and new optical properties (colors). Dyes that encompass classes of molecules absorbing in the UV-visible part of the electromagnetic spectrum now have a wider range of applications, including coloring (textiles, food, paintings), energy production (photovoltaic cells, OLEDs), or pharmaceuticals (diagnostics, drugs). Parallel to the growth in dye applications, researchers have increased their efforts to design and synthesize new dyes to customize absorption and emission properties. In particular, dyes containing one or more metallic centers allow for the construction of fairly sophisticated systems capable of selectively reacting to light of a given wavelength and behaving as molecular devices (photochemical molecular devices, PMDs).Theoretical tools able to predict and interpret the excited-state properties of organic and inorganic dyes allow for an efficient screening of photochemical centers. In this Account, we report recent developments defining a quantitative ab initio protocol (based on time-dependent density functional theory) for modeling dye spectral properties. In particular, we discuss the importance of several parameters, such as the methods used for electronic structure calculations, solvent effects, and statistical treatments. In addition, we illustrate the performance of such simulation tools through case studies. We also comment on current weak points of these methods and ways to improve them. PMID:19113946
Computationally efficient multibody simulations
NASA Technical Reports Server (NTRS)
Ramakrishnan, Jayant; Kumar, Manoj
1994-01-01
Computationally efficient approaches to the solution of the dynamics of multibody systems are presented in this work. The computational efficiency is derived from both the algorithmic and implementational standpoint. Order(n) approaches provide a new formulation of the equations of motion eliminating the assembly and numerical inversion of a system mass matrix as required by conventional algorithms. Computational efficiency is also gained in the implementation phase by the symbolic processing and parallel implementation of these equations. Comparison of this algorithm with existing multibody simulation programs illustrates the increased computational efficiency.
Efficient and accurate computation of generalized singular-value decompositions
NASA Astrophysics Data System (ADS)
Drmac, Zlatko
2001-11-01
We present a new family of algorithms for accurate floating--point computation of the singular value decomposition (SVD) of various forms of products (quotients) of two or three matrices. The main goal of such an algorithm is to compute all singular values to high relative accuracy. This means that we are seeking guaranteed number of accurate digits even in the smallest singular values. We also want to achieve computational efficiency, while maintaining high accuracy. To illustrate, consider the SVD of the product A=BTSC. The new algorithm uses certain preconditioning (based on diagonal scalings, the LU and QR factorizations) to replace A with A'=(B')TS'C', where A and A' have the same singular values and the matrix A' is computed explicitly. Theoretical analysis and numerical evidence show that, in the case of full rank B, C, S, the accuracy of the new algorithm is unaffected by replacing B, S, C with, respectively, D1B, D2SD3, D4C, where Di, i=1,...,4 are arbitrary diagonal matrices. As an application, the paper proposes new accurate algorithms for computing the (H,K)-SVD and (H1,K)-SVD of S.
Computer Modeling and Simulation
Pronskikh, V. S.
2014-05-09
Verification and validation of computer codes and models used in simulation are two aspects of the scientific practice of high importance and have recently been discussed by philosophers of science. While verification is predominantly associated with the correctness of the way a model is represented by a computer code or algorithm, validation more often refers to model’s relation to the real world and its intended use. It has been argued that because complex simulations are generally not transparent to a practitioner, the Duhem problem can arise for verification and validation due to their entanglement; such an entanglement makes it impossible to distinguish whether a coding error or model’s general inadequacy to its target should be blamed in the case of the model failure. I argue that in order to disentangle verification and validation, a clear distinction between computer modeling (construction of mathematical computer models of elementary processes) and simulation (construction of models of composite objects and processes by means of numerical experimenting with them) needs to be made. Holding on to that distinction, I propose to relate verification (based on theoretical strategies such as inferences) to modeling and validation, which shares the common epistemology with experimentation, to simulation. To explain reasons of their intermittent entanglement I propose a weberian ideal-typical model of modeling and simulation as roles in practice. I suggest an approach to alleviate the Duhem problem for verification and validation generally applicable in practice and based on differences in epistemic strategies and scopes
Accelerator simulation using computers
Lee, M.; Zambre, Y.; Corbett, W.
1992-01-01
Every accelerator or storage ring system consists of a charged particle beam propagating through a beam line. Although a number of computer programs exits that simulate the propagation of a beam in a given beam line, only a few provide the capabilities for designing, commissioning and operating the beam line. This paper shows how a multi-track'' simulation and analysis code can be used for these applications.
Accelerator simulation using computers
Lee, M.; Zambre, Y.; Corbett, W.
1992-01-01
Every accelerator or storage ring system consists of a charged particle beam propagating through a beam line. Although a number of computer programs exits that simulate the propagation of a beam in a given beam line, only a few provide the capabilities for designing, commissioning and operating the beam line. This paper shows how a ``multi-track`` simulation and analysis code can be used for these applications.
Computer-simulated phacoemulsification
NASA Astrophysics Data System (ADS)
Laurell, Carl-Gustaf; Nordh, Leif; Skarman, Eva; Andersson, Mats; Nordqvist, Per
2001-06-01
Phacoemulsification makes the cataract operation easier for the patient but involves a demanding technique for the surgeon. It is therefore important to increase the quality of surgical training in order to shorten the learning period for the beginner. This should diminish the risks of the patient. We are developing a computer-based simulator for training of phacoemulsification. The simulator is built on a platform that can be used as a basis for several different training simulators. A prototype has been made that has been partly tested by experienced surgeons.
Probabilistic Fatigue: Computational Simulation
NASA Technical Reports Server (NTRS)
Chamis, Christos C.
2002-01-01
Fatigue is a primary consideration in the design of aerospace structures for long term durability and reliability. There are several types of fatigue that must be considered in the design. These include low cycle, high cycle, combined for different cyclic loading conditions - for example, mechanical, thermal, erosion, etc. The traditional approach to evaluate fatigue has been to conduct many tests in the various service-environment conditions that the component will be subjected to in a specific design. This approach is reasonable and robust for that specific design. However, it is time consuming, costly and needs to be repeated for designs in different operating conditions in general. Recent research has demonstrated that fatigue of structural components/structures can be evaluated by computational simulation based on a novel paradigm. Main features in this novel paradigm are progressive telescoping scale mechanics, progressive scale substructuring and progressive structural fracture, encompassed with probabilistic simulation. These generic features of this approach are to probabilistically telescope scale local material point damage all the way up to the structural component and to probabilistically scale decompose structural loads and boundary conditions all the way down to material point. Additional features include a multifactor interaction model that probabilistically describes material properties evolution, any changes due to various cyclic load and other mutually interacting effects. The objective of the proposed paper is to describe this novel paradigm of computational simulation and present typical fatigue results for structural components. Additionally, advantages, versatility and inclusiveness of computational simulation versus testing are discussed. Guidelines for complementing simulated results with strategic testing are outlined. Typical results are shown for computational simulation of fatigue in metallic composite structures to demonstrate the
Computer simulation of earthquakes
NASA Technical Reports Server (NTRS)
Cohen, S. C.
1977-01-01
In a computer simulation study of earthquakes a seismically active strike slip fault is represented by coupled mechanical blocks which are driven by a moving plate and which slide on a friction surface. Elastic forces and time independent friction are used to generate main shock events, while viscoelastic forces and time dependent friction add aftershock features. The study reveals that the size, length, and time and place of event occurrence are strongly influenced by the magnitude and degree of homogeneity in the elastic, viscous, and friction parameters of the fault region. For example, periodically reoccurring similar events are observed in simulations with near-homogeneous parameters along the fault, whereas seismic gaps are a common feature of simulations employing large variations in the fault parameters. The study also reveals correlations between strain energy release and fault length and average displacement and between main shock and aftershock displacements.
Neutron supermirrors: an accurate theory for layer thickness computation
NASA Astrophysics Data System (ADS)
Bray, Michael
2001-11-01
We present a new theory for the computation of Super-Mirror stacks, using accurate formulas derived from the classical optics field. Approximations are introduced into the computation, but at a later stage than existing theories, providing a more rigorous treatment of the problem. The final result is a continuous thickness stack, whose properties can be determined at the outset of the design. We find that the well-known fourth power dependence of number of layers versus maximum angle is (of course) asymptotically correct. We find a formula giving directly the relation between desired reflectance, maximum angle, and number of layers (for a given pair of materials). Note: The author of this article, a classical opticist, has limited knowledge of the Neutron world, and begs forgiveness for any shortcomings, erroneous assumptions and/or misinterpretation of previous authors' work on the subject.
Accurate Computation of Survival Statistics in Genome-Wide Studies
Vandin, Fabio; Papoutsaki, Alexandra; Raphael, Benjamin J.; Upfal, Eli
2015-01-01
A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations. PMID:25950620
Computer simulation of earthquakes
NASA Technical Reports Server (NTRS)
Cohen, S. C.
1976-01-01
Two computer simulation models of earthquakes were studied for the dependence of the pattern of events on the model assumptions and input parameters. Both models represent the seismically active region by mechanical blocks which are connected to one another and to a driving plate. The blocks slide on a friction surface. In the first model elastic forces were employed and time independent friction to simulate main shock events. The size, length, and time and place of event occurrence were influenced strongly by the magnitude and degree of homogeniety in the elastic and friction parameters of the fault region. Periodically reoccurring similar events were frequently observed in simulations with near homogeneous parameters along the fault, whereas, seismic gaps were a common feature of simulations employing large variations in the fault parameters. The second model incorporated viscoelastic forces and time-dependent friction to account for aftershock sequences. The periods between aftershock events increased with time and the aftershock region was confined to that which moved in the main event.
NASA Technical Reports Server (NTRS)
Alter, Stephen J.; Brauckmann, Gregory J.; Kleb, Bil; Streett, Craig L; Glass, Christopher E.; Schuster, David M.
2015-01-01
Using the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics code, an unsteady, time-accurate flow field about a Space Launch System configuration was simulated at a transonic wind tunnel condition (Mach = 0.9). Delayed detached eddy simulation combined with Reynolds Averaged Naiver-Stokes and a Spallart-Almaras turbulence model were employed for the simulation. Second order accurate time evolution scheme was used to simulate the flow field, with a minimum of 0.2 seconds of simulated time to as much as 1.4 seconds. Data was collected at 480 pressure taps at locations, 139 of which matched a 3% wind tunnel model, tested in the Transonic Dynamic Tunnel (TDT) facility at NASA Langley Research Center. Comparisons between computation and experiment showed agreement within 5% in terms of location for peak RMS levels, and 20% for frequency and magnitude of power spectral densities. Grid resolution and time step sensitivity studies were performed to identify methods for improved accuracy comparisons to wind tunnel data. With limited computational resources, accurate trends for reduced vibratory loads on the vehicle were observed. Exploratory methods such as determining minimized computed errors based on CFL number and sub-iterations, as well as evaluating frequency content of the unsteady pressures and evaluation of oscillatory shock structures were used in this study to enhance computational efficiency and solution accuracy. These techniques enabled development of a set of best practices, for the evaluation of future flight vehicle designs in terms of vibratory loads.
Direct computation of parameters for accurate polarizable force fields
Verstraelen, Toon Vandenbrande, Steven; Ayers, Paul W.
2014-11-21
We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.
An Accurate and Dynamic Computer Graphics Muscle Model
NASA Technical Reports Server (NTRS)
Levine, David Asher
1997-01-01
A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.
Intelligence Assessment with Computer Simulations
ERIC Educational Resources Information Center
Kroner, S.; Plass, J.L.; Leutner, D.
2005-01-01
It has been suggested that computer simulations may be used for intelligence assessment. This study investigates what relationships exist between intelligence and computer-simulated tasks that mimic real-world problem-solving behavior, and discusses design requirements that simulations have to meet in order to be suitable for intelligence…
Massively Parallel Processing for Fast and Accurate Stamping Simulations
NASA Astrophysics Data System (ADS)
Gress, Jeffrey J.; Xu, Siguang; Joshi, Ramesh; Wang, Chuan-tao; Paul, Sabu
2005-08-01
The competitive automotive market drives automotive manufacturers to speed up the vehicle development cycles and reduce the lead-time. Fast tooling development is one of the key areas to support fast and short vehicle development programs (VDP). In the past ten years, the stamping simulation has become the most effective validation tool in predicting and resolving all potential formability and quality problems before the dies are physically made. The stamping simulation and formability analysis has become an critical business segment in GM math-based die engineering process. As the simulation becomes as one of the major production tools in engineering factory, the simulation speed and accuracy are the two of the most important measures for stamping simulation technology. The speed and time-in-system of forming analysis becomes an even more critical to support the fast VDP and tooling readiness. Since 1997, General Motors Die Center has been working jointly with our software vendor to develop and implement a parallel version of simulation software for mass production analysis applications. By 2001, this technology was matured in the form of distributed memory processing (DMP) of draw die simulations in a networked distributed memory computing environment. In 2004, this technology was refined to massively parallel processing (MPP) and extended to line die forming analysis (draw, trim, flange, and associated spring-back) running on a dedicated computing environment. The evolution of this technology and the insight gained through the implementation of DM0P/MPP technology as well as performance benchmarks are discussed in this publication.
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
Exploring accurate Poisson–Boltzmann methods for biomolecular simulations
Wang, Changhao; Wang, Jun; Cai, Qin; Li, Zhilin; Zhao, Hong-Kai; Luo, Ray
2013-01-01
Accurate and efficient treatment of electrostatics is a crucial step in computational analyses of biomolecular structures and dynamics. In this study, we have explored a second-order finite-difference numerical method to solve the widely used Poisson–Boltzmann equation for electrostatic analyses of realistic bio-molecules. The so-called immersed interface method was first validated and found to be consistent with the classical weighted harmonic averaging method for a diversified set of test biomolecules. The numerical accuracy and convergence behaviors of the new method were next analyzed in its computation of numerical reaction field grid potentials, energies, and atomic solvation forces. Overall similar convergence behaviors were observed as those by the classical method. Interestingly, the new method was found to deliver more accurate and better-converged grid potentials than the classical method on or nearby the molecular surface, though the numerical advantage of the new method is reduced when grid potentials are extrapolated to the molecular surface. Our exploratory study indicates the need for further improving interpolation/extrapolation schemes in addition to the developments of higher-order numerical methods that have attracted most attention in the field. PMID:24443709
A fast and accurate computational approach to protein ionization
Spassov, Velin Z.; Yan, Lisa
2008-01-01
We report a very fast and accurate physics-based method to calculate pH-dependent electrostatic effects in protein molecules and to predict the pK values of individual sites of titration. In addition, a CHARMm-based algorithm is included to construct and refine the spatial coordinates of all hydrogen atoms at a given pH. The present method combines electrostatic energy calculations based on the Generalized Born approximation with an iterative mobile clustering approach to calculate the equilibria of proton binding to multiple titration sites in protein molecules. The use of the GBIM (Generalized Born with Implicit Membrane) CHARMm module makes it possible to model not only water-soluble proteins but membrane proteins as well. The method includes a novel algorithm for preliminary refinement of hydrogen coordinates. Another difference from existing approaches is that, instead of monopeptides, a set of relaxed pentapeptide structures are used as model compounds. Tests on a set of 24 proteins demonstrate the high accuracy of the method. On average, the RMSD between predicted and experimental pK values is close to 0.5 pK units on this data set, and the accuracy is achieved at very low computational cost. The pH-dependent assignment of hydrogen atoms also shows very good agreement with protonation states and hydrogen-bond network observed in neutron-diffraction structures. The method is implemented as a computational protocol in Accelrys Discovery Studio and provides a fast and easy way to study the effect of pH on many important mechanisms such as enzyme catalysis, ligand binding, protein–protein interactions, and protein stability. PMID:18714088
Photoacoustic computed tomography without accurate ultrasonic transducer responses
NASA Astrophysics Data System (ADS)
Sheng, Qiwei; Wang, Kun; Xia, Jun; Zhu, Liren; Wang, Lihong V.; Anastasio, Mark A.
2015-03-01
Conventional photoacoustic computed tomography (PACT) image reconstruction methods assume that the object and surrounding medium are described by a constant speed-of-sound (SOS) value. In order to accurately recover fine structures, SOS heterogeneities should be quantified and compensated for during PACT reconstruction. To address this problem, several groups have proposed hybrid systems that combine PACT with ultrasound computed tomography (USCT). In such systems, a SOS map is reconstructed first via USCT. Consequently, this SOS map is employed to inform the PACT reconstruction method. Additionally, the SOS map can provide structural information regarding tissue, which is complementary to the functional information from the PACT image. We propose a paradigm shift in the way that images are reconstructed in hybrid PACT-USCT imaging. Inspired by our observation that information about the SOS distribution is encoded in PACT measurements, we propose to jointly reconstruct the absorbed optical energy density and SOS distributions from a combined set of USCT and PACT measurements, thereby reducing the two reconstruction problems into one. This innovative approach has several advantages over conventional approaches in which PACT and USCT images are reconstructed independently: (1) Variations in the SOS will automatically be accounted for, optimizing PACT image quality; (2) The reconstructed PACT and USCT images will possess minimal systematic artifacts because errors in the imaging models will be optimally balanced during the joint reconstruction; (3) Due to the exploitation of information regarding the SOS distribution in the full-view PACT data, our approach will permit high-resolution reconstruction of the SOS distribution from sparse array data.
D-BRAIN: Anatomically Accurate Simulated Diffusion MRI Brain Data.
Perrone, Daniele; Jeurissen, Ben; Aelterman, Jan; Roine, Timo; Sijbers, Jan; Pizurica, Aleksandra; Leemans, Alexander; Philips, Wilfried
2016-01-01
Diffusion Weighted (DW) MRI allows for the non-invasive study of water diffusion inside living tissues. As such, it is useful for the investigation of human brain white matter (WM) connectivity in vivo through fiber tractography (FT) algorithms. Many DW-MRI tailored restoration techniques and FT algorithms have been developed. However, it is not clear how accurately these methods reproduce the WM bundle characteristics in real-world conditions, such as in the presence of noise, partial volume effect, and a limited spatial and angular resolution. The difficulty lies in the lack of a realistic brain phantom on the one hand, and a sufficiently accurate way of modeling the acquisition-related degradation on the other. This paper proposes a software phantom that approximates a human brain to a high degree of realism and that can incorporate complex brain-like structural features. We refer to it as a Diffusion BRAIN (D-BRAIN) phantom. Also, we propose an accurate model of a (DW) MRI acquisition protocol to allow for validation of methods in realistic conditions with data imperfections. The phantom model simulates anatomical and diffusion properties for multiple brain tissue components, and can serve as a ground-truth to evaluate FT algorithms, among others. The simulation of the acquisition process allows one to include noise, partial volume effects, and limited spatial and angular resolution in the images. In this way, the effect of image artifacts on, for instance, fiber tractography can be investigated with great detail. The proposed framework enables reliable and quantitative evaluation of DW-MR image processing and FT algorithms at the level of large-scale WM structures. The effect of noise levels and other data characteristics on cortico-cortical connectivity and tractography-based grey matter parcellation can be investigated as well. PMID:26930054
D-BRAIN: Anatomically Accurate Simulated Diffusion MRI Brain Data
Perrone, Daniele; Jeurissen, Ben; Aelterman, Jan; Roine, Timo; Sijbers, Jan; Pizurica, Aleksandra; Leemans, Alexander; Philips, Wilfried
2016-01-01
Diffusion Weighted (DW) MRI allows for the non-invasive study of water diffusion inside living tissues. As such, it is useful for the investigation of human brain white matter (WM) connectivity in vivo through fiber tractography (FT) algorithms. Many DW-MRI tailored restoration techniques and FT algorithms have been developed. However, it is not clear how accurately these methods reproduce the WM bundle characteristics in real-world conditions, such as in the presence of noise, partial volume effect, and a limited spatial and angular resolution. The difficulty lies in the lack of a realistic brain phantom on the one hand, and a sufficiently accurate way of modeling the acquisition-related degradation on the other. This paper proposes a software phantom that approximates a human brain to a high degree of realism and that can incorporate complex brain-like structural features. We refer to it as a Diffusion BRAIN (D-BRAIN) phantom. Also, we propose an accurate model of a (DW) MRI acquisition protocol to allow for validation of methods in realistic conditions with data imperfections. The phantom model simulates anatomical and diffusion properties for multiple brain tissue components, and can serve as a ground-truth to evaluate FT algorithms, among others. The simulation of the acquisition process allows one to include noise, partial volume effects, and limited spatial and angular resolution in the images. In this way, the effect of image artifacts on, for instance, fiber tractography can be investigated with great detail. The proposed framework enables reliable and quantitative evaluation of DW-MR image processing and FT algorithms at the level of large-scale WM structures. The effect of noise levels and other data characteristics on cortico-cortical connectivity and tractography-based grey matter parcellation can be investigated as well. PMID:26930054
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
An Accurate and Computationally Efficient Model for Membrane-Type Circular-Symmetric Micro-Hotplates
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
How Accurate Are Transition States from Simulations of Enzymatic Reactions?
2015-01-01
The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics. PMID:24860275
The FLUKA Code: An Accurate Simulation Tool for Particle Therapy
Battistoni, Giuseppe; Bauer, Julia; Boehlen, Till T.; Cerutti, Francesco; Chin, Mary P. W.; Dos Santos Augusto, Ricardo; Ferrari, Alfredo; Ortega, Pablo G.; Kozłowska, Wioletta; Magro, Giuseppe; Mairani, Andrea; Parodi, Katia; Sala, Paola R.; Schoofs, Philippe; Tessonnier, Thomas; Vlachoudis, Vasilis
2016-01-01
Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models capable of handling all components of the expected radiation field. This becomes extremely important for correctly performing not only physical but also biologically based dose calculations, especially in cases where ions heavier than protons are involved. In addition, accurate prediction of emerging secondary radiation is of utmost importance in innovative areas of research aiming at in vivo treatment verification. This contribution will address the recent developments of the FLUKA MC code and its practical applications in this field. Refinements of the FLUKA nuclear models in the therapeutic energy interval lead to an improved description of the mixed radiation field as shown in the presented benchmarks against experimental data with both 4He and 12C ion beams. Accurate description of ionization energy losses and of particle scattering and interactions lead to the excellent agreement of calculated depth–dose profiles with those measured at leading European hadron therapy centers, both with proton and ion beams. In order to support the application of FLUKA in hospital-based environments, Flair, the FLUKA graphical interface, has been enhanced with the capability of translating CT DICOM images into voxel-based computational phantoms in a fast and well-structured way. The interface is capable of importing also radiotherapy treatment data described in DICOM RT standard. In addition, the interface is equipped with an intuitive PET scanner geometry generator and automatic recording of coincidence events. Clinically, similar cases will be presented both in terms of absorbed dose and biological dose calculations describing the various available features. PMID:27242956
The FLUKA Code: An Accurate Simulation Tool for Particle Therapy.
Battistoni, Giuseppe; Bauer, Julia; Boehlen, Till T; Cerutti, Francesco; Chin, Mary P W; Dos Santos Augusto, Ricardo; Ferrari, Alfredo; Ortega, Pablo G; Kozłowska, Wioletta; Magro, Giuseppe; Mairani, Andrea; Parodi, Katia; Sala, Paola R; Schoofs, Philippe; Tessonnier, Thomas; Vlachoudis, Vasilis
2016-01-01
Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models capable of handling all components of the expected radiation field. This becomes extremely important for correctly performing not only physical but also biologically based dose calculations, especially in cases where ions heavier than protons are involved. In addition, accurate prediction of emerging secondary radiation is of utmost importance in innovative areas of research aiming at in vivo treatment verification. This contribution will address the recent developments of the FLUKA MC code and its practical applications in this field. Refinements of the FLUKA nuclear models in the therapeutic energy interval lead to an improved description of the mixed radiation field as shown in the presented benchmarks against experimental data with both (4)He and (12)C ion beams. Accurate description of ionization energy losses and of particle scattering and interactions lead to the excellent agreement of calculated depth-dose profiles with those measured at leading European hadron therapy centers, both with proton and ion beams. In order to support the application of FLUKA in hospital-based environments, Flair, the FLUKA graphical interface, has been enhanced with the capability of translating CT DICOM images into voxel-based computational phantoms in a fast and well-structured way. The interface is capable of importing also radiotherapy treatment data described in DICOM RT standard. In addition, the interface is equipped with an intuitive PET scanner geometry generator and automatic recording of coincidence events. Clinically, similar cases will be presented both in terms of absorbed dose and biological dose calculations describing the various available features. PMID:27242956
Anisotropic Turbulence Modeling for Accurate Rod Bundle Simulations
Baglietto, Emilio
2006-07-01
An improved anisotropic eddy viscosity model has been developed for accurate predictions of the thermal hydraulic performances of nuclear reactor fuel assemblies. The proposed model adopts a non-linear formulation of the stress-strain relationship in order to include the reproduction of the anisotropic phenomena, and in combination with an optimized low-Reynolds-number formulation based on Direct Numerical Simulation (DNS) to produce correct damping of the turbulent viscosity in the near wall region. This work underlines the importance of accurate anisotropic modeling to faithfully reproduce the scale of the turbulence driven secondary flows inside the bundle subchannels, by comparison with various isothermal and heated experimental cases. The very low scale secondary motion is responsible for the increased turbulence transport which produces a noticeable homogenization of the velocity distribution and consequently of the circumferential cladding temperature distribution, which is of main interest in bundle design. Various fully developed bare bundles test cases are shown for different geometrical and flow conditions, where the proposed model shows clearly improved predictions, in close agreement with experimental findings, for regular as well as distorted geometries. Finally the applicability of the model for practical bundle calculations is evaluated through its application in the high-Reynolds form on coarse grids, with excellent results. (author)
CgWind: A high-order accurate simulation tool for wind turbines and wind farms
Chand, K K; Henshaw, W D; Lundquist, K A; Singer, M A
2010-02-22
CgWind is a high-fidelity large eddy simulation (LES) tool designed to meet the modeling needs of wind turbine and wind park engineers. This tool combines several advanced computational technologies in order to model accurately the complex and dynamic nature of wind energy applications. The composite grid approach provides high-quality structured grids for the efficient implementation of high-order accurate discretizations of the incompressible Navier-Stokes equations. Composite grids also provide a natural mechanism for modeling bodies in relative motion and complex geometry. Advanced algorithms such as matrix-free multigrid, compact discretizations and approximate factorization will allow CgWind to perform highly resolved calculations efficiently on a wide class of computing resources. Also in development are nonlinear LES subgrid-scale models required to simulate the many interacting scales present in large wind turbine applications. This paper outlines our approach, the current status of CgWind and future development plans.
Massively parallel quantum computer simulator
NASA Astrophysics Data System (ADS)
De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.
2007-01-01
We describe portable software to simulate universal quantum computers on massive parallel computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray X1E, a SGI Altix 3700 and clusters of PCs running Windows XP. We study the performance of the software by simulating quantum computers containing up to 36 qubits, using up to 4096 processors and up to 1 TB of memory. Our results demonstrate that the simulator exhibits nearly ideal scaling as a function of the number of processors and suggest that the simulation software described in this paper may also serve as benchmark for testing high-end parallel computers.
Zhang, Hao; Zhao, Yan; Cao, Liangcai; Jin, Guofan
2015-02-23
We propose an algorithm based on fully computed holographic stereogram for calculating full-parallax computer-generated holograms (CGHs) with accurate depth cues. The proposed method integrates point source algorithm and holographic stereogram based algorithm to reconstruct the three-dimensional (3D) scenes. Precise accommodation cue and occlusion effect can be created, and computer graphics rendering techniques can be employed in the CGH generation to enhance the image fidelity. Optical experiments have been performed using a spatial light modulator (SLM) and a fabricated high-resolution hologram, the results show that our proposed algorithm can perform quality reconstructions of 3D scenes with arbitrary depth information. PMID:25836429
Symphony: a framework for accurate and holistic WSN simulation.
Riliskis, Laurynas; Osipov, Evgeny
2015-01-01
Research on wireless sensor networks has progressed rapidly over the last decade, and these technologies have been widely adopted for both industrial and domestic uses. Several operating systems have been developed, along with a multitude of network protocols for all layers of the communication stack. Industrial Wireless Sensor Network (WSN) systems must satisfy strict criteria and are typically more complex and larger in scale than domestic systems. Together with the non-deterministic behavior of network hardware in real settings, this greatly complicates the debugging and testing of WSN functionality. To facilitate the testing, validation, and debugging of large-scale WSN systems, we have developed a simulation framework that accurately reproduces the processes that occur inside real equipment, including both hardware- and software-induced delays. The core of the framework consists of a virtualized operating system and an emulated hardware platform that is integrated with the general purpose network simulator ns-3. Our framework enables the user to adjust the real code base as would be done in real deployments and also to test the boundary effects of different hardware components on the performance of distributed applications and protocols. Additionally we have developed a clock emulator with several different skew models and a component that handles sensory data feeds. The new framework should substantially shorten WSN application development cycles. PMID:25723144
Symphony: A Framework for Accurate and Holistic WSN Simulation
Riliskis, Laurynas; Osipov, Evgeny
2015-01-01
Research on wireless sensor networks has progressed rapidly over the last decade, and these technologies have been widely adopted for both industrial and domestic uses. Several operating systems have been developed, along with a multitude of network protocols for all layers of the communication stack. Industrial Wireless Sensor Network (WSN) systems must satisfy strict criteria and are typically more complex and larger in scale than domestic systems. Together with the non-deterministic behavior of network hardware in real settings, this greatly complicates the debugging and testing of WSN functionality. To facilitate the testing, validation, and debugging of large-scale WSN systems, we have developed a simulation framework that accurately reproduces the processes that occur inside real equipment, including both hardware- and software-induced delays. The core of the framework consists of a virtualized operating system and an emulated hardware platform that is integrated with the general purpose network simulator ns-3. Our framework enables the user to adjust the real code base as would be done in real deployments and also to test the boundary effects of different hardware components on the performance of distributed applications and protocols. Additionally we have developed a clock emulator with several different skew models and a component that handles sensory data feeds. The new framework should substantially shorten WSN application development cycles. PMID:25723144
Measurement of Fracture Geometry for Accurate Computation of Hydraulic Conductivity
NASA Astrophysics Data System (ADS)
Chae, B.; Ichikawa, Y.; Kim, Y.
2003-12-01
Fluid flow in rock mass is controlled by geometry of fractures which is mainly characterized by roughness, aperture and orientation. Fracture roughness and aperture was observed by a new confocal laser scanning microscope (CLSM; Olympus OLS1100). The wavelength of laser is 488nm, and the laser scanning is managed by a light polarization method using two galvano-meter scanner mirrors. The system improves resolution in the light axis (namely z) direction because of the confocal optics. The sampling is managed in a spacing 2.5 μ m along x and y directions. The highest measurement resolution of z direction is 0.05 μ m, which is the more accurate than other methods. For the roughness measurements, core specimens of coarse and fine grained granites were provided. Measurements were performed along three scan lines on each fracture surface. The measured data were represented as 2-D and 3-D digital images showing detailed features of roughness. Spectral analyses by the fast Fourier transform (FFT) were performed to characterize on the roughness data quantitatively and to identify influential frequency of roughness. The FFT results showed that components of low frequencies were dominant in the fracture roughness. This study also verifies that spectral analysis is a good approach to understand complicate characteristics of fracture roughness. For the aperture measurements, digital images of the aperture were acquired under applying five stages of uniaxial normal stresses. This method can characterize the response of aperture directly using the same specimen. Results of measurements show that reduction values of aperture are different at each part due to rough geometry of fracture walls. Laboratory permeability tests were also conducted to evaluate changes of hydraulic conductivities related to aperture variation due to different stress levels. The results showed non-uniform reduction of hydraulic conductivity under increase of the normal stress and different values of
Recommendations for accurate numerical blood flow simulations of stented intracranial aneurysms.
Janiga, Gábor; Berg, Philipp; Beuing, Oliver; Neugebauer, Mathias; Gasteiger, Rocco; Preim, Bernhard; Rose, Georg; Skalej, Martin; Thévenin, Dominique
2013-06-01
The number of scientific publications dealing with stented intracranial aneurysms is rapidly increasing. Powerful computational facilities are now available; an accurate computational modeling of hemodynamics in patient-specific configurations is, however, still being sought. Furthermore, there is still no general agreement on the quantities that should be computed and on the most adequate analysis for intervention support. In this article, the accurate representation of patient geometry is first discussed, involving successive improvements. Concerning the second step, the mesh required for the numerical simulation is especially challenging when deploying a stent with very fine wire structures. Third, the description of the fluid properties is a major challenge. Finally, a founded quantitative analysis of the simulation results is obviously needed to support interventional decisions. In the present work, an attempt has been made to review the most important steps for a high-quality computational fluid dynamics computation of virtually stented intracranial aneurysms. In consequence, this leads to concrete recommendations, whereby the obtained results are not discussed for their medical relevance but for the evaluation of their quality. This investigation might hopefully be helpful for further studies considering stent deployment in patient-specific geometries, in particular regarding the generation of the most appropriate computational model. PMID:23729530
Computer simulation of space charge
NASA Astrophysics Data System (ADS)
Yu, K. W.; Chung, W. K.; Mak, S. S.
1991-05-01
Using the particle-mesh (PM) method, a one-dimensional simulation of the well-known Langmuir-Child's law is performed on an INTEL 80386-based personal computer system. The program is coded in turbo basic (trademark of Borland International, Inc.). The numerical results obtained were in excellent agreement with theoretical predictions and the computational time required is quite modest. This simulation exercise demonstrates that some simple computer simulation using particles may be implemented successfully on PC's that are available today, and hopefully this will provide the necessary incentives for newcomers to the field who wish to acquire a flavor of the elementary aspects of the practice.
Accurate direct Eulerian simulation of dynamic elastic-plastic flow
Kamm, James R; Walter, John W
2009-01-01
The simulation of dynamic, large strain deformation is an important, difficult, and unsolved computational challenge. Existing Eulerian schemes for dynamic material response are plagued by unresolved issues. We present a new scheme for the first-order system of elasto-plasticity equations in the Eulerian frame. This system has an intrinsic constraint on the inverse deformation gradient. Standard Godunov schemes do not satisfy this constraint. The method of Flux Distributions (FD) was devised to discretely enforce such constraints for numerical schemes with cell-centered variables. We describe a Flux Distribution approach that enforces the inverse deformation gradient constraint. As this approach is new and novel, we do not yet have numerical results to validate our claims. This paper is the first installment of our program to develop this new method.
Toward the Accurate Simulation of Two-Dimensional Electronic Spectra
NASA Astrophysics Data System (ADS)
Giussani, Angelo; Nenov, Artur; Segarra-Martí, Javier; Jaiswal, Vishal K.; Rivalta, Ivan; Dumont, Elise; Mukamel, Shaul; Garavelli, Marco
2015-06-01
Two-dimensional pump-probe electronic spectroscopy is a powerful technique able to provide both high spectral and temporal resolution, allowing the analysis of ultrafast complex reactions occurring via complementary pathways by the identification of decay-specific fingerprints. [1-2] The understanding of the origin of the experimentally recorded signals in a two-dimensional electronic spectrum requires the characterization of the electronic states involved in the electronic transitions photoinduced by the pump/probe pulses in the experiment. Such a goal constitutes a considerable computational challenge, since up to 100 states need to be described, for which state-of-the-art methods as RASSCF and RASPT2 have to be wisely employed. [3] With the present contribution, the main features and potentialities of two-dimensional electronic spectroscopy are presented, together with the machinery in continuous development in our groups in order to compute two-dimensional electronic spectra. The results obtained using different level of theory and simulations are shown, bringing as examples the computed two-dimensional electronic spectra for some specific cases studied. [2-4] [1] Rivalta I, Nenov A, Cerullo G, Mukamel S, Garavelli M, Int. J. Quantum Chem., 2014, 114, 85 [2] Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal V K, Altavilla S, Mukamel S, Garavelli M, Faraday Discuss. 2015, DOI: 10.1039/C4FD00175C [3] Nenov A, Giussani A, Segarra-Martí J, Jaiswal V K, Rivalta I, Cerullo G, Mukamel S, Garavelli M, J. Chem. Phys. submitted [4] Nenov A, Giussani A, Fingerhut B P, Rivalta I, Dumont E, Mukamel S, Garavelli M, Phys. Chem. Chem. Phys. Submitted [5] Krebs N, Pugliesi I, Hauer J, Riedle E, New J. Phys., 2013,15, 08501
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.
Computer Simulation of Mutagenesis.
ERIC Educational Resources Information Center
North, J. C.; Dent, M. T.
1978-01-01
A FORTRAN program is described which simulates point-substitution mutations in the DNA strands of typical organisms. Its objective is to help students to understand the significance and structure of the genetic code, and the mechanisms and effect of mutagenesis. (Author/BB)
Liquid propellant rocket engine combustion simulation with a time-accurate CFD method
NASA Technical Reports Server (NTRS)
Chen, Y. S.; Shang, H. M.; Liaw, Paul; Hutt, J.
1993-01-01
Time-accurate computational fluid dynamics (CFD) algorithms are among the basic requirements as an engineering or research tool for realistic simulations of transient combustion phenomena, such as combustion instability, transient start-up, etc., inside the rocket engine combustion chamber. A time-accurate pressure based method is employed in the FDNS code for combustion model development. This is in connection with other program development activities such as spray combustion model development and efficient finite-rate chemistry solution method implementation. In the present study, a second-order time-accurate time-marching scheme is employed. For better spatial resolutions near discontinuities (e.g., shocks, contact discontinuities), a 3rd-order accurate TVD scheme for modeling the convection terms is implemented in the FDNS code. Necessary modification to the predictor/multi-corrector solution algorithm in order to maintain time-accurate wave propagation is also investigated. Benchmark 1-D and multidimensional test cases, which include the classical shock tube wave propagation problems, resonant pipe test case, unsteady flow development of a blast tube test case, and H2/O2 rocket engine chamber combustion start-up transient simulation, etc., are investigated to validate and demonstrate the accuracy and robustness of the present numerical scheme and solution algorithm.
Cluster computing software for GATE simulations
Beenhouwer, Jan de; Staelens, Steven; Kruecker, Dirk; Ferrer, Ludovic; D'Asseler, Yves; Lemahieu, Ignace; Rannou, Fernando R.
2007-06-15
Geometry and tracking (GEANT4) is a Monte Carlo package designed for high energy physics experiments. It is used as the basis layer for Monte Carlo simulations of nuclear medicine acquisition systems in GEANT4 Application for Tomographic Emission (GATE). GATE allows the user to realistically model experiments using accurate physics models and time synchronization for detector movement through a script language contained in a macro file. The downside of this high accuracy is long computation time. This paper describes a platform independent computing approach for running GATE simulations on a cluster of computers in order to reduce the overall simulation time. Our software automatically creates fully resolved, nonparametrized macros accompanied with an on-the-fly generated cluster specific submit file used to launch the simulations. The scalability of GATE simulations on a cluster is investigated for two imaging modalities, positron emission tomography (PET) and single photon emission computed tomography (SPECT). Due to a higher sensitivity, PET simulations are characterized by relatively high data output rates that create rather large output files. SPECT simulations, on the other hand, have lower data output rates but require a long collimator setup time. Both of these characteristics hamper scalability as a function of the number of CPUs. The scalability of PET simulations is improved here by the development of a fast output merger. The scalability of SPECT simulations is improved by greatly reducing the collimator setup time. Accordingly, these two new developments result in higher scalability for both PET and SPECT simulations and reduce the computation time to more practical values.
Cluster computing software for GATE simulations.
De Beenhouwer, Jan; Staelens, Steven; Kruecker, Dirk; Ferrer, Ludovic; D'Asseler, Yves; Lemahieu, Ignace; Rannou, Fernando R
2007-06-01
Geometry and tracking (GEANT4) is a Monte Carlo package designed for high energy physics experiments. It is used as the basis layer for Monte Carlo simulations of nuclear medicine acquisition systems in GEANT4 Application for Tomographic Emission (GATE). GATE allows the user to realistically model experiments using accurate physics models and time synchronization for detector movement through a script language contained in a macro file. The downside of this high accuracy is long computation time. This paper describes a platform independent computing approach for running GATE simulations on a cluster of computers in order to reduce the overall simulation time. Our software automatically creates fully resolved, nonparametrized macros accompanied with an on-the-fly generated cluster specific submit file used to launch the simulations. The scalability of GATE simulations on a cluster is investigated for two imaging modalities, positron emission tomography (PET) and single photon emission computed tomography (SPECT). Due to a higher sensitivity, PET simulations are characterized by relatively high data output rates that create rather large output files. SPECT simulations, on the other hand, have lower data output rates but require a long collimator setup time. Both of these characteristics hamper scalability as a function of the number of CPUs. The scalability of PET simulations is improved here by the development of a fast output merger. The scalability of SPECT simulations is improved by greatly reducing the collimator setup time. Accordingly, these two new developments result in higher scalability for both PET and SPECT simulations and reduce the computation time to more practical values. PMID:17654895
Accurate computation of Stokes flow driven by an open immersed interface
NASA Astrophysics Data System (ADS)
Li, Yi; Layton, Anita T.
2012-06-01
We present numerical methods for computing two-dimensional Stokes flow driven by forces singularly supported along an open, immersed interface. Two second-order accurate methods are developed: one for accurately evaluating boundary integral solutions at a point, and another for computing Stokes solution values on a rectangular mesh. We first describe a method for computing singular or nearly singular integrals, such as a double layer potential due to sources on a curve in the plane, evaluated at a point on or near the curve. To improve accuracy of the numerical quadrature, we add corrections for the errors arising from discretization, which are found by asymptotic analysis. When used to solve the Stokes equations with sources on an open, immersed interface, the method generates second-order approximations, for both the pressure and the velocity, and preserves the jumps in the solutions and their derivatives across the boundary. We then combine the method with a mesh-based solver to yield a hybrid method for computing Stokes solutions at N2 grid points on a rectangular grid. Numerical results are presented which exhibit second-order accuracy. To demonstrate the applicability of the method, we use the method to simulate fluid dynamics induced by the beating motion of a cilium. The method preserves the sharp jumps in the Stokes solution and their derivatives across the immersed boundary. Model results illustrate the distinct hydrodynamic effects generated by the effective stroke and by the recovery stroke of the ciliary beat cycle.
Computer Simulation and Library Management.
ERIC Educational Resources Information Center
Main, Linda
1992-01-01
Reviews the literature on computer simulation modeling for library management and examines whether simulation is underutilized because the models are too complex and mathematical. Other problems with implementation are considered, including incomplete problem definition, lack of a conceptual framework, system constraints, lack of interaction…
Plasma physics via computer simulation
Birdsall, C.K.; Langdon, A.B.
1985-01-01
This book describes the computerized simulation of plasma kinetics. Topics considered include why attempting to do plasma physics via computer simulation using particles makes good physical sense; overall view of a one-dimensional electrostatic program; a one-dimensional electrostatic program; introduction to the numerical methods used; a 1d electromagnetic program; projects for EM1; effects of the spatial grid; effects of the finite time step; energy-conserving simulation models; multipole models; kinetic theory for fluctuations and noise; collisions; statistical mechanics of a sheet plasma; electrostatic programs in two and three dimensions; electromagnetic programs in 2D and 3D; design of computer experiments; and the choice of parameters.
Passeri, A; Formiconi, A R; De Cristofaro, M T; Pupi, A; Meldolesi, U
1997-04-01
It is well known that the quantitative potential of emission computed tomography (ECT) relies on the ability to compensate for resolution, attenuation and scatter effects. Reconstruction algorithms which are able to take these effects into account are highly demanding in terms of computing resources. The reported work aimed to investigate the use of a parallel high-performance computing platform for ECT reconstruction taking into account an accurate model of the acquisition of single-photon emission tomographic (SPET) data. An iterative algorithm with an accurate model of the variable system response was ported on the MIMD (Multiple Instruction Multiple Data) parallel architecture of a 64-node Cray T3D massively parallel computer. The system was organized to make it easily accessible even from low-cost PC-based workstations through standard TCP/IP networking. A complete brain study of 30 (64x64) slices could be reconstructed from a set of 90 (64x64) projections with ten iterations of the conjugate gradients algorithm in 9 s, corresponding to an actual speed-up factor of 135. This work demonstrated the possibility of exploiting remote high-performance computing and networking resources from hospital sites by means of low-cost workstations using standard communication protocols without particular problems for routine use. The achievable speed-up factors allow the assessment of the clinical benefit of advanced reconstruction techniques which require a heavy computational burden for the compensation effects such as variable spatial resolution, scatter and attenuation. The possibility of using the same software on the same hardware platform with data acquired in different laboratories with various kinds of SPET instrumentation is appealing for software quality control and for the evaluation of the clinical impact of the reconstruction methods. PMID:9096089
Direct Simulations of Transition and Turbulence Using High-Order Accurate Finite-Difference Schemes
NASA Technical Reports Server (NTRS)
Rai, Man Mohan
1997-01-01
In recent years the techniques of computational fluid dynamics (CFD) have been used to compute flows associated with geometrically complex configurations. However, success in terms of accuracy and reliability has been limited to cases where the effects of turbulence and transition could be modeled in a straightforward manner. Even in simple flows, the accurate computation of skin friction and heat transfer using existing turbulence models has proved to be a difficult task, one that has required extensive fine-tuning of the turbulence models used. In more complex flows (for example, in turbomachinery flows in which vortices and wakes impinge on airfoil surfaces causing periodic transitions from laminar to turbulent flow) the development of a model that accounts for all scales of turbulence and predicts the onset of transition may prove to be impractical. Fortunately, current trends in computing suggest that it may be possible to perform direct simulations of turbulence and transition at moderate Reynolds numbers in some complex cases in the near future. This seminar will focus on direct simulations of transition and turbulence using high-order accurate finite-difference methods. The advantage of the finite-difference approach over spectral methods is that complex geometries can be treated in a straightforward manner. Additionally, finite-difference techniques are the prevailing methods in existing application codes. In this seminar high-order-accurate finite-difference methods for the compressible and incompressible formulations of the unsteady Navier-Stokes equations and their applications to direct simulations of turbulence and transition will be presented.
Composite Erosion by Computational Simulation
NASA Technical Reports Server (NTRS)
Chamis, Christos C.
2006-01-01
Composite degradation is evaluated by computational simulation when the erosion degradation occurs on a ply-by-ply basis and the degrading medium (device) is normal to the ply. The computational simulation is performed by a multi factor interaction model and by a multi scale and multi physics available computer code. The erosion process degrades both the fiber and the matrix simultaneously in the same slice (ply). Both the fiber volume ratio and the matrix volume ratio approach zero while the void volume ratio increases as the ply degrades. The multi factor interaction model simulates the erosion degradation, provided that the exponents and factor ratios are selected judiciously. Results obtained by the computational composite mechanics show that most composite characterization properties degrade monotonically and approach "zero" as the ply degrades completely.
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.
Computational algorithms for simulations in atmospheric optics.
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. PMID:27140113
NASA Astrophysics Data System (ADS)
Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A.; Siepmann, J. Ilja
2015-09-01
Since the seminal paper by Panagiotopoulos [Mol. Phys. 61, 813 (1997)], the Gibbs ensemble Monte Carlo (GEMC) method has been the most popular particle-based simulation approach for the computation of vapor-liquid phase equilibria. However, the validity of GEMC simulations in the near-critical region has been questioned because rigorous finite-size scaling approaches cannot be applied to simulations with fluctuating volume. Valleau [Mol. Simul. 29, 627 (2003)] has argued that GEMC simulations would lead to a spurious overestimation of the critical temperature. More recently, Patel et al. [J. Chem. Phys. 134, 024101 (2011)] opined that the use of analytical tail corrections would be problematic in the near-critical region. To address these issues, we perform extensive GEMC simulations for Lennard-Jones particles in the near-critical region varying the system size, the overall system density, and the cutoff distance. For a system with N = 5500 particles, potential truncation at 8σ and analytical tail corrections, an extrapolation of GEMC simulation data at temperatures in the range from 1.27 to 1.305 yields Tc = 1.3128 ± 0.0016, ρc = 0.316 ± 0.004, and pc = 0.1274 ± 0.0013 in excellent agreement with the thermodynamic limit determined by Potoff and Panagiotopoulos [J. Chem. Phys. 109, 10914 (1998)] using grand canonical Monte Carlo simulations and finite-size scaling. Critical properties estimated using GEMC simulations with different overall system densities (0.296 ≤ ρt ≤ 0.336) agree to within the statistical uncertainties. For simulations with tail corrections, data obtained using rcut = 3.5σ yield Tc and pc that are higher by 0.2% and 1.4% than simulations with rcut = 5 and 8σ but still with overlapping 95% confidence intervals. In contrast, GEMC simulations with a truncated and shifted potential show that rcut = 8σ is insufficient to obtain accurate results. Additional GEMC simulations for hard-core square-well particles with various ranges of the
Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A.; Siepmann, J. Ilja
2015-09-21
Since the seminal paper by Panagiotopoulos [Mol. Phys. 61, 813 (1997)], the Gibbs ensemble Monte Carlo (GEMC) method has been the most popular particle-based simulation approach for the computation of vapor–liquid phase equilibria. However, the validity of GEMC simulations in the near-critical region has been questioned because rigorous finite-size scaling approaches cannot be applied to simulations with fluctuating volume. Valleau [Mol. Simul. 29, 627 (2003)] has argued that GEMC simulations would lead to a spurious overestimation of the critical temperature. More recently, Patel et al. [J. Chem. Phys. 134, 024101 (2011)] opined that the use of analytical tail corrections would be problematic in the near-critical region. To address these issues, we perform extensive GEMC simulations for Lennard-Jones particles in the near-critical region varying the system size, the overall system density, and the cutoff distance. For a system with N = 5500 particles, potential truncation at 8σ and analytical tail corrections, an extrapolation of GEMC simulation data at temperatures in the range from 1.27 to 1.305 yields T{sub c} = 1.3128 ± 0.0016, ρ{sub c} = 0.316 ± 0.004, and p{sub c} = 0.1274 ± 0.0013 in excellent agreement with the thermodynamic limit determined by Potoff and Panagiotopoulos [J. Chem. Phys. 109, 10914 (1998)] using grand canonical Monte Carlo simulations and finite-size scaling. Critical properties estimated using GEMC simulations with different overall system densities (0.296 ≤ ρ{sub t} ≤ 0.336) agree to within the statistical uncertainties. For simulations with tail corrections, data obtained using r{sub cut} = 3.5σ yield T{sub c} and p{sub c} that are higher by 0.2% and 1.4% than simulations with r{sub cut} = 5 and 8σ but still with overlapping 95% confidence intervals. In contrast, GEMC simulations with a truncated and shifted potential show that r{sub cut} = 8σ is insufficient to obtain accurate results. Additional GEMC simulations for hard
Computing accurate age and distance factors in cosmology
NASA Astrophysics Data System (ADS)
Christiansen, Jodi L.; Siver, Andrew
2012-05-01
As the universe expands astronomical observables such as brightness and angular size on the sky change in ways that differ from our simple Cartesian expectation. We show how observed quantities depend on the expansion of space and demonstrate how to calculate such quantities using the Friedmann equations. The general solution to the Friedmann equations requires a numerical solution, which is easily coded in any computing language (including excel). We use these numerical calculations in four projects that help students build their understanding of high-redshift phenomena and cosmology. Instructions for these projects are available as supplementary materials.
Computer Simulation of Aircraft Aerodynamics
NASA Technical Reports Server (NTRS)
Inouye, Mamoru
1989-01-01
The role of Ames Research Center in conducting basic aerodynamics research through computer simulations is described. The computer facilities, including supercomputers and peripheral equipment that represent the state of the art, are described. The methodology of computational fluid dynamics is explained briefly. Fundamental studies of turbulence and transition are being pursued to understand these phenomena and to develop models that can be used in the solution of the Reynolds-averaged Navier-Stokes equations. Four applications of computer simulations for aerodynamics problems are described: subsonic flow around a fuselage at high angle of attack, subsonic flow through a turbine stator-rotor stage, transonic flow around a flexible swept wing, and transonic flow around a wing-body configuration that includes an inlet and a tail.
High-Resolution Tsunami Inundation Simulations Based on Accurate Estimations of Coastal Waveforms
NASA Astrophysics Data System (ADS)
Oishi, Y.; Imamura, F.; Sugawara, D.; Furumura, T.
2015-12-01
We evaluate the accuracy of high-resolution tsunami inundation simulations in detail using the actual observational data of the 2011 Tohoku-Oki earthquake (Mw9.0) and investigate the methodologies to improve the simulation accuracy.Due to the recent development of parallel computing technologies, high-resolution tsunami inundation simulations are conducted more commonly than before. To evaluate how accurately these simulations can reproduce inundation processes, we test several types of simulation configurations on a parallel computer, where we can utilize the observational data (e.g., offshore and coastal waveforms and inundation properties) that are recorded during the Tohoku-Oki earthquake.Before discussing the accuracy of inundation processes on land, the incident waves at coastal sites must be accurately estimated. However, for megathrust earthquakes, it is difficult to find the tsunami source that can provide accurate estimations of tsunami waveforms at every coastal site because of the complex spatiotemporal distribution of the source and the limitation of observation. To overcome this issue, we employ a site-specific source inversion approach that increases the estimation accuracy within a specific coastal site by applying appropriate weighting to the observational data in the inversion process.We applied our source inversion technique to the Tohoku tsunami and conducted inundation simulations using 5-m resolution digital elevation model data (DEM) for the coastal area around Miyako Bay and Sendai Bay. The estimated waveforms at the coastal wave gauges of these bays successfully agree with the observed waveforms. However, the simulations overestimate the inundation extent indicating the necessity to improve the inundation model. We find that the value of Manning's roughness coefficient should be modified from the often-used value of n = 0.025 to n = 0.033 to obtain proper results at both cities.In this presentation, the simulation results with several
NASA Astrophysics Data System (ADS)
Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.
2016-07-01
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.
Taxis through Computer Simulation Programs.
ERIC Educational Resources Information Center
Park, David
1983-01-01
Describes a sequence of five computer programs (listings for Apple II available from author) on tactic responses (oriented movement of a cell, cell group, or whole organism in reponse to stimuli). The simulation programs are useful in helping students examine mechanisms at work in real organisms. (JN)
Computer Simulation of Diffraction Patterns.
ERIC Educational Resources Information Center
Dodd, N. A.
1983-01-01
Describes an Apple computer program (listing available from author) which simulates Fraunhofer and Fresnel diffraction using vector addition techniques (vector chaining) and allows user to experiment with different shaped multiple apertures. Graphics output include vector resultants, phase difference, diffraction patterns, and the Cornu spiral…
Accurate and efficient halo-based galaxy clustering modelling with simulations
NASA Astrophysics Data System (ADS)
Zheng, Zheng; Guo, Hong
2016-06-01
Small- and intermediate-scale galaxy clustering can be used to establish the galaxy-halo connection to study galaxy formation and evolution and to tighten constraints on cosmological parameters. With the increasing precision of galaxy clustering measurements from ongoing and forthcoming large galaxy surveys, accurate models are required to interpret the data and extract relevant information. We introduce a method based on high-resolution N-body simulations to accurately and efficiently model the galaxy two-point correlation functions (2PCFs) in projected and redshift spaces. The basic idea is to tabulate all information of haloes in the simulations necessary for computing the galaxy 2PCFs within the framework of halo occupation distribution or conditional luminosity function. It is equivalent to populating galaxies to dark matter haloes and using the mock 2PCF measurements as the model predictions. Besides the accurate 2PCF calculations, the method is also fast and therefore enables an efficient exploration of the parameter space. As an example of the method, we decompose the redshift-space galaxy 2PCF into different components based on the type of galaxy pairs and show the redshift-space distortion effect in each component. The generalizations and limitations of the method are discussed.
Linaro, Daniele; Storace, Marco; Giugliano, Michele
2011-01-01
Stochastic channel gating is the major source of intrinsic neuronal noise whose functional consequences at the microcircuit- and network-levels have been only partly explored. A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availability of fast numerical methods. In fact, exact techniques employ the microscopic simulation of the random opening and closing of individual ion channels, usually based on Markov models, whose computational loads are prohibitive for next generation massive computer models of the brain. In this work, we operatively define a procedure for translating any Markov model describing voltage- or ligand-gated membrane ion-conductances into an effective stochastic version, whose computer simulation is efficient, without compromising accuracy. Our approximation is based on an improved Langevin-like approach, which employs stochastic differential equations and no Montecarlo methods. As opposed to an earlier proposal recently debated in the literature, our approximation reproduces accurately the statistical properties of the exact microscopic simulations, under a variety of conditions, from spontaneous to evoked response features. In addition, our method is not restricted to the Hodgkin-Huxley sodium and potassium currents and is general for a variety of voltage- and ligand-gated ion currents. As a by-product, the analysis of the properties emerging in exact Markov schemes by standard probability calculus enables us for the first time to analytically identify the sources of inaccuracy of the previous proposal, while providing solid ground for its modification and improvement we present here. PMID:21423712
Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
NASA Astrophysics Data System (ADS)
Grønbech-Jensen, Niels; Hayre, Natha Robert; Farago, Oded
2014-02-01
A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as an example that can be easily simulated by all three packages. Contrary to existing methods, the new thermostat exhibits no detectable changes in the sampling statistics as the time step is varied in the entire numerical stability range. The simple form of the method, which we express in the three common forms (Velocity-Explicit, Störmer-Verlet, and Leap-Frog), allows for easy implementation within existing molecular simulation packages to achieve faster and more accurate results with no cost in either computing time or programming complexity.
Computer simulation of martensitic transformations
Xu, Ping
1993-11-01
The characteristics of martensitic transformations in solids are largely determined by the elastic strain that develops as martensite particles grow and interact. To study the development of microstructure, a finite-element computer simulation model was constructed to mimic the transformation process. The transformation is athermal and simulated at each incremental step by transforming the cell which maximizes the decrease in the free energy. To determine the free energy change, the elastic energy developed during martensite growth is calculated from the theory of linear elasticity for elastically homogeneous media, and updated as the transformation proceeds.
Temperature estimators in computer simulation
NASA Astrophysics Data System (ADS)
Jara, César; González-Cataldo, Felipe; Davis, Sergio; Gutiérrez, Gonzalo
2016-05-01
Temperature is a key physical quantity that is used to describe equilibrium between two bodies in thermal contact. In computer simulations, the temperature is usually estimated by means of the equipartition theorem, as an average over the kinetic energy. However, recent studies have shown that the temperature can be estimated using only the particles positions, which has been called configurational temperature. Through classical molecular dynamics simulations of 108-argon-atoms system, we compare the performance of four different temperature estimators: the usual kinetic temperature and three configurational temperatures, Our results show that the different estimators converge to the same value, but their fluctuations are different.
Developing accurate simulations for high-speed fiber links
NASA Astrophysics Data System (ADS)
Searcy, Steven; Stark, Andrew; Hsueh, Yu-Ting; Detwiler, Thomas; Tibuleac, Sorin; Chang, GK; Ralph, Stephen E.
2011-01-01
Reliable simulations of high-speed fiber optic links are necessary to understand, design, and deploy fiber networks. Laboratory experiments cannot explore all possible component variations and fiber environments that are found in today's deployed systems. Simulations typically depict relative penalties compared to a reference link. However, absolute performance metrics are required to assess actual deployment configurations. Here we detail the efforts within the Georgia Tech 100G Consortium towards achieving high absolute accuracy between simulation and experimental performance with a goal of +/-0.25 dB for back-to-back configuration, and +/-0.5 dB for transmission over multiple spans with different dispersion maps. We measure all possible component parameters including fiber length, loss, and dispersion for use in simulation. We also validate experimental methods of performance evaluation including OSNR assessment and DSP-based demodulation. We investigate a wide range of parameters including modulator chirp, polarization state, polarization dependent loss, transmit spectrum, laser linewidth, and fiber nonlinearity. We evaluate 56 Gb/s (single-polarization) and 112 Gb/s (dual-polarization) DQPSK and coherent QPSK within a 50 GHz DWDM environment with 10 Gb/s OOK adjacent channels for worst-case XPM effects. We demonstrate good simulation accuracy within linear and some nonlinear regimes for a wide range of OSNR in both back-to-back configuration and up to eight spans, over a range of launch powers. This allows us to explore a wide range of environments not available in the lab, including different fiber types, ROADM passbands, and levels of crosstalk. Continued exploration is required to validate robustness over various demodulation algorithms.
Computer Simulations of Space Plasmas
NASA Astrophysics Data System (ADS)
Goertz, C. K.
Even a superficial scanning of the latest issues of the Journal of Geophysical Research reveals that numerical simulation of space plasma processes is an active and growing field. The complexity and sophistication of numerically produced “data” rivals that of the real stuff. Sometimes numerical results need interpretation in terms of a simple “theory,” very much as the results of real experiments and observations do. Numerical simulation has indeed become a third independent tool of space physics, somewhere between observations and analytic theory. There is thus a strong need for textbooks and monographs that report the latest techniques and results in an easily accessible form. This book is an attempt to satisfy this need. The editors want it not only to be “proceedings of selected lectures (given) at the first ISSS (International School of Space Simulations in Kyoto, Japan, November 1-2, 1982) but rather…a form of textbook of computer simulations of space plasmas.” This is, of course, a difficult task when many authors are involved. Unavoidable redundancies and differences in notation may confuse the beginner. Some important questions, like numerical stability, are not discussed in sufficient detail. The recent book by C.K. Birdsall and A.B. Langdon (Plasma Physics via Computer Simulations, McGraw-Hill, New York, 1985) is more complete and detailed and seems more suitable as a textbook for simulations. Nevertheless, this book is useful to the beginner and the specialist because it contains not only descriptions of various numerical techniques but also many applications of simulations to space physics phenomena.
Biomes computed from simulated climatologies
Claussen, M.; Esch, M.
1994-01-01
The biome model of Prentice et al. is used to predict global patterns of potential natural plant formations, or biomes, from climatologies simulated by ECHAM, a model used for climate simulations at the Max-Planck-Institut fuer Meteorologie. This study undertaken in order to show the advantage of this biome model in diagnosing the performance of a climate model and assessing effects of past and future climate changes predicted by a climate model. Good overall agreement is found between global patterns of biomes computed from observed and simulated data of present climate. But there are also major discrepancies indicated by a difference in biomes in Australia, in the Kalahari Desert, and in the Middle West of North America. These discrepancies can be traced back to in simulated rainfall as well as summer or winter temperatures. Global patterns of biomes computed from an ice age simulation reveal that North America, Europe, and Siberia should have been covered largely by tundra and taiga, whereas only small differences are for the tropical rain forests. A potential northeast shift of biomes is expected from a simulation with enhanced CO{sub 2} concentration according to the IPCC Scenario A. Little change is seen in the tropical rain forest and the Sahara. Since the biome model used is not capable of predicting chances in vegetation patterns due to a rapid climate change, the latter simulation to be taken as a prediction of chances in conditions favourable for the existence of certain biomes, not as a reduction of a future distribution of biomes. 15 refs., 8 figs., 2 tabs.
Computer simulation of nonequilibrium processes
Wallace, D.C.
1985-07-01
The underlying concepts of nonequilibrium statistical mechanics, and of irreversible thermodynamics, will be described. The question at hand is then, how are these concepts to be realize in computer simulations of many-particle systems. The answer will be given for dissipative deformation processes in solids, on three hierarchical levels: heterogeneous plastic flow, dislocation dynamics, an molecular dynamics. Aplication to the shock process will be discussed.
Accurate, practical simulation of satellite infrared radiometer spectral data
Sullivan, T.J.
1982-09-01
This study's purpose is to determine whether a relatively simple random band model formulation of atmospheric radiation transfer in the infrared region can provide valid simulations of narrow interval satellite-borne infrared sounder system data. Detailed ozonesondes provide the pertinent atmospheric information and sets of calibrated satellite measurements provide the validation. High resolution line-by-line model calculations are included to complete the evaluation.
NASA Astrophysics Data System (ADS)
Rensonnet, Gaëtan; Jacobs, Damien; Macq, Benoît.; Taquet, Maxime
2016-03-01
Diffusion-weighted magnetic resonance imaging (DW-MRI) is a powerful tool to probe the diffusion of water through tissues. Through the application of magnetic gradients of appropriate direction, intensity and duration constituting the acquisition parameters, information can be retrieved about the underlying microstructural organization of the brain. In this context, an important and open question is to determine an optimal sequence of such acquisition parameters for a specific purpose. The use of simulated DW-MRI data for a given microstructural configuration provides a convenient and efficient way to address this problem. We first present a novel hybrid method for the synthetic simulation of DW-MRI signals that combines analytic expressions in simple geometries such as spheres and cylinders and Monte Carlo (MC) simulations elsewhere. Our hybrid method remains valid for any acquisition parameters and provides identical levels of accuracy with a computational time that is 90% shorter than that required by MC simulations for commonly-encountered microstructural configurations. We apply our novel simulation technique to estimate the radius of axons under various noise levels with different acquisition protocols commonly used in the literature. The results of our comparison suggest that protocols favoring a large number of gradient intensities such as a Cube and Sphere (CUSP) imaging provide more accurate radius estimation than conventional single-shell HARDI acquisitions for an identical acquisition time.
Inversion based on computational simulations
Hanson, K.M.; Cunningham, G.S.; Saquib, S.S.
1998-09-01
A standard approach to solving inversion problems that involve many parameters uses gradient-based optimization to find the parameters that best match the data. The authors discuss enabling techniques that facilitate application of this approach to large-scale computational simulations, which are the only way to investigate many complex physical phenomena. Such simulations may not seem to lend themselves to calculation of the gradient with respect to numerous parameters. However, adjoint differentiation allows one to efficiently compute the gradient of an objective function with respect to all the variables of a simulation. When combined with advanced gradient-based optimization algorithms, adjoint differentiation permits one to solve very large problems of optimization or parameter estimation. These techniques will be illustrated through the simulation of the time-dependent diffusion of infrared light through tissue, which has been used to perform optical tomography. The techniques discussed have a wide range of applicability to modeling including the optimization of models to achieve a desired design goal.
An accurate and efficient 3-D micromagnetic simulation of metal evaporated tape
NASA Astrophysics Data System (ADS)
Jones, M.; Miles, J. J.
1997-07-01
Metal evaporated tape (MET) has a complex column-like structure in which magnetic domains are arranged randomly. In order to accurately simulate the behaviour of MET it is important to capture these aspects of the material in a high-resolution 3-D micromagnetic model. The scale of this problem prohibits the use of traditional scalar computers and leads us to develop algorithms for a vector processor architecture. We demonstrate that despite the materials highly non-uniform structure, it is possible to develop fast vector algorithms for the computation of the magnetostatic interaction field. We do this by splitting the field calculation into near and far components. The near field component is calculated exactly using an efficient vector algorithm, whereas the far field is calculated approximately using a novel fast Fourier transform (FFT) technique. Results are presented which demonstrate that, in practice, the algorithms require sub-O( N log( N)) computation time. In addition results of highly realistic simulation of hysteresis in MET are presented.
NASA Astrophysics Data System (ADS)
Garrison, Stephen L.
2005-07-01
The combination of molecular simulations and potentials obtained from quantum chemistry is shown to be able to provide reasonably accurate thermodynamic property predictions. Gibbs ensemble Monte Carlo simulations are used to understand the effects of small perturbations to various regions of the model Lennard-Jones 12-6 potential. However, when the phase behavior and second virial coefficient are scaled by the critical properties calculated for each potential, the results obey a corresponding states relation suggesting a non-uniqueness problem for interaction potentials fit to experimental phase behavior. Several variations of a procedure collectively referred to as quantum mechanical Hybrid Methods for Interaction Energies (HM-IE) are developed and used to accurately estimate interaction energies from CCSD(T) calculations with a large basis set in a computationally efficient manner for the neon-neon, acetylene-acetylene, and nitrogen-benzene systems. Using these results and methods, an ab initio, pairwise-additive, site-site potential for acetylene is determined and then improved using results from molecular simulations using this initial potential. The initial simulation results also indicate that a limited range of energies important for accurate phase behavior predictions. Second virial coefficients calculated from the improved potential indicate that one set of experimental data in the literature is likely erroneous. This prescription is then applied to methanethiol. Difficulties in modeling the effects of the lone pair electrons suggest that charges on the lone pair sites negatively impact the ability of the intermolecular potential to describe certain orientations, but that the lone pair sites may be necessary to reasonably duplicate the interaction energies for several orientations. Two possible methods for incorporating the effects of three-body interactions into simulations within the pairwise-additivity formulation are also developed. A low density
Lee, M.W.; Meuwly, M.
2013-01-01
The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.
Lee, Myung Won; Meuwly, Markus
2013-12-14
The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories. PMID:24170171
Development of modified cable models to simulate accurate neuronal active behaviors
2014-01-01
In large network and single three-dimensional (3-D) neuron simulations, high computing speed dictates using reduced cable models to simulate neuronal firing behaviors. However, these models are unwarranted under active conditions and lack accurate representation of dendritic active conductances that greatly shape neuronal firing. Here, realistic 3-D (R3D) models (which contain full anatomical details of dendrites) of spinal motoneurons were systematically compared with their reduced single unbranched cable (SUC, which reduces the dendrites to a single electrically equivalent cable) counterpart under passive and active conditions. The SUC models matched the R3D model's passive properties but failed to match key active properties, especially active behaviors originating from dendrites. For instance, persistent inward currents (PIC) hysteresis, frequency-current (FI) relationship secondary range slope, firing hysteresis, plateau potential partial deactivation, staircase currents, synaptic current transfer ratio, and regional FI relationships were not accurately reproduced by the SUC models. The dendritic morphology oversimplification and lack of dendritic active conductances spatial segregation in the SUC models caused significant underestimation of those behaviors. Next, SUC models were modified by adding key branching features in an attempt to restore their active behaviors. The addition of primary dendritic branching only partially restored some active behaviors, whereas the addition of secondary dendritic branching restored most behaviors. Importantly, the proposed modified models successfully replicated the active properties without sacrificing model simplicity, making them attractive candidates for running R3D single neuron and network simulations with accurate firing behaviors. The present results indicate that using reduced models to examine PIC behaviors in spinal motoneurons is unwarranted. PMID:25277743
Accurate simulation of terahertz transmission through doped silicon junctions
NASA Astrophysics Data System (ADS)
Jen, Chih-Yu; Richter, Christiaan
2015-03-01
In the previous work we presented results demonstrating the ability of transmission mode terahertz time domain spectroscopy (THz-TDS) to detect doping profile differences and deviations in silicon. This capability is potentially useful for quality control in the semiconductor and photovoltaic industry. We shared subsequent experimental results revealing that terahertz interactions with both electrons and holes are strong enough to recognize both n- and p-type doping profile changes. We also displayed that the relatively long wavelength (~ 1 mm) of THz radiation allows this approach to be compatible with surface treatments like for instance the texturing (scattering layer) typically used in the solar industry. In this work we continuously demonstrate the accuracy with which current terahertz optical models can simulate the power spectrum of terahertz radiation transmitted through junctions with known doping profiles (as determined with SIMS). We conclude that current optical models predict the terahertz transmission and absorption in silicon junctions well.
Accurate Position Sensing of Defocused Beams Using Simulated Beam Templates
Awwal, A; Candy, J; Haynam, C; Widmayer, C; Bliss, E; Burkhart, S
2004-09-29
In position detection using matched filtering one is faced with the challenge of determining the best position in the presence of distortions such as defocus and diffraction noise. This work evaluates the performance of simulated defocused images as the template against the real defocused beam. It was found that an amplitude modulated phase-only filter is better equipped to deal with real defocused images that suffer from diffraction noise effects resulting in a textured spot intensity pattern. It is shown that the there is a tradeoff of performance dependent upon the type and size of the defocused image. A novel automated system was developed that can automatically select the right template type and size. Results of this automation for real defocused images are presented.
NASA Technical Reports Server (NTRS)
Liu, Yen; Vinokur, Marcel
1989-01-01
This paper treats the accurate and efficient calculation of thermodynamic properties of arbitrary gas mixtures for equilibrium flow computations. New improvements in the Stupochenko-Jaffe model for the calculation of thermodynamic properties of diatomic molecules are presented. A unified formulation of equilibrium calculations for gas mixtures in terms of irreversible entropy is given. Using a highly accurate thermo-chemical data base, a new, efficient and vectorizable search algorithm is used to construct piecewise interpolation procedures with generate accurate thermodynamic variable and their derivatives required by modern computational algorithms. Results are presented for equilibrium air, and compared with those given by the Srinivasan program.
Computer simulation of metal-organic materials
NASA Astrophysics Data System (ADS)
Stern, Abraham C.
Computer simulations of metal-organic frameworks are conducted to both investigate the mechanism of hydrogen sorption and to elucidate a detailed, molecular-level understanding of the physical interactions that can lead to successful material design strategies. To this end, important intermolecular interactions are identified and individually parameterized to yield a highly accurate representation of the potential energy landscape. Polarization, one such interaction found to play a significant role in H 2 sorption, is included explicitly for the first time in simulations of metal-organic frameworks. Permanent electrostatics are usually accounted for by means of an approximate fit to model compounds. The application of this method to simulations involving metal-organic frameworks introduces several substantial problems that are characterized in this work. To circumvent this, a method is developed and tested in which atomic point partial charges are computed more directly, fit to the fully periodic electrostatic potential. In this manner, long-range electrostatics are explicitly accounted for via Ewald summation. Grand canonical Monte Carlo simulations are conducted employing the force field parameterization developed here. Several of the major findings of this work are: Polarization is found to play a critical role in determining the overall structure of H2 sorbed in metal-organic frameworks, although not always the determining factor in uptake. The parameterization of atomic point charges by means of a fit to the periodic electrostatic potential is a robust, efficient method and consistently results in a reliable description of Coulombic interactions without introducing ambiguity associated with other procedures. After careful development of both hydrogen and framework potential energy functions, quantitatively accurate results have been obtained. Such predictive accuracy will aid greatly in the rational, iterative design cycle between experimental and theoretical
Nielsen, Jens; D’Avezac, Mayeul; Hetherington, James; Stamatakis, Michail
2013-12-14
Ab initio kinetic Monte Carlo (KMC) simulations have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These simulations necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. More recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for simulating catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce parallelization with OpenMP. We further benchmark our framework by simulating a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.
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.
Cartesian Off-Body Grid Adaption for Viscous Time- Accurate Flow Simulation
NASA Technical Reports Server (NTRS)
Buning, Pieter G.; Pulliam, Thomas H.
2011-01-01
An improved solution adaption capability has been implemented in the OVERFLOW overset grid CFD code. Building on the Cartesian off-body approach inherent in OVERFLOW and the original adaptive refinement method developed by Meakin, the new scheme provides for automated creation of multiple levels of finer Cartesian grids. Refinement can be based on the undivided second-difference of the flow solution variables, or on a specific flow quantity such as vorticity. Coupled with load-balancing and an inmemory solution interpolation procedure, the adaption process provides very good performance for time-accurate simulations on parallel compute platforms. A method of using refined, thin body-fitted grids combined with adaption in the off-body grids is presented, which maximizes the part of the domain subject to adaption. Two- and three-dimensional examples are used to illustrate the effectiveness and performance of the adaption scheme.
Pacheco, P; Miller, P; Kim, J; Leese, T; Zabiyaka, Y
2003-05-07
Object-oriented NeuroSys (ooNeuroSys) is a collection of programs for simulating very large networks of biologically accurate neurons on distributed memory parallel computers. It includes two principle programs: ooNeuroSys, a parallel program for solving the large systems of ordinary differential equations arising from the interconnected neurons, and Neurondiz, a parallel program for visualizing the results of ooNeuroSys. Both programs are designed to be run on clusters and use the MPI library to obtain parallelism. ooNeuroSys also includes an easy-to-use Python interface. This interface allows neuroscientists to quickly develop and test complex neuron models. Both ooNeuroSys and Neurondiz have a design that allows for both high performance and relative ease of maintenance.
Computational Methods for Jet Noise Simulation
NASA Technical Reports Server (NTRS)
Goodrich, John W. (Technical Monitor); Hagstrom, Thomas
2003-01-01
The purpose of our project is to develop, analyze, and test novel numerical technologies central to the long term goal of direct simulations of subsonic jet noise. Our current focus is on two issues: accurate, near-field domain truncations and high-order, single-step discretizations of the governing equations. The Direct Numerical Simulation (DNS) of jet noise poses a number of extreme challenges to computational technique. In particular, the problem involves multiple temporal and spatial scales as well as flow instabilities and is posed on an unbounded spatial domain. Moreover, the basic phenomenon of interest, the radiation of acoustic waves to the far field, involves only a minuscule fraction of the total energy. The best current simulations of jet noise are at low Reynolds number. It is likely that an increase of one to two orders of magnitude will be necessary to reach a regime where the separation between the energy-containing and dissipation scales is sufficient to make the radiated noise essentially independent of the Reynolds number. Such an increase in resolution cannot be obtained in the near future solely through increases in computing power. Therefore, new numerical methodologies of maximal efficiency and accuracy are required.
Meek, Garrett A; Levine, Benjamin G
2014-07-01
Spikes in the time-derivative coupling (TDC) near surface crossings make the accurate integration of the time-dependent Schrödinger equation in nonadiabatic molecular dynamics simulations a challenge. To address this issue, we present an approximation to the TDC based on a norm-preserving interpolation (NPI) of the adiabatic electronic wave functions within each time step. We apply NPI and two other schemes for computing the TDC in numerical simulations of the Landau-Zener model, comparing the simulated transfer probabilities to the exact solution. Though NPI does not require the analytical calculation of nonadiabatic coupling matrix elements, it consistently yields unsigned population transfer probability errors of ∼0.001, whereas analytical calculation of the TDC yields errors of 0.0-1.0 depending on the time step, the offset of the maximum in the TDC from the beginning of the time step, and the coupling strength. The approximation of Hammes-Schiffer and Tully yields errors intermediate between NPI and the analytical scheme. PMID:26279558
Computer simulations of particle packing
Cesarano, J. III; McEuen, M.J.; Swiler, T.
1996-09-01
Computer code has been developed to rapidly simulate the random packing of disks and spheres in two and three dimensions. Any size distribution may be packed. The code simulates varying degrees of inter particle conditions ranging from sticky to free flowing. The code will also calculate the overall packing density, density distributions, and void size distributions (in two dimensions). An important aspect of the code is that it is written in C++ and incorporates a user-friendly graphical interface for standard Macintosh and Power PC platforms. Investigations as to how well the code simulates the realistic random packing have begun. The code has been developed in consideration of the problem of filling a container (or die) with spray-dried granules of ceramic powder (represented by spheres). Although not presented here, the futuristic goal of this work is to give users the ability to predict homogeneity of filled dies prior to dry pressing. Additionally, this software has educational utility for studying relationships between particle size distributions and macrostructures.
Computation simulation of the nonlinear response of suspension bridges
McCallen, D.B.; Astaneh-Asl, A.
1997-10-01
Accurate computational simulation of the dynamic response of long- span bridges presents one of the greatest challenges facing the earthquake engineering community The size of these structures, in terms of physical dimensions and number of main load bearing members, makes computational simulation of transient response an arduous task. Discretization of a large bridge with general purpose finite element software often results in a computational model of such size that excessive computational effort is required for three dimensional nonlinear analyses. The aim of the current study was the development of efficient, computationally based methodologies for the nonlinear analysis of cable supported bridge systems which would allow accurate characterization of a bridge with a relatively small number of degrees of freedom. This work has lead to the development of a special purpose software program for the nonlinear analysis of cable supported bridges and the methodologies and software are described and illustrated in this paper.
Determining Peptide Partitioning Properties via Computer Simulation
Ulmschneider, Jakob P.; Ulmschneider, Martin B.
2010-01-01
The transfer of polypeptide segments into lipid bilayers to form transmembrane helices represents the crucial first step in cellular membrane protein folding and assembly. This process is driven by complex and poorly understood atomic interactions of peptides with the lipid bilayer environment. The lack of suitable experimental techniques that can resolve these processes both at atomic resolution and nanosecond timescales has spurred the development of computational techniques. In this review, we summarize the significant progress achieved in the last few years in elucidating the partitioning of peptides into lipid bilayer membranes using atomic detail molecular dynamics simulations. Indeed, partitioning simulations can now provide a wealth of structural and dynamic information. Furthermore, we show that peptide-induced bilayer distortions, insertion pathways, transfer free energies, and kinetic insertion barriers are now accurate enough to complement experiments. Further advances in simulation methods and force field parameter accuracy promise to turn molecular dynamics simulations into a powerful tool for investigating a wide range of membrane active peptide phenomena. PMID:21107546
Haley, William E.; Ibrahim, El-Sayed H.; Qu, Mingliang; Cernigliaro, Joseph G.; Goldfarb, David S.; McCollough, Cynthia H.
2015-01-01
Dual-energy computed tomography (DECT) has recently been suggested as the imaging modality of choice for kidney stones due to its ability to provide information on stone composition. Standard postprocessing of the dual-energy images accurately identifies uric acid stones, but not other types. Cystine stones can be identified from DECT images when analyzed with advanced postprocessing. This case report describes clinical implications of accurate diagnosis of cystine stones using DECT. PMID:26688770
Haley, William E; Ibrahim, El-Sayed H; Qu, Mingliang; Cernigliaro, Joseph G; Goldfarb, David S; McCollough, Cynthia H
2015-01-01
Dual-energy computed tomography (DECT) has recently been suggested as the imaging modality of choice for kidney stones due to its ability to provide information on stone composition. Standard postprocessing of the dual-energy images accurately identifies uric acid stones, but not other types. Cystine stones can be identified from DECT images when analyzed with advanced postprocessing. This case report describes clinical implications of accurate diagnosis of cystine stones using DECT. PMID:26688770
Unfitted Two-Phase Flow Simulations in Pore-Geometries with Accurate
NASA Astrophysics Data System (ADS)
Heimann, Felix; Engwer, Christian; Ippisch, Olaf; Bastian, Peter
2013-04-01
The development of better macro scale models for multi-phase flow in porous media is still impeded by the lack of suitable methods for the simulation of such flow regimes on the pore scale. The highly complicated geometry of natural porous media imposes requirements with regard to stability and computational efficiency which current numerical methods fail to meet. Therefore, current simulation environments are still unable to provide a thorough understanding of porous media in multi-phase regimes and still fail to reproduce well known effects like hysteresis or the more peculiar dynamics of the capillary fringe with satisfying accuracy. Although flow simulations in pore geometries were initially the domain of Lattice-Boltzmann and other particle methods, the development of Galerkin methods for such applications is important as they complement the range of feasible flow and parameter regimes. In the recent past, it has been shown that unfitted Galerkin methods can be applied efficiently to topologically demanding geometries. However, in the context of two-phase flows, the interface of the two immiscible fluids effectively separates the domain in two sub-domains. The exact representation of such setups with multiple independent and time depending geometries exceeds the functionality of common unfitted methods. We present a new approach to pore scale simulations with an unfitted discontinuous Galerkin (UDG) method. Utilizing a recursive sub-triangulation algorithm, we extent the UDG method to setups with multiple independent geometries. This approach allows an accurate representation of the moving contact line and the interface conditions, i.e. the pressure jump across the interface. Example simulations in two and three dimensions illustrate and verify the stability and accuracy of this approach.
A Three Dimensional Parallel Time Accurate Turbopump Simulation Procedure Using Overset Grid Systems
NASA Technical Reports Server (NTRS)
Kiris, Cetin; Chan, William; Kwak, Dochan
2001-01-01
The objective of the current effort is to provide a computational framework for design and analysis of the entire fuel supply system of a liquid rocket engine, including high-fidelity unsteady turbopump flow analysis. This capability is needed to support the design of pump sub-systems for advanced space transportation vehicles that are likely to involve liquid propulsion systems. To date, computational tools for design/analysis of turbopump flows are based on relatively lower fidelity methods. An unsteady, three-dimensional viscous flow analysis tool involving stationary and rotational components for the entire turbopump assembly has not been available for real-world engineering applications. The present effort provides developers with information such as transient flow phenomena at start up, and non-uniform inflows, and will eventually impact on system vibration and structures. In the proposed paper, the progress toward the capability of complete simulation of the turbo-pump for a liquid rocket engine is reported. The Space Shuttle Main Engine (SSME) turbo-pump is used as a test case for evaluation of the hybrid MPI/Open-MP and MLP versions of the INS3D code. CAD to solution auto-scripting capability is being developed for turbopump applications. The relative motion of the grid systems for the rotor-stator interaction was obtained using overset grid techniques. Unsteady computations for the SSME turbo-pump, which contains 114 zones with 34.5 million grid points, are carried out on Origin 3000 systems at NASA Ames Research Center. Results from these time-accurate simulations with moving boundary capability will be presented along with the performance of parallel versions of the code.
A Three-Dimensional Parallel Time-Accurate Turbopump Simulation Procedure Using Overset Grid System
NASA Technical Reports Server (NTRS)
Kiris, Cetin; Chan, William; Kwak, Dochan
2002-01-01
The objective of the current effort is to provide a computational framework for design and analysis of the entire fuel supply system of a liquid rocket engine, including high-fidelity unsteady turbopump flow analysis. This capability is needed to support the design of pump sub-systems for advanced space transportation vehicles that are likely to involve liquid propulsion systems. To date, computational tools for design/analysis of turbopump flows are based on relatively lower fidelity methods. An unsteady, three-dimensional viscous flow analysis tool involving stationary and rotational components for the entire turbopump assembly has not been available for real-world engineering applications. The present effort provides developers with information such as transient flow phenomena at start up, and nonuniform inflows, and will eventually impact on system vibration and structures. In the proposed paper, the progress toward the capability of complete simulation of the turbo-pump for a liquid rocket engine is reported. The Space Shuttle Main Engine (SSME) turbo-pump is used as a test case for evaluation of the hybrid MPI/Open-MP and MLP versions of the INS3D code. CAD to solution auto-scripting capability is being developed for turbopump applications. The relative motion of the grid systems for the rotor-stator interaction was obtained using overset grid techniques. Unsteady computations for the SSME turbo-pump, which contains 114 zones with 34.5 million grid points, are carried out on Origin 3000 systems at NASA Ames Research Center. Results from these time-accurate simulations with moving boundary capability are presented along with the performance of parallel versions of the code.
Computer simulation of microstructural dynamics
Grest, G.S.; Anderson, M.P.; Srolovitz, D.J.
1985-01-01
Since many of the physical properties of materials are determined by their microstructure, it is important to be able to predict and control microstructural development. A number of approaches have been taken to study this problem, but they assume that the grains can be described as spherical or hexagonal and that growth occurs in an average environment. We have developed a new technique to bridge the gap between the atomistic interactions and the macroscopic scale by discretizing the continuum system such that the microstructure retains its topological connectedness, yet is amenable to computer simulations. Using this technique, we have studied grain growth in polycrystalline aggregates. The temporal evolution and grain morphology of our model are in excellent agreement with experimental results for metals and ceramics.
Priority Queues for Computer Simulations
NASA Technical Reports Server (NTRS)
Steinman, Jeffrey S. (Inventor)
1998-01-01
The present invention is embodied in new priority queue data structures for event list management of computer simulations, and includes a new priority queue data structure and an improved event horizon applied to priority queue data structures. ne new priority queue data structure is a Qheap and is made out of linked lists for robust, fast, reliable, and stable event list management and uses a temporary unsorted list to store all items until one of the items is needed. Then the list is sorted, next, the highest priority item is removed, and then the rest of the list is inserted in the Qheap. Also, an event horizon is applied to binary tree and splay tree priority queue data structures to form the improved event horizon for event management.
Creation of Anatomically Accurate Computer-Aided Design (CAD) Solid Models from Medical Images
NASA Technical Reports Server (NTRS)
Stewart, John E.; Graham, R. Scott; Samareh, Jamshid A.; Oberlander, Eric J.; Broaddus, William C.
1999-01-01
Most surgical instrumentation and implants used in the world today are designed with sophisticated Computer-Aided Design (CAD)/Computer-Aided Manufacturing (CAM) software. This software automates the mechanical development of a product from its conceptual design through manufacturing. CAD software also provides a means of manipulating solid models prior to Finite Element Modeling (FEM). Few surgical products are designed in conjunction with accurate CAD models of human anatomy because of the difficulty with which these models are created. We have developed a novel technique that creates anatomically accurate, patient specific CAD solids from medical images in a matter of minutes.
A Mass Spectrometer Simulator in Your Computer
NASA Astrophysics Data System (ADS)
Gagnon, Michel
2012-12-01
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, it is not possible for instructors to take full advantage of this equipment. Therefore, to facilitate accessibility to this tool, we have developed a realistic computer-based simulator. Using this software, students are able to practice their ability to identify the components of the original gas, thereby gaining a better understanding of the underlying physical laws. The software is available as a free download.
Computer simulations of liquid crystals
NASA Astrophysics Data System (ADS)
Smondyrev, Alexander M.
Liquid crystal physics is an exciting interdisciplinary field of research with important practical applications. Their complexity and the presence of strong translational and orientational fluctuations require a computational approach, especially in the studies of nonequlibrium phenomena. In this dissertation we present the results of computer simulation studies of liquid crystals using the molecular dynamics technique. We employed the Gay-Berne phenomenological model of liquid crystals to describe the interaction between the molecules. Both equilibrium and non-equilibrium phenomena were studied. In the first case we studied the flow properties of the liquid crystal system in equilibrium as well as the dynamics of the director. We measured the viscosities of the Gay-Berne model in the nematic and isotropic phases. The temperature-dependence of the rotational and shear viscosities, including the nonmonotonic behavior of one shear viscosity, are in good agreement with experimental data. The bulk viscosities are significantly larger than the shear viscosities, again in agreement with experiment. The director motion was found to be ballistic at short times and diffusive at longer times. The second class of problems we focused on is the properties of the system which was rapidly quenched to very low temperatures from the nematic phase. We find a glass transition to a metastable phase with nematic order and frozen translational and orientational degrees of freedom. For fast quench rates the local structure is nematic-like, while for slower quench rates smectic order is present as well. Finally, we considered a system in the isotropic phase which is then cooled to temperatures below the isotropic-nematic transition temperature. We expect topological defects to play a central role in the subsequent equilibration of the system. To identify and study these defects we require a simulation of a system with several thousand particles. We present the results of large
Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets.
Wagoner, Jason A; Pande, Vijay S
2013-12-21
We extend the theory of hybrid explicit/implicit solvent models to include an explicit domain that grows and shrinks in response to a solute's evolving configuration. The goal of this model is to provide an appropriate but not excessive amount of solvent detail, and the inclusion of an adjustable boundary provides a significant computational advantage for solutes that explore a range of configurations. In addition to the theoretical development, a successful implementation of this method requires (1) an efficient moveset that propagates the boundary as a new coordinate of the system, and (2) an accurate continuum solvent model with parameters that are transferable to an explicit domain of any size. We address these challenges and develop boundary updates using Monte Carlo moves biased by nonequilibrium paths. We obtain the desired level of accuracy using a "decoupling interface" that we have previously shown to remove boundary artifacts common to hybrid solvent models. Using an uncharged, coarse-grained solvent model, we then study the efficiency of nonequilibrium paths that a simulation takes by quantifying the dissipation. In the spirit of optimization, we study this quantity over a range of simulation parameters. PMID:24359359
Margot Gerritsen
2008-10-31
Gas-injection processes are widely and increasingly used for enhanced oil recovery (EOR). In the United States, for example, EOR production by gas injection accounts for approximately 45% of total EOR production and has tripled since 1986. The understanding of the multiphase, multicomponent flow taking place in any displacement process is essential for successful design of gas-injection projects. Due to complex reservoir geometry, reservoir fluid properties and phase behavior, the design of accurate and efficient numerical simulations for the multiphase, multicomponent flow governing these processes is nontrivial. In this work, we developed, implemented and tested a streamline based solver for gas injection processes that is computationally very attractive: as compared to traditional Eulerian solvers in use by industry it computes solutions with a computational speed orders of magnitude higher and a comparable accuracy provided that cross-flow effects do not dominate. We contributed to the development of compositional streamline solvers in three significant ways: improvement of the overall framework allowing improved streamline coverage and partial streamline tracing, amongst others; parallelization of the streamline code, which significantly improves wall clock time; and development of new compositional solvers that can be implemented along streamlines as well as in existing Eulerian codes used by industry. We designed several novel ideas in the streamline framework. First, we developed an adaptive streamline coverage algorithm. Adding streamlines locally can reduce computational costs by concentrating computational efforts where needed, and reduce mapping errors. Adapting streamline coverage effectively controls mass balance errors that mostly result from the mapping from streamlines to pressure grid. We also introduced the concept of partial streamlines: streamlines that do not necessarily start and/or end at wells. This allows more efficient coverage and avoids
The Shuttle Mission Simulator computer generated imagery
NASA Technical Reports Server (NTRS)
Henderson, T. H.
1984-01-01
Equipment available in the primary training facility for the Space Transportation System (STS) flight crews includes the Fixed Base Simulator, the Motion Base Simulator, the Spacelab Simulator, and the Guidance and Navigation Simulator. The Shuttle Mission Simulator (SMS) consists of the Fixed Base Simulator and the Motion Base Simulator. The SMS utilizes four visual Computer Generated Image (CGI) systems. The Motion Base Simulator has a forward crew station with six-degrees of freedom motion simulation. Operation of the Spacelab Simulator is planned for the spring of 1983. The Guidance and Navigation Simulator went into operation in 1982. Aspects of orbital visual simulation are discussed, taking into account the earth scene, payload simulation, the generation and display of 1079 stars, the simulation of sun glare, and Reaction Control System jet firing plumes. Attention is also given to landing site visual simulation, and night launch and landing simulation.
Understanding Islamist political violence through computational social simulation
Watkins, Jennifer H; Mackerrow, Edward P; Patelli, Paolo G; Eberhardt, Ariane; Stradling, Seth G
2008-01-01
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 the 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.
Development of simulation computer complex specification
NASA Technical Reports Server (NTRS)
1973-01-01
The Training Simulation Computer Complex Study was one of three studies contracted in support of preparations for procurement of a shuttle mission simulator for shuttle crew training. The subject study was concerned with definition of the software loads to be imposed on the computer complex to be associated with the shuttle mission simulator and the development of procurement specifications based on the resulting computer requirements. These procurement specifications cover the computer hardware and system software as well as the data conversion equipment required to interface the computer to the simulator hardware. The development of the necessary hardware and software specifications required the execution of a number of related tasks which included, (1) simulation software sizing, (2) computer requirements definition, (3) data conversion equipment requirements definition, (4) system software requirements definition, (5) a simulation management plan, (6) a background survey, and (7) preparation of the specifications.
Chen, Chun-Chi; Chen, Chao-Lieh; Lin, You-Ting
2016-01-01
This study proposes a new behavioral simulator that uses SIMULINK for all-digital CMOS time-domain smart temperature sensors (TDSTSs) for performing rapid and accurate simulations. Inverter-based TDSTSs offer the benefits of low cost and simple structure for temperature-to-digital conversion and have been developed. Typically, electronic design automation tools, such as HSPICE, are used to simulate TDSTSs for performance evaluations. However, such tools require extremely long simulation time and complex procedures to analyze the results and generate figures. In this paper, we organize simple but accurate equations into a temperature-dependent model (TDM) by which the TDSTSs evaluate temperature behavior. Furthermore, temperature-sensing models of a single CMOS NOT gate were devised using HSPICE simulations. Using the TDM and these temperature-sensing models, a novel simulator in SIMULINK environment was developed to substantially accelerate the simulation and simplify the evaluation procedures. Experiments demonstrated that the simulation results of the proposed simulator have favorable agreement with those obtained from HSPICE simulations, showing that the proposed simulator functions successfully. This is the first behavioral simulator addressing the rapid simulation of TDSTSs. PMID:27509507
Accurate charge capture and cost allocation: cost justification for bedside computing.
Grewal, R.; Reed, R. L.
1993-01-01
This paper shows that cost justification for bedside clinical computing can be made by recouping charges with accurate charge capture. Twelve months worth of professional charges for a sixteen bed surgical intensive care unit are computed from charted data in a bedside clinical database and are compared to the professional charges actually billed by the unit. A substantial difference in predicted charges and billed charges was found. This paper also discusses the concept of appropriate cost allocation in the inpatient environment and the feasibility of appropriate allocation as a by-product of bedside computing. PMID:8130444
Space Ultrareliable Modular Computer (SUMC) instruction simulator
NASA Technical Reports Server (NTRS)
Curran, R. T.
1972-01-01
The design principles, description, functional operation, and recommended expansion and enhancements are presented for the Space Ultrareliable Modular Computer interpretive simulator. Included as appendices are the user's manual, program module descriptions, target instruction descriptions, simulator source program listing, and a sample program printout. In discussing the design and operation of the simulator, the key problems involving host computer independence and target computer architectural scope are brought into focus.
NASA Technical Reports Server (NTRS)
Goodwin, Sabine A.; Raj, P.
1999-01-01
Progress to date towards the development and validation of a fast, accurate and cost-effective aeroelastic method for advanced parallel computing platforms such as the IBM SP2 and the SGI Origin 2000 is presented in this paper. The ENSAERO code, developed at the NASA-Ames Research Center has been selected for this effort. The code allows for the computation of aeroelastic responses by simultaneously integrating the Euler or Navier-Stokes equations and the modal structural equations of motion. To assess the computational performance and accuracy of the ENSAERO code, this paper reports the results of the Navier-Stokes simulations of the transonic flow over a flexible aeroelastic wing body configuration. In addition, a forced harmonic oscillation analysis in the frequency domain and an analysis in the time domain are done on a wing undergoing a rigid pitch and plunge motion. Finally, to demonstrate the ENSAERO flutter-analysis capability, aeroelastic Euler and Navier-Stokes computations on an L-1011 wind tunnel model including pylon, nacelle and empennage are underway. All computational solutions are compared with experimental data to assess the level of accuracy of ENSAERO. As the computations described above are performed, a meticulous log of computational performance in terms of wall clock time, execution speed, memory and disk storage is kept. Code scalability is also demonstrated by studying the impact of varying the number of processors on computational performance on the IBM SP2 and the Origin 2000 systems.
Simulating Drosophila Genetics with the Computer.
ERIC Educational Resources Information Center
Small, James W., Jr.; Edwards, Kathryn L.
1979-01-01
Presents some techniques developed to help improve student understanding of Mendelian principles through the use of a computer simulation model by the genetic system of the fruit fly. Includes discussion and evaluation of this computer assisted program. (MA)
Protocols for Handling Messages Between Simulation Computers
NASA Technical Reports Server (NTRS)
Balcerowski, John P.; Dunnam, Milton
2006-01-01
Practical Simulator Network (PSimNet) is a set of data-communication protocols designed especially for use in handling messages between computers that are engaging cooperatively in real-time or nearly-real-time training simulations. In a typical application, computers that provide individualized training at widely dispersed locations would communicate, by use of PSimNet, with a central host computer that would provide a common computational- simulation environment and common data. Originally intended for use in supporting interfaces between training computers and computers that simulate the responses of spacecraft scientific payloads, PSimNet could be especially well suited for a variety of other applications -- for example, group automobile-driver training in a classroom. Another potential application might lie in networking of automobile-diagnostic computers at repair facilities to a central computer that would compile the expertise of numerous technicians and engineers and act as an expert consulting technician.
Chip level simulation of fault tolerant computers
NASA Technical Reports Server (NTRS)
Armstrong, J. R.
1982-01-01
Chip-level modeling techniques in the evaluation of fault tolerant systems were researched. A fault tolerant computer was modeled. An efficient approach to functional fault simulation was developed. Simulation software was also developed.
Monte Carlo Computer Simulation of a Rainbow.
ERIC Educational Resources Information Center
Olson, Donald; And Others
1990-01-01
Discusses making a computer-simulated rainbow using principles of physics, such as reflection and refraction. Provides BASIC program for the simulation. Appends a program illustrating the effects of dispersion of the colors. (YP)
Computer Based Simulation of Laboratory Experiments.
ERIC Educational Resources Information Center
Edward, Norrie S.
1997-01-01
Examines computer based simulations of practical laboratory experiments in engineering. Discusses the aims and achievements of lab work (cognitive, process, psychomotor, and affective); types of simulations (model building and behavioral); and the strengths and weaknesses of simulations. Describes the development of a centrifugal pump simulation,…
Constructivist Design of Graphic Computer Simulations.
ERIC Educational Resources Information Center
Black, John B.; And Others
Two graphic computer simulations have been prepared for teaching high school and middle school students about how business organizations and financial systems work: "Parkside," which simulates managing a hotel; and "Guestwear," which simulates managing a clothing manufacturer. Both simulations are based on six principles of constructivist design…
Computer-based personality judgments are more accurate than those made by humans
Youyou, Wu; Kosinski, Michal; Stillwell, David
2015-01-01
Judging others’ personalities is an essential skill in successful social living, as personality is a key driver behind people’s interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants’ Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507
Computer-based personality judgments are more accurate than those made by humans.
Youyou, Wu; Kosinski, Michal; Stillwell, David
2015-01-27
Judging others' personalities is an essential skill in successful social living, as personality is a key driver behind people's interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants' Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507
Computer Simulation in Chemical Kinetics
ERIC Educational Resources Information Center
Anderson, Jay Martin
1976-01-01
Discusses the use of the System Dynamics technique in simulating a chemical reaction for kinetic analysis. Also discusses the use of simulation modelling in biology, ecology, and the social sciences, where experimentation may be impractical or impossible. (MLH)
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.
NASA Technical Reports Server (NTRS)
Vatsa, Veer N.; Singer, Bart A.
2003-01-01
We evaluate the applicability of a production computational fluid dynamics code for conducting detached eddy simulation for unsteady flows. A second-order accurate Navier-Stokes code developed at NASA Langley Research Center, known as TLNS3D, is used for these simulations. We focus our attention on high Reynolds number flow (Re = 5 x 10(sup 4) - 1.4 x 10(sup 5)) past a circular cylinder to simulate flows with large-scale separations. We consider two types of flow situations: one in which the flow at the separation point is laminar, and the other in which the flow is already turbulent when it detaches from the surface of the cylinder. Solutions are presented for two- and three-dimensional calculations using both the unsteady Reynolds-averaged Navier-Stokes paradigm and the detached eddy simulation treatment. All calculations use the standard Spalart-Allmaras turbulence model as the base model.
Computer simulation of CPM dye lasers
Wang Qingyue; Zhao Xingjun )
1990-01-01
Quantative analysis of the laser pulses of various intracavity elements in a CPM dye laser is carried out in this study. The pulse formation is simulated with a computer, resulting in an asymmetric numerical solution for the pulse shape. The mechanisms of pulse formation are also discussed based on the results of computer simulation.
A Unified Methodology for Computing Accurate Quaternion Color Moments and Moment Invariants.
Karakasis, Evangelos G; Papakostas, George A; Koulouriotis, Dimitrios E; Tourassis, Vassilios D
2014-02-01
In this paper, a general framework for computing accurate quaternion color moments and their corresponding invariants is proposed. The proposed unified scheme arose by studying the characteristics of different orthogonal polynomials. These polynomials are used as kernels in order to form moments, the invariants of which can easily be derived. The resulted scheme permits the usage of any polynomial-like kernel in a unified and consistent way. The resulted moments and moment invariants demonstrate robustness to noisy conditions and high discriminative power. Additionally, in the case of continuous moments, accurate computations take place to avoid approximation errors. Based on this general methodology, the quaternion Tchebichef, Krawtchouk, Dual Hahn, Legendre, orthogonal Fourier-Mellin, pseudo Zernike and Zernike color moments, and their corresponding invariants are introduced. A selected paradigm presents the reconstruction capability of each moment family, whereas proper classification scenarios evaluate the performance of color moment invariants. PMID:24216719
VLSI circuit simulation using a vector computer
NASA Technical Reports Server (NTRS)
Mcgrogan, S. K.
1984-01-01
Simulation of circuits having more than 2000 active devices requires the largest, fastest computers available. A vector computer, such as the CYBER 205, can yield great speed and cost advantages if efforts are made to adapt the simulation program to the strengths of the computer. ASPEC and SPICE (1), two widely used circuit simulation programs, are discussed. ASPECV and VAMOS (5) are respectively vector adaptations of these two simulators. They demonstrate the substantial performance enhancements possible for this class of algorithm on the CYBER 205.
NASA Astrophysics Data System (ADS)
Shukla, Ratnesh K.
2014-11-01
Single fluid schemes that rely on an interface function for phase identification in multicomponent compressible flows are widely used to study hydrodynamic flow phenomena in several diverse applications. Simulations based on standard numerical implementation of these schemes suffer from an artificial increase in the width of the interface function owing to the numerical dissipation introduced by an upwind discretization of the governing equations. In addition, monotonicity requirements which ensure that the sharp interface function remains bounded at all times necessitate use of low-order accurate discretization strategies. This results in a significant reduction in accuracy along with a loss of intricate flow features. In this paper we develop a nonlinear transformation based interface capturing method which achieves superior accuracy without compromising the simplicity, computational efficiency and robustness of the original flow solver. A nonlinear map from the signed distance function to the sigmoid type interface function is used to effectively couple a standard single fluid shock and interface capturing scheme with a high-order accurate constrained level set reinitialization method in a way that allows for oscillation-free transport of the sharp material interface. Imposition of a maximum principle, which ensures that the multidimensional preconditioned interface capturing method does not produce new maxima or minima even in the extreme events of interface merger or breakup, allows for an explicit determination of the interface thickness in terms of the grid spacing. A narrow band method is formulated in order to localize computations pertinent to the preconditioned interface capturing method. Numerical tests in one dimension reveal a significant improvement in accuracy and convergence; in stark contrast to the conventional scheme, the proposed method retains its accuracy and convergence characteristics in a shifted reference frame. Results from the test
Optimum spaceborne computer system design by simulation
NASA Technical Reports Server (NTRS)
Williams, T.; Kerner, H.; Weatherbee, J. E.; Taylor, D. S.; Hodges, B.
1973-01-01
A deterministic simulator is described which models the Automatically Reconfigurable Modular Multiprocessor System (ARMMS), a candidate computer system for future manned and unmanned space missions. Its use as a tool to study and determine the minimum computer system configuration necessary to satisfy the on-board computational requirements of a typical mission is presented. The paper describes how the computer system configuration is determined in order to satisfy the data processing demand of the various shuttle booster subsytems. The configuration which is developed as a result of studies with the simulator is optimal with respect to the efficient use of computer system resources.
Analyzing Robotic Kinematics Via Computed Simulations
NASA Technical Reports Server (NTRS)
Carnahan, Timothy M.
1992-01-01
Computing system assists in evaluation of kinematics of conceptual robot. Displays positions and motions of robotic manipulator within work cell. Also displays interactions between robotic manipulator and other objects. Results of simulation displayed on graphical computer workstation. System includes both off-the-shelf software originally developed for automotive industry and specially developed software. Simulation system also used to design human-equivalent hand, to model optical train in infrared system, and to develop graphical interface for teleoperator simulation system.
Computationally Lightweight Air-Traffic-Control Simulation
NASA Technical Reports Server (NTRS)
Knight, Russell
2005-01-01
An algorithm for computationally lightweight simulation of automated air traffic control (ATC) at a busy airport has been derived. The algorithm is expected to serve as the basis for development of software that would be incorporated into flight-simulator software, the ATC component of which is not yet capable of handling realistic airport loads. Software based on this algorithm could also be incorporated into other computer programs that simulate a variety of scenarios for purposes of training or amusement.
NASA Astrophysics Data System (ADS)
Yoshidome, Takashi; Ekimoto, Toru; Matubayasi, Nobuyuki; Harano, Yuichi; Kinoshita, Masahiro; Ikeguchi, Mitsunori
2015-05-01
The hydration free energy (HFE) is a crucially important physical quantity to discuss various chemical processes in aqueous solutions. Although an explicit-solvent computation with molecular dynamics (MD) simulations is a preferable treatment of the HFE, huge computational load has been inevitable for large, complex solutes like proteins. In the present paper, we propose an efficient computation method for the HFE. In our method, the HFE is computed as a sum of
Computer Clinical Simulations in Health Sciences.
ERIC Educational Resources Information Center
Jones, Gary L; Keith, Kenneth D.
1983-01-01
Discusses the key characteristics of clinical simulation, some developmental foundations, two current research studies, and some implications for the future of health science education. Investigations of the effects of computer-based simulation indicate that acquisition of decision-making skills is greater than with noncomputerized simulations.…
Computer simulation of nonequilibrium processes
Hoover, W.G.; Moran, B.; Holian, B.L.; Posch, H.A.; Bestiale, S.
1987-01-01
Recent atomistic simulations of irreversible macroscopic hydrodynamic flows are illustrated. An extension of Nose's reversible atomistic mechanics makes it possible to simulate such non-equilibrium systems with completely reversible equations of motion. The new techniques show that macroscopic irreversibility is a natural inevitable consequence of time-reversible Lyapunov-unstable microscopic equations of motion.
NASA Technical Reports Server (NTRS)
Tranter, W. H.; Ziemer, R. E.; Fashano, M. J.
1975-01-01
This paper reviews the SYSTID technique for performance evaluation of communication systems using time-domain computer simulation. An example program illustrates the language. The inclusion of both Gaussian and impulse noise models make accurate simulation possible in a wide variety of environments. A very flexible postprocessor makes possible accurate and efficient performance evaluation.
NASA Astrophysics Data System (ADS)
Wosnik, M.; Bachant, P.
2014-12-01
Cross-flow turbines, often referred to as vertical-axis turbines, show potential for success in marine hydrokinetic (MHK) and wind energy applications, ranging from small- to utility-scale installations in tidal/ocean currents and offshore wind. As turbine designs mature, the research focus is shifting from individual devices to the optimization of turbine arrays. It would be expensive and time-consuming to conduct physical model studies of large arrays at large model scales (to achieve sufficiently high Reynolds numbers), and hence numerical techniques are generally better suited to explore the array design parameter space. However, since the computing power available today is not sufficient to conduct simulations of the flow in and around large arrays of turbines with fully resolved turbine geometries (e.g., grid resolution into the viscous sublayer on turbine blades), the turbines' interaction with the energy resource (water current or wind) needs to be parameterized, or modeled. Models used today--a common model is the actuator disk concept--are not able to predict the unique wake structure generated by cross-flow turbines. This wake structure has been shown to create "constructive" interference in some cases, improving turbine performance in array configurations, in contrast with axial-flow, or horizontal axis devices. Towards a more accurate parameterization of cross-flow turbines, an extensive experimental study was carried out using a high-resolution turbine test bed with wake measurement capability in a large cross-section tow tank. The experimental results were then "interpolated" using high-fidelity Navier--Stokes simulations, to gain insight into the turbine's near-wake. The study was designed to achieve sufficiently high Reynolds numbers for the results to be Reynolds number independent with respect to turbine performance and wake statistics, such that they can be reliably extrapolated to full scale and used for model validation. The end product of
Filtration theory using computer simulations
Bergman, W.; Corey, I.
1997-08-01
We have used commercially available fluid dynamics codes based on Navier-Stokes theory and the Langevin particle equation of motion to compute the particle capture efficiency and pressure drop through selected two- and three-dimensional fiber arrays. The approach we used was to first compute the air velocity vector field throughout a defined region containing the fiber matrix. The particle capture in the fiber matrix is then computed by superimposing the Langevin particle equation of motion over the flow velocity field. Using the Langevin equation combines the particle Brownian motion, inertia and interception mechanisms in a single equation. In contrast, most previous investigations treat the different capture mechanisms separately. We have computed the particle capture efficiency and the pressure drop through one, 2-D and two, 3-D fiber matrix elements. 5 refs., 11 figs.
Accurate calculation of computer-generated holograms using angular-spectrum layer-oriented method.
Zhao, Yan; Cao, Liangcai; Zhang, Hao; Kong, Dezhao; Jin, Guofan
2015-10-01
Fast calculation and correct depth cue are crucial issues in the calculation of computer-generated hologram (CGH) for high quality three-dimensional (3-D) display. An angular-spectrum based algorithm for layer-oriented CGH is proposed. Angular spectra from each layer are synthesized as a layer-corresponded sub-hologram based on the fast Fourier transform without paraxial approximation. The proposed method can avoid the huge computational cost of the point-oriented method and yield accurate predictions of the whole diffracted field compared with other layer-oriented methods. CGHs of versatile formats of 3-D digital scenes, including computed tomography and 3-D digital models, are demonstrated with precise depth performance and advanced image quality. PMID:26480062
Material Models for Accurate Simulation of Sheet Metal Forming and Springback
NASA Astrophysics Data System (ADS)
Yoshida, Fusahito
2010-06-01
For anisotropic sheet metals, modeling of anisotropy and the Bauschinger effect is discussed in the framework of Yoshida-Uemori kinematic hardening model incorporating with anisotropic yield functions. The performances of the models in predicting yield loci, cyclic stress-strain responses on several types of steel and aluminum sheets are demonstrated by comparing the numerical simulation results with the corresponding experimental observations. From some examples of FE simulation of sheet metal forming and springback, it is concluded that modeling of both the anisotropy and the Bauschinger effect is essential for the accurate numerical simulation.
Time accurate application of the MacCormack 2-4 scheme on massively parallel computers
NASA Technical Reports Server (NTRS)
Hudson, Dale A.; Long, Lyle N.
1995-01-01
Many recent computational efforts in turbulence and acoustics research have used higher order numerical algorithms. One popular method has been the explicit MacCormack 2-4 scheme. The MacCormack 2-4 scheme is second order accurate in time and fourth order accurate in space, and is stable for CFL's below 2/3. Current research has shown that the method can give accurate results but does exhibit significant Gibbs phenomena at sharp discontinuities. The impact of adding Jameson type second, third, and fourth order artificial viscosity was examined here. Category 2 problems, the nonlinear traveling wave and the Riemann problem, were computed using a CFL number of 0.25. This research has found that dispersion errors can be significantly reduced or nearly eliminated by using a combination of second and third order terms in the damping. Use of second and fourth order terms reduced the magnitude of dispersion errors but not as effectively as the second and third order combination. The program was coded using Thinking Machine's CM Fortran, a variant of Fortran 90/High Performance Fortran, and was executed on a 2K CM-200. Simple extrapolation boundary conditions were used for both problems.
Palm computer demonstrates a fast and accurate means of burn data collection.
Lal, S O; Smith, F W; Davis, J P; Castro, H Y; Smith, D W; Chinkes, D L; Barrow, R E
2000-01-01
Manual biomedical data collection and entry of the data into a personal computer is time-consuming and can be prone to errors. The purpose of this study was to compare data entry into a hand-held computer versus hand written data followed by entry of the data into a personal computer. A Palm (3Com Palm IIIx, Santa, Clara, Calif) computer with a custom menu-driven program was used for the entry and retrieval of burn-related variables. These variables were also used to create an identical sheet that was filled in by hand. Identical data were retrieved twice from 110 charts 48 hours apart and then used to create an Excel (Microsoft, Redmond, Wash) spreadsheet. One time data were recorded by the Palm entry method, and the other time the data were handwritten. The method of retrieval was alternated between the Palm system and handwritten system every 10 charts. The total time required to log data and to generate an Excel spreadsheet was recorded and used as a study endpoint. The total time for the Palm method of data collection and downloading to a personal computer was 23% faster than hand recording with the personal computer entry method (P < 0.05), and 58% fewer errors were generated with the Palm method.) The Palm is a faster and more accurate means of data collection than a handwritten technique. PMID:11194811
Evaluation of Visual Computer Simulator for Computer Architecture Education
ERIC Educational Resources Information Center
Imai, Yoshiro; Imai, Masatoshi; Moritoh, Yoshio
2013-01-01
This paper presents trial evaluation of a visual computer simulator in 2009-2011, which has been developed to play some roles of both instruction facility and learning tool simultaneously. And it illustrates an example of Computer Architecture education for University students and usage of e-Learning tool for Assembly Programming in order to…
High performance computing for domestic petroleum reservoir simulation
Zyvoloski, G.; Auer, L.; Dendy, J.
1996-06-01
This is the final report of a two-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory. High-performance computing offers the prospect of greatly increasing the resolution at which petroleum reservoirs can be represented in simulation models. The increases in resolution can be achieved through large increases in computational speed and memory, if machine architecture and numerical methods for solution of the multiphase flow equations can be used to advantage. Perhaps more importantly, the increased speed and size of today`s computers make it possible to add physical processes to simulation codes that heretofore were too expensive in terms of computer time and memory to be practical. These factors combine to allow the development of new, more accurate methods for optimizing petroleum reservoir production.
Computer simulation of upset welding
Spingarn, J R; Mason, W E; Swearengen, J C
1982-04-01
Useful process modeling of upset welding requires contributions from metallurgy, welding engineering, thermal analysis and experimental mechanics. In this report, the significant milestones for such an effort are outlined and probable difficult areas are pointed out. Progress to date is summarized and directions for future research are offered. With regard to the computational aspects of this problem, a 2-D heat conduction computer code has been modified to incorporate electrical heating, and computations have been run for an axisymmetric problem with simple viscous material laws and d.c. electrical boundary conditions. In the experimental endeavor, the boundary conditions have been measured during the welding process, although interpretation of voltage drop measurements is not straightforward. The ranges of strain, strain rate and temperature encountered during upset welding have been measured or calculated, and the need for a unifying constitutive law is described. Finally, the possible complications of microstructure and interfaces are clarified.
Erguel, Ozguer; Guerel, Levent
2008-12-01
We present a novel stabilization procedure for accurate surface formulations of electromagnetic scattering problems involving three-dimensional dielectric objects with arbitrarily low contrasts. Conventional surface integral equations provide inaccurate results for the scattered fields when the contrast of the object is low, i.e., when the electromagnetic material parameters of the scatterer and the host medium are close to each other. We propose a stabilization procedure involving the extraction of nonradiating currents and rearrangement of the right-hand side of the equations using fictitious incident fields. Then, only the radiating currents are solved to calculate the scattered fields accurately. This technique can easily be applied to the existing implementations of conventional formulations, it requires negligible extra computational cost, and it is also appropriate for the solution of large problems with the multilevel fast multipole algorithm. We show that the stabilization leads to robust formulations that are valid even for the solutions of extremely low-contrast objects.
An accurate quadrature technique for the contact boundary in 3D finite element computations
NASA Astrophysics Data System (ADS)
Duong, Thang X.; Sauer, Roger A.
2015-01-01
This paper presents a new numerical integration technique for 3D contact finite element implementations, focusing on a remedy for the inaccurate integration due to discontinuities at the boundary of contact surfaces. The method is based on the adaptive refinement of the integration domain along the boundary of the contact surface, and is accordingly denoted RBQ for refined boundary quadrature. It can be used for common element types of any order, e.g. Lagrange, NURBS, or T-Spline elements. In terms of both computational speed and accuracy, RBQ exhibits great advantages over a naive increase of the number of quadrature points. Also, the RBQ method is shown to remain accurate for large deformations. Furthermore, since the sharp boundary of the contact surface is determined, it can be used for various purposes like the accurate post-processing of the contact pressure. Several examples are presented to illustrate the new technique.
Computational Spectrum of Agent Model Simulation
Perumalla, Kalyan S
2010-01-01
The study of human social behavioral systems is finding renewed interest in military, homeland security and other applications. Simulation is the most generally applied approach to studying complex scenarios in such systems. Here, we outline some of the important considerations that underlie the computational aspects of simulation-based study of human social systems. The fundamental imprecision underlying questions and answers in social science makes it necessary to carefully distinguish among different simulation problem classes and to identify the most pertinent set of computational dimensions associated with those classes. We identify a few such classes and present their computational implications. The focus is then shifted to the most challenging combinations in the computational spectrum, namely, large-scale entity counts at moderate to high levels of fidelity. Recent developments in furthering the state-of-the-art in these challenging cases are outlined. A case study of large-scale agent simulation is provided in simulating large numbers (millions) of social entities at real-time speeds on inexpensive hardware. Recent computational results are identified that highlight the potential of modern high-end computing platforms to push the envelope with respect to speed, scale and fidelity of social system simulations. Finally, the problem of shielding the modeler or domain expert from the complex computational aspects is discussed and a few potential solution approaches are identified.
A Generic Scheduling Simulator for High Performance Parallel Computers
Yoo, B S; Choi, G S; Jette, M A
2001-08-01
It is well known that efficient job scheduling plays a crucial role in achieving high system utilization in large-scale high performance computing environments. A good scheduling algorithm should schedule jobs to achieve high system utilization while satisfying various user demands in an equitable fashion. Designing such a scheduling algorithm is a non-trivial task even in a static environment. In practice, the computing environment and workload are constantly changing. There are several reasons for this. First, the computing platforms constantly evolve as the technology advances. For example, the availability of relatively powerful commodity off-the-shelf (COTS) components at steadily diminishing prices have made it feasible to construct ever larger massively parallel computers in recent years [1, 4]. Second, the workload imposed on the system also changes constantly. The rapidly increasing compute resources have provided many applications developers with the opportunity to radically alter program characteristics and take advantage of these additional resources. New developments in software technology may also trigger changes in user applications. Finally, political climate change may alter user priorities or the mission of the organization. System designers in such dynamic environments must be able to accurately forecast the effect of changes in the hardware, software, and/or policies under consideration. If the environmental changes are significant, one must also reassess scheduling algorithms. Simulation has frequently been relied upon for this analysis, because other methods such as analytical modeling or actual measurements are usually too difficult or costly. A drawback of the simulation approach, however, is that developing a simulator is a time-consuming process. Furthermore, an existing simulator cannot be easily adapted to a new environment. In this research, we attempt to develop a generic job-scheduling simulator, which facilitates the evaluation of
NASA Astrophysics Data System (ADS)
Peng, Liang-You; Gong, Qihuang
2010-12-01
The accurate computations of hydrogenic continuum wave functions are very important in many branches of physics such as electron-atom collisions, cold atom physics, and atomic ionization in strong laser fields, etc. Although there already exist various algorithms and codes, most of them are only reliable in a certain ranges of parameters. In some practical applications, accurate continuum wave functions need to be calculated at extremely low energies, large radial distances and/or large angular momentum number. Here we provide such a code, which can generate accurate hydrogenic continuum wave functions and corresponding Coulomb phase shifts at a wide range of parameters. Without any essential restrict to angular momentum number, the present code is able to give reliable results at the electron energy range [10,10] eV for radial distances of [10,10] a.u. We also find the present code is very efficient, which should find numerous applications in many fields such as strong field physics. Program summaryProgram title: HContinuumGautchi Catalogue identifier: AEHD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1233 No. of bytes in distributed program, including test data, etc.: 7405 Distribution format: tar.gz Programming language: Fortran90 in fixed format Computer: AMD Processors Operating system: Linux RAM: 20 MBytes Classification: 2.7, 4.5 Nature of problem: The accurate computation of atomic continuum wave functions is very important in many research fields such as strong field physics and cold atom physics. Although there have already existed various algorithms and codes, most of them can only be applicable and reliable in a certain range of parameters. We present here an accurate FORTRAN program for
Towards fast and accurate algorithms for processing fuzzy data: interval computations revisited
NASA Astrophysics Data System (ADS)
Xiang, Gang; Kreinovich, Vladik
2013-02-01
In many practical applications, we need to process data, e.g. to predict the future values of different quantities based on their current values. Often, the only information that we have about the current values comes from experts, and is described in informal ('fuzzy') terms like 'small'. To process such data, it is natural to use fuzzy techniques, techniques specifically designed by Lotfi Zadeh to handle such informal information. In this survey, we start by revisiting the motivation behind Zadeh's formulae for processing fuzzy data, and explain how the algorithmic problem of processing fuzzy data can be described in terms of interval computations (α-cuts). Many fuzzy practitioners claim 'I tried interval computations, they did not work' - meaning that they got estimates which are much wider than the desired α-cuts. We show that such statements are usually based on a (widely spread) misunderstanding - that interval computations simply mean replacing each arithmetic operation with the corresponding operation with intervals. We show that while such straightforward interval techniques indeed often lead to over-wide estimates, the current advanced interval computations techniques result in estimates which are much more accurate. We overview such advanced interval computations techniques, and show that by using them, we can efficiently and accurately process fuzzy data. We wrote this survey with three audiences in mind. First, we want fuzzy researchers and practitioners to understand the current advanced interval computations techniques and to use them to come up with faster and more accurate algorithms for processing fuzzy data. For this 'fuzzy' audience, we explain these current techniques in detail. Second, we also want interval researchers to better understand this important application area for their techniques. For this 'interval' audience, we want to explain where fuzzy techniques come from, what are possible variants of these techniques, and what are the
Economic Analysis. Computer Simulation Models.
ERIC Educational Resources Information Center
Sterling Inst., Washington, DC. Educational Technology Center.
A multimedia course in economic analysis was developed and used in conjunction with the United States Naval Academy. (See ED 043 790 and ED 043 791 for final reports of the project evaluation and development model.) This volume of the text discusses the simulation of behavioral relationships among variable elements in an economy and presents…
Astronomy Simulation with Computer Graphics.
ERIC Educational Resources Information Center
Thomas, William E.
1982-01-01
"Planetary Motion Simulations" is a system of programs designed for students to observe motions of a superior planet (one whose orbit lies outside the orbit of the earth). Programs run on the Apple II microcomputer and employ high-resolution graphics to present the motions of Saturn. (Author/JN)
Computer simulation of engine systems
NASA Technical Reports Server (NTRS)
Fishbach, L. H.
1980-01-01
The use of computerized simulations of the steady state and transient performance of jet engines throughout the flight regime is discussed. In addition, installation effects on thrust and specific fuel consumption is accounted for as well as engine weight, dimensions and cost. The availability throughout the government and industry of analytical methods for calculating these quantities are pointed out.
Fiber Composite Sandwich Thermostructural Behavior: Computational Simulation
NASA Technical Reports Server (NTRS)
Chamis, C. C.; Aiello, R. A.; Murthy, P. L. N.
1986-01-01
Several computational levels of progressive sophistication/simplification are described to computationally simulate composite sandwich hygral, thermal, and structural behavior. The computational levels of sophistication include: (1) three-dimensional detailed finite element modeling of the honeycomb, the adhesive and the composite faces; (2) three-dimensional finite element modeling of the honeycomb assumed to be an equivalent continuous, homogeneous medium, the adhesive and the composite faces; (3) laminate theory simulation where the honeycomb (metal or composite) is assumed to consist of plies with equivalent properties; and (4) derivations of approximate, simplified equations for thermal and mechanical properties by simulating the honeycomb as an equivalent homogeneous medium. The approximate equations are combined with composite hygrothermomechanical and laminate theories to provide a simple and effective computational procedure for simulating the thermomechanical/thermostructural behavior of fiber composite sandwich structures.
Augmented Reality Simulations on Handheld Computers
ERIC Educational Resources Information Center
Squire, Kurt; Klopfer, Eric
2007-01-01
Advancements in handheld computing, particularly its portability, social interactivity, context sensitivity, connectivity, and individuality, open new opportunities for immersive learning environments. This article articulates the pedagogical potential of augmented reality simulations in environmental engineering education by immersing students in…
ERIC Educational Resources Information Center
Hayden, Howard C.
1984-01-01
Discusses a computer simulation which: (1) describes an experiment investigating F=m/a; (2) generates data; (3) allows students to see the data; and (4) generates the equation with a least-squares fit. (JN)
Computer simulation and optimization of radioelectronic devices
NASA Astrophysics Data System (ADS)
Benenson, Z. M.; Elistratov, M. R.; Ilin, L. K.; Kravchenko, S. V.; Sukhov, D. M.; Udler, M. A.
Methods of simulating and optimizing radioelectronic devices in an automated design system are discussed. Also treated are algorithms used in the computer-aided design of these devices. The special language of description for these devices is described.
NASA Technical Reports Server (NTRS)
Tamma, Kumar K.; Railkar, Sudhir B.
1988-01-01
This paper represents an attempt to apply extensions of a hybrid transfinite element computational approach for accurately predicting thermoelastic stress waves. The applicability of the present formulations for capturing the thermal stress waves induced by boundary heating for the well known Danilovskaya problems is demonstrated. A unique feature of the proposed formulations for applicability to the Danilovskaya problem of thermal stress waves in elastic solids lies in the hybrid nature of the unified formulations and the development of special purpose transfinite elements in conjunction with the classical Galerkin techniques and transformation concepts. Numerical test cases validate the applicability and superior capability to capture the thermal stress waves induced due to boundary heating.
Accurate Experiment to Computation Coupling for Understanding QH-mode physics using NIMROD
NASA Astrophysics Data System (ADS)
King, J. R.; Burrell, K. H.; Garofalo, A. M.; Groebner, R. J.; Hanson, J. D.; Hebert, J. D.; Hudson, S. R.; Pankin, A. Y.; Kruger, S. E.; Snyder, P. B.
2015-11-01
It is desirable to have an ITER H-mode regime that is quiescent to edge-localized modes (ELMs). The quiescent H-mode (QH-mode) with edge harmonic oscillations (EHO) is one such regime. High quality equilibria are essential for accurate EHO simulations with initial-value codes such as NIMROD. We include profiles outside the LCFS which generate associated currents when we solve the Grad-Shafranov equation with open-flux regions using the NIMEQ solver. The new solution is an equilibrium that closely resembles the original reconstruction (which does not contain open-flux currents). This regenerated equilibrium is consistent with the profiles that are measured by the high quality diagnostics on DIII-D. Results from nonlinear NIMROD simulations of the EHO are presented. The full measured rotation profiles are included in the simulation. The simulation develops into a saturated state. The saturation mechanism of the EHO is explored and simulation is compared to magnetic-coil measurements. This work is currently supported in part by the US DOE Office of Science under awards DE-FC02-04ER54698, DE-AC02-09CH11466 and the SciDAC Center for Extended MHD Modeling.
Computer-simulated phacoemulsification improvements
NASA Astrophysics Data System (ADS)
Soederberg, Per G.; Laurell, Carl-Gustaf; Artzen, D.; Nordh, Leif; Skarman, Eva; Nordqvist, P.; Andersson, Mats
2002-06-01
A simulator for phacoemulsification cataract extraction is developed. A three-dimensional visual interface and foot pedals for phacoemulsification power, x-y positioning, zoom and focus were established. An algorithm that allows real time visual feedback of the surgical field was developed. Cataract surgery is the most common surgical procedure. The operation requires input from both feet and both hands and provides visual feedback through the operation microscope essentially without tactile feedback. Experience demonstrates that the number of complications for an experienced surgeon learning phacoemulsification, decreases exponentially, reaching close to the asymptote after the first 500 procedures despite initial wet lab training on animal eyes. Simulator training is anticipated to decrease training time, decrease complication rate for the beginner and reduce expensive supervision by a high volume surgeon.
Teaching Environmental Systems Modelling Using Computer Simulation.
ERIC Educational Resources Information Center
Moffatt, Ian
1986-01-01
A computer modeling course in environmental systems and dynamics is presented. The course teaches senior undergraduates to analyze a system of interest, construct a system flow chart, and write computer programs to simulate real world environmental processes. An example is presented along with a course evaluation, figures, tables, and references.…
Psychology on Computers: Simulations, Experiments and Projects.
ERIC Educational Resources Information Center
Belcher, Duane M.; Smith, Stephen D.
PSYCOM is a unique mixed media package which combines high interest projects on the computer with a written text of expository material. It goes beyond most computer-assisted instruction which emphasizes drill and practice and testing of knowledge. A project might consist of a simulation or an actual experiment, or it might be a demonstration, a…
Computer Simulation Of A Small Turboshaft Engine
NASA Technical Reports Server (NTRS)
Ballin, Mark G.
1991-01-01
Component-type mathematical model of small turboshaft engine developed for use in real-time computer simulations of dynamics of helicopter flight. Yields shaft speeds, torques, fuel-consumption rates, and other operating parameters with sufficient accuracy for use in real-time simulation of maneuvers involving large transients in power and/or severe accelerations.
Simulations of Probabilities for Quantum Computing
NASA Technical Reports Server (NTRS)
Zak, M.
1996-01-01
It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-LIpschitz dynamics, without utilization of any man-made devices (such as random number generators). Self-organizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed.
Criterion Standards for Evaluating Computer Simulation Courseware.
ERIC Educational Resources Information Center
Wholeben, Brent Edward
This paper explores the role of computerized simulations as a decision-modeling intervention strategy, and views the strategy's different attribute biases based upon the varying primary missions of instruction versus application. The common goals associated with computer simulations as a training technique are discussed and compared with goals of…
Salesperson Ethics: An Interactive Computer Simulation
ERIC Educational Resources Information Center
Castleberry, Stephen
2014-01-01
A new interactive computer simulation designed to teach sales ethics is described. Simulation learner objectives include gaining a better understanding of legal issues in selling; realizing that ethical dilemmas do arise in selling; realizing the need to be honest when selling; seeing that there are conflicting demands from a salesperson's…
Improving light propagation Monte Carlo simulations with accurate 3D modeling of skin tissue
Paquit, Vincent C; Price, Jeffery R; Meriaudeau, Fabrice; Tobin Jr, Kenneth William
2008-01-01
In this paper, we present a 3D light propagation model to simulate multispectral reflectance images of large skin surface areas. In particular, we aim to simulate more accurately the effects of various physiological properties of the skin in the case of subcutaneous vein imaging compared to existing models. Our method combines a Monte Carlo light propagation model, a realistic three-dimensional model of the skin using parametric surfaces and a vision system for data acquisition. We describe our model in detail, present results from the Monte Carlo modeling and compare our results with those obtained with a well established Monte Carlo model and with real skin reflectance images.
Computer simulation of gear tooth manufacturing processes
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri; Huston, Ronald L.
1990-01-01
The use of computer graphics to simulate gear tooth manufacturing procedures is discussed. An analytical basis for the simulation is established for spur gears. The simulation itself, however, is developed not only for spur gears, but for straight bevel gears as well. The applications of the developed procedure extend from the development of finite element models of heretofore intractable geometrical forms, to exploring the fabrication of nonstandard tooth forms.
A Variable Coefficient Method for Accurate Monte Carlo Simulation of Dynamic Asset Price
NASA Astrophysics Data System (ADS)
Li, Yiming; Hung, Chih-Young; Yu, Shao-Ming; Chiang, Su-Yun; Chiang, Yi-Hui; Cheng, Hui-Wen
2007-07-01
In this work, we propose an adaptive Monte Carlo (MC) simulation technique to compute the sample paths for the dynamical asset price. In contrast to conventional MC simulation with constant drift and volatility (μ,σ), our MC simulation is performed with variable coefficient methods for (μ,σ) in the solution scheme, where the explored dynamic asset pricing model starts from the formulation of geometric Brownian motion. With the method of simultaneously updated (μ,σ), more than 5,000 runs of MC simulation are performed to fulfills basic accuracy of the large-scale computation and suppresses statistical variance. Daily changes of stock market index in Taiwan and Japan are investigated and analyzed.
Accurate methods for computing inviscid and viscous Kelvin-Helmholtz instability
NASA Astrophysics Data System (ADS)
Chen, Michael J.; Forbes, Lawrence K.
2011-02-01
The Kelvin-Helmholtz instability is modelled for inviscid and viscous fluids. Here, two bounded fluid layers flow parallel to each other with the interface between them growing in an unstable fashion when subjected to a small perturbation. In the various configurations of this problem, and the related problem of the vortex sheet, there are several phenomena associated with the evolution of the interface; notably the formation of a finite time curvature singularity and the ‘roll-up' of the interface. Two contrasting computational schemes will be presented. A spectral method is used to follow the evolution of the interface in the inviscid version of the problem. This allows the interface shape to be computed up to the time that a curvature singularity forms, with several computational difficulties overcome to reach that point. A weakly compressible viscous version of the problem is studied using finite difference techniques and a vorticity-streamfunction formulation. The two versions have comparable, but not identical, initial conditions and so the results exhibit some differences in timing. By including a small amount of viscosity the interface may be followed to the point that it rolls up into a classic ‘cat's-eye' shape. Particular attention was given to computing a consistent initial condition and solving the continuity equation both accurately and efficiently.
Subramanian, Swetha; Mast, T Douglas
2015-10-01
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. PMID:26352462
NASA Astrophysics Data System (ADS)
Subramanian, Swetha; Mast, T. Douglas
2015-09-01
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.
Optimum spaceborne computer system design by simulation
NASA Technical Reports Server (NTRS)
Williams, T.; Weatherbee, J. E.; Taylor, D. S.
1972-01-01
A deterministic digital simulation model is described which models the Automatically Reconfigurable Modular Multiprocessor System (ARMMS), a candidate computer system for future manned and unmanned space missions. Use of the model as a tool in configuring a minimum computer system for a typical mission is demonstrated. The configuration which is developed as a result of studies with the simulator is optimal with respect to the efficient use of computer system resources, i.e., the configuration derived is a minimal one. Other considerations such as increased reliability through the use of standby spares would be taken into account in the definition of a practical system for a given mission.
Computer simulation of bubble formation.
Insepov, Z.; Bazhirov, T.; Norman, G.; Stegailov, V.; Mathematics and Computer Science; Institute for High Energy Densities of Joint Institute for High Temperatures of RAS
2007-01-01
Properties of liquid metals (Li, Pb, Na) containing nanoscale cavities were studied by atomistic Molecular Dynamics (MD). Two atomistic models of cavity simulation were developed that cover a wide area in the phase diagram with negative pressure. In the first model, the thermodynamics of cavity formation, stability and the dynamics of cavity evolution in bulk liquid metals have been studied. Radial densities, pressures, surface tensions, and work functions of nano-scale cavities of various radii were calculated for liquid Li, Na, and Pb at various temperatures and densities, and at small negative pressures near the liquid-gas spinodal, and the work functions for cavity formation in liquid Li were calculated and compared with the available experimental data. The cavitation rate can further be obtained by using the classical nucleation theory (CNT). The second model is based on the stability study and on the kinetics of cavitation of the stretched liquid metals. A MD method was used to simulate cavitation in a metastable Pb and Li melts and determine the stability limits. States at temperatures below critical (T < 0.5Tc) and large negative pressures were considered. The kinetic boundary of liquid phase stability was shown to be different from the spinodal. The kinetics and dynamics of cavitation were studied. The pressure dependences of cavitation frequencies were obtained for several temperatures. The results of MD calculations were compared with estimates based on classical nucleation theory.
Computer Code for Nanostructure Simulation
NASA Technical Reports Server (NTRS)
Filikhin, Igor; Vlahovic, Branislav
2009-01-01
Due to their small size, nanostructures can have stress and thermal gradients that are larger than any macroscopic analogue. These gradients can lead to specific regions that are susceptible to failure via processes such as plastic deformation by dislocation emission, chemical debonding, and interfacial alloying. A program has been developed that rigorously simulates and predicts optoelectronic properties of nanostructures of virtually any geometrical complexity and material composition. It can be used in simulations of energy level structure, wave functions, density of states of spatially configured phonon-coupled electrons, excitons in quantum dots, quantum rings, quantum ring complexes, and more. The code can be used to calculate stress distributions and thermal transport properties for a variety of nanostructures and interfaces, transport and scattering at nanoscale interfaces and surfaces under various stress states, and alloy compositional gradients. The code allows users to perform modeling of charge transport processes through quantum-dot (QD) arrays as functions of inter-dot distance, array order versus disorder, QD orientation, shape, size, and chemical composition for applications in photovoltaics and physical properties of QD-based biochemical sensors. The code can be used to study the hot exciton formation/relation dynamics in arrays of QDs of different shapes and sizes at different temperatures. It also can be used to understand the relation among the deposition parameters and inherent stresses, strain deformation, heat flow, and failure of nanostructures.
Pseudospark discharges via computer simulation
Boeuf, J.P.; Pitchford, L.C. )
1991-04-01
The authors of this paper developed a hybrid fluid-particle (Monte Carlo) model to describe the initiation phase of pseudospark discharges. In this model, time-dependent fluid equations for the electrons and positive ions are solved self-consistently with Poisson's equation for the electric field in a two-dimensional, cylindrically symmetrical geometry. The Monte Carlo simulation is used to determine the ionization source term in the fluid equations. This model has been used to study the evolution of a discharge in helium at 0.5 torr, with an applied voltage of 2 kV and in a typical pseudospark geometry. From the numerical results, the authors have identified a sequence of physical events that lead to the rapid rise in current associated with the onset of the pseudospark discharge mode. For the conditions the authors have simulated, they find that there is a maximum in the electron multiplication at the time which corresponds to the onset of the hollow cathode effect, and although the multiplication later decreases, it is always greater than needed for a steady-state discharge. Thus the sheaths inside the hollow cathode tend to collapse against the walls, and eventually cathode emission mechanisms (such as field-enhanced thermionic emission) which the authors have not included will start to play a role. In spite of the approximation in this model, the picture which has emerged provides insight into the mechanisms controlling the onset of this potentially important discharge mode.
Computational simulations and experimental validation of a furnace brazing process
Hosking, F.M.; Gianoulakis, S.E.; Malizia, L.A.
1998-12-31
Modeling of a furnace brazing process is described. The computational tools predict the thermal response of loaded hardware in a hydrogen brazing furnace to programmed furnace profiles. Experiments were conducted to validate the model and resolve computational uncertainties. Critical boundary conditions that affect materials and processing response to the furnace environment were determined. {open_quotes}Global{close_quotes} and local issues (i.e., at the furnace/hardware and joint levels, respectively) are discussed. The ability to accurately simulate and control furnace conditions is examined.
Rotorcraft Damage Tolerance Evaluated by Computational Simulation
NASA Technical Reports Server (NTRS)
Chamis, Christos C.; Minnetyan, Levon; Abdi, Frank
2000-01-01
An integrally stiffened graphite/epoxy composite rotorcraft structure is evaluated via computational simulation. A computer code that scales up constituent micromechanics level material properties to the structure level and accounts for all possible failure modes is used for the simulation of composite degradation under loading. Damage initiation, growth, accumulation, and propagation to fracture are included in the simulation. Design implications with regard to defect and damage tolerance of integrally stiffened composite structures are examined. A procedure is outlined regarding the use of this type of information for setting quality acceptance criteria, design allowables, damage tolerance, and retirement-for-cause criteria.
Polymer Composites Corrosive Degradation: A Computational Simulation
NASA Technical Reports Server (NTRS)
Chamis, Christos C.; Minnetyan, Levon
2007-01-01
A computational simulation of polymer composites corrosive durability is presented. The corrosive environment is assumed to manage the polymer composite degradation on a ply-by-ply basis. The degradation is correlated with a measured pH factor and is represented by voids, temperature and moisture which vary parabolically for voids and linearly for temperature and moisture through the laminate thickness. The simulation is performed by a computational composite mechanics computer code which includes micro, macro, combined stress failure and laminate theories. This accounts for starting the simulation from constitutive material properties and up to the laminate scale which exposes the laminate to the corrosive environment. Results obtained for one laminate indicate that the ply-by-ply degradation degrades the laminate to the last one or the last several plies. Results also demonstrate that the simulation is applicable to other polymer composite systems as well.
Computer simulations of lung surfactant.
Baoukina, Svetlana; Tieleman, D Peter
2016-10-01
Lung surfactant lines the gas-exchange interface in the lungs and reduces the surface tension, which is necessary for breathing. Lung surfactant consists mainly of lipids with a small amount of proteins and forms a monolayer at the air-water interface connected to bilayer reservoirs. Lung surfactant function involves transfer of material between the monolayer and bilayers during the breathing cycle. Lipids and proteins are organized laterally in the monolayer; selected species are possibly preferentially transferred to bilayers. The complex 3D structure of lung surfactant and the exact roles of lipid organization and proteins remain important goals for research. We review recent simulation studies on the properties of lipid monolayers, monolayers with phase coexistence, monolayer-bilayer transformations, lipid-protein interactions, and effects of nanoparticles on lung surfactant. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26922885
Creating science simulations through Computational Thinking Patterns
NASA Astrophysics Data System (ADS)
Basawapatna, Ashok Ram
Computational thinking aims to outline fundamental skills from computer science that everyone should learn. As currently defined, with help from the National Science Foundation (NSF), these skills include problem formulation, logically organizing data, automating solutions through algorithmic thinking, and representing data through abstraction. One aim of the NSF is to integrate these and other computational thinking concepts into the classroom. End-user programming tools offer a unique opportunity to accomplish this goal. An end-user programming tool that allows students with little or no prior experience the ability to create simulations based on phenomena they see in-class could be a first step towards meeting most, if not all, of the above computational thinking goals. This thesis describes the creation, implementation and initial testing of a programming tool, called the Simulation Creation Toolkit, with which users apply high-level agent interactions called Computational Thinking Patterns (CTPs) to create simulations. Employing Computational Thinking Patterns obviates lower behavior-level programming and allows users to directly create agent interactions in a simulation by making an analogy with real world phenomena they are trying to represent. Data collected from 21 sixth grade students with no prior programming experience and 45 seventh grade students with minimal programming experience indicates that this is an effective first step towards enabling students to create simulations in the classroom environment. Furthermore, an analogical reasoning study that looked at how users might apply patterns to create simulations from high- level descriptions with little guidance shows promising results. These initial results indicate that the high level strategy employed by the Simulation Creation Toolkit is a promising strategy towards incorporating Computational Thinking concepts in the classroom environment.
Computer simulation of space station computer steered high gain antenna
NASA Technical Reports Server (NTRS)
Beach, S. W.
1973-01-01
The mathematical modeling and programming of a complete simulation program for a space station computer-steered high gain antenna are described. The program provides for reading input data cards, numerically integrating up to 50 first order differential equations, and monitoring up to 48 variables on printed output and on plots. The program system consists of a high gain antenna, an antenna gimbal control system, an on board computer, and the environment in which all are to operate.
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.
A simplified approach to characterizing a kilovoltage source spectrum for accurate dose computation
Poirier, Yannick; Kouznetsov, Alexei; Tambasco, Mauro
2012-06-15
% for the homogeneous and heterogeneous block phantoms, and agreement for the transverse dose profiles was within 6%. Conclusions: The HVL and kVp are sufficient for characterizing a kV x-ray source spectrum for accurate dose computation. As these parameters can be easily and accurately measured, they provide for a clinically feasible approach to characterizing a kV energy spectrum to be used for patient specific x-ray dose computations. Furthermore, these results provide experimental validation of our novel hybrid dose computation algorithm.
Optical computed tomography of radiochromic gels for accurate three-dimensional dosimetry
NASA Astrophysics Data System (ADS)
Babic, Steven
In this thesis, three-dimensional (3-D) radiochromic Ferrous Xylenol-orange (FX) and Leuco Crystal Violet (LCV) micelles gels were imaged by laser and cone-beam (Vista(TM)) optical computed tomography (CT) scanners. The objective was to develop optical CT of radiochromic gels for accurate 3-D dosimetry of intensity-modulated radiation therapy (IMRT) and small field techniques used in modern radiotherapy. First, the cause of a threshold dose response in FX gel dosimeters when scanned with a yellow light source was determined. This effect stems from a spectral sensitivity to multiple chemical complexes that are at different dose levels between ferric ions and xylenol-orange. To negate the threshold dose, an initial concentration of ferric ions is needed in order to shift the chemical equilibrium so that additional dose results in a linear production of a coloured complex that preferentially absorbs at longer wavelengths. Second, a low diffusion leuco-based radiochromic gel consisting of Triton X-100 micelles was developed. The diffusion coefficient of the LCV micelle gel was found to be minimal (0.036 + 0.001 mm2 hr-1 ). Although a dosimetric characterization revealed a reduced sensitivity to radiation, this was offset by a lower auto-oxidation rate and base optical density, higher melting point and no spectral sensitivity. Third, the Radiological Physics Centre (RPC) head-and-neck IMRT protocol was extended to 3-D dose verification using laser and cone-beam (Vista(TM)) optical CT scans of FX gels. Both optical systems yielded comparable measured dose distributions in high-dose regions and low gradients. The FX gel dosimetry results were crossed checked against independent thermoluminescent dosimeter and GAFChromicRTM EBT film measurements made by the RPC. It was shown that optical CT scanned FX gels can be used for accurate IMRT dose verification in 3-D. Finally, corrections for FX gel diffusion and scattered stray light in the Vista(TM) scanner were developed to
Accurate 3-D finite difference computation of traveltimes in strongly heterogeneous media
NASA Astrophysics Data System (ADS)
Noble, M.; Gesret, A.; Belayouni, N.
2014-12-01
Seismic traveltimes and their spatial derivatives are the basis of many imaging methods such as pre-stack depth migration and tomography. A common approach to compute these quantities is to solve the eikonal equation with a finite-difference scheme. If many recently published algorithms for resolving the eikonal equation do now yield fairly accurate traveltimes for most applications, the spatial derivatives of traveltimes remain very approximate. To address this accuracy issue, we develop a new hybrid eikonal solver that combines a spherical approximation when close to the source and a plane wave approximation when far away. This algorithm reproduces properly the spherical behaviour of wave fronts in the vicinity of the source. We implement a combination of 16 local operators that enables us to handle velocity models with sharp vertical and horizontal velocity contrasts. We associate to these local operators a global fast sweeping method to take into account all possible directions of wave propagation. Our formulation allows us to introduce a variable grid spacing in all three directions of space. We demonstrate the efficiency of this algorithm in terms of computational time and the gain in accuracy of the computed traveltimes and their derivatives on several numerical examples.
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul
2015-03-14
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 10(3)-10(5) 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. PMID:25770527
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul
2015-03-14
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 10{sup 3}-10{sup 5} 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.
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.
Airport Simulations Using Distributed Computational Resources
NASA Technical Reports Server (NTRS)
McDermott, William J.; Maluf, David A.; Gawdiak, Yuri; Tran, Peter; Clancy, Daniel (Technical Monitor)
2002-01-01
The Virtual National Airspace Simulation (VNAS) will improve the safety of Air Transportation. In 2001, using simulation and information management software running over a distributed network of super-computers, researchers at NASA Ames, Glenn, and Langley Research Centers developed a working prototype of a virtual airspace. This VNAS prototype modeled daily operations of the Atlanta airport by integrating measured operational data and simulation data on up to 2,000 flights a day. The concepts and architecture developed by NASA for this prototype are integral to the National Airspace Simulation to support the development of strategies improving aviation safety, identifying precursors to component failure.
Highly Accurate Frequency Calculations of Crab Cavities Using the VORPAL Computational Framework
Austin, T.M.; Cary, J.R.; Bellantoni, L.; /Argonne
2009-05-01
We have applied the Werner-Cary method [J. Comp. Phys. 227, 5200-5214 (2008)] for extracting modes and mode frequencies from time-domain simulations of crab cavities, as are needed for the ILC and the beam delivery system of the LHC. This method for frequency extraction relies on a small number of simulations, and post-processing using the SVD algorithm with Tikhonov regularization. The time-domain simulations were carried out using the VORPAL computational framework, which is based on the eminently scalable finite-difference time-domain algorithm. A validation study was performed on an aluminum model of the 3.9 GHz RF separators built originally at Fermi National Accelerator Laboratory in the US. Comparisons with measurements of the A15 cavity show that this method can provide accuracy to within 0.01% of experimental results after accounting for manufacturing imperfections. To capture the near degeneracies two simulations, requiring in total a few hours on 600 processors were employed. This method has applications across many areas including obtaining MHD spectra from time-domain simulations.
NASA Astrophysics Data System (ADS)
Zhang, Xiang; Vu-Quoc, Loc
2007-07-01
We present in this paper the displacement-driven version of a tangential force-displacement (TFD) model that accounts for both elastic and plastic deformations together with interfacial friction occurring in collisions of spherical particles. This elasto-plastic frictional TFD model, with its force-driven version presented in [L. Vu-Quoc, L. Lesburg, X. Zhang. An accurate tangential force-displacement model for granular-flow simulations: contacting spheres with plastic deformation, force-driven formulation, Journal of Computational Physics 196(1) (2004) 298-326], is consistent with the elasto-plastic frictional normal force-displacement (NFD) model presented in [L. Vu-Quoc, X. Zhang. An elasto-plastic contact force-displacement model in the normal direction: displacement-driven version, Proceedings of the Royal Society of London, Series A 455 (1991) 4013-4044]. Both the NFD model and the present TFD model are based on the concept of additive decomposition of the radius of contact area into an elastic part and a plastic part. The effect of permanent indentation after impact is represented by a correction to the radius of curvature. The effect of material softening due to plastic flow is represented by a correction to the elastic moduli. The proposed TFD model is accurate, and is validated against nonlinear finite element analyses involving plastic flows in both the loading and unloading conditions. The proposed consistent displacement-driven, elasto-plastic NFD and TFD models are designed for implementation in computer codes using the discrete-element method (DEM) for granular-flow simulations. The model is shown to be accurate and is validated against nonlinear elasto-plastic finite-element analysis.
Time Accurate CFD Simulations of the Orion Launch Abort Vehicle in the Transonic Regime
NASA Technical Reports Server (NTRS)
Ruf, Joseph; Rojahn, Josh
2011-01-01
Significant asymmetries in the fluid dynamics were calculated for some cases in the CFD simulations of the Orion Launch Abort Vehicle through its abort trajectories. The CFD simulations were performed steady state with symmetric boundary conditions and geometries. The trajectory points at issue were in the transonic regime, at 0 and 5 angles of attack with the Abort Motors with and without the Attitude Control Motors (ACM) firing. In some of the cases the asymmetric fluid dynamics resulted in aerodynamic side forces that were large enough that would overcome the control authority of the ACMs. MSFC s Fluid Dynamics Group supported the investigation into the cause of the flow asymmetries with time accurate CFD simulations, utilizing a hybrid RANS-LES turbulence model. The results show that the flow over the vehicle and the subsequent interaction with the AB and ACM motor plumes were unsteady. The resulting instantaneous aerodynamic forces were oscillatory with fairly large magnitudes. Time averaged aerodynamic forces were essentially symmetric.
NASA Technical Reports Server (NTRS)
VanZante, Dale E.; Strazisar, Anthony J.; Wood, Jerry R,; Hathaway, Michael D.; Okiishi, Theodore H.
2000-01-01
The tip clearance flows of transonic compressor rotors are important because they have a significant impact on rotor and stage performance. While numerical simulations of these flows are quite sophisticated. they are seldom verified through rigorous comparisons of numerical and measured data because these kinds of measurements are rare in the detail necessary to be useful in high-speed machines. In this paper we compare measured tip clearance flow details (e.g. trajectory and radial extent) with corresponding data obtained from a numerical simulation. Recommendations for achieving accurate numerical simulation of tip clearance flows are presented based on this comparison. Laser Doppler Velocimeter (LDV) measurements acquired in a transonic compressor rotor, NASA Rotor 35, are used. The tip clearance flow field of this transonic rotor was simulated using a Navier-Stokes turbomachinery solver that incorporates an advanced k-epsilon turbulence model derived for flows that are not in local equilibrium. Comparison between measured and simulated results indicates that simulation accuracy is primarily dependent upon the ability of the numerical code to resolve important details of a wall-bounded shear layer formed by the relative motion between the over-tip leakage flow and the shroud wall. A simple method is presented for determining the strength of this shear layer.
NASA Technical Reports Server (NTRS)
Kory, Carol L.
1999-01-01
The phenomenal growth of commercial communications has created a great demand for traveling-wave tube (TWT) amplifiers. 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. For the first time, an accurate three-dimensional helical model was developed that allows accurate prediction of TWT cold-test characteristics including operating frequency, interaction impedance, and attenuation. This computational model, which was developed at the NASA Lewis Research Center, allows TWT designers to obtain a more accurate value of interaction impedance than is possible using experimental methods. Obtaining helical slow-wave circuit interaction impedance is an important part of the design process for a TWT because it is related to the gain and efficiency of the tube. This impedance cannot be measured directly; thus, conventional methods involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit and obtaining the difference in resonant frequency between the perturbed and unperturbed circuits. A mathematical relationship has been derived between this frequency difference and the interaction impedance (ref. 1). However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. In addition, this experimental procedure is time-consuming and expensive, but until recently it was widely accepted as the most accurate means of determining interaction impedance. The advent of an accurate three-dimensional helical circuit model (ref. 2) made it possible for Lewis researchers to fully investigate standard approximations made in deriving the relationship between measured perturbation data and interaction impedance. The most prominent approximations made
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval
Karim, Rezaul; Aziz, Mohd. Momin Al; Shatabda, Swakkhar; Rahman, M. Sohel; Mia, Md. Abul Kashem; Zaman, Farhana; Rakin, Salman
2015-01-01
The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval.
Karim, Rezaul; Aziz, Mohd Momin Al; Shatabda, Swakkhar; Rahman, M Sohel; Mia, Md Abul Kashem; Zaman, Farhana; Rakin, Salman
2015-01-01
The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226
Symbolic computation in system simulation and design
NASA Astrophysics Data System (ADS)
Evans, Brian L.; Gu, Steve X.; Kalavade, Asa; Lee, Edward A.
1995-06-01
This paper examines some of the roles that symbolic computation plays in assisting system- level simulation and design. By symbolic computation, we mean programs like Mathematica that perform symbolic algebra and apply transformation rules based on algebraic identities. At a behavioral level, symbolic computation can compute parameters, generate new models, and optimize parameter settings. At the synthesis level, symbolic computation can work in tandem with synthesis tools to rewrite cascade and parallel combinations on components in sub- systems to meet design constraints. Symbolic computation represents one type of tool that may be invoked in the complex flow of the system design process. The paper discusses the qualities that a formal infrastructure for managing system design should have. The paper also describes an implementation of this infrastructure called DesignMaker, implemented in the Ptolemy environment, which manages the flow of tool invocations in an efficient manner using a graphical file dependency mechanism.
Computer Series, 108. Computer Simulation of Chemical Equilibrium.
ERIC Educational Resources Information Center
Cullen, John F., Jr.
1989-01-01
Presented is a computer simulation called "The Great Chemical Bead Game" which can be used to teach the concepts of equilibrium and kinetics to introductory chemistry students more clearly than through an experiment. Discussed are the rules of the game, the application of rate laws and graphical analysis. (CW)
Enabling Computational Technologies for Terascale Scientific Simulations
Ashby, S.F.
2000-08-24
We develop scalable algorithms and object-oriented code frameworks for terascale scientific simulations on massively parallel processors (MPPs). Our research in multigrid-based linear solvers and adaptive mesh refinement enables Laboratory programs to use MPPs to explore important physical phenomena. For example, our research aids stockpile stewardship by making practical detailed 3D simulations of radiation transport. The need to solve large linear systems arises in many applications, including radiation transport, structural dynamics, combustion, and flow in porous media. These systems result from discretizations of partial differential equations on computational meshes. Our first research objective is to develop multigrid preconditioned iterative methods for such problems and to demonstrate their scalability on MPPs. Scalability describes how total computational work grows with problem size; it measures how effectively additional resources can help solve increasingly larger problems. Many factors contribute to scalability: computer architecture, parallel implementation, and choice of algorithm. Scalable algorithms have been shown to decrease simulation times by several orders of magnitude.
Computer simulation of breathing systems for divers
Sexton, P.G.; Nuckols, M.L.
1983-02-01
A powerful new tool for the analysis and design of underwater breathing gas systems is being developed. A versatile computer simulator is described which makes possible the modular ''construction'' of any conceivable breathing gas system from computer memory-resident components. The analysis of a typical breathing gas system is demonstrated using this simulation technique, and the effects of system modifications on performance of the breathing system are shown. This modeling technique will ultimately serve as the foundation for a proposed breathing system simulator under development by the Navy. The marriage of this computer modeling technique with an interactive graphics system will provide the designer with an efficient, cost-effective tool for the development of new and improved diving systems.
NASA Astrophysics Data System (ADS)
Hochlaf, M.; Puzzarini, C.; Senent, M. L.
2015-07-01
We present multi-component computations for rotational constants, vibrational and torsional levels of medium-sized molecules. Through the treatment of two organic sulphur molecules, ethyl mercaptan and dimethyl sulphide, which are relevant for atmospheric and astrophysical media, we point out the outstanding capabilities of explicitly correlated coupled clusters (CCSD(T)-F12) method in conjunction with the cc-pVTZ-F12 basis set for the accurate predictions of such quantities. Indeed, we show that the CCSD(T)-F12/cc-pVTZ-F12 equilibrium rotational constants are in good agreement with those obtained by means of a composite scheme based on CCSD(T) calculations that accounts for the extrapolation to the complete basis set (CBS) limit and core-correlation effects [CCSD(T)/CBS+CV], thus leading to values of ground-state rotational constants rather close to the corresponding experimental data. For vibrational and torsional levels, our analysis reveals that the anharmonic frequencies derived from CCSD(T)-F12/cc-pVTZ-F12 harmonic frequencies and anharmonic corrections (Δν = ω - ν) at the CCSD/cc-pVTZ level closely agree with experimental results. The pattern of the torsional transitions and the shape of the potential energy surfaces along the torsional modes are also well reproduced using the CCSD(T)-F12/cc-pVTZ-F12 energies. Interestingly, this good accuracy is accompanied with a strong reduction of the computational costs. This makes the procedures proposed here as schemes of choice for effective and accurate prediction of spectroscopic properties of organic compounds. Finally, popular density functional approaches are compared with the coupled cluster (CC) methodologies in torsional studies. The long-range CAM-B3LYP functional of Handy and co-workers is recommended for large systems.
Software Engineering for Scientific Computer Simulations
NASA Astrophysics Data System (ADS)
Post, Douglass E.; Henderson, Dale B.; Kendall, Richard P.; Whitney, Earl M.
2004-11-01
Computer simulation is becoming a very powerful tool for analyzing and predicting the performance of fusion experiments. Simulation efforts are evolving from including only a few effects to many effects, from small teams with a few people to large teams, and from workstations and small processor count parallel computers to massively parallel platforms. Successfully making this transition requires attention to software engineering issues. We report on the conclusions drawn from a number of case studies of large scale scientific computing projects within DOE, academia and the DoD. The major lessons learned include attention to sound project management including setting reasonable and achievable requirements, building a good code team, enforcing customer focus, carrying out verification and validation and selecting the optimum computational mathematics approaches.
Time-Accurate Computation of Viscous Flow Around Deforming Bodies Using Overset Grids
Fast, P; Henshaw, W D
2001-04-02
Dynamically evolving boundaries and deforming bodies interacting with a flow are commonly encountered in fluid dynamics. However, the numerical simulation of flows with dynamic boundaries is difficult with current methods. We propose a new method for studying such problems. The key idea is to use the overset grid method with a thin, body-fitted grid near the deforming boundary, while using fixed Cartesian grids to cover most of the computational domain. Our approach combines the strengths of earlier moving overset grid methods for rigid body motion, and unstructured grid methods for Aow-structure interactions. Large scale deformation of the flow boundaries can be handled without a global regridding, and in a computationally efficient way. In terms of computational cost, even a full overset grid regridding is significantly cheaper than a full regridding of an unstructured grid for the same domain, especially in three dimensions. Numerical studies are used to verify accuracy and convergence of our flow solver. As a computational example, we consider two-dimensional incompressible flow past a flexible filament with prescribed dynamics.
Structural Composites Corrosive Management by Computational Simulation
NASA Technical Reports Server (NTRS)
Chamis, Christos C.; Minnetyan, Levon
2006-01-01
A simulation of corrosive management on polymer composites durability is presented. The corrosive environment is assumed to manage the polymer composite degradation on a ply-by-ply basis. The degradation is correlated with a measured Ph factor and is represented by voids, temperature, and moisture which vary parabolically for voids and linearly for temperature and moisture through the laminate thickness. The simulation is performed by a computational composite mechanics computer code which includes micro, macro, combined stress failure, and laminate theories. This accounts for starting the simulation from constitutive material properties and up to the laminate scale which exposes the laminate to the corrosive environment. Results obtained for one laminate indicate that the ply-by-ply managed degradation degrades the laminate to the last one or the last several plies. Results also demonstrate that the simulation is applicable to other polymer composite systems as well.
Learning features in computer simulation skills training.
Johannesson, Eva; Olsson, Mats; Petersson, Göran; Silén, Charlotte
2010-09-01
New simulation tools imply new opportunities to teach skills and train health care professionals. The aim of this study was to investigate the learning gained from computer simulation skills training. The study was designed for optimal educational settings, which benefit student-centred learning. Twenty-four second year undergraduate nursing students practised intravenous catheterization with the computer simulation program CathSim. Questionnaires were answered before and after the skills training, and after the skills examination. When using CathSim, the students appreciated the variation in patient cases, the immediate feedback, and a better understanding of anatomy, but they missed having an arm model to hold. We concluded that CathSim was useful in the students' learning process and skills training when appropriately integrated into the curriculum. Learning features to be aware of when organizing curricula with simulators are motivation, realism, variation, meaningfulness and feedback. PMID:20015690
Task simulation in computer-based training
Gardner, P.R.
1988-02-01
Westinghouse Hanford Company (WHC) makes extensive use of job-task simulations in company-developed computer-based training (CBT) courseware. This courseware is different from most others because it does not simulate process control machinery or other computer programs, instead the WHC Excerises model day-to-day tasks such as physical work preparations, progress, and incident handling. These Exercises provide a higher level of motivation and enable the testing of more complex patterns of behavior than those typically measured by multiple-choice and short questions. Examples from the WHC Radiation Safety and Crane Safety courses will be used as illustrations. 3 refs.
Student Choices when Learning with Computer Simulations
NASA Astrophysics Data System (ADS)
Podolefsky, Noah S.; Adams, Wendy K.; Wieman, Carl E.
2009-11-01
We examine student choices while using PhET computer simulations (sims) to learn physics content. In interviews, students were given questions from the Force Concept Inventory (FCI) and were allowed to choose from 12 computer simulations in order to answer these questions. We investigate students' choices when answering FCI questions with sims. We find that while students' initially choose sims that match problem situations at a surface level, deeper connections may be noticed by students later on. These results inform us on how people may choose education resources when learning on their own.
Computer simulation: A modern day crystal ball?
NASA Technical Reports Server (NTRS)
Sham, Michael; Siprelle, Andrew
1994-01-01
It has long been the desire of managers to be able to look into the future and predict the outcome of decisions. With the advent of computer simulation and the tremendous capability provided by personal computers, that desire can now be realized. This paper presents an overview of computer simulation and modeling, and discusses the capabilities of Extend. Extend is an iconic-driven Macintosh-based software tool that brings the power of simulation to the average computer user. An example of an Extend based model is presented in the form of the Space Transportation System (STS) Processing Model. The STS Processing Model produces eight shuttle launches per year, yet it takes only about ten minutes to run. In addition, statistical data such as facility utilization, wait times, and processing bottlenecks are produced. The addition or deletion of resources, such as orbiters or facilities, can be easily modeled and their impact analyzed. Through the use of computer simulation, it is possible to look into the future to see the impact of today's decisions.
Li, Xiangrui; Lu, Zhong-Lin
2012-01-01
Display systems based on conventional computer graphics cards are capable of generating images with 8-bit gray level resolution. However, most experiments in vision research require displays with more than 12 bits of luminance resolution. Several solutions are available. Bit++ (1) and DataPixx (2) use the Digital Visual Interface (DVI) output from graphics cards and high resolution (14 or 16-bit) digital-to-analog converters to drive analog display devices. The VideoSwitcher (3) described here combines analog video signals from the red and blue channels of graphics cards with different weights using a passive resister network (4) and an active circuit to deliver identical video signals to the three channels of color monitors. The method provides an inexpensive way to enable high-resolution monochromatic displays using conventional graphics cards and analog monitors. It can also provide trigger signals that can be used to mark stimulus onsets, making it easy to synchronize visual displays with physiological recordings or response time measurements. Although computer keyboards and mice are frequently used in measuring response times (RT), the accuracy of these measurements is quite low. The RTbox is a specialized hardware and software solution for accurate RT measurements. Connected to the host computer through a USB connection, the driver of the RTbox is compatible with all conventional operating systems. It uses a microprocessor and high-resolution clock to record the identities and timing of button events, which are buffered until the host computer retrieves them. The recorded button events are not affected by potential timing uncertainties or biases associated with data transmission and processing in the host computer. The asynchronous storage greatly simplifies the design of user programs. Several methods are available to synchronize the clocks of the RTbox and the host computer. The RTbox can also receive external triggers and be used to measure RT with respect
Virtual ambulatory care. Computer simulation applications.
Zilm, Frank; Culp, Kristyna; Dorney, Beverley
2003-01-01
Computer simulation modeling has evolved during the past twenty years into an effective tool for analyzing and planning ambulatory care facilities. This article explains the use of this tool in three case-study, ambulatory care settings--a GI lab, holding beds for a cardiac catheterization laboratory, and in emergency services. These examples also illustrate the use of three software packages currently available: MedModel, Simul8, and WITNESS. PMID:12545512
NASA Astrophysics Data System (ADS)
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10-4 Ha/Bohr.
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10^{-4} Ha/Bohr.
Loco, Daniele; Jurinovich, Sandro; Di Bari, Lorenzo; Mennucci, Benedetta
2016-01-14
We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties. PMID:26646952
Development of highly accurate approximate scheme for computing the charge transfer integral.
Pershin, Anton; Szalay, Péter G
2015-08-21
The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the "exact" scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the "exact" calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature. PMID:26298117
Development of highly accurate approximate scheme for computing the charge transfer integral
Pershin, Anton; Szalay, Péter G.
2015-08-21
The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the “exact” scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the “exact” calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.
A fast and accurate simulator for the design of birdcage coils in MRI.
Giovannetti, Giulio; Landini, Luigi; Santarelli, Maria Filomena; Positano, Vincenzo
2002-11-01
The birdcage coils are extensively used in MRI systems since they introduce a high signal to noise ratio and a high radiofrequency magnetic field homogeneity that guarantee a large field of view. The present article describes the implementation of a birdcage coil simulator, operating in high-pass and low-pass modes, using magnetostatic analysis of the coil. Respect to other simulators described in literature, our simulator allows to obtain in short time not only the dominant frequency mode, but also the complete resonant frequency spectrum and the relevant magnetic field pattern with high accuracy. Our simulator accounts for all the inductances including the mutual inductances between conductors. Moreover, the inductance calculation includes an accurately birdcage geometry description and the effect of a radiofrequency shield. The knowledge of all the resonance modes introduced by a birdcage coil is twofold useful during birdcage coil design: --higher order modes should be pushed far from the fundamental one, --for particular applications, it is necessary to localize other resonant modes (as the Helmholtz mode) jointly to the dominant mode. The knowledge of the magnetic field pattern allows to a priori verify the field homogeneity created inside the coil, when varying the coil dimension and mainly the number of the coil legs. The coil is analyzed using equivalent circuit method. Finally, the simulator is validated by implementing a low-pass birdcage coil and comparing our data with the literature. PMID:12413563
NASA Astrophysics Data System (ADS)
Jiang, Xikai; Karpeev, Dmitry; Li, Jiyuan; de Pablo, Juan; Hernandez-Ortiz, Juan; Heinonen, Olle
Boundary integrals arise in many electrostatic and magnetostatic problems. In computational modeling of these problems, although the integral is performed only on the boundary of a domain, its direct evaluation needs O(N2) operations, where N is number of unknowns on the boundary. The O(N2) scaling impedes a wider usage of the boundary integral method in scientific and engineering communities. We have developed a parallel computational approach that utilize the Fast Multipole Method to evaluate the boundary integral in O(N) operations. To demonstrate the accuracy, efficiency, and scalability of our approach, we consider two test cases. In the first case, we solve a boundary value problem for a ferroelectric/ferromagnetic volume in free space using a hybrid finite element-boundary integral method. In the second case, we solve an electrostatic problem involving the polarization of dielectric objects in free space using the boundary element method. The results from test cases show that our parallel approach can enable highly efficient and accurate simulations of mesoscale electrostatic/magnetostatic problems. Computing resources was provided by Blues, a high-performance cluster operated by the Laboratory Computing Resource Center at Argonne National Laboratory. Work at Argonne was supported by U. S. DOE, Office of Science under Contract No. DE-AC02-06CH11357.
Perspective: Computer simulations of long time dynamics.
Elber, Ron
2016-02-14
Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473
Perspective: Computer simulations of long time dynamics
Elber, Ron
2016-01-01
Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473
Accurate Time-Dependent Traveling-Wave Tube Model Developed for Computational Bit-Error-Rate Testing
NASA Technical Reports Server (NTRS)
Kory, Carol L.
2001-01-01
The phenomenal growth of the satellite communications industry has created a large demand for traveling-wave tubes (TWT's) operating with unprecedented specifications requiring the design and production of many novel devices in record time. To achieve this, the TWT industry heavily relies on computational modeling. However, the TWT industry's computational modeling capabilities need to be improved because there are often discrepancies between measured TWT data and that predicted by conventional two-dimensional helical TWT interaction codes. This limits the analysis and design of novel devices or TWT's with parameters differing from what is conventionally manufactured. In addition, the inaccuracy of current computational tools limits achievable TWT performance because optimized designs require highly accurate models. To address these concerns, a fully three-dimensional, time-dependent, helical TWT interaction model was developed using the electromagnetic particle-in-cell code MAFIA (Solution of MAxwell's equations by the Finite-Integration-Algorithm). The model includes a short section of helical slow-wave circuit with excitation fed by radiofrequency input/output couplers, and an electron beam contained by periodic permanent magnet focusing. A cutaway view of several turns of the three-dimensional helical slow-wave circuit with input/output couplers is shown. This has been shown to be more accurate than conventionally used two-dimensional models. The growth of the communications industry has also imposed a demand for increased data rates for the transmission of large volumes of data. To achieve increased data rates, complex modulation and multiple access techniques are employed requiring minimum distortion of the signal as it is passed through the TWT. Thus, intersymbol interference (ISI) becomes a major consideration, as well as suspected causes such as reflections within the TWT. To experimentally investigate effects of the physical TWT on ISI would be
Maudlin, P.J.; Stout, M.G.
1996-09-01
Strength and fracture constitutive relationships containing strain rate dependence and thermal softening are important for accurate simulation of metal cutting. The mechanical behavior of a hardened 4340 steel was characterized using the von Mises yield function, the Mechanical Threshold Stress model and the Johnson- Cook fracture model. This constitutive description was implemented into the explicit Lagrangian FEM continuum-mechanics code EPIC, and orthogonal plane-strain metal cutting calculations were performed. Heat conduction and friction at the toolwork-piece interface were included in the simulations. These transient calculations were advanced in time until steady state machining behavior (force) was realized. Experimental cutting force data (cutting and thrust forces) were measured for a planning operation and compared to the calculations. 13 refs., 6 figs.
Uncertainty and error in computational simulations
Oberkampf, W.L.; Diegert, K.V.; Alvin, K.F.; Rutherford, B.M.
1997-10-01
The present paper addresses the question: ``What are the general classes of uncertainty and error sources in complex, computational simulations?`` This is the first step of a two step process to develop a general methodology for quantitatively estimating the global modeling and simulation uncertainty in computational modeling and simulation. The second step is to develop a general mathematical procedure for representing, combining and propagating all of the individual sources through the simulation. The authors develop a comprehensive view of the general phases of modeling and simulation. The phases proposed are: conceptual modeling of the physical system, mathematical modeling of the system, discretization of the mathematical model, computer programming of the discrete model, numerical solution of the model, and interpretation of the results. This new view is built upon combining phases recognized in the disciplines of operations research and numerical solution methods for partial differential equations. The characteristics and activities of each of these phases is discussed in general, but examples are given for the fields of computational fluid dynamics and heat transfer. They argue that a clear distinction should be made between uncertainty and error that can arise in each of these phases. The present definitions for uncertainty and error are inadequate and. therefore, they propose comprehensive definitions for these terms. Specific classes of uncertainty and error sources are then defined that can occur in each phase of modeling and simulation. The numerical sources of error considered apply regardless of whether the discretization procedure is based on finite elements, finite volumes, or finite differences. To better explain the broad types of sources of uncertainty and error, and the utility of their categorization, they discuss a coupled-physics example simulation.
Simulating physical phenomena with a quantum computer
NASA Astrophysics Data System (ADS)
Ortiz, Gerardo
2003-03-01
In a keynote speech at MIT in 1981 Richard Feynman raised some provocative questions in connection to the exact simulation of physical systems using a special device named a ``quantum computer'' (QC). At the time it was known that deterministic simulations of quantum phenomena in classical computers required a number of resources that scaled exponentially with the number of degrees of freedom, and also that the probabilistic simulation of certain quantum problems were limited by the so-called sign or phase problem, a problem believed to be of exponential complexity. Such a QC was intended to mimick physical processes exactly the same as Nature. Certainly, remarks coming from such an influential figure generated widespread interest in these ideas, and today after 21 years there are still some open questions. What kind of physical phenomena can be simulated with a QC?, How?, and What are its limitations? Addressing and attempting to answer these questions is what this talk is about. Definitively, the goal of physics simulation using controllable quantum systems (``physics imitation'') is to exploit quantum laws to advantage, and thus accomplish efficient imitation. Fundamental is the connection between a quantum computational model and a physical system by transformations of operator algebras. This concept is a necessary one because in Quantum Mechanics each physical system is naturally associated with a language of operators and thus can be considered as a possible model of quantum computation. The remarkable result is that an arbitrary physical system is naturally simulatable by another physical system (or QC) whenever a ``dictionary'' between the two operator algebras exists. I will explain these concepts and address some of Feynman's concerns regarding the simulation of fermionic systems. Finally, I will illustrate the main ideas by imitating simple physical phenomena borrowed from condensed matter physics using quantum algorithms, and present experimental
Numerical Simulation of the 2004 Indian Ocean Tsunami: Accurate Flooding and drying in Banda Aceh
NASA Astrophysics Data System (ADS)
Cui, Haiyang; Pietrzak, Julie; Stelling, Guus; Androsov, Alexey; Harig, Sven
2010-05-01
The Indian Ocean Tsunami on December 26, 2004 caused one of the largest tsunamis in recent times and led to widespread devastation and loss of life. One of the worst hit regions was Banda Aceh, which is the capital of the Aceh province, located in the northern part of Sumatra, 150km from the source of the earthquake. A German-Indonesian Tsunami Early Warning System (GITEWS) (www.gitews.de) is currently under active development. The work presented here is carried out within the GITEWS framework. One of the aims of this project is the development of accurate models with which to simulate the propagation, flooding and drying, and run-up of a tsunami. In this context, TsunAWI has been developed by the Alfred Wegener Institute; it is an explicit, () finite element model. However, the accurate numerical simulation of flooding and drying requires the conservation of mass and momentum. This is not possible in the current version of TsunAWi. The P1NC - P1element guarantees mass conservation in a global sense, yet as we show here it is important to guarantee mass conservation at the local level, that is within each individual cell. Here an unstructured grid, finite volume ocean model is presented. It is derived from the P1NC - P1 element, and is shown to be mass and momentum conserving. Then a number of simulations are presented, including dam break problems flooding over both a wet and a dry bed. Excellent agreement is found. Then we present simulations for Banda Aceh, and compare the results to on-site survey data, as well as to results from the original TsunAWI code.
Quantitative computer simulations of extraterrestrial processing operations
NASA Technical Reports Server (NTRS)
Vincent, T. L.; Nikravesh, P. E.
1989-01-01
The automation of a small, solid propellant mixer was studied. Temperature control is under investigation. A numerical simulation of the system is under development and will be tested using different control options. Control system hardware is currently being put into place. The construction of mathematical models and simulation techniques for understanding various engineering processes is also studied. Computer graphics packages were utilized for better visualization of the simulation results. The mechanical mixing of propellants is examined. Simulation of the mixing process is being done to study how one can control for chaotic behavior to meet specified mixing requirements. An experimental mixing chamber is also being built. It will allow visual tracking of particles under mixing. The experimental unit will be used to test ideas from chaos theory, as well as to verify simulation results. This project has applications to extraterrestrial propellant quality and reliability.
Computer simulation of screw dislocation in aluminum
NASA Technical Reports Server (NTRS)
Esterling, D. M.
1976-01-01
The atomic structure in a 110 screw dislocation core for aluminum is obtained by computer simulation. The lattice statics technique is employed since it entails no artificially imposed elastic boundary around the defect. The interatomic potential has no adjustable parameters and was derived from pseudopotential theory. The resulting atomic displacements were allowed to relax in all three dimensions.
Eliminating Computational Instability In Multibody Simulations
NASA Technical Reports Server (NTRS)
Watts, Gaines L.
1994-01-01
TWOBODY implements improved version of Lagrange multiplier method. Program ultilizes programming technique eliminating computational instability in multibody simulations in which Lagrange multipliers used. In technique, one uses constraint equations, instead of integration, to determine coordinates that are not independent. To illustrate technique, it includes simple mathematical model of solid rocket booster and parachute connected by frictionless swivel. Written in FORTRAN 77.
Macromod: Computer Simulation For Introductory Economics
ERIC Educational Resources Information Center
Ross, Thomas
1977-01-01
The Macroeconomic model (Macromod) is a computer assisted instruction simulation model designed for introductory economics courses. An evaluation of its utilization at a community college indicates that it yielded a 10 percent to 13 percent greater economic comprehension than lecture classes and that it met with high student approval. (DC)
Designing Online Scaffolds for Interactive Computer Simulation
ERIC Educational Resources Information Center
Chen, Ching-Huei; Wu, I-Chia; Jen, Fen-Lan
2013-01-01
The purpose of this study was to examine the effectiveness of online scaffolds in computer simulation to facilitate students' science learning. We first introduced online scaffolds to assist and model students' science learning and to demonstrate how a system embedded with online scaffolds can be designed and implemented to help high…
Assessing Moderator Variables: Two Computer Simulation Studies.
ERIC Educational Resources Information Center
Mason, Craig A.; And Others
1996-01-01
A strategy is proposed for conceptualizing moderating relationships based on their type (strictly correlational and classically correlational) and form, whether continuous, noncontinuous, logistic, or quantum. Results of computer simulations comparing three statistical approaches for assessing moderator variables are presented, and advantages of…
Decision Making in Computer-Simulated Experiments.
ERIC Educational Resources Information Center
Suits, J. P.; Lagowski, J. J.
A set of interactive, computer-simulated experiments was designed to respond to the large range of individual differences in aptitude and reasoning ability generally exhibited by students enrolled in first-semester general chemistry. These experiments give students direct experience in the type of decision making needed in an experimental setting.…
Progress in Computational Simulation of Earthquakes
NASA Technical Reports Server (NTRS)
Donnellan, Andrea; Parker, Jay; Lyzenga, Gregory; Judd, Michele; Li, P. Peggy; Norton, Charles; Tisdale, Edwin; Granat, Robert
2006-01-01
GeoFEST(P) is a computer program written for use in the QuakeSim project, which is devoted to development and improvement of means of computational simulation of earthquakes. GeoFEST(P) models interacting earthquake fault systems from the fault-nucleation to the tectonic scale. The development of GeoFEST( P) has involved coupling of two programs: GeoFEST and the Pyramid Adaptive Mesh Refinement Library. GeoFEST is a message-passing-interface-parallel code that utilizes a finite-element technique to simulate evolution of stress, fault slip, and plastic/elastic deformation in realistic materials like those of faulted regions of the crust of the Earth. The products of such simulations are synthetic observable time-dependent surface deformations on time scales from days to decades. Pyramid Adaptive Mesh Refinement Library is a software library that facilitates the generation of computational meshes for solving physical problems. In an application of GeoFEST(P), a computational grid can be dynamically adapted as stress grows on a fault. Simulations on workstations using a few tens of thousands of stress and displacement finite elements can now be expanded to multiple millions of elements with greater than 98-percent scaled efficiency on over many hundreds of parallel processors (see figure).
Computation applied to particle accelerator simulations
Herrmannsfeldt, W.B. ); Yan, Y.T. )
1991-07-01
The rapid growth in the power of large-scale computers has had a revolutionary effect on the study of charged-particle accelerators that is similar to the impact of smaller computers on everyday life. Before an accelerator is built, it is now the absolute rule to simulate every component and subsystem by computer to establish modes of operation and tolerances. We will bypass the important and fruitful areas of control and operation and consider only application to design and diagnostic interpretation. Applications of computers can be divided into separate categories including: component design, system design, stability studies, cost optimization, and operating condition simulation. For the purposes of this report, we will choose a few examples taken from the above categories to illustrate the methods and we will discuss the significance of the work to the project, and also briefly discuss the accelerator project itself. The examples that will be discussed are: (1) the tracking analysis done for the main ring of the Superconducting Supercollider, which contributed to the analysis which ultimately resulted in changing the dipole coil diameter to 5 cm from the earlier design for a 4-cm coil-diameter dipole magnet; (2) the design of accelerator structures for electron-positron linear colliders and circular colliding beam systems (B-factories); (3) simulation of the wake fields from multibunch electron beams for linear colliders; and (4) particle-in-cell simulation of space-charge dominated beams for an experimental liner induction accelerator for Heavy Ion Fusion. 8 refs., 9 figs.
Factors Promoting Engaged Exploration with Computer Simulations
ERIC Educational Resources Information Center
Podolefsky, Noah S.; Perkins, Katherine K.; Adams, Wendy K.
2010-01-01
This paper extends prior research on student use of computer simulations (sims) to engage with and explore science topics, in this case wave interference. We describe engaged exploration; a process that involves students actively interacting with educational materials, sense making, and exploring primarily via their own questioning. We analyze…
Spiking network simulation code for petascale computers.
Kunkel, Susanne; Schmidt, Maximilian; Eppler, Jochen M; Plesser, Hans E; Masumoto, Gen; Igarashi, Jun; Ishii, Shin; Fukai, Tomoki; Morrison, Abigail; Diesmann, Markus; Helias, Moritz
2014-01-01
Brain-scale networks exhibit a breathtaking heterogeneity in the dynamical properties and parameters of their constituents. At cellular resolution, the entities of theory are neurons and synapses and over the past decade researchers have learned to manage the heterogeneity of neurons and synapses with efficient data structures. Already early parallel simulation codes stored synapses in a distributed fashion such that a synapse solely consumes memory on the compute node harboring the target neuron. As petaflop computers with some 100,000 nodes become increasingly available for neuroscience, new challenges arise for neuronal network simulation software: Each neuron contacts on the order of 10,000 other neurons and thus has targets only on a fraction of all compute nodes; furthermore, for any given source neuron, at most a single synapse is typically created on any compute node. From the viewpoint of an individual compute node, the heterogeneity in the synaptic target lists thus collapses along two dimensions: the dimension of the types of synapses and the dimension of the number of synapses of a given type. Here we present a data structure taking advantage of this double collapse using metaprogramming techniques. After introducing the relevant scaling scenario for brain-scale simulations, we quantitatively discuss the performance on two supercomputers. We show that the novel architecture scales to the largest petascale supercomputers available today. PMID:25346682