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

NASA Technical Reports Server (NTRS)

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

2015-01-01

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

Compact Method for Modeling and Simulation of Memristor Devices

DTIC Science & Technology

2011-08-01

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

Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal.

PubMed

Shibuta, Yasushi; Sakane, Shinji; Miyoshi, Eisuke; Okita, Shin; Takaki, Tomohiro; Ohno, Munekazu

2017-04-05

Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue. Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi-graphics processing unit parallel computation combined with the rapid progress in high-performance computational environments.Nucleation is a fundamental physical process, however it is a long-standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion-atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.

Using a Commercial Simulator to Teach Sorption Separations

ERIC Educational Resources Information Center

Wankat, Phillip C.

2006-01-01

The commercial simulator Aspen Chromatography was used in the computer laboratory of a dual-level course. The lab assignments used a cookbook approach to teach basic simulator operation and open-ended exploration to understand adsorption. The students learned theory better than in previous years despite having less lecture time. Students agreed…

CUDA-based real time surgery simulation.

PubMed

Liu, Youquan; De, Suvranu

2008-01-01

In this paper we present a general software platform that enables real time surgery simulation on the newly available compute unified device architecture (CUDA)from NVIDIA. CUDA-enabled GPUs harness the power of 128 processors which allow data parallel computations. Compared to the previous GPGPU, it is significantly more flexible with a C language interface. We report implementation of both collision detection and consequent deformation computation algorithms. Our test results indicate that the CUDA enables a twenty times speedup for collision detection and about fifteen times speedup for deformation computation on an Intel Core 2 Quad 2.66 GHz machine with GeForce 8800 GTX.

Simulation of Nonlinear Instabilities in an Attachment-Line Boundary Layer

NASA Technical Reports Server (NTRS)

Joslin, Ronald D.

1996-01-01

The linear and the nonlinear stability of disturbances that propagate along the attachment line of a three-dimensional boundary layer is considered. The spatially evolving disturbances in the boundary layer are computed by direct numerical simulation (DNS) of the unsteady, incompressible Navier-Stokes equations. Disturbances are introduced either by forcing at the in ow or by applying suction and blowing at the wall. Quasi-parallel linear stability theory and a nonparallel theory yield notably different stability characteristics for disturbances near the critical Reynolds number; the DNS results con rm the latter theory. Previously, a weakly nonlinear theory and computations revealed a high wave-number region of subcritical disturbance growth. More recent computations have failed to achieve this subcritical growth. The present computational results indicate the presence of subcritically growing disturbances; the results support the weakly nonlinear theory. Furthermore, an explanation is provided for the previous theoretical and computational discrepancy. In addition, the present results demonstrate that steady suction can be used to stabilize disturbances that otherwise grow subcritically along the attachment line.

Design analysis and computer-aided performance evaluation of shuttle orbiter electrical power system. Volume 1: Summary

NASA Technical Reports Server (NTRS)

1974-01-01

Studies were conducted to develop appropriate space shuttle electrical power distribution and control (EPDC) subsystem simulation models and to apply the computer simulations to systems analysis of the EPDC. A previously developed software program (SYSTID) was adapted for this purpose. The following objectives were attained: (1) significant enhancement of the SYSTID time domain simulation software, (2) generation of functionally useful shuttle EPDC element models, and (3) illustrative simulation results in the analysis of EPDC performance, under the conditions of fault, current pulse injection due to lightning, and circuit protection sizing and reaction times.

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

Boundary conditions for simulating large SAW devices using ANSYS.

PubMed

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

2010-08-01

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

Surrogates for numerical simulations; optimization of eddy-promoter heat exchangers

NASA Technical Reports Server (NTRS)

Patera, Anthony T.; Patera, Anthony

1993-01-01

Although the advent of fast and inexpensive parallel computers has rendered numerous previously intractable calculations feasible, many numerical simulations remain too resource-intensive to be directly inserted in engineering optimization efforts. An attractive alternative to direct insertion considers models for computational systems: the expensive simulation is evoked only to construct and validate a simplified, input-output model; this simplified input-output model then serves as a simulation surrogate in subsequent engineering optimization studies. A simple 'Bayesian-validated' statistical framework for the construction, validation, and purposive application of static computer simulation surrogates is presented. As an example, dissipation-transport optimization of laminar-flow eddy-promoter heat exchangers are considered: parallel spectral element Navier-Stokes calculations serve to construct and validate surrogates for the flowrate and Nusselt number; these surrogates then represent the originating Navier-Stokes equations in the ensuing design process.

Generalized Maintenance Trainer Simulator: Development of Hardware and Software. Final Report.

ERIC Educational Resources Information Center

Towne, Douglas M.; Munro, Allen

A general purpose maintenance trainer, which has the potential to simulate a wide variety of electronic equipments without hardware changes or new computer programs, has been developed and field tested by the Navy. Based on a previous laboratory model, the Generalized Maintenance Trainer Simulator (GMTS) is a relatively low cost trainer that…

Practical Unitary Simulator for Non-Markovian Complex Processes

NASA Astrophysics Data System (ADS)

Binder, Felix C.; Thompson, Jayne; Gu, Mile

2018-06-01

Stochastic processes are as ubiquitous throughout the quantitative sciences as they are notorious for being difficult to simulate and predict. In this Letter, we propose a unitary quantum simulator for discrete-time stochastic processes which requires less internal memory than any classical analogue throughout the simulation. The simulator's internal memory requirements equal those of the best previous quantum models. However, in contrast to previous models, it only requires a (small) finite-dimensional Hilbert space. Moreover, since the simulator operates unitarily throughout, it avoids any unnecessary information loss. We provide a stepwise construction for simulators for a large class of stochastic processes hence directly opening the possibility for experimental implementations with current platforms for quantum computation. The results are illustrated for an example process.

A computational modeling of semantic knowledge in reading comprehension: Integrating the landscape model with latent semantic analysis.

PubMed

Yeari, Menahem; van den Broek, Paul

2016-09-01

It is a well-accepted view that the prior semantic (general) knowledge that readers possess plays a central role in reading comprehension. Nevertheless, computational models of reading comprehension have not integrated the simulation of semantic knowledge and online comprehension processes under a unified mathematical algorithm. The present article introduces a computational model that integrates the landscape model of comprehension processes with latent semantic analysis representation of semantic knowledge. In three sets of simulations of previous behavioral findings, the integrated model successfully simulated the activation and attenuation of predictive and bridging inferences during reading, as well as centrality estimations and recall of textual information after reading. Analyses of the computational results revealed new theoretical insights regarding the underlying mechanisms of the various comprehension phenomena.

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

NASA Astrophysics Data System (ADS)

Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

2014-01-01

Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

Relation of Parallel Discrete Event Simulation algorithms with physical models

NASA Astrophysics Data System (ADS)

Shchur, L. N.; Shchur, L. V.

2015-09-01

We extend concept of local simulation times in parallel discrete event simulation (PDES) in order to take into account architecture of the current hardware and software in high-performance computing. We shortly review previous research on the mapping of PDES on physical problems, and emphasise how physical results may help to predict parallel algorithms behaviour.

Coupling fast fluid dynamics and multizone airflow models in Modelica Buildings library to simulate the dynamics of HVAC systems

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

Tian, Wei; Sevilla, Thomas Alonso; Zuo, Wangda

Historically, multizone models are widely used in building airflow and energy performance simulations due to their fast computing speed. However, multizone models assume that the air in a room is well mixed, consequently limiting their application. In specific rooms where this assumption fails, the use of computational fluid dynamics (CFD) models may be an alternative option. Previous research has mainly focused on coupling CFD models and multizone models to study airflow in large spaces. While significant, most of these analyses did not consider the coupled simulation of the building airflow with the building's Heating, Ventilation, and Air-Conditioning (HVAC) systems. Thismore » paper tries to fill the gap by integrating the models for HVAC systems with coupled multizone and CFD simulations for airflows, using the Modelica simul ation platform. To improve the computational efficiency, we incorporated a simplified CFD model named fast fluid dynamics (FFD). We first introduce the data synchronization strategy and implementation in Modelica. Then, we verify the implementation using two case studies involving an isothermal and a non-isothermal flow by comparing model simulations to experiment data. Afterward, we study another three cases that are deemed more realistic. This is done by attaching a variable air volume (VAV) terminal box and a VAV system to previous flows to assess the capability of the models in studying the dynamic control of HVAC systems. Finally, we discuss further research needs on the coupled simulation using the models.« less

The ensemble switch method for computing interfacial tensions

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

Schmitz, Fabian; Virnau, Peter

2015-04-14

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

A Computational Study of the Flow Physics of Acoustic Liners

NASA Technical Reports Server (NTRS)

Tam, Christopher

2006-01-01

The present investigation is a continuation of a previous joint project between the Florida State University and the NASA Langley Research Center Liner Physics Team. In the previous project, a study of acoustic liners, in two dimensions, inside a normal incidence impedance tube was carried out. The study consisted of two parts. The NASA team was responsible for the experimental part of the project. This involved performing measurements in an impedance tube with a large aspect ratio slit resonator. The FSU team was responsible for the computation part of the project. This involved performing direct numerical simulation (DNS) of the NASA experiment in two dimensions using CAA methodology. It was agreed that upon completion of numerical simulation, the computed values of the liner impedance were to be sent to NASA for validation with experimental results. On following this procedure good agreements were found between numerical results and experimental measurements over a wide range of frequencies and sound-pressure-level. Broadband incident sound waves were also simulated numerically and measured experimentally. Overall, good agreements were also found.

Computer model to simulate testing at the National Transonic Facility

NASA Technical Reports Server (NTRS)

Mineck, Raymond E.; Owens, Lewis R., Jr.; Wahls, Richard A.; Hannon, Judith A.

1995-01-01

A computer model has been developed to simulate the processes involved in the operation of the National Transonic Facility (NTF), a large cryogenic wind tunnel at the Langley Research Center. The simulation was verified by comparing the simulated results with previously acquired data from three experimental wind tunnel test programs in the NTF. The comparisons suggest that the computer model simulates reasonably well the processes that determine the liquid nitrogen (LN2) consumption, electrical consumption, fan-on time, and the test time required to complete a test plan at the NTF. From these limited comparisons, it appears that the results from the simulation model are generally within about 10 percent of the actual NTF test results. The use of actual data acquisition times in the simulation produced better estimates of the LN2 usage, as expected. Additional comparisons are needed to refine the model constants. The model will typically produce optimistic results since the times and rates included in the model are typically the optimum values. Any deviation from the optimum values will lead to longer times or increased LN2 and electrical consumption for the proposed test plan. Computer code operating instructions and listings of sample input and output files have been included.

A study of application of remote sensing to river forecasting. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1975-01-01

A project is described whose goal was to define, implement and evaluate a pilot demonstration test to show the practicability of applying remotely sensed data to operational river forecasting in gaged or previously ungaged watersheds. A secondary objective was to provide NASA with documentation describing the computer programs that comprise the streamflow forecasting simulation model used. A computer-based simulation model was adapted to a streamflow forecasting application and implemented in an IBM System/360 Model 44 computer, operating in a dedicated mode, with operator interactive control through a Model 2250 keyboard/graphic CRT terminal. The test site whose hydrologic behavior was simulated is a small basin (365 square kilometers) designated Town Creek near Geraldine, Alabama.

Teaching and Learning with SimCity 2000.

ERIC Educational Resources Information Center

Adams, Paul C.

1998-01-01

Introduces "SimCity 2000," a computer simulation, as a tool for teaching urban geography. Argues that, combined with other activities, it can enhance computer literacy, geographical knowledge, and critical skills. Notes gender differences in students' previous exposure to the software; argues that instructors must consider this when…

Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model.

PubMed

Liu, Fang; Velikina, Julia V; Block, Walter F; Kijowski, Richard; Samsonov, Alexey A

2017-02-01

We present MRiLab, a new comprehensive simulator for large-scale realistic MRI simulations on a regular PC equipped with a modern graphical processing unit (GPU). MRiLab combines realistic tissue modeling with numerical virtualization of an MRI system and scanning experiment to enable assessment of a broad range of MRI approaches including advanced quantitative MRI methods inferring microstructure on a sub-voxel level. A flexible representation of tissue microstructure is achieved in MRiLab by employing the generalized tissue model with multiple exchanging water and macromolecular proton pools rather than a system of independent proton isochromats typically used in previous simulators. The computational power needed for simulation of the biologically relevant tissue models in large 3D objects is gained using parallelized execution on GPU. Three simulated and one actual MRI experiments were performed to demonstrate the ability of the new simulator to accommodate a wide variety of voxel composition scenarios and demonstrate detrimental effects of simplified treatment of tissue micro-organization adapted in previous simulators. GPU execution allowed  ∼ 200× improvement in computational speed over standard CPU. As a cross-platform, open-source, extensible environment for customizing virtual MRI experiments, MRiLab streamlines the development of new MRI methods, especially those aiming to infer quantitatively tissue composition and microstructure.

Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model

PubMed Central

Velikina, Julia V.; Block, Walter F.; Kijowski, Richard; Samsonov, Alexey A.

2017-01-01

We present MRiLab, a new comprehensive simulator for large-scale realistic MRI simulations on a regular PC equipped with a modern graphical processing unit (GPU). MRiLab combines realistic tissue modeling with numerical virtualization of an MRI system and scanning experiment to enable assessment of a broad range of MRI approaches including advanced quantitative MRI methods inferring microstructure on a sub-voxel level. A flexibl representation of tissue microstructure is achieved in MRiLab by employing the generalized tissue model with multiple exchanging water and macromolecular proton pools rather than a system of independent proton isochromats typically used in previous simulators. The computational power needed for simulation of the biologically relevant tissue models in large 3D objects is gained using parallelized execution on GPU. Three simulated and one actual MRI experiments were performed to demonstrate the ability of the new simulator to accommodate a wide variety of voxel composition scenarios and demonstrate detrimental effects of simplifie treatment of tissue micro-organization adapted in previous simulators. GPU execution allowed ∼200× improvement in computational speed over standard CPU. As a cross-platform, open-source, extensible environment for customizing virtual MRI experiments, MRiLab streamlines the development of new MRI methods, especially those aiming to infer quantitatively tissue composition and microstructure. PMID:28113746

Evaluation of the Virtual Squad Training System

DTIC Science & Technology

2010-01-01

ABSTRACT (Maximum 200 words): The Virtual Squad Training System ( VSTS ) is a network of nine individual immersive simulators with Helmet-Mounted...Displays (HMDs), and a command station for controlling computer generated entities. The VSTS includes both tethered and wearable simulators. The VSTS was...affected Soldiers’ ratings of the VSTS . Simulator sickness incidence was low compared to previous evaluations of antecedent systems using HMDs

Simulation optimization of PSA-threshold based prostate cancer screening policies

PubMed Central

Zhang, Jingyu; Denton, Brian T.; Shah, Nilay D.; Inman, Brant A.

2013-01-01

We describe a simulation optimization method to design PSA screening policies based on expected quality adjusted life years (QALYs). Our method integrates a simulation model in a genetic algorithm which uses a probabilistic method for selection of the best policy. We present computational results about the efficiency of our algorithm. The best policy generated by our algorithm is compared to previously recommended screening policies. Using the policies determined by our model, we present evidence that patients should be screened more aggressively but for a shorter length of time than previously published guidelines recommend. PMID:22302420

Remediating Physics Misconceptions Using an Analogy-Based Computer Tutor. Draft.

ERIC Educational Resources Information Center

Murray, Tom; And Others

Described is a computer tutor designed to help students gain a qualitative understanding of important physics concepts. The tutor simulates a teaching strategy called "bridging analogies" that previous research has demonstrated to be successful in one-on-one tutoring and written explanation studies. The strategy is designed to remedy…

Identifying Secondary-School Students' Difficulties When Reading Visual Representations Displayed in Physics Simulations

ERIC Educational Resources Information Center

López, Víctor; Pintó, Roser

2017-01-01

Computer simulations are often considered effective educational tools, since their visual and communicative power enable students to better understand physical systems and phenomena. However, previous studies have found that when students read visual representations some reading difficulties can arise, especially when these are complex or dynamic…

A simulation study of homogeneous ice nucleation in supercooled salty water

NASA Astrophysics Data System (ADS)

Soria, Guiomar D.; Espinosa, Jorge R.; Ramirez, Jorge; Valeriani, Chantal; Vega, Carlos; Sanz, Eduardo

2018-06-01

We use computer simulations to investigate the effect of salt on homogeneous ice nucleation. The melting point of the employed solution model was obtained both by direct coexistence simulations and by thermodynamic integration from previous calculations of the water chemical potential. Using a seeding approach, in which we simulate ice seeds embedded in a supercooled aqueous solution, we compute the nucleation rate as a function of temperature for a 1.85 NaCl mol per water kilogram solution at 1 bar. To improve the accuracy and reliability of our calculations, we combine seeding with the direct computation of the ice-solution interfacial free energy at coexistence using the Mold Integration method. We compare the results with previous simulation work on pure water to understand the effect caused by the solute. The model captures the experimental trend that the nucleation rate at a given supercooling decreases when adding salt. Despite the fact that the thermodynamic driving force for ice nucleation is higher for salty water for a given supercooling, the nucleation rate slows down with salt due to a significant increase of the ice-fluid interfacial free energy. The salty water model predicts an ice nucleation rate that is in good agreement with experimental measurements, bringing confidence in the predictive ability of the model. We expect that the combination of state-of-the-art simulation methods here employed to study ice nucleation from solution will be of much use in forthcoming numerical investigations of crystallization in mixtures.

A simulation study of homogeneous ice nucleation in supercooled salty water.

PubMed

Soria, Guiomar D; Espinosa, Jorge R; Ramirez, Jorge; Valeriani, Chantal; Vega, Carlos; Sanz, Eduardo

2018-06-14

We use computer simulations to investigate the effect of salt on homogeneous ice nucleation. The melting point of the employed solution model was obtained both by direct coexistence simulations and by thermodynamic integration from previous calculations of the water chemical potential. Using a seeding approach, in which we simulate ice seeds embedded in a supercooled aqueous solution, we compute the nucleation rate as a function of temperature for a 1.85 NaCl mol per water kilogram solution at 1 bar. To improve the accuracy and reliability of our calculations, we combine seeding with the direct computation of the ice-solution interfacial free energy at coexistence using the Mold Integration method. We compare the results with previous simulation work on pure water to understand the effect caused by the solute. The model captures the experimental trend that the nucleation rate at a given supercooling decreases when adding salt. Despite the fact that the thermodynamic driving force for ice nucleation is higher for salty water for a given supercooling, the nucleation rate slows down with salt due to a significant increase of the ice-fluid interfacial free energy. The salty water model predicts an ice nucleation rate that is in good agreement with experimental measurements, bringing confidence in the predictive ability of the model. We expect that the combination of state-of-the-art simulation methods here employed to study ice nucleation from solution will be of much use in forthcoming numerical investigations of crystallization in mixtures.

Synapse-Centric Mapping of Cortical Models to the SpiNNaker Neuromorphic Architecture

PubMed Central

Knight, James C.; Furber, Steve B.

2016-01-01

While the adult human brain has approximately 8.8 × 1010 neurons, this number is dwarfed by its 1 × 1015 synapses. From the point of view of neuromorphic engineering and neural simulation in general this makes the simulation of these synapses a particularly complex problem. SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Current solutions for simulating spiking neural networks on SpiNNaker are heavily inspired by work on distributed high-performance computing. However, while SpiNNaker shares many characteristics with such distributed systems, its component nodes have much more limited resources and, as the system lacks global synchronization, the computation performed on each node must complete within a fixed time step. We first analyze the performance of the current SpiNNaker neural simulation software and identify several problems that occur when it is used to simulate networks of the type often used to model the cortex which contain large numbers of sparsely connected synapses. We then present a new, more flexible approach for mapping the simulation of such networks to SpiNNaker which solves many of these problems. Finally we analyze the performance of our new approach using both benchmarks, designed to represent cortical connectivity, and larger, functional cortical models. In a benchmark network where neurons receive input from 8000 STDP synapses, our new approach allows 4× more neurons to be simulated on each SpiNNaker core than has been previously possible. We also demonstrate that the largest plastic neural network previously simulated on neuromorphic hardware can be run in real time using our new approach: double the speed that was previously achieved. Additionally this network contains two types of plastic synapse which previously had to be trained separately but, using our new approach, can be trained simultaneously. PMID:27683540

Slat Cove Unsteadiness Effect of 3D Flow Structures

NASA Technical Reports Server (NTRS)

Choudhari, Meelan M.; Khorrami, Mehdi R.

2006-01-01

Previous studies have indicated that 2D, time accurate computations based on a pseudo-laminar zonal model of the slat cove region (within the framework of the Reynolds-Averaged Navier-Stokes equations) are inadequate for predicting the full unsteady dynamics of the slat cove flow field. Even though such computations could capture the large-scale, unsteady vorticity structures in the slat cove region without requiring any external forcing, the simulated vortices were excessively strong and the recirculation zone was unduly energetic in comparison with the PIV measurements for a generic high-lift configuration. To resolve this discrepancy and to help enable physics based predictions of slat aeroacoustics, the present paper is focused on 3D simulations of the slat cove flow over a computational domain of limited spanwise extent. Maintaining the pseudo-laminar approach, current results indicate that accounting for the three-dimensionality of flow fluctuations leads to considerable improvement in the accuracy of the unsteady, nearfield solution. Analysis of simulation data points to the likely significance of turbulent fluctuations near the reattachment region toward the generation of broadband slat noise. The computed acoustic characteristics (in terms of the frequency spectrum and spatial distribution) within short distances from the slat resemble the previously reported, subscale measurements of slat noise.

Discharge Chamber Primary Electron Modeling Activities in Three-Dimensions

NASA Technical Reports Server (NTRS)

Steuber, Thomas J.

2004-01-01

Designing discharge chambers for ion thrusters involves many geometric configuration decisions. Various decisions will impact discharge chamber performance with respect to propellant utilization efficiency, ion production costs, and grid lifetime. These hardware design decisions can benefit from the assistance of computational modeling. Computational modeling for discharge chambers has been limited to two-dimensional codes that leveraged symmetry for interpretation into three-dimensional analysis. This paper presents model development activities towards a three-dimensional discharge chamber simulation to aid discharge chamber design decisions. Specifically, of the many geometric configuration decisions toward attainment of a worthy discharge chamber, this paper focuses on addressing magnetic circuit considerations with a three-dimensional discharge chamber simulation as a tool. With this tool, candidate discharge chamber magnetic circuit designs can be analyzed computationally to gain insight into factors that may influence discharge chamber performance such as: primary electron loss width in magnetic cusps, cathode tip position with respect to the low magnetic field volume, definition of a low magnetic field region, and maintenance of a low magnetic field region across the grid span. Corroborating experimental data will be obtained from mockup hardware tests. Initially, simulated candidate magnetic circuit designs will resemble previous successful thruster designs. To provide opportunity to improve beyond previous performance benchmarks, off-design modifications will be simulated and experimentally tested.

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

NASA Astrophysics Data System (ADS)

Czerepicki, A.; Koniak, M.

2017-06-01

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

Investigation on aerodynamic characteristics of baseline-II E-2 blended wing-body aircraft with canard via computational simulation

NASA Astrophysics Data System (ADS)

Nasir, Rizal E. M.; Ali, Zurriati; Kuntjoro, Wahyu; Wisnoe, Wirachman

2012-06-01

Previous wind tunnel test has proven the improved aerodynamic charasteristics of Baseline-II E-2 Blended Wing-Body (BWB) aircraft studied in Universiti Teknologi Mara. The E-2 is a version of Baseline-II BWB with modified outer wing and larger canard, solely-designed to gain favourable longitudinal static stability during flight. This paper highlights some results from current investigation on the said aircraft via computational fluid dynamics simulation as a mean to validate the wind tunnel test results. The simulation is conducted based on standard one-equation turbulence, Spalart-Allmaras model with polyhedral mesh. The ambience of the flight simulation is made based on similar ambience of wind tunnel test. The simulation shows lift, drag and moment results to be near the values found in wind tunnel test but only within angles of attack where the lift change is linear. Beyond the linear region, clear differences between computational simulation and wind tunnel test results are observed. It is recommended that different type of mathematical model be used to simulate flight conditions beyond linear lift region.

A computational approach for hypersonic nonequilibrium radiation utilizing space partition algorithm and Gauss quadrature

NASA Astrophysics Data System (ADS)

Shang, J. S.; Andrienko, D. A.; Huang, P. G.; Surzhikov, S. T.

2014-06-01

An efficient computational capability for nonequilibrium radiation simulation via the ray tracing technique has been accomplished. The radiative rate equation is iteratively coupled with the aerodynamic conservation laws including nonequilibrium chemical and chemical-physical kinetic models. The spectral properties along tracing rays are determined by a space partition algorithm of the nearest neighbor search process, and the numerical accuracy is further enhanced by a local resolution refinement using the Gauss-Lobatto polynomial. The interdisciplinary governing equations are solved by an implicit delta formulation through the diminishing residual approach. The axisymmetric radiating flow fields over the reentry RAM-CII probe have been simulated and verified with flight data and previous solutions by traditional methods. A computational efficiency gain nearly forty times is realized over that of the existing simulation procedures.

Digital multishaker modal testing

NASA Technical Reports Server (NTRS)

Blair, M.; Craig, R. R., Jr.

1983-01-01

A review of several modal testing techniques is made, along with brief discussions of their advantages and limitations. A new technique is presented which overcomes many of the previous limitations. Several simulated experiments are included to verify the validity and accuracy of the new method. Conclusions are drawn from the simulation studies and recommendations for further work are presented. The complete computer code configured for the simulation study is presented.

Interval sampling methods and measurement error: a computer simulation.

PubMed

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

2014-01-01

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

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

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

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

2015-03-28

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

Duality quantum algorithm efficiently simulates open quantum systems

PubMed Central

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

2016-01-01

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

A physics-based algorithm for real-time simulation of electrosurgery procedures in minimally invasive surgery.

PubMed

Lu, Zhonghua; Arikatla, Venkata S; Han, Zhongqing; Allen, Brian F; De, Suvranu

2014-12-01

High-frequency electricity is used in the majority of surgical interventions. However, modern computer-based training and simulation systems rely on physically unrealistic models that fail to capture the interplay of the electrical, mechanical and thermal properties of biological tissue. We present a real-time and physically realistic simulation of electrosurgery by modelling the electrical, thermal and mechanical properties as three iteratively solved finite element models. To provide subfinite-element graphical rendering of vaporized tissue, a dual-mesh dynamic triangulation algorithm based on isotherms is proposed. The block compressed row storage (BCRS) structure is shown to be critical in allowing computationally efficient changes in the tissue topology due to vaporization. We have demonstrated our physics-based electrosurgery cutting algorithm through various examples. Our matrix manipulation algorithms designed for topology changes have shown low computational cost. Our simulator offers substantially greater physical fidelity compared to previous simulators that use simple geometry-based heat characterization. Copyright © 2013 John Wiley & Sons, Ltd.

Enhancements to the Image Analysis Tool for Core Punch Experiments and Simulations (vs. 2014)

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

Hogden, John Edward; Unal, Cetin

A previous paper (Hogden & Unal, 2012, Image Analysis Tool for Core Punch Experiments and Simulations) described an image processing computer program developed at Los Alamos National Laboratory. This program has proven useful so developement has been continued. In this paper we describe enhacements to the program as of 2014.

Improving Decision Making Skill Using an Online Volcanic Crisis Simulation: Impact of Data Presentation Format

ERIC Educational Resources Information Center

Barclay, Elizabeth J.; Renshaw, Carl E.; Taylor, Holly A.; Bilge, A. Reyan

2011-01-01

Creating effective computer-based learning exercises requires an understanding of optimal user interface designs for improving higher order cognitive skills. Using an online volcanic crisis simulation previously shown to improve decision making skill, we find that a user interface using a graphical presentation of the volcano monitoring data…

Fusion Simulation Project Workshop Report

NASA Astrophysics Data System (ADS)

Kritz, Arnold; Keyes, David

2009-03-01

The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved 46 physicists, applied mathematicians and computer scientists, from 21 institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a 3-day workshop in May 2007.

Software for Simulating a Complex Robot

NASA Technical Reports Server (NTRS)

Goza, S. Michael

2003-01-01

RoboSim (Robot Simulation) is a computer program that simulates the poses and motions of the Robonaut a developmental anthropomorphic robot that has a complex system of joints with 43 degrees of freedom and multiple modes of operation and control. RoboSim performs a full kinematic simulation of all degrees of freedom. It also includes interface components that duplicate the functionality of the real Robonaut interface with control software and human operators. Basically, users see no difference between the real Robonaut and the simulation. Consequently, new control algorithms can be tested by computational simulation, without risk to the Robonaut hardware, and without using excessive Robonaut-hardware experimental time, which is always at a premium. Previously developed software incorporated into RoboSim includes Enigma (for graphical displays), OSCAR (for kinematical computations), and NDDS (for communication between the Robonaut and external software). In addition, RoboSim incorporates unique inverse-kinematical algorithms for chains of joints that have fewer than six degrees of freedom (e.g., finger joints). In comparison with the algorithms of OSCAR, these algorithms are more readily adaptable and provide better results when using equivalent sets of data.

Catastrophic Disruption of Asteroids: First Simulations with Explicit Formation of Spinning Rigid and Semi-rigid Aggregates

NASA Astrophysics Data System (ADS)

Michel, Patrick; Richardson, D. C.

2007-10-01

We have made major improvements in simulations of asteroid disruption by computing explicitly aggregate formations during the gravitational reaccumulation of small fragments, allowing us to obtain information on their spin and shape. First results will be presented taking as examples asteroid families that we reproduced successfully with previous less sophisticated simulations. In the last years, we have simulated successfully the formation of asteroid families using a SPH hydrocode to compute the fragmentation following the impact of a projectile on the parent body, and the N-body code pkdgrav to compute the mutual interactions of the fragments. We found that fragments generated by the disruption of a km-size asteroid can have large enough masses to be attracted by each other during their ejection. Consequently, many reaccumulations take place. Eventually most large fragments correspond to gravitational aggregates formed by reaccumulation of smaller ones. Moreover, formation of satellites occurs around the largest and other big remnants. In these previous simulations, when fragments reaccumulate, they merge into a single sphere whose mass is the sum of their masses. Thus, no information is obtained on the actual shape of the aggregates, their spin, ... For the first time, we have now simulated the disruption of a family parent body by computing explicitly the formation of aggregates, along with the above-mentioned properties. Once formed these aggregates can interact and/or collide with each other and break up during their evolution. We will present these first simulations and their possible implications on properties of asteroids generated by disruption. Results can for instance be compared with data provided by the Japanese space mission Hayabusa of the asteroid Itokawa, a body now understood to be a reaccumulated fragment from a larger parent body. Acknowledgments: PM and DCR acknowledge supports from the French Programme National de Planétologie and grants NSF AST0307549&AST0708110.

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

NASA Technical Reports Server (NTRS)

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

1974-01-01

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

Efficient and Extensible Quasi-Explicit Modular Nonlinear Multiscale Battery Model: GH-MSMD

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

Kim, Gi-Heon; Smith, Kandler; Lawrence-Simon, Jake

Complex physics and long computation time hinder the adoption of computer aided engineering models in the design of large-format battery cells and systems. A modular, efficient battery simulation model -- the multiscale multidomain (MSMD) model -- was previously introduced to aid the scale-up of Li-ion material and electrode designs to complete cell and pack designs, capturing electrochemical interplay with 3-D electronic current pathways and thermal response. Here, this paper enhances the computational efficiency of the MSMD model using a separation of time-scales principle to decompose model field variables. The decomposition provides a quasi-explicit linkage between the multiple length-scale domains andmore » thus reduces time-consuming nested iteration when solving model equations across multiple domains. In addition to particle-, electrode- and cell-length scales treated in the previous work, the present formulation extends to bus bar- and multi-cell module-length scales. We provide example simulations for several variants of GH electrode-domain models.« less

Efficient and Extensible Quasi-Explicit Modular Nonlinear Multiscale Battery Model: GH-MSMD

DOE PAGES

Kim, Gi-Heon; Smith, Kandler; Lawrence-Simon, Jake; ...

2017-03-24

Complex physics and long computation time hinder the adoption of computer aided engineering models in the design of large-format battery cells and systems. A modular, efficient battery simulation model -- the multiscale multidomain (MSMD) model -- was previously introduced to aid the scale-up of Li-ion material and electrode designs to complete cell and pack designs, capturing electrochemical interplay with 3-D electronic current pathways and thermal response. Here, this paper enhances the computational efficiency of the MSMD model using a separation of time-scales principle to decompose model field variables. The decomposition provides a quasi-explicit linkage between the multiple length-scale domains andmore » thus reduces time-consuming nested iteration when solving model equations across multiple domains. In addition to particle-, electrode- and cell-length scales treated in the previous work, the present formulation extends to bus bar- and multi-cell module-length scales. We provide example simulations for several variants of GH electrode-domain models.« less

Computational Design of a Thermostable Mutant of Cocaine Esterase via Molecular Dynamics Simulations

PubMed Central

Huang, Xiaoqin; Gao, Daquan; Zhan, Chang-Guo

2015-01-01

Cocaine esterase (CocE) has been known as the most efficient native enzyme for metabolizing the naturally occurring cocaine. A major obstacle to the clinical application of CocE is the thermoinstability of native CocE with a half-life of only ~11 min at physiological temperature (37°C). It is highly desirable to develop a thermostable mutant of CocE for therapeutic treatment of cocaine overdose and addiction. To establish a structure-thermostability relationship, we carried out molecular dynamics (MD) simulations at 400 K on wild-type CocE and previously known thermostable mutants, demonstrating that the thermostability of the active form of the enzyme correlates with the fluctuation (characterized as the RMSD and RMSF of atomic positions) of the catalytic residues (Y44, S117, Y118, H287, and D259) in the simulated enzyme. In light of the structure-thermostability correlation, further computational modeling including MD simulations at 400 K predicted that the active site structure of the L169K mutant should be more thermostable. The prediction has been confirmed by wet experimental tests showing that the active form of the L169K mutant had a half-life of 570 min at 37°C, which is significantly longer than those of the wild-type and previously known thermostable mutants. The encouraging outcome suggests that the high-temperature MD simulations and the structure-thermostability may be considered as a valuable tool for computational design of thermostable mutants of an enzyme. PMID:21373712

Acceleration of Monte Carlo simulation of photon migration in complex heterogeneous media using Intel many-integrated core architecture.

PubMed

Gorshkov, Anton V; Kirillin, Mikhail Yu

2015-08-01

Over two decades, the Monte Carlo technique has become a gold standard in simulation of light propagation in turbid media, including biotissues. Technological solutions provide further advances of this technique. The Intel Xeon Phi coprocessor is a new type of accelerator for highly parallel general purpose computing, which allows execution of a wide range of applications without substantial code modification. We present a technical approach of porting our previously developed Monte Carlo (MC) code for simulation of light transport in tissues to the Intel Xeon Phi coprocessor. We show that employing the accelerator allows reducing computational time of MC simulation and obtaining simulation speed-up comparable to GPU. We demonstrate the performance of the developed code for simulation of light transport in the human head and determination of the measurement volume in near-infrared spectroscopy brain sensing.

Using Palm Technology in Participatory Simulations of Complex Systems: A New Take on Ubiquitous and Accessible Mobile Computing

NASA Astrophysics Data System (ADS)

Klopfer, Eric; Yoon, Susan; Perry, Judy

2005-09-01

This paper reports on teachers' perceptions of the educational affordances of a handheld application called Participatory Simulations. It presents evidence from five cases representing each of the populations who work with these computational tools. Evidence across multiple data sources yield similar results to previous research evaluations of handheld activities with respect to enhancing motivation, engagement and self-directed learning. Three additional themes are discussed that provide insight into understanding curricular applicability of Participatory Simulations that suggest a new take on ubiquitous and accessible mobile computing. These themes generally point to the multiple layers of social and cognitive flexibility intrinsic to their design: ease of adaptation to subject-matter content knowledge and curricular integration; facility in attending to teacher-individualized goals; and encouraging the adoption of learner-centered strategies.

Progress in fast, accurate multi-scale climate simulations

DOE PAGES

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

2015-06-01

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

The Application of High Energy Resolution Green's Functions to Threat Scenario Simulation

NASA Astrophysics Data System (ADS)

Thoreson, Gregory G.; Schneider, Erich A.

2012-04-01

Radiation detectors installed at key interdiction points provide defense against nuclear smuggling attempts by scanning vehicles and traffic for illicit nuclear material. These hypothetical threat scenarios may be modeled using radiation transport simulations. However, high-fidelity models are computationally intensive. Furthermore, the range of smuggler attributes and detector technologies create a large problem space not easily overcome by brute-force methods. Previous research has demonstrated that decomposing the scenario into independently simulated components using Green's functions can simulate photon detector signals with coarse energy resolution. This paper extends this methodology by presenting physics enhancements and numerical treatments which allow for an arbitrary level of energy resolution for photon transport. As a result, spectroscopic detector signals produced from full forward transport simulations can be replicated while requiring multiple orders of magnitude less computation time.

Computational fluid dynamics uses in fluid dynamics/aerodynamics education

NASA Technical Reports Server (NTRS)

Holst, Terry L.

1994-01-01

The field of computational fluid dynamics (CFD) has advanced to the point where it can now be used for the purpose of fluid dynamics physics education. Because of the tremendous wealth of information available from numerical simulation, certain fundamental concepts can be efficiently communicated using an interactive graphical interrogation of the appropriate numerical simulation data base. In other situations, a large amount of aerodynamic information can be communicated to the student by interactive use of simple CFD tools on a workstation or even in a personal computer environment. The emphasis in this presentation is to discuss ideas for how this process might be implemented. Specific examples, taken from previous publications, will be used to highlight the presentation.

Computational chemistry

NASA Technical Reports Server (NTRS)

Arnold, J. O.

1987-01-01

With the advent of supercomputers, modern computational chemistry algorithms and codes, a powerful tool was created to help fill NASA's continuing need for information on the properties of matter in hostile or unusual environments. Computational resources provided under the National Aerodynamics Simulator (NAS) program were a cornerstone for recent advancements in this field. Properties of gases, materials, and their interactions can be determined from solutions of the governing equations. In the case of gases, for example, radiative transition probabilites per particle, bond-dissociation energies, and rates of simple chemical reactions can be determined computationally as reliably as from experiment. The data are proving to be quite valuable in providing inputs to real-gas flow simulation codes used to compute aerothermodynamic loads on NASA's aeroassist orbital transfer vehicles and a host of problems related to the National Aerospace Plane Program. Although more approximate, similar solutions can be obtained for ensembles of atoms simulating small particles of materials with and without the presence of gases. Computational chemistry has application in studying catalysis, properties of polymers, all of interest to various NASA missions, including those previously mentioned. In addition to discussing these applications of computational chemistry within NASA, the governing equations and the need for supercomputers for their solution is outlined.

Effects on Training Using Illumination in Virtual Environments

NASA Technical Reports Server (NTRS)

Maida, James C.; Novak, M. S. Jennifer; Mueller, Kristian

1999-01-01

Camera based tasks are commonly performed during orbital operations, and orbital lighting conditions, such as high contrast shadowing and glare, are a factor in performance. Computer based training using virtual environments is a common tool used to make and keep CTW members proficient. If computer based training included some of these harsh lighting conditions, would the crew increase their proficiency? The project goal was to determine whether computer based training increases proficiency if one trains for a camera based task using computer generated virtual environments with enhanced lighting conditions such as shadows and glare rather than color shaded computer images normally used in simulators. Previous experiments were conducted using a two degree of freedom docking system. Test subjects had to align a boresight camera using a hand controller with one axis of rotation and one axis of rotation. Two sets of subjects were trained on two computer simulations using computer generated virtual environments, one with lighting, and one without. Results revealed that when subjects were constrained by time and accuracy, those who trained with simulated lighting conditions performed significantly better than those who did not. To reinforce these results for speed and accuracy, the task complexity was increased.

Spatial adaptive sampling in multiscale simulation

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

Moving target, distributed, real-time simulation using Ada

NASA Technical Reports Server (NTRS)

Collins, W. R.; Feyock, S.; King, L. A.; Morell, L. J.

1985-01-01

Research on a precompiler solution is described for the moving target compiler problem encountered when trying to run parallel simulation algorithms on several microcomputers. The precompiler is under development at NASA-Lewis for simulating jet engines. Since the behavior of any component of a jet engine, e.g., the fan inlet, rear duct, forward sensor, etc., depends on the previous behaviors and not the current behaviors of other components, the behaviors can be modeled on different processors provided the outputs of the processors reach other processors in appropriate time intervals. The simulator works in compute and transfer modes. The Ada procedure sets for the behaviors of different components are divided up and routed by the precompiler, which essentially receives a multitasking program. The subroutines are synchronized after each computation cycle.

A Computational and Experimental Study of Resonators in Three Dimensions

NASA Technical Reports Server (NTRS)

Tam, C. K. W.; Ju, H.; Jones, Michael G.; Watson, Willie R.; Parrott, Tony L.

2009-01-01

In a previous work by the present authors, a computational and experimental investigation of the acoustic properties of two-dimensional slit resonators was carried out. The present paper reports the results of a study extending the previous work to three dimensions. This investigation has two basic objectives. The first is to validate the computed results from direct numerical simulations of the flow and acoustic fields of slit resonators in three dimensions by comparing with experimental measurements in a normal incidence impedance tube. The second objective is to study the flow physics of resonant liners responsible for sound wave dissipation. Extensive comparisons are provided between computed and measured acoustic liner properties with both discrete frequency and broadband sound sources. Good agreements are found over a wide range of frequencies and sound pressure levels. Direct numerical simulation confirms the previous finding in two dimensions that vortex shedding is the dominant dissipation mechanism at high sound pressure intensity. However, it is observed that the behavior of the shed vortices in three dimensions is quite different from those of two dimensions. In three dimensions, the shed vortices tend to evolve into ring (circular in plan form) vortices, even though the slit resonator opening from which the vortices are shed has an aspect ratio of 2.5. Under the excitation of discrete frequency sound, the shed vortices align themselves into two regularly spaced vortex trains moving away from the resonator opening in opposite directions. This is different from the chaotic shedding of vortices found in two-dimensional simulations. The effect of slit aspect ratio at a fixed porosity is briefly studied. For the range of liners considered in this investigation, it is found that the absorption coefficient of a liner increases when the open area of the single slit is subdivided into multiple, smaller slits.

Uniform rovibrational collisional N2 bin model for DSMC, with application to atmospheric entry flows

NASA Astrophysics Data System (ADS)

Torres, E.; Bondar, Ye. A.; Magin, T. E.

2016-11-01

A state-to-state model for internal energy exchange and molecular dissociation allows for high-fidelity DSMC simulations. Elementary reaction cross sections for the N2 (v, J)+ N system were previously extracted from a quantum-chemical database, originally compiled at NASA Ames Research Center. Due to the high computational cost of simulating the full range of inelastic collision processes (approx. 23 million reactions), a coarse-grain model, called the Uniform RoVibrational Collisional (URVC) bin model can be used instead. This allows to reduce the original 9390 rovibrational levels of N2 to 10 energy bins. In the present work, this reduced model is used to simulate a 2D flow configuration, which more closely reproduces the conditions of high-speed entry into Earth's atmosphere. For this purpose, the URVC bin model had to be adapted for integration into the "Rarefied Gas Dynamics Analysis System" (RGDAS), a separate high-performance DSMC code capable of handling complex geometries and parallel computations. RGDAS was developed at the Institute of Theoretical and Applied Mechanics in Novosibirsk, Russia for use by the European Space Agency (ESA) and shares many features with the well-known SMILE code developed by the same group. We show that the reduced mechanism developed previously can be implemented in RGDAS, and the results exhibit nonequilibrium effects consistent with those observed in previous 1D-simulations.

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads.

PubMed

Stone, John E; Hallock, Michael J; Phillips, James C; Peterson, Joseph R; Luthey-Schulten, Zaida; Schulten, Klaus

2016-05-01

Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers.

Effects of Geometric Details on Slat Noise Generation and Propagation

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Lockard, David P.

2009-01-01

The relevance of geometric details to the generation and propagation of noise from leading-edge slats is considered. Typically, such details are omitted in computational simulations and model-scale experiments thereby creating ambiguities in comparisons with acoustic results from flight tests. The current study uses two-dimensional, computational simulations in conjunction with a Ffowcs Williams-Hawkings (FW-H) solver to investigate the effects of previously neglected slat "bulb" and "blade" seals on the local flow field and the associated acoustic radiation. The computations show that the presence of the "blade" seal at the cusp in the simulated geometry significantly changes the slat cove flow dynamics, reduces the amplitudes of the radiated sound, and to a lesser extent, alters the directivity beneath the airfoil. Furthermore, the computations suggest that a modest extension of the baseline "blade" seal further enhances the suppression of slat noise. As a side issue, the utility and equivalence of FW-H methodology for calculating far-field noise as opposed to a more direct approach is examined and demonstrated.

Dynamic Mesh CFD Simulations of Orion Parachute Pendulum Motion During Atmospheric Entry

NASA Technical Reports Server (NTRS)

Halstrom, Logan D.; Schwing, Alan M.; Robinson, Stephen K.

2016-01-01

This paper demonstrates the usage of computational fluid dynamics to study the effects of pendulum motion dynamics of the NASAs Orion Multi-Purpose Crew Vehicle parachute system on the stability of the vehicles atmospheric entry and decent. Significant computational fluid dynamics testing has already been performed at NASAs Johnson Space Center, but this study sought to investigate the effect of bulk motion of the parachute, such as pitching, on the induced aerodynamic forces. Simulations were performed with a moving grid geometry oscillating according to the parameters observed in flight tests. As with the previous simulations, OVERFLOW computational fluid dynamics tool is used with the assumption of rigid, non-permeable geometry. Comparison to parachute wind tunnel tests is included for a preliminary validation of the dynamic mesh model. Results show qualitative differences in the flow fields of the static and dynamic simulations and quantitative differences in the induced aerodynamic forces, suggesting that dynamic mesh modeling of the parachute pendulum motion may uncover additional dynamic effects.

Bravyi-Kitaev Superfast simulation of electronic structure on a quantum computer.

PubMed

Setia, Kanav; Whitfield, James D

2018-04-28

Present quantum computers often work with distinguishable qubits as their computational units. In order to simulate indistinguishable fermionic particles, it is first required to map the fermionic state to the state of the qubits. The Bravyi-Kitaev Superfast (BKSF) algorithm can be used to accomplish this mapping. The BKSF mapping has connections to quantum error correction and opens the door to new ways of understanding fermionic simulation in a topological context. Here, we present the first detailed exposition of the BKSF algorithm for molecular simulation. We provide the BKSF transformed qubit operators and report on our implementation of the BKSF fermion-to-qubits transform in OpenFermion. In this initial study of a hydrogen molecule we have compared BKSF, Jordan-Wigner, and Bravyi-Kitaev transforms under the Trotter approximation. The gate count to implement BKSF is lower than Jordan-Wigner but higher than Bravyi-Kitaev. We considered different orderings of the exponentiated terms and found lower Trotter errors than the previously reported for Jordan-Wigner and Bravyi-Kitaev algorithms. These results open the door to the further study of the BKSF algorithm for quantum simulation.

Confirmation of a realistic reactor model for BNCT dosimetry at the TRIGA Mainz

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

Ziegner, Markus, E-mail: Markus.Ziegner.fl@ait.ac.at; Schmitz, Tobias; Hampel, Gabriele

2014-11-01

Purpose: In order to build up a reliable dose monitoring system for boron neutron capture therapy (BNCT) applications at the TRIGA reactor in Mainz, a computer model for the entire reactor was established, simulating the radiation field by means of the Monte Carlo method. The impact of different source definition techniques was compared and the model was validated by experimental fluence and dose determinations. Methods: The depletion calculation code ORIGEN2 was used to compute the burn-up and relevant material composition of each burned fuel element from the day of first reactor operation to its current core. The material composition ofmore » the current core was used in a MCNP5 model of the initial core developed earlier. To perform calculations for the region outside the reactor core, the model was expanded to include the thermal column and compared with the previously established ATTILA model. Subsequently, the computational model is simplified in order to reduce the calculation time. Both simulation models are validated by experiments with different setups using alanine dosimetry and gold activation measurements with two different types of phantoms. Results: The MCNP5 simulated neutron spectrum and source strength are found to be in good agreement with the previous ATTILA model whereas the photon production is much lower. Both MCNP5 simulation models predict all experimental dose values with an accuracy of about 5%. The simulations reveal that a Teflon environment favorably reduces the gamma dose component as compared to a polymethyl methacrylate phantom. Conclusions: A computer model for BNCT dosimetry was established, allowing the prediction of dosimetric quantities without further calibration and within a reasonable computation time for clinical applications. The good agreement between the MCNP5 simulations and experiments demonstrates that the ATTILA model overestimates the gamma dose contribution. The detailed model can be used for the planning of structural modifications in the thermal column irradiation channel or the use of different irradiation sites than the thermal column, e.g., the beam tubes.« less

Improving Simulated Annealing by Recasting it as a Non-Cooperative Game

NASA Technical Reports Server (NTRS)

Wolpert, David; Bandari, Esfandiar; Tumer, Kagan

2001-01-01

The game-theoretic field of COllective INtelligence (COIN) concerns the design of computer-based players engaged in a non-cooperative game so that as those players pursue their self-interests, a pre-specified global goal for the collective computational system is achieved "as a side-effect". Previous implementations of COIN algorithms have outperformed conventional techniques by up to several orders of magnitude, on domains ranging from telecommunications control to optimization in congestion problems. Recent mathematical developments have revealed that these previously developed game-theory-motivated algorithms were based on only two of the three factors determining performance. Consideration of only the third factor would instead lead to conventional optimization techniques like simulated annealing that have little to do with non-cooperative games. In this paper we present an algorithm based on all three terms at once. This algorithm can be viewed as a way to modify simulated annealing by recasting it as a non-cooperative game, with each variable replaced by a player. This recasting allows us to leverage the intelligent behavior of the individual players to substantially improve the exploration step of the simulated annealing. Experiments are presented demonstrating that this recasting improves simulated annealing by several orders of magnitude for spin glass relaxation and bin-packing.

Efficient generation of connectivity in neuronal networks from simulator-independent descriptions

PubMed Central

Djurfeldt, Mikael; Davison, Andrew P.; Eppler, Jochen M.

2014-01-01

Simulator-independent descriptions of connectivity in neuronal networks promise greater ease of model sharing, improved reproducibility of simulation results, and reduced programming effort for computational neuroscientists. However, until now, enabling the use of such descriptions in a given simulator in a computationally efficient way has entailed considerable work for simulator developers, which must be repeated for each new connectivity-generating library that is developed. We have developed a generic connection generator interface that provides a standard way to connect a connectivity-generating library to a simulator, such that one library can easily be replaced by another, according to the modeler's needs. We have used the connection generator interface to connect C++ and Python implementations of the previously described connection-set algebra to the NEST simulator. We also demonstrate how the simulator-independent modeling framework PyNN can transparently take advantage of this, passing a connection description through to the simulator layer for rapid processing in C++ where a simulator supports the connection generator interface and falling-back to slower iteration in Python otherwise. A set of benchmarks demonstrates the good performance of the interface. PMID:24795620

Review of Real-Time Simulator and the Steps Involved for Implementation of a Model from MATLAB/SIMULINK to Real-Time

NASA Astrophysics Data System (ADS)

Mikkili, Suresh; Panda, Anup Kumar; Prattipati, Jayanthi

2015-06-01

Nowadays the researchers want to develop their model in real-time environment. Simulation tools have been widely used for the design and improvement of electrical systems since the mid twentieth century. The evolution of simulation tools has progressed in step with the evolution of computing technologies. In recent years, computing technologies have improved dramatically in performance and become widely available at a steadily decreasing cost. Consequently, simulation tools have also seen dramatic performance gains and steady cost decreases. Researchers and engineers now have the access to affordable, high performance simulation tools that were previously too cost prohibitive, except for the largest manufacturers. This work has introduced a specific class of digital simulator known as a real-time simulator by answering the questions "what is real-time simulation", "why is it needed" and "how it works". The latest trend in real-time simulation consists of exporting simulation models to FPGA. In this article, the Steps involved for implementation of a model from MATLAB to REAL-TIME are provided in detail.

Simulating urban land cover changes at sub-pixel level in a coastal city

NASA Astrophysics Data System (ADS)

Zhao, Xiaofeng; Deng, Lei; Feng, Huihui; Zhao, Yanchuang

2014-10-01

The simulation of urban expansion or land cover changes is a major theme in both geographic information science and landscape ecology. Yet till now, almost all of previous studies were based on grid computations at pixel level. With the prevalence of spectral mixture analysis in urban land cover research, the simulation of urban land cover at sub-pixel level is being put into agenda. This study provided a new approach of land cover simulation at sub-pixel level. Landsat TM/ETM+ images of Xiamen city, China on both the January of 2002 and 2007 were used to acquire land cover data through supervised classification. Then the two classified land cover data were utilized to extract the transformation rule between 2002 and 2007 using logistic regression. The transformation possibility of each land cover type in a certain pixel was taken as its percent in the same pixel after normalization. And cellular automata (CA) based grid computation was carried out to acquire simulated land cover on 2007. The simulated 2007 sub-pixel land cover was testified with a validated sub-pixel land cover achieved by spectral mixture analysis in our previous studies on the same date. And finally the sub-pixel land cover of 2017 was simulated for urban planning and management. The results showed that our method is useful in land cover simulation at sub-pixel level. Although the simulation accuracy is not quite satisfactory for all the land cover types, it provides an important idea and a good start in the CA-based urban land cover simulation.

Design of a real-time wind turbine simulator using a custom parallel architecture

NASA Technical Reports Server (NTRS)

Hoffman, John A.; Gluck, R.; Sridhar, S.

1995-01-01

The design of a new parallel-processing digital simulator is described. The new simulator has been developed specifically for analysis of wind energy systems in real time. The new processor has been named: the Wind Energy System Time-domain simulator, version 3 (WEST-3). Like previous WEST versions, WEST-3 performs many computations in parallel. The modules in WEST-3 are pure digital processors, however. These digital processors can be programmed individually and operated in concert to achieve real-time simulation of wind turbine systems. Because of this programmability, WEST-3 is very much more flexible and general than its two predecessors. The design features of WEST-3 are described to show how the system produces high-speed solutions of nonlinear time-domain equations. WEST-3 has two very fast Computational Units (CU's) that use minicomputer technology plus special architectural features that make them many times faster than a microcomputer. These CU's are needed to perform the complex computations associated with the wind turbine rotor system in real time. The parallel architecture of the CU causes several tasks to be done in each cycle, including an IO operation and the combination of a multiply, add, and store. The WEST-3 simulator can be expanded at any time for additional computational power. This is possible because the CU's interfaced to each other and to other portions of the simulation using special serial buses. These buses can be 'patched' together in essentially any configuration (in a manner very similar to the programming methods used in analog computation) to balance the input/ output requirements. CU's can be added in any number to share a given computational load. This flexible bus feature is very different from many other parallel processors which usually have a throughput limit because of rigid bus architecture.

Convolutional coding results for the MVM '73 X-band telemetry experiment

NASA Technical Reports Server (NTRS)

Layland, J. W.

1978-01-01

Results of simulation of several short-constraint-length convolutional codes using a noisy symbol stream obtained via the turnaround ranging channels of the MVM'73 spacecraft are presented. First operational use of this coding technique is on the Voyager mission. The relative performance of these codes in this environment is as previously predicted from computer-based simulations.

Correction for spatial averaging in laser speckle contrast analysis

PubMed Central

Thompson, Oliver; Andrews, Michael; Hirst, Evan

2011-01-01

Practical laser speckle contrast analysis systems face a problem of spatial averaging of speckles, due to the pixel size in the cameras used. Existing practice is to use a system factor in speckle contrast analysis to account for spatial averaging. The linearity of the system factor correction has not previously been confirmed. The problem of spatial averaging is illustrated using computer simulation of time-integrated dynamic speckle, and the linearity of the correction confirmed using both computer simulation and experimental results. The valid linear correction allows various useful compromises in the system design. PMID:21483623

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

NASA Technical Reports Server (NTRS)

Menon, Suresh

2003-01-01

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

Simulating electron energy loss spectroscopy with the MNPBEM toolbox

NASA Astrophysics Data System (ADS)

Hohenester, Ulrich

2014-03-01

Within the MNPBEM toolbox, we show how to simulate electron energy loss spectroscopy (EELS) of plasmonic nanoparticles using a boundary element method approach. The methodology underlying our approach closely follows the concepts developed by García de Abajo and coworkers (Garcia de Abajo, 2010). We introduce two classes eelsret and eelsstat that allow in combination with our recently developed MNPBEM toolbox for a simple, robust, and efficient computation of EEL spectra and maps. The classes are accompanied by a number of demo programs for EELS simulation of metallic nanospheres, nanodisks, and nanotriangles, and for electron trajectories passing by or penetrating through the metallic nanoparticles. We also discuss how to compute electric fields induced by the electron beam and cathodoluminescence. Catalogue identifier: AEKJ_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKJ_v2_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.: 38886 No. of bytes in distributed program, including test data, etc.: 1222650 Distribution format: tar.gz Programming language: Matlab 7.11.0 (R2010b). Computer: Any which supports Matlab 7.11.0 (R2010b). Operating system: Any which supports Matlab 7.11.0 (R2010b). RAM:≥1 GB Classification: 18. Catalogue identifier of previous version: AEKJ_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 370 External routines: MESH2D available at www.mathworks.com Does the new version supersede the previous version?: Yes Nature of problem: Simulation of electron energy loss spectroscopy (EELS) for plasmonic nanoparticles. Solution method: Boundary element method using electromagnetic potentials. Reasons for new version: The new version of the toolbox includes two additional classes for the simulation of electron energy loss spectroscopy (EELS) of plasmonic nanoparticles, and corrects a few minor bugs and inconsistencies. Summary of revisions: New classes “eelsstat” and “eelsret” for the simulation of electron energy loss spectroscopy (EELS) of plasmonic nanoparticles have been added. A few minor errors in the implementation of dipole excitation have been corrected. Running time: Depending on surface discretization between seconds and hours.

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

PubMed

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

2018-04-20

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

Computational design of a thermostable mutant of cocaine esterase via molecular dynamics simulations.

PubMed

Huang, Xiaoqin; Gao, Daquan; Zhan, Chang-Guo

2011-06-07

Cocaine esterase (CocE) has been known as the most efficient native enzyme for metabolizing naturally occurring cocaine. A major obstacle to the clinical application of CocE is the thermoinstability of native CocE with a half-life of only ∼11 min at physiological temperature (37 °C). It is highly desirable to develop a thermostable mutant of CocE for therapeutic treatment of cocaine overdose and addiction. To establish a structure-thermostability relationship, we carried out molecular dynamics (MD) simulations at 400 K on wild-type CocE and previously known thermostable mutants, demonstrating that the thermostability of the active form of the enzyme correlates with the fluctuation (characterized as the root-mean square deviation and root-mean square fluctuation of atomic positions) of the catalytic residues (Y44, S117, Y118, H287, and D259) in the simulated enzyme. In light of the structure-thermostability correlation, further computational modelling including MD simulations at 400 K predicted that the active site structure of the L169K mutant should be more thermostable. The prediction has been confirmed by wet experimental tests showing that the active form of the L169K mutant had a half-life of 570 min at 37 °C, which is significantly longer than those of the wild-type and previously known thermostable mutants. The encouraging outcome suggests that the high-temperature MD simulations and the structure-thermostability relationship may be considered as a valuable tool for the computational design of thermostable mutants of an enzyme.

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

Not Available

Some of the major technical questions associated with the burial of radioactive high-level wastes in geologic formations are related to the thermal environments generated by the waste and the impact of this dissipated heat on the surrounding environment. The design of a high level waste storage facility must be such that the temperature variations that occur do not adversely affect operating personnel and equipment. The objective of this investigation was to assist OWI by determining the thermal environment that would be experienced by personnel and equipment in a waste storage facility in salt. Particular emphasis was placed on determining themore » maximum floor and air temperatures with and without ventilation in the first 30 years after waste emplacement. The assumed facility design differs somewhat from those previously analyzed and reported, but many of the previous parametric surveys are useful for comparison. In this investigation a number of 2-dimensional and 3-dimensional simulations of the heat flow in a repository have been performed on the HEATING5 and TRUMP heat transfer codes. The representative repository constructs used in the simulations are described, as well as the computational models and computer codes. Results of the simulations are presented and discussed. Comparisons are made between the recent results and those from previous analyses. Finally, a summary of study limitations, comparisons, and conclusions is given.« less

Evaluation of a subject-specific, torque-driven computer simulation model of one-handed tennis backhand groundstrokes.

PubMed

Kentel, Behzat B; King, Mark A; Mitchell, Sean R

2011-11-01

A torque-driven, subject-specific 3-D computer simulation model of the impact phase of one-handed tennis backhand strokes was evaluated by comparing performance and simulation results. Backhand strokes of an elite subject were recorded on an artificial tennis court. Over the 50-ms period after impact, good agreement was found with an overall RMS difference of 3.3° between matching simulation and performance in terms of joint and racket angles. Consistent with previous experimental research, the evaluation process showed that grip tightness and ball impact location are important factors that affect postimpact racket and arm kinematics. Associated with these factors, the model can be used for a better understanding of the eccentric contraction of the wrist extensors during one-handed backhand ground strokes, a hypothesized mechanism of tennis elbow.

Frequency and Clinical Significance of Previously Undetected Incidental Findings Detected on Computed Tomography Simulation Scans for Breast Cancer Patients

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

Nakamura, Naoki, E-mail: naokinak@luke.or.jp; Tsunoda, Hiroko; Takahashi, Osamu

2012-11-01

Purpose: To determine the frequency and clinical significance of previously undetected incidental findings found on computed tomography (CT) simulation images for breast cancer patients. Methods and Materials: All CT simulation images were first interpreted prospectively by radiation oncologists and then double-checked by diagnostic radiologists. The official reports of CT simulation images for 881 consecutive postoperative breast cancer patients from 2009 to 2010 were retrospectively reviewed. Potentially important incidental findings (PIIFs) were defined as any previously undetected benign or malignancy-related findings requiring further medical follow-up or investigation. For all patients in whom a PIIF was detected, we reviewed the clinical recordsmore » to determine the clinical significance of the PIIF. If the findings from the additional studies prompted by a PIIF required a change in management, the PIIF was also recorded as a clinically important incidental finding (CIIF). Results: There were a total of 57 (6%) PIIFs. The 57 patients in whom a PIIF was detected were followed for a median of 17 months (range, 3-26). Six cases of CIIFs (0.7% of total) were detected. Of the six CIIFs, three (50%) cases had not been noted by the radiation oncologist until the diagnostic radiologist detected the finding. On multivariate analysis, previous CT examination was an independent predictor for PIIF (p = 0.04). Patients who had not previously received chest CT examinations within 1 year had a statistically significantly higher risk of PIIF than those who had received CT examinations within 6 months (odds ratio, 3.54; 95% confidence interval, 1.32-9.50; p = 0.01). Conclusions: The rate of incidental findings prompting a change in management was low. However, radiation oncologists appear to have some difficulty in detecting incidental findings that require a change in management. Considering cost, it may be reasonable that routine interpretations are given to those who have not received previous chest CT examinations within 1 year.« less

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

PubMed Central

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

2013-01-01

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

Computational complexity of the landscape II-Cosmological considerations

NASA Astrophysics Data System (ADS)

Denef, Frederik; Douglas, Michael R.; Greene, Brian; Zukowski, Claire

2018-05-01

We propose a new approach for multiverse analysis based on computational complexity, which leads to a new family of "computational" measure factors. By defining a cosmology as a space-time containing a vacuum with specified properties (for example small cosmological constant) together with rules for how time evolution will produce the vacuum, we can associate global time in a multiverse with clock time on a supercomputer which simulates it. We argue for a principle of "limited computational complexity" governing early universe dynamics as simulated by this supercomputer, which translates to a global measure for regulating the infinities of eternal inflation. The rules for time evolution can be thought of as a search algorithm, whose details should be constrained by a stronger principle of "minimal computational complexity". Unlike previously studied global measures, ours avoids standard equilibrium considerations and the well-known problems of Boltzmann Brains and the youngness paradox. We also give various definitions of the computational complexity of a cosmology, and argue that there are only a few natural complexity classes.

Modelling total solar irradiance since 1878 from simulated magnetograms

NASA Astrophysics Data System (ADS)

Dasi-Espuig, M.; Jiang, J.; Krivova, N. A.; Solanki, S. K.

2014-10-01

Aims: We present a new model of total solar irradiance (TSI) based on magnetograms simulated with a surface flux transport model (SFTM) and the Spectral And Total Irradiance REconstructions (SATIRE) model. Our model provides daily maps of the distribution of the photospheric field and the TSI starting from 1878. Methods: The modelling is done in two main steps. We first calculate the magnetic flux on the solar surface emerging in active and ephemeral regions. The evolution of the magnetic flux in active regions (sunspots and faculae) is computed using a surface flux transport model fed with the observed record of sunspot group areas and positions. The magnetic flux in ephemeral regions is treated separately using the concept of overlapping cycles. We then use a version of the SATIRE model to compute the TSI. The area coverage and the distribution of different magnetic features as a function of time, which are required by SATIRE, are extracted from the simulated magnetograms and the modelled ephemeral region magnetic flux. Previously computed intensity spectra of the various types of magnetic features are employed. Results: Our model reproduces the PMOD composite of TSI measurements starting from 1978 at daily and rotational timescales more accurately than the previous version of the SATIRE model computing TSI over this period of time. The simulated magnetograms provide a more realistic representation of the evolution of the magnetic field on the photosphere and also allow us to make use of information on the spatial distribution of the magnetic fields before the times when observed magnetograms were available. We find that the secular increase in TSI since 1878 is fairly stable to modifications of the treatment of the ephemeral region magnetic flux.

Electron and ion heating by whistler turbulence: Three-dimensional particle-in-cell simulations

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

Hughes, R. Scott; Gary, S. Peter; Wang, Joseph

2014-12-17

Three-dimensional particle-in-cell simulations of decaying whistler turbulence are carried out on a collisionless, homogeneous, magnetized, electron-ion plasma model. In addition, the simulations use an initial ensemble of relatively long wavelength whistler modes with a broad range of initial propagation directions with an initial electron beta β e = 0.05. The computations follow the temporal evolution of the fluctuations as they cascade into broadband turbulent spectra at shorter wavelengths. Three simulations correspond to successively larger simulation boxes and successively longer wavelengths of the initial fluctuations. The computations confirm previous results showing electron heating is preferentially parallel to the background magnetic fieldmore » B o, and ion heating is preferentially perpendicular to B o. The new results here are that larger simulation boxes and longer initial whistler wavelengths yield weaker overall dissipation, consistent with linear dispersion theory predictions of decreased damping, stronger ion heating, consistent with a stronger ion Landau resonance, and weaker electron heating.« less

A Determination of the Minimum Frequency Requirements for a PATRIOT Battalion UHF Communication System.

DTIC Science & Technology

1982-12-01

a computer program which simulates the PATRIOT battalion UH1F communication system. *.-.The detailed description of how the model performs this...the Degree of Master of Science .AI . j tf ti on-i by 5 , .... . :it Lard/or Gregory H. Swanson DLt Captain USA Graduate Computer Science I...5 Model Application..... . . . .. .. . . .. .. . . 6 Thesnis Overviev ....... o.000000000000000000000. .6 Previous Studies

Consolidation of cloud computing in ATLAS

NASA Astrophysics Data System (ADS)

Taylor, Ryan P.; Domingues Cordeiro, Cristovao Jose; Giordano, Domenico; Hover, John; Kouba, Tomas; Love, Peter; McNab, Andrew; Schovancova, Jaroslava; Sobie, Randall; ATLAS Collaboration

2017-10-01

Throughout the first half of LHC Run 2, ATLAS cloud computing has undergone a period of consolidation, characterized by building upon previously established systems, with the aim of reducing operational effort, improving robustness, and reaching higher scale. This paper describes the current state of ATLAS cloud computing. Cloud activities are converging on a common contextualization approach for virtual machines, and cloud resources are sharing monitoring and service discovery components. We describe the integration of Vacuum resources, streamlined usage of the Simulation at Point 1 cloud for offline processing, extreme scaling on Amazon compute resources, and procurement of commercial cloud capacity in Europe. Finally, building on the previously established monitoring infrastructure, we have deployed a real-time monitoring and alerting platform which coalesces data from multiple sources, provides flexible visualization via customizable dashboards, and issues alerts and carries out corrective actions in response to problems.

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

PubMed Central

Stone, John E.; Hallock, Michael J.; Phillips, James C.; Peterson, Joseph R.; Luthey-Schulten, Zaida; Schulten, Klaus

2016-01-01

Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers. PMID:27516922

Determination of Physical Properties of Ionic Liquids Using Molecular Simulations

DTIC Science & Technology

2010-08-20

That is, most groups rely on relatively short (100-500 ps) simulations and evaluate the viscosity via conventional Green - Kubo integration . In this...and can contribute to higher than expected viscosities . The liquid structure of the energetic ionic liquid 2-hydroxyethylhydrizinium nitrate was...claimed previously that neglect of polarizability leads to inaccuracies in the computed transport properties of ionic liquids such as viscosities

Continued Development of Expert System Tools for NPSS Engine Diagnostics

NASA Technical Reports Server (NTRS)

Lewandowski, Henry

1996-01-01

The objectives of this grant were to work with previously developed NPSS (Numerical Propulsion System Simulation) tools and enhance their functionality; explore similar AI systems; and work with the High Performance Computing Communication (HPCC) K-12 program. Activities for this reporting period are briefly summarized and a paper addressing the implementation, monitoring and zooming in a distributed jet engine simulation is included as an attachment.

Numerical simulation of aerobic exercise as a countermeasure in human spaceflight

NASA Astrophysics Data System (ADS)

Perez-Poch, Antoni

The objective of this work is to analyse the efficacy of long-term regular exercise on relevant cardiovascular parameters when the human body is also exposed to microgravity. Computer simulations are an important tool which may be used to predict and analyse these possible effects, and compare them with in-flight experiments. We based our study on a electrical-like computer model (NELME: Numerical Evaluation of Long-term Microgravity Effects) which was developed in our laboratory and validated with the available data, focusing on the cardiovascu-lar parameters affected by changes in gravity exposure. NELME is based on an electrical-like control system model of the physiological changes, that are known to take place when grav-ity changes are applied. The computer implementation has a modular architecture. Hence, different output parameters, potential effects, organs and countermeasures can be easily imple-mented and evaluated. We added to the previous cardiovascular system module a perturbation module to evaluate the effect of regular exercise on the output parameters previously studied. Therefore, we simulated a well-known countermeasure with different protocols of exercising, as a pattern of input electric-like perturbations on the basic module. Different scenarios have been numerically simulated for both men and women, in different patterns of microgravity, reduced gravity and time exposure. Also EVAs were simulated as perturbations to the system. Results show slight differences in gender, with more risk reduction for women than for men after following an aerobic exercise pattern during a simulated mission. Also, risk reduction of a cardiovascular malfunction is evaluated, with a ceiling effect found in all scenarios. A turning point in vascular resistance for a long-term exposure of microgravity below 0.4g has been found of particular interest. In conclusion, we show that computer simulations are a valuable tool to analyse different effects of long-term microgravity exposure on the human body. Potential countermeasures such as physical exercise can also be evaluated as an induced perturbation into the system. Relevant results are compatible with existing data, and are of valuable interest as an assessment of the efficacy of aerobic exercise as a countermeasure in future missions to Mars.

SIM_EXPLORE: Software for Directed Exploration of Complex Systems

NASA Technical Reports Server (NTRS)

Burl, Michael; Wang, Esther; Enke, Brian; Merline, William J.

2013-01-01

Physics-based numerical simulation codes are widely used in science and engineering to model complex systems that would be infeasible to study otherwise. While such codes may provide the highest- fidelity representation of system behavior, they are often so slow to run that insight into the system is limited. Trying to understand the effects of inputs on outputs by conducting an exhaustive grid-based sweep over the input parameter space is simply too time-consuming. An alternative approach called "directed exploration" has been developed to harvest information from numerical simulators more efficiently. The basic idea is to employ active learning and supervised machine learning to choose cleverly at each step which simulation trials to run next based on the results of previous trials. SIM_EXPLORE is a new computer program that uses directed exploration to explore efficiently complex systems represented by numerical simulations. The software sequentially identifies and runs simulation trials that it believes will be most informative given the results of previous trials. The results of new trials are incorporated into the software's model of the system behavior. The updated model is then used to pick the next round of new trials. This process, implemented as a closed-loop system wrapped around existing simulation code, provides a means to improve the speed and efficiency with which a set of simulations can yield scientifically useful results. The software focuses on the case in which the feedback from the simulation trials is binary-valued, i.e., the learner is only informed of the success or failure of the simulation trial to produce a desired output. The software offers a number of choices for the supervised learning algorithm (the method used to model the system behavior given the results so far) and a number of choices for the active learning strategy (the method used to choose which new simulation trials to run given the current behavior model). The software also makes use of the LEGION distributed computing framework to leverage the power of a set of compute nodes. The approach has been demonstrated on a planetary science application in which numerical simulations are used to study the formation of asteroid families.

Grace: A cross-platform micromagnetic simulator on graphics processing units

NASA Astrophysics Data System (ADS)

Zhu, Ru

2015-12-01

A micromagnetic simulator running on graphics processing units (GPUs) is presented. Different from GPU implementations of other research groups which are predominantly running on NVidia's CUDA platform, this simulator is developed with C++ Accelerated Massive Parallelism (C++ AMP) and is hardware platform independent. It runs on GPUs from venders including NVidia, AMD and Intel, and achieves significant performance boost as compared to previous central processing unit (CPU) simulators, up to two orders of magnitude. The simulator paved the way for running large size micromagnetic simulations on both high-end workstations with dedicated graphics cards and low-end personal computers with integrated graphics cards, and is freely available to download.

Probabilistic analysis algorithm for UA slope software program.

DOT National Transportation Integrated Search

2013-12-01

A reliability-based computational algorithm for using a single row and equally spaced drilled shafts to : stabilize an unstable slope has been developed in this research. The Monte-Carlo simulation (MCS) : technique was used in the previously develop...

Using Modeling and Simulation to Complement Testing for Increased Understanding of Weapon Subassembly Response.

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

Wong, Michael K.; Davidson, Megan

As part of Sandia’s nuclear deterrence mission, the B61-12 Life Extension Program (LEP) aims to modernize the aging weapon system. Modernization requires requalification and Sandia is using high performance computing to perform advanced computational simulations to better understand, evaluate, and verify weapon system performance in conjunction with limited physical testing. The Nose Bomb Subassembly (NBSA) of the B61-12 is responsible for producing a fuzing signal upon ground impact. The fuzing signal is dependent upon electromechanical impact sensors producing valid electrical fuzing signals at impact. Computer generated models were used to assess the timing between the impact sensor’s response to themore » deceleration of impact and damage to major components and system subassemblies. The modeling and simulation team worked alongside the physical test team to design a large-scale reverse ballistic test to not only assess system performance, but to also validate their computational models. The reverse ballistic test conducted at Sandia’s sled test facility sent a rocket sled with a representative target into a stationary B61-12 (NBSA) to characterize the nose crush and functional response of NBSA components. Data obtained from data recorders and high-speed photometrics were integrated with previously generated computer models in order to refine and validate the model’s ability to reliably simulate real-world effects. Large-scale tests are impractical to conduct for every single impact scenario. By creating reliable computer models, we can perform simulations that identify trends and produce estimates of outcomes over the entire range of required impact conditions. Sandia’s HPCs enable geometric resolution that was unachievable before, allowing for more fidelity and detail, and creating simulations that can provide insight to support evaluation of requirements and performance margins. As computing resources continue to improve, researchers at Sandia are hoping to improve these simulations so they provide increasingly credible analysis of the system response and performance over the full range of conditions.« less

Scaling a Convection-Resolving RCM to Near-Global Scales

NASA Astrophysics Data System (ADS)

Leutwyler, D.; Fuhrer, O.; Chadha, T.; Kwasniewski, G.; Hoefler, T.; Lapillonne, X.; Lüthi, D.; Osuna, C.; Schar, C.; Schulthess, T. C.; Vogt, H.

2017-12-01

In the recent years, first decade-long kilometer-scale resolution RCM simulations have been performed on continental-scale computational domains. However, the size of the planet Earth is still an order of magnitude larger and thus the computational implications of performing global climate simulations at this resolution are challenging. We explore the gap between the currently established RCM simulations and global simulations by scaling the GPU accelerated version of the COSMO model to a near-global computational domain. To this end, the evolution of an idealized moist baroclinic wave has been simulated over the course of 10 days with a grid spacing of up to 930 m. The computational mesh employs 36'000 x 16'001 x 60 grid points and covers 98.4% of the planet's surface. The code shows perfect weak scaling up to 4'888 Nodes of the Piz Daint supercomputer and yields 0.043 simulated years per day (SYPD) which is approximately one seventh of the 0.2-0.3 SYPD required to conduct AMIP-type simulations. However, at half the resolution (1.9 km) we've observed 0.23 SYPD. Besides formation of frontal precipitating systems containing embedded explicitly-resolved convective motions, the simulations reveal a secondary instability that leads to cut-off warm-core cyclonic vortices in the cyclone's core, once the grid spacing is refined to the kilometer scale. The explicit representation of embedded moist convection and the representation of the previously unresolved instabilities exhibit a physically different behavior in comparison to coarser-resolution simulations. The study demonstrates that global climate simulations using kilometer-scale resolution are imminent and serves as a baseline benchmark for global climate model applications and future exascale supercomputing systems.

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

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

Badal, A; Zbijewski, W; Bolch, W

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

Computer Simulations of Coronary Blood Flow Through a Constriction

DTIC Science & Technology

2014-03-01

interventional procedures (e.g., stent deployment). Building off previous models that have been partially validated with experimental data, this thesis... stent deployment). Building off previous models that have been partially validated with experimental data, this thesis continues to develop the...the artery and increase blood flow. Generally a stent , or a mesh wire tube, is permanently inserted in order to scaffold open the artery wall

Physically-Based Modelling and Real-Time Simulation of Fluids.

NASA Astrophysics Data System (ADS)

Chen, Jim Xiong

1995-01-01

Simulating physically realistic complex fluid behaviors presents an extremely challenging problem for computer graphics researchers. Such behaviors include the effects of driving boats through water, blending differently colored fluids, rain falling and flowing on a terrain, fluids interacting in a Distributed Interactive Simulation (DIS), etc. Such capabilities are useful in computer art, advertising, education, entertainment, and training. We present a new method for physically-based modeling and real-time simulation of fluids in computer graphics and dynamic virtual environments. By solving the 2D Navier -Stokes equations using a CFD method, we map the surface into 3D using the corresponding pressures in the fluid flow field. This achieves realistic real-time fluid surface behaviors by employing the physical governing laws of fluids but avoiding extensive 3D fluid dynamics computations. To complement the surface behaviors, we calculate fluid volume and external boundary changes separately to achieve full 3D general fluid flow. To simulate physical activities in a DIS, we introduce a mechanism which uses a uniform time scale proportional to the clock-time and variable time-slicing to synchronize physical models such as fluids in the networked environment. Our approach can simulate many different fluid behaviors by changing the internal or external boundary conditions. It can model different kinds of fluids by varying the Reynolds number. It can simulate objects moving or floating in fluids. It can also produce synchronized general fluid flows in a DIS. Our model can serve as a testbed to simulate many other fluid phenomena which have never been successfully modeled previously.

Parameter inference in small world network disease models with approximate Bayesian Computational methods

NASA Astrophysics Data System (ADS)

Walker, David M.; Allingham, David; Lee, Heung Wing Joseph; Small, Michael

2010-02-01

Small world network models have been effective in capturing the variable behaviour of reported case data of the SARS coronavirus outbreak in Hong Kong during 2003. Simulations of these models have previously been realized using informed “guesses” of the proposed model parameters and tested for consistency with the reported data by surrogate analysis. In this paper we attempt to provide statistically rigorous parameter distributions using Approximate Bayesian Computation sampling methods. We find that such sampling schemes are a useful framework for fitting parameters of stochastic small world network models where simulation of the system is straightforward but expressing a likelihood is cumbersome.

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

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

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

2007-01-20

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

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

NASA Astrophysics Data System (ADS)

Moran, Kenneth J.; Beran, Philip S.

1994-07-01

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

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

NASA Astrophysics Data System (ADS)

Furuichi, Mikito; Nishiura, Daisuke

2017-10-01

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

Quantitative computational infrared imaging of buoyant diffusion flames

NASA Astrophysics Data System (ADS)

Newale, Ashish S.

Studies of infrared radiation from turbulent buoyant diffusion flames impinging on structural elements have applications to the development of fire models. A numerical and experimental study of radiation from buoyant diffusion flames with and without impingement on a flat plate is reported. Quantitative images of the radiation intensity from the flames are acquired using a high speed infrared camera. Large eddy simulations are performed using fire dynamics simulator (FDS version 6). The species concentrations and temperature from the simulations are used in conjunction with a narrow-band radiation model (RADCAL) to solve the radiative transfer equation. The computed infrared radiation intensities rendered in the form of images and compared with the measurements. The measured and computed radiation intensities reveal necking and bulging with a characteristic frequency of 7.1 Hz which is in agreement with previous empirical correlations. The results demonstrate the effects of stagnation point boundary layer on the upstream buoyant shear layer. The coupling between these two shear layers presents a model problem for sub-grid scale modeling necessary for future large eddy simulations.

Simulation using computer-piloted point excitations of vibrations induced on a structure by an acoustic environment

NASA Astrophysics Data System (ADS)

Monteil, P.

1981-11-01

Computation of the overall levels and spectral densities of the responses measured on a launcher skin, the fairing for instance, merged into a random acoustic environment during take off, was studied. The analysis of transmission of these vibrations to the payload required the simulation of these responses by a shaker control system, using a small number of distributed shakers. Results show that this closed loop computerized digital system allows the acquisition of auto and cross spectral densities equal to those of the responses previously computed. However, wider application is sought, e.g., road and runway profiles. The problems of multiple input-output system identification, multiple true random signal generation, and real time programming are evoked. The system should allow for the control of four shakers.

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

PubMed

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

Scalable Domain Decomposed Monte Carlo Particle Transport

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

O'Brien, Matthew Joseph

2013-12-05

In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation.

Microsecond Simulations of DNA and Ion Transport in Nanopores with Novel Ion-Ion and Ion-Nucleotides Effective Potentials

PubMed Central

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei

2014-01-01

We developed a novel scheme based on the Grand-Canonical Monte-Carlo/Brownian Dynamics (GCMC/BD) simulations and have extended it to studies of ion currents across three nanopores with the potential for ssDNA sequencing: solid-state nanopore Si3N4, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the Inverse Monte-Carlo protocol, which maps the relevant ion-nucleotide distribution functions from an all-atom MD simulations. Combined with the previously developed simulation platform for Brownian Dynamic (BD) simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations. PMID:24738152

Improving Simulated Annealing by Replacing Its Variables with Game-Theoretic Utility Maximizers

NASA Technical Reports Server (NTRS)

Wolpert, David H.; Bandari, Esfandiar; Tumer, Kagan

2001-01-01

The game-theory field of Collective INtelligence (COIN) concerns the design of computer-based players engaged in a non-cooperative game so that as those players pursue their self-interests, a pre-specified global goal for the collective computational system is achieved as a side-effect. Previous implementations of COIN algorithms have outperformed conventional techniques by up to several orders of magnitude, on domains ranging from telecommunications control to optimization in congestion problems. Recent mathematical developments have revealed that these previously developed algorithms were based on only two of the three factors determining performance. Consideration of only the third factor would instead lead to conventional optimization techniques like simulated annealing that have little to do with non-cooperative games. In this paper we present an algorithm based on all three terms at once. This algorithm can be viewed as a way to modify simulated annealing by recasting it as a non-cooperative game, with each variable replaced by a player. This recasting allows us to leverage the intelligent behavior of the individual players to substantially improve the exploration step of the simulated annealing. Experiments are presented demonstrating that this recasting significantly improves simulated annealing for a model of an economic process run over an underlying small-worlds topology. Furthermore, these experiments reveal novel small-worlds phenomena, and highlight the shortcomings of conventional mechanism design in bounded rationality domains.

Advances in computational design and analysis of airbreathing propulsion systems

NASA Technical Reports Server (NTRS)

Klineberg, John M.

1989-01-01

The development of commercial and military aircraft depends, to a large extent, on engine manufacturers being able to achieve significant increases in propulsion capability through improved component aerodynamics, materials, and structures. The recent history of propulsion has been marked by efforts to develop computational techniques that can speed up the propulsion design process and produce superior designs. The availability of powerful supercomputers, such as the NASA Numerical Aerodynamic Simulator, and the potential for even higher performance offered by parallel computer architectures, have opened the door to the use of multi-dimensional simulations to study complex physical phenomena in propulsion systems that have previously defied analysis or experimental observation. An overview of several NASA Lewis research efforts is provided that are contributing toward the long-range goal of a numerical test-cell for the integrated, multidisciplinary design, analysis, and optimization of propulsion systems. Specific examples in Internal Computational Fluid Mechanics, Computational Structural Mechanics, Computational Materials Science, and High Performance Computing are cited and described in terms of current capabilities, technical challenges, and future research directions.

Reducing the latency of the Fractal Iterative Method to half an iteration

NASA Astrophysics Data System (ADS)

Béchet, Clémentine; Tallon, Michel

2013-12-01

The fractal iterative method for atmospheric tomography (FRiM-3D) has been introduced to solve the wavefront reconstruction at the dimensions of an ELT with a low-computational cost. Previous studies reported the requirement of only 3 iterations of the algorithm in order to provide the best adaptive optics (AO) performance. Nevertheless, any iterative method in adaptive optics suffer from the intrinsic latency induced by the fact that one iteration can start only once the previous one is completed. Iterations hardly match the low-latency requirement of the AO real-time computer. We present here a new approach to avoid iterations in the computation of the commands with FRiM-3D, thus allowing low-latency AO response even at the scale of the European ELT (E-ELT). The method highlights the importance of "warm-start" strategy in adaptive optics. To our knowledge, this particular way to use the "warm-start" has not been reported before. Futhermore, removing the requirement of iterating to compute the commands, the computational cost of the reconstruction with FRiM-3D can be simplified and at least reduced to half the computational cost of a classical iteration. Thanks to simulations of both single-conjugate and multi-conjugate AO for the E-ELT,with FRiM-3D on Octopus ESO simulator, we demonstrate the benefit of this approach. We finally enhance the robustness of this new implementation with respect to increasing measurement noise, wind speed and even modeling errors.

Accelerating 3D Hall MHD Magnetosphere Simulations with Graphics Processing Units

NASA Astrophysics Data System (ADS)

Bard, C.; Dorelli, J.

2017-12-01

The resolution required to simulate planetary magnetospheres with Hall magnetohydrodynamics result in program sizes approaching several hundred million grid cells. These would take years to run on a single computational core and require hundreds or thousands of computational cores to complete in a reasonable time. However, this requires access to the largest supercomputers. Graphics processing units (GPUs) provide a viable alternative: one GPU can do the work of roughly 100 cores, bringing Hall MHD simulations of Ganymede within reach of modest GPU clusters ( 8 GPUs). We report our progress in developing a GPU-accelerated, three-dimensional Hall magnetohydrodynamic code and present Hall MHD simulation results for both Ganymede (run on 8 GPUs) and Mercury (56 GPUs). We benchmark our Ganymede simulation with previous results for the Galileo G8 flyby, namely that adding the Hall term to ideal MHD simulations changes the global convection pattern within the magnetosphere. Additionally, we present new results for the G1 flyby as well as initial results from Hall MHD simulations of Mercury and compare them with the corresponding ideal MHD runs.

Richardson-Lucy/maximum likelihood image restoration algorithm for fluorescence microscopy: further testing.

PubMed

Holmes, T J; Liu, Y H

1989-11-15

A maximum likelihood based iterative algorithm adapted from nuclear medicine imaging for noncoherent optical imaging was presented in a previous publication with some initial computer-simulation testing. This algorithm is identical in form to that previously derived in a different way by W. H. Richardson "Bayesian-Based Iterative Method of Image Restoration," J. Opt. Soc. Am. 62, 55-59 (1972) and L. B. Lucy "An Iterative Technique for the Rectification of Observed Distributions," Astron. J. 79, 745-765 (1974). Foreseen applications include superresolution and 3-D fluorescence microscopy. This paper presents further simulation testing of this algorithm and a preliminary experiment with a defocused camera. The simulations show quantified resolution improvement as a function of iteration number, and they show qualitatively the trend in limitations on restored resolution when noise is present in the data. Also shown are results of a simulation in restoring missing-cone information for 3-D imaging. Conclusions are in support of the feasibility of using these methods with real systems, while computational cost and timing estimates indicate that it should be realistic to implement these methods. Itis suggested in the Appendix that future extensions to the maximum likelihood based derivation of this algorithm will address some of the limitations that are experienced with the nonextended form of the algorithm presented here.

Fast ray-tracing of human eye optics on Graphics Processing Units.

PubMed

Wei, Qi; Patkar, Saket; Pai, Dinesh K

2014-05-01

We present a new technique for simulating retinal image formation by tracing a large number of rays from objects in three dimensions as they pass through the optic apparatus of the eye to objects. Simulating human optics is useful for understanding basic questions of vision science and for studying vision defects and their corrections. Because of the complexity of computing such simulations accurately, most previous efforts used simplified analytical models of the normal eye. This makes them less effective in modeling vision disorders associated with abnormal shapes of the ocular structures which are hard to be precisely represented by analytical surfaces. We have developed a computer simulator that can simulate ocular structures of arbitrary shapes, for instance represented by polygon meshes. Topographic and geometric measurements of the cornea, lens, and retina from keratometer or medical imaging data can be integrated for individualized examination. We utilize parallel processing using modern Graphics Processing Units (GPUs) to efficiently compute retinal images by tracing millions of rays. A stable retinal image can be generated within minutes. We simulated depth-of-field, accommodation, chromatic aberrations, as well as astigmatism and correction. We also show application of the technique in patient specific vision correction by incorporating geometric models of the orbit reconstructed from clinical medical images. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

A Pilot Study of Computer-Based Simulation Training for Enhancing Family Medicine Residents' Competence in Computerized Settings.

PubMed

Shachak, Aviv; Domb, Sharon; Borycki, Elizabeth; Fong, Nancy; Skyrme, Alison; Kushniruk, Andre; Reis, Shmuel; Ziv, Amitai

2015-01-01

We previously developed a prototype computer-based simulation to teach residents how to integrate better EMR use in the patient-physician interaction. To evaluate the prototype, we conducted usability tests with three non-clinician students, followed by a pilot study with 16 family medicine residents. The pilot study included pre- and post-test surveys of competencies and attitudes related to using the EMR in the consultation and the acceptability of the simulation, as well as 'think aloud' observations. After using the simulation prototypes, the mean scores for competencies and attitudes improved from 14.88/20 to 15.63/20 and from 22.25/30 to 23.13/30, respectively; however, only the difference for competencies was significant (paired t-test; t=-2.535, p=0.023). Mean scores for perceived usefulness and ease of use of the simulation were good (3.81 and 4.10 on a 5-point scale, respectively). Issues identified in usability testing include confusing interaction with some features, preferences for a more interactive representation of the EMR, and more options for shared decision making. In conclusion, computer-based simulation may be an effective and acceptable tool for teaching residents how to better use EMRs in clinical encounters.

Simulated hydrologic effects of possible ground-water and surface-water management alternatives in and near the Platte River, south-central Nebraska

USGS Publications Warehouse

Burns, Alan W.

1981-01-01

Digital computer models were developed and used to simulate the hydrologic effects of hypothetical water-management alternatives on the wetland habitat area near Grand Island, Nebr. Areally distributed recharge to and discharge from the aquifer system adjacent to the Platte River between Overton and Grand Island were computed for four hypothetical water-management alternatives. Using stream-aquifer response functions, the stream depletions resulting from the different alternatives ranged from 53,000 acre-feet per year for increased surface-water irrigation to 177,000 acre-feet per year for increased ground-water pumpage. Current conditions would result in stream depletions of 125,000 acre-feet per year. Using the relationship between discharge and river stage, frequency curves of the stage in the river near the wildlife habitat area were computed using a 50-year sequence of historical streamflow at Overton, minus the stream depletions resulting from various management practices. For the management alternatives previously discussed, differences in the stage-frequency curves were minimal. For comparative purposes, three additional water-management alternatives whose application would change the incoming streamflow at Overton were simulated. Although in these alternatives the amounts of water that were diverted or imported were similar to the amounts in the previous alternatives, their effects on the stage-frequency curves were much more dramatic. (USGS)

A method to incorporate the effect of beam quality on image noise in a digitally reconstructed radiograph (DRR) based computer simulation for optimisation of digital radiography

NASA Astrophysics Data System (ADS)

Moore, Craig S.; Wood, Tim J.; Saunderson, John R.; Beavis, Andrew W.

2017-09-01

The use of computer simulated digital x-radiographs for optimisation purposes has become widespread in recent years. To make these optimisation investigations effective, it is vital simulated radiographs contain accurate anatomical and system noise. Computer algorithms that simulate radiographs based solely on the incident detector x-ray intensity (‘dose’) have been reported extensively in the literature. However, while it has been established for digital mammography that x-ray beam quality is an important factor when modelling noise in simulated images there are no such studies for diagnostic imaging of the chest, abdomen and pelvis. This study investigates the influence of beam quality on image noise in a digital radiography (DR) imaging system, and incorporates these effects into a digitally reconstructed radiograph (DRR) computer simulator. Image noise was measured on a real DR imaging system as a function of dose (absorbed energy) over a range of clinically relevant beam qualities. Simulated ‘absorbed energy’ and ‘beam quality’ DRRs were then created for each patient and tube voltage under investigation. Simulated noise images, corrected for dose and beam quality, were subsequently produced from the absorbed energy and beam quality DRRs, using the measured noise, absorbed energy and beam quality relationships. The noise images were superimposed onto the noiseless absorbed energy DRRs to create the final images. Signal-to-noise measurements in simulated chest, abdomen and spine images were within 10% of the corresponding measurements in real images. This compares favourably to our previous algorithm where images corrected for dose only were all within 20%.

Anticipation of the landing shock phenomenon in flight simulation

NASA Technical Reports Server (NTRS)

Mcfarland, Richard E.

1987-01-01

An aircraft landing may be described as a controlled crash because a runway surface is intercepted. In a simulation model the transition from aerodynamic flight to weight on wheels involves a single computational cycle during which stiff differential equations are activated; with a significant probability these initial conditions are unrealistic. This occurs because of the finite cycle time, during which large restorative forces will accompany unrealistic initial oleo compressions. This problem was recognized a few years ago at Ames Research Center during simulation studies of a supersonic transport. The mathematical model of this vehicle severely taxed computational resources, and required a large cycle time. The ground strike problem was solved by a described technique called anticipation equations. This extensively used technique has not been previously reported. The technique of anticipating a significant event is a useful tool in the general field of discrete flight simulation. For the differential equations representing a landing gear model stiffness, rate of interception and cycle time may combine to produce an unrealistic simulation of the continuum.

Multiscale Computer Simulation of Failure in Aerogels

NASA Technical Reports Server (NTRS)

Good, Brian S.

2008-01-01

Aerogels have been of interest to the aerospace community primarily for their thermal properties, notably their low thermal conductivities. While such gels are typically fragile, recent advances in the application of conformal polymer layers to these gels has made them potentially useful as lightweight structural materials as well. We have previously performed computer simulations of aerogel thermal conductivity and tensile and compressive failure, with results that are in qualitative, and sometimes quantitative, agreement with experiment. However, recent experiments in our laboratory suggest that gels having similar densities may exhibit substantially different properties. In this work, we extend our original diffusion limited cluster aggregation (DLCA) model for gel structure to incorporate additional variation in DLCA simulation parameters, with the aim of producing DLCA clusters of similar densities that nevertheless have different fractal dimension and secondary particle coordination. We perform particle statics simulations of gel strain on these clusters, and consider the effects of differing DLCA simulation conditions, and the resultant differences in fractal dimension and coordination, on gel strain properties.

Detailed Comparison of DNS to PSE for Oblique Breakdown at Mach 3

NASA Technical Reports Server (NTRS)

Mayer, Christian S. J.; Fasel, Hermann F.; Choudhari, Meelan; Chang, Chau-Lyan

2010-01-01

A pair of oblique waves at low amplitudes is introduced in a supersonic flat-plate boundary layer. Their downstream development and the concomitant process of laminar to turbulent transition is then investigated numerically using Direct Numerical Simulations (DNS) and Parabolized Stability Equations (PSE). This abstract is the last part of an extensive study of the complete transition process initiated by oblique breakdown at Mach 3. In contrast to the previous simulations, the symmetry condition in the spanwise direction is removed for the simulation presented in this abstract. By removing the symmetry condition, we are able to confirm that the flow is indeed symmetric over the entire computational domain. Asymmetric modes grow in the streamwise direction but reach only small amplitude values at the outflow. Furthermore, this abstract discusses new time-averaged data from our previous simulation CASE 3 and compares PSE data obtained from NASA's LASTRAC code to DNS results.

Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation

PubMed Central

Smith, Gregory R.; Xie, Lu; Schwartz, Russell

2016-01-01

The environment of a living cell is vastly different from that of an in vitro reaction system, an issue that presents great challenges to the use of in vitro models, or computer simulations based on them, for understanding biochemistry in vivo. Virus capsids make an excellent model system for such questions because they typically have few distinct components, making them amenable to in vitro and modeling studies, yet their assembly can involve complex networks of possible reactions that cannot be resolved in detail by any current experimental technology. We previously fit kinetic simulation parameters to bulk in vitro assembly data to yield a close match between simulated and real data, and then used the simulations to study features of assembly that cannot be monitored experimentally. The present work seeks to project how assembly in these simulations fit to in vitro data would be altered by computationally adding features of the cellular environment to the system, specifically the presence of nucleic acid about which many capsids assemble. The major challenge of such work is computational: simulating fine-scale assembly pathways on the scale and in the parameter domains of real viruses is far too computationally costly to allow for explicit models of nucleic acid interaction. We bypass that limitation by applying analytical models of nucleic acid effects to adjust kinetic rate parameters learned from in vitro data to see how these adjustments, singly or in combination, might affect fine-scale assembly progress. The resulting simulations exhibit surprising behavioral complexity, with distinct effects often acting synergistically to drive efficient assembly and alter pathways relative to the in vitro model. The work demonstrates how computer simulations can help us understand how assembly might differ between the in vitro and in vivo environments and what features of the cellular environment account for these differences. PMID:27244559

Storm Water Management Model Applications Manual

EPA Science Inventory

The EPA Storm Water Management Model (SWMM) is a dynamic rainfall-runoff simulation model that computes runoff quantity and quality from primarily urban areas. This manual is a practical application guide for new SWMM users who have already had some previous training in hydrolog...

[Low Fidelity Simulation of a Zero-Y Robot

NASA Technical Reports Server (NTRS)

Sweet, Adam

2001-01-01

The item to be cleared is a low-fidelity software simulation model of a hypothetical freeflying robot designed for use in zero gravity environments. This simulation model works with the HCC simulation system that was developed by Xerox PARC and NASA Ames Research Center. HCC has been previously cleared for distribution. When used with the HCC software, the model computes the location and orientation of the simulated robot over time. Failures (such as a broken motor) can be injected into the simulation to produce simulated behavior corresponding to the failure. Release of this simulation will allow researchers to test their software diagnosis systems by attempting to diagnose the simulated failure from the simulated behavior. This model does not contain any encryption software nor can it perform any control tasks that might be export controlled.

Using a million cell simulation of the cerebellum: network scaling and task generality.

PubMed

Li, Wen-Ke; Hausknecht, Matthew J; Stone, Peter; Mauk, Michael D

2013-11-01

Several factors combine to make it feasible to build computer simulations of the cerebellum and to test them in biologically realistic ways. These simulations can be used to help understand the computational contributions of various cerebellar components, including the relevance of the enormous number of neurons in the granule cell layer. In previous work we have used a simulation containing 12000 granule cells to develop new predictions and to account for various aspects of eyelid conditioning, a form of motor learning mediated by the cerebellum. Here we demonstrate the feasibility of scaling up this simulation to over one million granule cells using parallel graphics processing unit (GPU) technology. We observe that this increase in number of granule cells requires only twice the execution time of the smaller simulation on the GPU. We demonstrate that this simulation, like its smaller predecessor, can emulate certain basic features of conditioned eyelid responses, with a slight improvement in performance in one measure. We also use this simulation to examine the generality of the computation properties that we have derived from studying eyelid conditioning. We demonstrate that this scaled up simulation can learn a high level of performance in a classic machine learning task, the cart-pole balancing task. These results suggest that this parallel GPU technology can be used to build very large-scale simulations whose connectivity ratios match those of the real cerebellum and that these simulations can be used guide future studies on cerebellar mediated tasks and on machine learning problems. Copyright © 2012 Elsevier Ltd. All rights reserved.

Improving Hall Thruster Plume Simulation through Refined Characterization of Near-field Plasma Properties

NASA Astrophysics Data System (ADS)

Huismann, Tyler D.

Due to the rapidly expanding role of electric propulsion (EP) devices, it is important to evaluate their integration with other spacecraft systems. Specifically, EP device plumes can play a major role in spacecraft integration, and as such, accurate characterization of plume structure bears on mission success. This dissertation addresses issues related to accurate prediction of plume structure in a particular type of EP device, a Hall thruster. This is done in two ways: first, by coupling current plume simulation models with current models that simulate a Hall thruster's internal plasma behavior; second, by improving plume simulation models and thereby increasing physical fidelity. These methods are assessed by comparing simulated results to experimental measurements. Assessment indicates the two methods improve plume modeling capabilities significantly: using far-field ion current density as a metric, these approaches used in conjunction improve agreement with measurements by a factor of 2.5, as compared to previous methods. Based on comparison to experimental measurements, recent computational work on discharge chamber modeling has been largely successful in predicting properties of internal thruster plasmas. This model can provide detailed information on plasma properties at a variety of locations. Frequently, experimental data is not available at many locations that are of interest regarding computational models. Excepting the presence of experimental data, there are limited alternatives for scientifically determining plasma properties that are necessary as inputs into plume simulations. Therefore, this dissertation focuses on coupling current models that simulate internal thruster plasma behavior with plume simulation models. Further, recent experimental work on atom-ion interactions has provided a better understanding of particle collisions within plasmas. This experimental work is used to update collision models in a current plume simulation code. Previous versions of the code assume an unknown dependence between particles' pre-collision velocities and post-collision scattering angles. This dissertation focuses on updating several of these types of collisions by assuming a curve fit based on the measurements of atom-ion interactions, such that previously unknown angular dependences are well-characterized.

The influence of anesthesia and fluid-structure interaction on simulated shear stress patterns in the carotid bifurcation of mice.

PubMed

De Wilde, David; Trachet, Bram; De Meyer, Guido; Segers, Patrick

2016-09-06

Low and oscillatory wall shear stresses (WSS) near aortic bifurcations have been linked to the onset of atherosclerosis. In previous work, we calculated detailed WSS patterns in the carotid bifurcation of mice using a Fluid-structure interaction (FSI) approach. We subsequently fed the animals a high-fat diet and linked the results of the FSI simulations to those of atherosclerotic plaque location on a within-subject basis. However, these simulations were based on boundary conditions measured under anesthesia, while active mice might experience different hemodynamics. Moreover, the FSI technique for mouse-specific simulations is both time- and labor-intensive, and might be replaced by simpler and easier Computational Fluid Dynamics (CFD) simulations. The goal of the current work was (i) to compare WSS patterns based on anesthesia conditions to those representing active resting and exercising conditions; and (ii) to compare WSS patterns based on FSI simulations to those based on steady-state and transient CFD simulations. For each of the 3 computational techniques (steady state CFD, transient CFD, FSI) we performed 5 simulations: 1 for anesthesia, 2 for conscious resting conditions and 2 more for conscious active conditions. The inflow, pressure and heart rate were scaled according to representative in vivo measurements obtained from literature. When normalized by the maximal shear stress value, shear stress patterns were similar for the 3 computational techniques. For all activity levels, steady state CFD led to an overestimation of WSS values, while FSI simulations yielded a clear increase in WSS reversal at the outer side of the sinus of the external carotid artery that was not visible in transient CFD-simulations. Furthermore, the FSI simulations in the highest locomotor activity state showed a flow recirculation zone in the external carotid artery that was not present under anesthesia. This recirculation went hand in hand with locally increased WSS reversal. Our data show that FSI simulations are not necessary to obtain normalized WSS patterns, but indispensable to assess the oscillatory behavior of the WSS in mice. Flow recirculation and WSS reversal at the external carotid artery may occur during high locomotor activity while they are not present under anesthesia. These phenomena might thus influence plaque formation to a larger extent than what was previously assumed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Single Axis Attitude Control and DC Bus Regulation with Two Flywheels

NASA Technical Reports Server (NTRS)

Kascak, Peter E.; Jansen, Ralph H.; Kenny, Barbara; Dever, Timothy P.

2002-01-01

A computer simulation of a flywheel energy storage single axis attitude control system is described. The simulation models hardware which will be experimentally tested in the future. This hardware consists of two counter rotating flywheels mounted to an air table. The air table allows one axis of rotational motion. An inertia DC bus coordinator is set forth that allows the two control problems, bus regulation and attitude control, to be separated. Simulation results are presented with a previously derived flywheel bus regulator and a simple PID attitude controller.

A dynamical-systems approach for computing ice-affected streamflow

USGS Publications Warehouse

Holtschlag, David J.

1996-01-01

A dynamical-systems approach was developed and evaluated for computing ice-affected streamflow. The approach provides for dynamic simulation and parameter estimation of site-specific equations relating ice effects to routinely measured environmental variables. Comparison indicates that results from the dynamical-systems approach ranked higher than results from 11 analytical methods previously investigated on the basis of accuracy and feasibility criteria. Additional research will likely lead to further improvements in the approach.

Mathematic models for a ray tracing method and its applications in wireless optical communications.

PubMed

Zhang, Minglun; Zhang, Yangan; Yuan, Xueguang; Zhang, Jinnan

2010-08-16

This paper presents a new ray tracing method, which contains a whole set of mathematic models, and its validity is verified by simulations. In addition, both theoretical analysis and simulation results show that the computational complexity of the method is much lower than that of previous ones. Therefore, the method can be used to rapidly calculate the impulse response of wireless optical channels for complicated systems.

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

NASA Astrophysics Data System (ADS)

Wan, Tian

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

Two transducer formula for more precise determination of ultrasonic phase velocity from standing wave measurements

NASA Technical Reports Server (NTRS)

Ringermacher, H. I.; Moerner, W. E.; Miller, J. G.

1974-01-01

A two transducer correction formula valid for both solid and liquid specimens is presented. Using computer simulations of velocity measurements, the accuracy and range of validity of the results are discussed and are compared with previous approximations.

Physical Processes and Applications of the Monte Carlo Radiative Energy Deposition (MRED) Code

NASA Astrophysics Data System (ADS)

Reed, Robert A.; Weller, Robert A.; Mendenhall, Marcus H.; Fleetwood, Daniel M.; Warren, Kevin M.; Sierawski, Brian D.; King, Michael P.; Schrimpf, Ronald D.; Auden, Elizabeth C.

2015-08-01

MRED is a Python-language scriptable computer application that simulates radiation transport. It is the computational engine for the on-line tool CRÈME-MC. MRED is based on c++ code from Geant4 with additional Fortran components to simulate electron transport and nuclear reactions with high precision. We provide a detailed description of the structure of MRED and the implementation of the simulation of physical processes used to simulate radiation effects in electronic devices and circuits. Extensive discussion and references are provided that illustrate the validation of models used to implement specific simulations of relevant physical processes. Several applications of MRED are summarized that demonstrate its ability to predict and describe basic physical phenomena associated with irradiation of electronic circuits and devices. These include effects from single particle radiation (including both direct ionization and indirect ionization effects), dose enhancement effects, and displacement damage effects. MRED simulations have also helped to identify new single event upset mechanisms not previously observed by experiment, but since confirmed, including upsets due to muons and energetic electrons.

Further developments in cloud statistics for computer simulations

NASA Technical Reports Server (NTRS)

Chang, D. T.; Willand, J. H.

1972-01-01

This study is a part of NASA's continued program to provide global statistics of cloud parameters for computer simulation. The primary emphasis was on the development of the data bank of the global statistical distributions of cloud types and cloud layers and their applications in the simulation of the vertical distributions of in-cloud parameters such as liquid water content. These statistics were compiled from actual surface observations as recorded in Standard WBAN forms. Data for a total of 19 stations were obtained and reduced. These stations were selected to be representative of the 19 primary cloud climatological regions defined in previous studies of cloud statistics. Using the data compiled in this study, a limited study was conducted of the hemogeneity of cloud regions, the latitudinal dependence of cloud-type distributions, the dependence of these statistics on sample size, and other factors in the statistics which are of significance to the problem of simulation. The application of the statistics in cloud simulation was investigated. In particular, the inclusion of the new statistics in an expanded multi-step Monte Carlo simulation scheme is suggested and briefly outlined.

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.

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

Lai, Canhai; Xu, Zhijie; Li, Tingwen

In virtual design and scale up of pilot-scale carbon capture systems, the coupled reactive multiphase flow problem must be solved to predict the adsorber’s performance and capture efficiency under various operation conditions. This paper focuses on the detailed computational fluid dynamics (CFD) modeling of a pilot-scale fluidized bed adsorber equipped with vertical cooling tubes. Multiphase Flow with Interphase eXchanges (MFiX), an open-source multiphase flow CFD solver, is used for the simulations with custom code to simulate the chemical reactions and filtered models to capture the effect of the unresolved details in the coarser mesh for simulations with reasonable simulations andmore » manageable computational effort. Previously developed two filtered models for horizontal cylinder drag, heat transfer, and reaction kinetics have been modified to derive the 2D filtered models representing vertical cylinders in the coarse-grid CFD simulations. The effects of the heat exchanger configurations (i.e., horizontal or vertical) on the adsorber’s hydrodynamics and CO2 capture performance are then examined. The simulation result subsequently is compared and contrasted with another predicted by a one-dimensional three-region process model.« less

Physiology driven adaptivity for the numerical solution of the bidomain equations.

PubMed

Whiteley, Jonathan P

2007-09-01

Previous work [Whiteley, J. P. IEEE Trans. Biomed. Eng. 53:2139-2147, 2006] derived a stable, semi-implicit numerical scheme for solving the bidomain equations. This scheme allows the timestep used when solving the bidomain equations numerically to be chosen by accuracy considerations rather than stability considerations. In this study we modify this scheme to allow an adaptive numerical solution in both time and space. The spatial mesh size is determined by the gradient of the transmembrane and extracellular potentials while the timestep is determined by the values of: (i) the fast sodium current; and (ii) the calcium release from junctional sarcoplasmic reticulum to myoplasm current. For two-dimensional simulations presented here, combining the numerical algorithm in the paper cited above with the adaptive algorithm presented here leads to an increase in computational efficiency by a factor of around 250 over previous work, together with significantly less computational memory being required. The speedup for three-dimensional simulations is likely to be more impressive.

TRIM—3D: a three-dimensional model for accurate simulation of shallow water flow

USGS Publications Warehouse

Casulli, Vincenzo; Bertolazzi, Enrico; Cheng, Ralph T.

1993-01-01

A semi-implicit finite difference formulation for the numerical solution of three-dimensional tidal circulation is discussed. The governing equations are the three-dimensional Reynolds equations in which the pressure is assumed to be hydrostatic. A minimal degree of implicitness has been introduced in the finite difference formula so that the resulting algorithm permits the use of large time steps at a minimal computational cost. This formulation includes the simulation of flooding and drying of tidal flats, and is fully vectorizable for an efficient implementation on modern vector computers. The high computational efficiency of this method has made it possible to provide the fine details of circulation structure in complex regions that previous studies were unable to obtain. For proper interpretation of the model results suitable interactive graphics is also an essential tool.

Hydrodynamic Simulations of Protoplanetary Disks with GIZMO

NASA Astrophysics Data System (ADS)

Rice, Malena; Laughlin, Greg

2018-01-01

Over the past several decades, the field of computational fluid dynamics has rapidly advanced as the range of available numerical algorithms and computationally feasible physical problems has expanded. The development of modern numerical solvers has provided a compelling opportunity to reconsider previously obtained results in search for yet undiscovered effects that may be revealed through longer integration times and more precise numerical approaches. In this study, we compare the results of past hydrodynamic disk simulations with those obtained from modern analytical resources. We focus our study on the GIZMO code (Hopkins 2015), which uses meshless methods to solve the homogeneous Euler equations of hydrodynamics while eliminating problems arising as a result of advection between grid cells. By comparing modern simulations with prior results, we hope to provide an improved understanding of the impact of fluid mechanics upon the evolution of protoplanetary disks.

Molecular simulation investigation into the performance of Cu-BTC metal-organic frameworks for carbon dioxide-methane separations.

PubMed

Gutiérrez-Sevillano, Juan José; Caro-Pérez, Alejandro; Dubbeldam, David; Calero, Sofía

2011-12-07

We report a molecular simulation study for Cu-BTC metal-organic frameworks as carbon dioxide-methane separation devices. For this study we have computed adsorption and diffusion of methane and carbon dioxide in the structure, both as pure components and mixtures over the full range of bulk gas compositions. From the single component isotherms, mixture adsorption is predicted using the ideal adsorbed solution theory. These predictions are in very good agreement with our computed mixture isotherms and with previously reported data. Adsorption and diffusion selectivities and preferential sitings are also discussed with the aim to provide new molecular level information for all studied systems.

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

PubMed

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

2003-04-15

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

Evaluation of Airframe Noise Reduction Concepts via Simulations Using a Lattice Boltzmann Approach

NASA Technical Reports Server (NTRS)

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

2015-01-01

Unsteady computations are presented for a high-fidelity, 18% scale, semi-span Gulfstream aircraft model in landing configuration, i.e. flap deflected at 39 degree and main landing gear deployed. The simulations employ the lattice Boltzmann solver PowerFLOW® to simultaneously capture the flow physics and acoustics in the near field. Sound propagation to the far field is obtained using a Ffowcs Williams and Hawkings acoustic analogy approach. In addition to the baseline geometry, which was presented previously, various noise reduction concepts for the flap and main landing gear are simulated. In particular, care is taken to fully resolve the complex geometrical details associated with these concepts in order to capture the resulting intricate local flow field thus enabling accurate prediction of their acoustic behavior. To determine aeroacoustic performance, the farfield noise predicted with the concepts applied is compared to high-fidelity simulations of the untreated baseline configurations. To assess the accuracy of the computed results, the aerodynamic and aeroacoustic impact of the noise reduction concepts is evaluated numerically and compared to experimental results for the same model. The trends and effectiveness of the simulated noise reduction concepts compare well with measured values and demonstrate that the computational approach is capable of capturing the primary effects of the acoustic treatment on a full aircraft model.

Optimization of Simplex Atomizer Inlet Port Configuration through Computational Fluid Dynamics and Experimental Study for Aero-Gas Turbine Applications

NASA Astrophysics Data System (ADS)

Marudhappan, Raja; Chandrasekhar, Udayagiri; Hemachandra Reddy, Koni

2017-10-01

The design of plain orifice simplex atomizer for use in the annular combustion system of 1100 kW turbo shaft engine is optimized. The discrete flow field of jet fuel inside the swirl chamber of the atomizer and up to 1.0 mm downstream of the atomizer exit are simulated using commercial Computational Fluid Dynamics (CFD) software. The Euler-Euler multiphase model is used to solve two sets of momentum equations for liquid and gaseous phases and the volume fraction of each phase is tracked throughout the computational domain. The atomizer design is optimized after performing several 2D axis symmetric analyses with swirl and the optimized inlet port design parameters are used for 3D simulation. The Volume Of Fluid (VOF) multiphase model is used in the simulation. The orifice exit diameter is 0.6 mm. The atomizer is fabricated with the optimized geometric parameters. The performance of the atomizer is tested in the laboratory. The experimental observations are compared with the results obtained from 2D and 3D CFD simulations. The simulated velocity components, pressure field, streamlines and air core dynamics along the atomizer axis are compared to previous research works and found satisfactory. The work has led to a novel approach in the design of pressure swirl atomizer.

Simple, efficient allocation of modelling runs on heterogeneous clusters with MPI

USGS Publications Warehouse

Donato, David I.

2017-01-01

In scientific modelling and computation, the choice of an appropriate method for allocating tasks for parallel processing depends on the computational setting and on the nature of the computation. The allocation of independent but similar computational tasks, such as modelling runs or Monte Carlo trials, among the nodes of a heterogeneous computational cluster is a special case that has not been specifically evaluated previously. A simulation study shows that a method of on-demand (that is, worker-initiated) pulling from a bag of tasks in this case leads to reliably short makespans for computational jobs despite heterogeneity both within and between cluster nodes. A simple reference implementation in the C programming language with the Message Passing Interface (MPI) is provided.

The Application of Neutron Transport Green's Functions to Threat Scenario Simulation

NASA Astrophysics Data System (ADS)

Thoreson, Gregory G.; Schneider, Erich A.; Armstrong, Hirotatsu; van der Hoeven, Christopher A.

2015-02-01

Radiation detectors provide deterrence and defense against nuclear smuggling attempts by scanning vehicles, ships, and pedestrians for radioactive material. Understanding detector performance is crucial to developing novel technologies, architectures, and alarm algorithms. Detection can be modeled through radiation transport simulations; however, modeling a spanning set of threat scenarios over the full transport phase-space is computationally challenging. Previous research has demonstrated Green's functions can simulate photon detector signals by decomposing the scenario space into independently simulated submodels. This paper presents decomposition methods for neutron and time-dependent transport. As a result, neutron detector signals produced from full forward transport simulations can be efficiently reconstructed by sequential application of submodel response functions.

Large Eddy Simulation of "turbulent-like" flow in intracranial aneurysms

NASA Astrophysics Data System (ADS)

Khan, Muhammad Owais; Chnafa, Christophe; Steinman, David A.; Mendez, Simon; Nicoud, Franck

2016-11-01

Hemodynamic forces are thought to contribute to pathogenesis and rupture of intracranial aneurysms (IA). Recent high-resolution patient-specific computational fluid dynamics (CFD) simulations have highlighted the presence of "turbulent-like" flow features, characterized by transient high-frequency flow instabilities. In-vitro studies have shown that such "turbulent-like" flows can lead to lack of endothelial cell orientation and cell depletion, and thus, may also have relevance to IA rupture risk assessment. From a modelling perspective, previous studies have relied on DNS to resolve the small-scale structures in these flows. While accurate, DNS is clinically infeasible due to high computational cost and long simulation times. In this study, we present the applicability of LES for IAs using a LES/blood flow dedicated solver (YALES2BIO) and compare against respective DNS. As a qualitative analysis, we compute time-averaged WSS and OSI maps, as well as, novel frequency-based WSS indices. As a quantitative analysis, we show the differences in POD eigenspectra for LES vs. DNS and wavelet analysis of intra-saccular velocity traces. Differences in two SGS models (i.e. Dynamic Smagorinsky vs. Sigma) are also compared against DNS, and computational gains of LES are discussed.

Validation of Magnetic Resonance Thermometry by Computational Fluid Dynamics

NASA Astrophysics Data System (ADS)

Rydquist, Grant; Owkes, Mark; Verhulst, Claire M.; Benson, Michael J.; Vanpoppel, Bret P.; Burton, Sascha; Eaton, John K.; Elkins, Christopher P.

2016-11-01

Magnetic Resonance Thermometry (MRT) is a new experimental technique that can create fully three-dimensional temperature fields in a noninvasive manner. However, validation is still required to determine the accuracy of measured results. One method of examination is to compare data gathered experimentally to data computed with computational fluid dynamics (CFD). In this study, large-eddy simulations have been performed with the NGA computational platform to generate data for a comparison with previously run MRT experiments. The experimental setup consisted of a heated jet inclined at 30° injected into a larger channel. In the simulations, viscosity and density were scaled according to the local temperature to account for differences in buoyant and viscous forces. A mesh-independent study was performed with 5 mil-, 15 mil- and 45 mil-cell meshes. The program Star-CCM + was used to simulate the complete experimental geometry. This was compared to data generated from NGA. Overall, both programs show good agreement with the experimental data gathered with MRT. With this data, the validity of MRT as a diagnostic tool has been shown and the tool can be used to further our understanding of a range of flows with non-trivial temperature distributions.

Tetrahedral and polyhedral mesh evaluation for cerebral hemodynamic simulation--a comparison.

PubMed

Spiegel, Martin; Redel, Thomas; Zhang, Y; Struffert, Tobias; Hornegger, Joachim; Grossman, Robert G; Doerfler, Arnd; Karmonik, Christof

2009-01-01

Computational fluid dynamic (CFD) based on patient-specific medical imaging data has found widespread use for visualizing and quantifying hemodynamics in cerebrovascular disease such as cerebral aneurysms or stenotic vessels. This paper focuses on optimizing mesh parameters for CFD simulation of cerebral aneurysms. Valid blood flow simulations strongly depend on the mesh quality. Meshes with a coarse spatial resolution may lead to an inaccurate flow pattern. Meshes with a large number of elements will result in unnecessarily high computation time which is undesirable should CFD be used for planning in the interventional setting. Most CFD simulations reported for these vascular pathologies have used tetrahedral meshes. We illustrate the use of polyhedral volume elements in comparison to tetrahedral meshing on two different geometries, a sidewall aneurysm of the internal carotid artery and a basilar bifurcation aneurysm. The spatial mesh resolution ranges between 5,119 and 228,118 volume elements. The evaluation of the different meshes was based on the wall shear stress previously identified as a one possible parameter for assessing aneurysm growth. Polyhedral meshes showed better accuracy, lower memory demand, shorter computational speed and faster convergence behavior (on average 369 iterations less).

Streaming parallel GPU acceleration of large-scale filter-based spiking neural networks.

PubMed

Slażyński, Leszek; Bohte, Sander

2012-01-01

The arrival of graphics processing (GPU) cards suitable for massively parallel computing promises affordable large-scale neural network simulation previously only available at supercomputing facilities. While the raw numbers suggest that GPUs may outperform CPUs by at least an order of magnitude, the challenge is to develop fine-grained parallel algorithms to fully exploit the particulars of GPUs. Computation in a neural network is inherently parallel and thus a natural match for GPU architectures: given inputs, the internal state for each neuron can be updated in parallel. We show that for filter-based spiking neurons, like the Spike Response Model, the additive nature of membrane potential dynamics enables additional update parallelism. This also reduces the accumulation of numerical errors when using single precision computation, the native precision of GPUs. We further show that optimizing simulation algorithms and data structures to the GPU's architecture has a large pay-off: for example, matching iterative neural updating to the memory architecture of the GPU speeds up this simulation step by a factor of three to five. With such optimizations, we can simulate in better-than-realtime plausible spiking neural networks of up to 50 000 neurons, processing over 35 million spiking events per second.

Approximate Algorithms for Computing Spatial Distance Histograms with Accuracy Guarantees

PubMed Central

Grupcev, Vladimir; Yuan, Yongke; Tu, Yi-Cheng; Huang, Jin; Chen, Shaoping; Pandit, Sagar; Weng, Michael

2014-01-01

Particle simulation has become an important research tool in many scientific and engineering fields. Data generated by such simulations impose great challenges to database storage and query processing. One of the queries against particle simulation data, the spatial distance histogram (SDH) query, is the building block of many high-level analytics, and requires quadratic time to compute using a straightforward algorithm. Previous work has developed efficient algorithms that compute exact SDHs. While beating the naive solution, such algorithms are still not practical in processing SDH queries against large-scale simulation data. In this paper, we take a different path to tackle this problem by focusing on approximate algorithms with provable error bounds. We first present a solution derived from the aforementioned exact SDH algorithm, and this solution has running time that is unrelated to the system size N. We also develop a mathematical model to analyze the mechanism that leads to errors in the basic approximate algorithm. Our model provides insights on how the algorithm can be improved to achieve higher accuracy and efficiency. Such insights give rise to a new approximate algorithm with improved time/accuracy tradeoff. Experimental results confirm our analysis. PMID:24693210

Organ radiation exposure with EOS: GATE simulations versus TLD measurements

NASA Astrophysics Data System (ADS)

Clavel, A. H.; Thevenard-Berger, P.; Verdun, F. R.; Létang, J. M.; Darbon, A.

2016-03-01

EOS® is an innovative X-ray imaging system allowing the acquisition of two simultaneous images of a patient in the standing position, during the vertical scan of two orthogonal fan beams. This study aimed to compute organs radiation exposure to a patient, in the particular geometry of this system. Two different positions of the patient in the machine were studied, corresponding to postero-anterior plus left lateral projections (PA-LLAT) and antero-posterior plus right lateral projections (AP-RLAT). To achieve this goal, a Monte-Carlo simulation was developed based on a GATE environment. To model the physical properties of the patient, a computational phantom was produced based on computed tomography scan data of an anthropomorphic phantom. The simulations provided several organs doses, which were compared to previously published dose results measured with Thermo Luminescent Detectors (TLD) in the same conditions and with the same phantom. The simulation results showed a good agreement with measured doses at the TLD locations, for both AP-RLAT and PA-LLAT projections. This study also showed that the organ dose assessed only from a sample of locations, rather than considering the whole organ, introduced significant bias, depending on organs and projections.

Intercomparison of 3D pore-scale flow and solute transport simulation methods

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

Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.

2016-09-01

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include methods that 1) explicitly model the three-dimensional geometry of pore spaces and 2) those that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of class 1, based on direct numerical simulation using computational fluid dynamics (CFD) codes, against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of class 1 based on the immersed-boundary method (IMB),more » lattice Boltzmann method (LBM), smoothed particle hydrodynamics (SPH), as well as a model of class 2 (a pore-network model or PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and nonreactive solute transport, and intercompare the model results with previously reported experimental observations. Experimental observations are limited to measured pore-scale velocities, so solute transport comparisons are made only among the various models. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations).« less

Evaluation of a Computational Model of Situational Awareness

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Acceleration of the chemistry solver for modeling DI engine combustion using dynamic adaptive chemistry (DAC) schemes

NASA Astrophysics Data System (ADS)

Shi, Yu; Liang, Long; Ge, Hai-Wen; Reitz, Rolf D.

2010-03-01

Acceleration of the chemistry solver for engine combustion is of much interest due to the fact that in practical engine simulations extensive computational time is spent solving the fuel oxidation and emission formation chemistry. A dynamic adaptive chemistry (DAC) scheme based on a directed relation graph error propagation (DRGEP) method has been applied to study homogeneous charge compression ignition (HCCI) engine combustion with detailed chemistry (over 500 species) previously using an R-value-based breadth-first search (RBFS) algorithm, which significantly reduced computational times (by as much as 30-fold). The present paper extends the use of this on-the-fly kinetic mechanism reduction scheme to model combustion in direct-injection (DI) engines. It was found that the DAC scheme becomes less efficient when applied to DI engine simulations using a kinetic mechanism of relatively small size and the accuracy of the original DAC scheme decreases for conventional non-premixed combustion engine. The present study also focuses on determination of search-initiating species, involvement of the NOx chemistry, selection of a proper error tolerance, as well as treatment of the interaction of chemical heat release and the fuel spray. Both the DAC schemes were integrated into the ERC KIVA-3v2 code, and simulations were conducted to compare the two schemes. In general, the present DAC scheme has better efficiency and similar accuracy compared to the previous DAC scheme. The efficiency depends on the size of the chemical kinetics mechanism used and the engine operating conditions. For cases using a small n-heptane kinetic mechanism of 34 species, 30% of the computational time is saved, and 50% for a larger n-heptane kinetic mechanism of 61 species. The paper also demonstrates that by combining the present DAC scheme with an adaptive multi-grid chemistry (AMC) solver, it is feasible to simulate a direct-injection engine using a detailed n-heptane mechanism with 543 species with practical computer time.

Virtual reality simulators: valuable surgical skills trainers or video games?

PubMed

Willis, Ross E; Gomez, Pedro Pablo; Ivatury, Srinivas J; Mitra, Hari S; Van Sickle, Kent R

2014-01-01

Virtual reality (VR) and physical model (PM) simulators differ in terms of whether the trainee is manipulating actual 3-dimensional objects (PM) or computer-generated 3-dimensional objects (VR). Much like video games (VG), VR simulators utilize computer-generated graphics. These differences may have profound effects on the utility of VR and PM training platforms. In this study, we aimed to determine whether a relationship exists between VR, PM, and VG platforms. VR and PM simulators for laparoscopic camera navigation ([LCN], experiment 1) and flexible endoscopy ([FE] experiment 2) were used in this study. In experiment 1, 20 laparoscopic novices played VG and performed 0° and 30° LCN exercises on VR and PM simulators. In experiment 2, 20 FE novices played VG and performed colonoscopy exercises on VR and PM simulators. In both experiments, VG performance was correlated with VR performance but not with PM performance. Performance on VR simulators did not correlate with performance on respective PM models. VR environments may be more like VG than previously thought. © 2013 Published by Association of Program Directors in Surgery on behalf of Association of Program Directors in Surgery.

Relativistic interpretation of Newtonian simulations for cosmic structure formation

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

Fidler, Christian; Tram, Thomas; Crittenden, Robert

2016-09-01

The standard numerical tools for studying non-linear collapse of matter are Newtonian N -body simulations. Previous work has shown that these simulations are in accordance with General Relativity (GR) up to first order in perturbation theory, provided that the effects from radiation can be neglected. In this paper we show that the present day matter density receives more than 1% corrections from radiation on large scales if Newtonian simulations are initialised before z =50. We provide a relativistic framework in which unmodified Newtonian simulations are compatible with linear GR even in the presence of radiation. Our idea is to usemore » GR perturbation theory to keep track of the evolution of relativistic species and the relativistic space-time consistent with the Newtonian trajectories computed in N -body simulations. If metric potentials are sufficiently small, they can be computed using a first-order Einstein–Boltzmann code such as CLASS. We make this idea rigorous by defining a class of GR gauges, the Newtonian motion gauges, which are defined such that matter particles follow Newtonian trajectories. We construct a simple example of a relativistic space-time within which unmodified Newtonian simulations can be interpreted.« less

Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits

NASA Astrophysics Data System (ADS)

Spiriti, Justin; Zuckerman, Daniel M.

2015-12-01

Traditional coarse-graining based on a reduced number of interaction sites often entails a significant sacrifice of chemical accuracy. As an alternative, we present a method for simulating large systems composed of interacting macromolecules using an energy tabulation strategy previously devised for small rigid molecules or molecular fragments [S. Lettieri and D. M. Zuckerman, J. Comput. Chem. 33, 268-275 (2012); J. Spiriti and D. M. Zuckerman, J. Chem. Theory Comput. 10, 5161-5177 (2014)]. We treat proteins as rigid and construct distance and orientation-dependent tables of the interaction energy between them. Arbitrarily detailed interactions may be incorporated into the tables, but as a proof-of-principle, we tabulate a simple α-carbon Gō-like model for interactions between dimeric subunits of the hepatitis B viral capsid. This model is significantly more structurally realistic than previous models used in capsid assembly studies. We are able to increase the speed of Monte Carlo simulations by a factor of up to 6700 compared to simulations without tables, with only minimal further loss in accuracy. To obtain further enhancement of sampling, we combine tabulation with the weighted ensemble (WE) method, in which multiple parallel simulations are occasionally replicated or pruned in order to sample targeted regions of a reaction coordinate space. In the initial study reported here, WE is able to yield pathways of the final ˜25% of the assembly process.

Validation of the SimSET simulation package for modeling the Siemens Biograph mCT PET scanner

NASA Astrophysics Data System (ADS)

Poon, Jonathan K.; Dahlbom, Magnus L.; Casey, Michael E.; Qi, Jinyi; Cherry, Simon R.; Badawi, Ramsey D.

2015-02-01

Monte Carlo simulation provides a valuable tool in performance assessment and optimization of system design parameters for PET scanners. SimSET is a popular Monte Carlo simulation toolkit that features fast simulation time, as well as variance reduction tools to further enhance computational efficiency. However, SimSET has lacked the ability to simulate block detectors until its most recent release. Our goal is to validate new features of SimSET by developing a simulation model of the Siemens Biograph mCT PET scanner and comparing the results to a simulation model developed in the GATE simulation suite and to experimental results. We used the NEMA NU-2 2007 scatter fraction, count rates, and spatial resolution protocols to validate the SimSET simulation model and its new features. The SimSET model overestimated the experimental results of the count rate tests by 11-23% and the spatial resolution test by 13-28%, which is comparable to previous validation studies of other PET scanners in the literature. The difference between the SimSET and GATE simulation was approximately 4-8% for the count rate test and approximately 3-11% for the spatial resolution test. In terms of computational time, SimSET performed simulations approximately 11 times faster than GATE simulations. The new block detector model in SimSET offers a fast and reasonably accurate simulation toolkit for PET imaging applications.

[Acquiring skills in malignant hyperthermia crisis management: comparison of high-fidelity simulation versus computer-based case study].

PubMed

Mejía, Vilma; Gonzalez, Carlos; Delfino, Alejandro E; Altermatt, Fernando R; Corvetto, Marcia A

The primary purpose of this study was to compare the effect of high fidelity simulation versus a computer-based case solving self-study, in skills acquisition about malignant hyperthermia on first year anesthesiology residents. After institutional ethical committee approval, 31 first year anesthesiology residents were enrolled in this prospective randomized single-blinded study. Participants were randomized to either a High Fidelity Simulation Scenario or a computer-based Case Study about malignant hyperthermia. After the intervention, all subjects' performance in was assessed through a high fidelity simulation scenario using a previously validated assessment rubric. Additionally, knowledge tests and a satisfaction survey were applied. Finally, a semi-structured interview was done to assess self-perception of reasoning process and decision-making. 28 first year residents finished successfully the study. Resident's management skill scores were globally higher in High Fidelity Simulation versus Case Study, however they were significant in 4 of the 8 performance rubric elements: recognize signs and symptoms (p = 0.025), prioritization of initial actions of management (p = 0.003), recognize complications (p = 0.025) and communication (p = 0.025). Average scores from pre- and post-test knowledge questionnaires improved from 74% to 85% in the High Fidelity Simulation group, and decreased from 78% to 75% in the Case Study group (p = 0.032). Regarding the qualitative analysis, there was no difference in factors influencing the student's process of reasoning and decision-making with both teaching strategies. Simulation-based training with a malignant hyperthermia high-fidelity scenario was superior to computer-based case study, improving knowledge and skills in malignant hyperthermia crisis management, with a very good satisfaction level in anesthesia residents. Copyright © 2018 Sociedade Brasileira de Anestesiologia. Publicado por Elsevier Editora Ltda. All rights reserved.

Parametric Simulations of the Great Dark Spots of Neptune

NASA Astrophysics Data System (ADS)

Deng, Xiaolong; Le Beau, R.

2006-09-01

Observations by Voyager II and the Hubble Space Telescope of the Great Dark Spots (GDS) of Neptune suggest that large vortices with lifespans of years are not uncommon occurrences in the atmosphere of Neptune. The variability of these features over time, in particular the complex motions of GDS-89, make them challenging candidates to simulate in atmospheric models. Previously, using the Explicit Planetary Isentropic-Coordinate (EPIC) General Circulation Model, LeBeau and Dowling (1998) simulated the GDS-like vortex features. Qualitatively, the drift, oscillation, and tail-like features of GDS-89 were recreated, although precise numerical matches were only achieved for the meridional drift rate. In 2001, Stratman et al. applied EPIC to simulate the formation of bright companion clouds to the Great Dark Spots. In 2006, Dowling et al. presented a new version of EPIC, which includes hybrid vertical coordinate, cloud physics, advanced chemistry, and new turbulence models. With the new version of EPIC, more observation results, and more powerful computers, it is the time to revisit CFD simulations of the Neptune's atmosphere and do more detailed work on GDS-like vortices. In this presentation, we apply the new version of EPIC to simulate GDS-89. We test the influences of different parameters in the EPIC model: potential vorticity gradient, wind profile, initial latitude, vortex shape, and vertical structure. The observed motions, especially the latitudinal drift and oscillations in orientation angle and aspect ratio, are used as diagnostics of these unobserved atmospheric conditions. Increased computing power allows for more refined and longer simulations and greater coverage of the parameter space than previous efforts. Improved quantitative results have been achieved, including voritices with near eight-day oscillations and comparable variations in shape to GDS-89. This research has been supported by Kentucky NASA EPSCoR.

Influence of grid resolution, parcel size and drag models on bubbling fluidized bed simulation

DOE PAGES

Lu, Liqiang; Konan, Arthur; Benyahia, Sofiane

2017-06-02

Here in this paper, a bubbling fluidized bed is simulated with different numerical parameters, such as grid resolution and parcel size. We examined also the effect of using two homogeneous drag correlations and a heterogeneous drag based on the energy minimization method. A fast and reliable bubble detection algorithm was developed based on the connected component labeling. The radial and axial solids volume fraction profiles are compared with experiment data and previous simulation results. These results show a significant influence of drag models on bubble size and voidage distributions and a much less dependence on numerical parameters. With a heterogeneousmore » drag model that accounts for sub-scale structures, the void fraction in the bubbling fluidized bed can be well captured with coarse grid and large computation parcels. Refining the CFD grid and reducing the parcel size can improve the simulation results but with a large increase in computation cost.« less

Eulerian-Lagrangian Simulations of Transonic Flutter Instabilities

NASA Technical Reports Server (NTRS)

Bendiksen, Oddvar O.

1994-01-01

This paper presents an overview of recent applications of Eulerian-Lagrangian computational schemes in simulating transonic flutter instabilities. This approach, the fluid-structure system is treated as a single continuum dynamics problem, by switching from an Eulerian to a Lagrangian formulation at the fluid-structure boundary. This computational approach effectively eliminates the phase integration errors associated with previous methods, where the fluid and structure are integrated sequentially using different schemes. The formulation is based on Hamilton's Principle in mixed coordinates, and both finite volume and finite element discretization schemes are considered. Results from numerical simulations of transonic flutter instabilities are presented for isolated wings, thin panels, and turbomachinery blades. The results suggest that the method is capable of reproducing the energy exchange between the fluid and the structure with significantly less error than existing methods. Localized flutter modes and panel flutter modes involving traveling waves can also be simulated effectively with no a priori knowledge of the type of instability involved.

Dual-energy contrast-enhanced digital mammography (DE-CEDM): optimization on digital subtraction with practical x-ray low/high-energy spectra

NASA Astrophysics Data System (ADS)

Chen, Biao; Jing, Zhenxue; Smith, Andrew P.; Parikh, Samir; Parisky, Yuri

2006-03-01

Dual-energy contrast enhanced digital mammography (DE-CEDM), which is based upon the digital subtraction of low/high-energy image pairs acquired before/after the administration of contrast agents, may provide physicians physiologic and morphologic information of breast lesions and help characterize their probability of malignancy. This paper proposes to use only one pair of post-contrast low / high-energy images to obtain digitally subtracted dual-energy contrast-enhanced images with an optimal weighting factor deduced from simulated characteristics of the imaging chain. Based upon our previous CEDM framework, quantitative characteristics of the materials and imaging components in the x-ray imaging chain, including x-ray tube (tungsten) spectrum, filters, breast tissues / lesions, contrast agents (non-ionized iodine solution), and selenium detector, were systemically modeled. Using the base-material (polyethylene-PMMA) decomposition method based on entrance low / high-energy x-ray spectra and breast thickness, the optimal weighting factor was calculated to cancel the contrast between fatty and glandular tissues while enhancing the contrast of iodized lesions. By contrast, previous work determined the optimal weighting factor through either a calibration step or through acquisition of a pre-contrast low/high-energy image pair. Computer simulations were conducted to determine weighting factors, lesions' contrast signal values, and dose levels as functions of x-ray techniques and breast thicknesses. Phantom and clinical feasibility studies were performed on a modified Selenia full field digital mammography system to verify the proposed method and computer-simulated results. The resultant conclusions from the computer simulations and phantom/clinical feasibility studies will be used in the upcoming clinical study.

Using Virtual Reality with and without Gaming Attributes for Academic Achievement

ERIC Educational Resources Information Center

Vogel, Jennifer J.; Greenwood-Ericksen, Adams; Cannon-Bowers, Jan; Bowers, Clint A.

2006-01-01

A subcategory of computer-assisted instruction (CAI), games have additional attributes such as motivation, reward, interactivity, score, and challenge. This study used a quasi-experimental design to determine if previous findings generalize to non simulation-based game designs. Researchers observed significant improvement in the overall population…

Problem Solving Under Time-Constraints.

ERIC Educational Resources Information Center

Richardson, Michael; Hunt, Earl

A model of how automated and controlled processing can be mixed in computer simulations of problem solving is proposed. It is based on previous work by Hunt and Lansman (1983), who developed a model of problem solving that could reproduce the data obtained with several attention and performance paradigms, extending production-system notation to…

Teaching Petri Nets Using P3

ERIC Educational Resources Information Center

Gasevic, Dragan; Devedzic, Vladan

2004-01-01

This paper presents Petri net software tool P3 that is developed for training purposes of the Architecture and organization of computers (AOC) course. The P3 has the following features: graphical modeling interface, interactive simulation by single and parallel (with previous conflict resolution) transition firing, two well-known Petri net…

Direct Numerical Simulation of an Airfoil with Sand Grain Roughness on the Leading Edge

NASA Technical Reports Server (NTRS)

Ribeiro, Andre F. P.; Casalino, Damiano; Fares, Ehab; Choudhari, Meelan

2016-01-01

As part of a computational study of acoustic radiation due to the passage of turbulent boundary layer eddies over the trailing edge of an airfoil, the Lattice-Boltzmann method is used to perform direct numerical simulations of compressible, low Mach number flow past an NACA 0012 airfoil at zero degrees angle of attack. The chord Reynolds number of approximately 0.657 million models one of the test conditions from a previous experiment by Brooks, Pope, and Marcolini at NASA Langley Research Center. A unique feature of these simulations involves direct modeling of the sand grain roughness on the leading edge, which was used in the abovementioned experiment to trip the boundary layer to fully turbulent flow. This report documents the findings of preliminary, proof-of-concept simulations based on a narrow spanwise domain and a limited time interval. The inclusion of fully-resolved leading edge roughness in this simulation leads to significantly earlier transition than that in the absence of any roughness. The simulation data is used in conjunction with both the Ffowcs Williams-Hawkings acoustic analogy and a semi-analytical model by Roger and Moreau to predict the farfield noise. The encouraging agreement between the computed noise spectrum and that measured in the experiment indicates the potential payoff from a full-fledged numerical investigation based on the current approach. Analysis of the computed data is used to identify the required improvements to the preliminary simulations described herein.

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

PubMed

Salis, Howard; Kaznessis, Yiannis

2005-02-01

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

A parallel interaction potential approach coupled with the immersed boundary method for fully resolved simulations of deformable interfaces and membranes

NASA Astrophysics Data System (ADS)

Spandan, Vamsi; Meschini, Valentina; Ostilla-Mónico, Rodolfo; Lohse, Detlef; Querzoli, Giorgio; de Tullio, Marco D.; Verzicco, Roberto

2017-11-01

In this paper we show and discuss how the deformation dynamics of closed liquid-liquid interfaces (for example drops and bubbles) can be replicated with use of a phenomenological interaction potential model. This new approach to simulate liquid-liquid interfaces is based on the fundamental principle of minimum potential energy where the total potential energy depends on the extent of deformation of a spring network distributed on the surface of the immersed drop or bubble. Simulating liquid-liquid interfaces using this model require computing ad-hoc elastic constants which is done through a reverse-engineered approach. The results from our simulations agree very well with previous studies on the deformation of drops in standard flow configurations such as a deforming drop in a shear flow or cross flow. The interaction potential model is highly versatile, computationally efficient and can be easily incorporated into generic single phase fluid solvers to also simulate complex fluid-structure interaction problems. This is shown by simulating flow in the left ventricle of the heart with mechanical and natural mitral valves where the imposed flow, motion of ventricle and valves dynamically govern the behaviour of each other. Results from these simulations are compared with ad-hoc in-house experimental measurements. Finally, we present a simple and easy to implement parallelisation scheme, as high performance computing is unavoidable when studying large scale problems involving several thousands of simultaneously deforming bodies in highly turbulent flows.

Stochastic Evolutionary Algorithms for Planning Robot Paths

NASA Technical Reports Server (NTRS)

Fink, Wolfgang; Aghazarian, Hrand; Huntsberger, Terrance; Terrile, Richard

2006-01-01

A computer program implements stochastic evolutionary algorithms for planning and optimizing collision-free paths for robots and their jointed limbs. Stochastic evolutionary algorithms can be made to produce acceptably close approximations to exact, optimal solutions for path-planning problems while often demanding much less computation than do exhaustive-search and deterministic inverse-kinematics algorithms that have been used previously for this purpose. Hence, the present software is better suited for application aboard robots having limited computing capabilities (see figure). The stochastic aspect lies in the use of simulated annealing to (1) prevent trapping of an optimization algorithm in local minima of an energy-like error measure by which the fitness of a trial solution is evaluated while (2) ensuring that the entire multidimensional configuration and parameter space of the path-planning problem is sampled efficiently with respect to both robot joint angles and computation time. Simulated annealing is an established technique for avoiding local minima in multidimensional optimization problems, but has not, until now, been applied to planning collision-free robot paths by use of low-power computers.

Allan deviation computations of a linear frequency synthesizer system using frequency domain techniques

NASA Technical Reports Server (NTRS)

Wu, Andy

1995-01-01

Allan Deviation computations of linear frequency synthesizer systems have been reported previously using real-time simulations. Even though it takes less time compared with the actual measurement, it is still very time consuming to compute the Allan Deviation for long sample times with the desired confidence level. Also noises, such as flicker phase noise and flicker frequency noise, can not be simulated precisely. The use of frequency domain techniques can overcome these drawbacks. In this paper the system error model of a fictitious linear frequency synthesizer is developed and its performance using a Cesium (Cs) atomic frequency standard (AFS) as a reference is evaluated using frequency domain techniques. For a linear timing system, the power spectral density at the system output can be computed with known system transfer functions and known power spectral densities from the input noise sources. The resulting power spectral density can then be used to compute the Allan Variance at the system output. Sensitivities of the Allan Variance at the system output to each of its independent input noises are obtained, and they are valuable for design trade-off and trouble-shooting.

Simulating and assessing boson sampling experiments with phase-space representations

NASA Astrophysics Data System (ADS)

Opanchuk, Bogdan; Rosales-Zárate, Laura; Reid, Margaret D.; Drummond, Peter D.

2018-04-01

The search for new, application-specific quantum computers designed to outperform any classical computer is driven by the ending of Moore's law and the quantum advantages potentially obtainable. Photonic networks are promising examples, with experimental demonstrations and potential for obtaining a quantum computer to solve problems believed classically impossible. This introduces a challenge: how does one design or understand such photonic networks? One must be able to calculate observables using general methods capable of treating arbitrary inputs, dissipation, and noise. We develop complex phase-space software for simulating these photonic networks, and apply this to boson sampling experiments. Our techniques give sampling errors orders of magnitude lower than experimental correlation measurements for the same number of samples. We show that these techniques remove systematic errors in previous algorithms for estimating correlations, with large improvements in errors in some cases. In addition, we obtain a scalable channel-combination strategy for assessment of boson sampling devices.

Test and evaluation of a multifunction keyboard and a dedicated keyboard for control of a flight management computer

NASA Technical Reports Server (NTRS)

Crane, J. M.; Boucek, G. P., Jr.; Smith, W. D.

1986-01-01

A flight management computer (FMC) control display unit (CDU) test was conducted to compare two types of input devices: a fixed legend (dedicated) keyboard and a programmable legend (multifunction) keyboard. The task used for comparison was operation of the flight management computer for the Boeing 737-300. The same tasks were performed by twelve pilots on the FMC control display unit configured with a programmable legend keyboard and with the currently used B737-300 dedicated keyboard. Flight simulator work activity levels and input task complexity were varied during each pilot session. Half of the points tested were previously familiar with the B737-300 dedicated keyboard CDU and half had no prior experience with it. The data collected included simulator flight parameters, keystroke time and sequences, and pilot questionnaire responses. A timeline analysis was also used for evaluation of the two keyboard concepts.

A Model of In vitro Plasticity at the Parallel Fiber—Molecular Layer Interneuron Synapses

PubMed Central

Lennon, William; Yamazaki, Tadashi; Hecht-Nielsen, Robert

2015-01-01

Theoretical and computational models of the cerebellum typically focus on the role of parallel fiber (PF)—Purkinje cell (PKJ) synapses for learned behavior, but few emphasize the role of the molecular layer interneurons (MLIs)—the stellate and basket cells. A number of recent experimental results suggest the role of MLIs is more important than previous models put forth. We investigate learning at PF—MLI synapses and propose a mathematical model to describe plasticity at this synapse. We perform computer simulations with this form of learning using a spiking neuron model of the MLI and show that it reproduces six in vitro experimental results in addition to simulating four novel protocols. Further, we show how this plasticity model can predict the results of other experimental protocols that are not simulated. Finally, we hypothesize what the biological mechanisms are for changes in synaptic efficacy that embody the phenomenological model proposed here. PMID:26733856

HIV-1 Strategies of Immune Evasion

NASA Astrophysics Data System (ADS)

Castiglione, F.; Bernaschi, M.

We simulate the progression of the HIV-1 infection in untreated host organisms. The phenotype features of the virus are represented by the replication rate, the probability of activating the transcription, the mutation rate and the capacity to stimulate an immune response (the so-called immunogenicity). It is very difficult to study in-vivo or in-vitro how these characteristics of the virus influence the evolution of the disease. Therefore we resorted to simulations based on a computer model validated in previous studies. We observe, by means of computer experiments, that the virus continuously evolves under the selective pressure of an immune response whose effectiveness downgrades along with the disease progression. The results of the simulations show that immunogenicity is the most important factor in determining the rate of disease progression but, by itself, it is not sufficient to drive the disease to a conclusion in all cases.

Down to the roughness scale assessment of piston-ring/liner contacts

NASA Astrophysics Data System (ADS)

Checo, H. M.; Jaramillo, A.; Ausas, R. F.; Jai, M.; Buscaglia, G. C.

2017-02-01

The effects of surface roughness in hydrodynamic bearings been accounted for through several approaches, the most widely used being averaging or stochastic techniques. With these the surface is not treated “as it is”, but by means of an assumed probability distribution for the roughness. The so called direct, deterministic or measured-surface simulation) solve the lubrication problem with realistic surfaces down to the roughness scale. This leads to expensive computational problems. Most researchers have tackled this problem considering non-moving surfaces and neglecting the ring dynamics to reduce the computational burden. What is proposed here is to solve the fully-deterministic simulation both in space and in time, so that the actual movement of the surfaces and the rings dynamics are taken into account. This simulation is much more complex than previous ones, as it is intrinsically transient. The feasibility of these fully-deterministic simulations is illustrated two cases: fully deterministic simulation of liner surfaces with diverse finishings (honed and coated bores) with constant piston velocity and load on the ring and also in real engine conditions.

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

Collins, William D; Johansen, Hans; Evans, Katherine J

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 andmore » 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.« less

Internet-based system for simulation-based medical planning for cardiovascular disease.

PubMed

Steele, Brooke N; Draney, Mary T; Ku, Joy P; Taylor, Charles A

2003-06-01

Current practice in vascular surgery utilizes only diagnostic and empirical data to plan treatments, which does not enable quantitative a priori prediction of the outcomes of interventions. We have previously described simulation-based medical planning methods to model blood flow in arteries and plan medical treatments based on physiologic models. An important consideration for the design of these patient-specific modeling systems is the accessibility to physicians with modest computational resources. We describe a simulation-based medical planning environment developed for the World Wide Web (WWW) using the Virtual Reality Modeling Language (VRML) and the Java programming language.

Transient Three-Dimensional Side Load Analysis of Out-of-Round Film Cooled Nozzles

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Lin, Jeff; Ruf, Joe; Guidos, Mike

2010-01-01

The objective of this study is to investigate the effect of nozzle out-of-roundness on the transient startup side loads. The out-of-roundness could be the result of asymmetric loads induced by hardware attached to the nozzle, asymmetric internal stresses induced by previous tests and/or deformation, such as creep, from previous tests. The rocket engine studied encompasses a regeneratively cooled thrust chamber and a film cooled nozzle extension with film coolant distributed from a turbine exhaust manifold. The computational methodology is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, and a transient inlet history based on an engine system simulation. Transient startup computations were performed with the out-of-roundness achieved by four degrees of ovalization of the nozzle: one perfectly round, one slightly out-of-round, one more out-of-round, and one significantly out-of-round. The computed side load physics caused by the nozzle out-of-roundness and its effect on nozzle side load are reported and discussed.

Enhancement of CFD validation exercise along the roof profile of a low-rise building

NASA Astrophysics Data System (ADS)

Deraman, S. N. C.; Majid, T. A.; Zaini, S. S.; Yahya, W. N. W.; Abdullah, J.; Ismail, M. A.

2018-04-01

The aim of this study is to enhance the validation of CFD exercise along the roof profile of a low-rise building. An isolated gabled-roof house having 26.6° roof pitch was simulated to obtain the pressure coefficient around the house. Validation of CFD analysis with experimental data requires many input parameters. This study performed CFD simulation based on the data from a previous study. Where the input parameters were not clearly stated, new input parameters were established from the open literatures. The numerical simulations were performed in FLUENT 14.0 by applying the Computational Fluid Dynamics (CFD) approach based on steady RANS equation together with RNG k-ɛ model. Hence, the result from CFD was analysed by using quantitative test (statistical analysis) and compared with CFD results from the previous study. The statistical analysis results from ANOVA test and error measure showed that the CFD results from the current study produced good agreement and exhibited the closest error compared to the previous study. All the input data used in this study can be extended to other types of CFD simulation involving wind flow over an isolated single storey house.

3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model.

PubMed

Spühler, Jeannette H; Jansson, Johan; Jansson, Niclas; Hoffman, Johan

2018-01-01

Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework.

3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model

PubMed Central

Spühler, Jeannette H.; Jansson, Johan; Jansson, Niclas; Hoffman, Johan

2018-01-01

Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework. PMID:29713288

Efficient generation of low-energy folded states of a model protein

NASA Astrophysics Data System (ADS)

Gordon, Heather L.; Kwan, Wai Kei; Gong, Chunhang; Larrass, Stefan; Rothstein, Stuart M.

2003-01-01

A number of short simulated annealing runs are performed on a highly-frustrated 46-"residue" off-lattice model protein. We perform, in an iterative fashion, a principal component analysis of the 946 nonbonded interbead distances, followed by two varieties of cluster analyses: hierarchical and k-means clustering. We identify several distinct sets of conformations with reasonably consistent cluster membership. Nonbonded distance constraints are derived for each cluster and are employed within a distance geometry approach to generate many new conformations, previously unidentified by the simulated annealing experiments. Subsequent analyses suggest that these new conformations are members of the parent clusters from which they were generated. Furthermore, several novel, previously unobserved structures with low energy were uncovered, augmenting the ensemble of simulated annealing results, and providing a complete distribution of low-energy states. The computational cost of this approach to generating low-energy conformations is small when compared to the expense of further Monte Carlo simulated annealing runs.

Direct Numerical Simulations of an Unpremixed Turbulent Jet Flame

DTIC Science & Technology

1988-03-01

shear layer. As the vortices reach the outflow boundary, the zero-gradient condition seems to allow them to travel out of the computational domain...ei Ii-t salp . Thiey- used pint ihe ustial d ependent variales. I1 Imerefre for r’- H(1/2 act1ig flows tile dimniensiomalit v of tilie vystveni call...seems to allow them to travel out of the computational domain. As mentioned in the previous section, the errors associated with this boundary condition

A Physics-driven Neural Networks-based Simulation System (PhyNNeSS) for multimodal interactive virtual environments involving nonlinear deformable objects

PubMed Central

De, Suvranu; Deo, Dhannanjay; Sankaranarayanan, Ganesh; Arikatla, Venkata S.

2012-01-01

Background While an update rate of 30 Hz is considered adequate for real time graphics, a much higher update rate of about 1 kHz is necessary for haptics. Physics-based modeling of deformable objects, especially when large nonlinear deformations and complex nonlinear material properties are involved, at these very high rates is one of the most challenging tasks in the development of real time simulation systems. While some specialized solutions exist, there is no general solution for arbitrary nonlinearities. Methods In this work we present PhyNNeSS - a Physics-driven Neural Networks-based Simulation System - to address this long-standing technical challenge. The first step is an off-line pre-computation step in which a database is generated by applying carefully prescribed displacements to each node of the finite element models of the deformable objects. In the next step, the data is condensed into a set of coefficients describing neurons of a Radial Basis Function network (RBFN). During real-time computation, these neural networks are used to reconstruct the deformation fields as well as the interaction forces. Results We present realistic simulation examples from interactive surgical simulation with real time force feedback. As an example, we have developed a deformable human stomach model and a Penrose-drain model used in the Fundamentals of Laparoscopic Surgery (FLS) training tool box. Conclusions A unique computational modeling system has been developed that is capable of simulating the response of nonlinear deformable objects in real time. The method distinguishes itself from previous efforts in that a systematic physics-based pre-computational step allows training of neural networks which may be used in real time simulations. We show, through careful error analysis, that the scheme is scalable, with the accuracy being controlled by the number of neurons used in the simulation. PhyNNeSS has been integrated into SoFMIS (Software Framework for Multimodal Interactive Simulation) for general use. PMID:22629108

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

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

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

2010-11-15

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

Automated social skills training with audiovisual information.

PubMed

Tanaka, Hiroki; Sakti, Sakriani; Neubig, Graham; Negoro, Hideki; Iwasaka, Hidemi; Nakamura, Satoshi

2016-08-01

People with social communication difficulties tend to have superior skills using computers, and as a result computer-based social skills training systems are flourishing. Social skills training, performed by human trainers, is a well-established method to obtain appropriate skills in social interaction. Previous works have attempted to automate one or several parts of social skills training through human-computer interaction. However, while previous work on simulating social skills training considered only acoustic and linguistic features, human social skills trainers take into account visual features (e.g. facial expression, posture). In this paper, we create and evaluate a social skills training system that closes this gap by considering audiovisual features regarding ratio of smiling, yaw, and pitch. An experimental evaluation measures the difference in effectiveness of social skill training when using audio features and audiovisual features. Results showed that the visual features were effective to improve users' social skills.

Simulating Self-Assembly with Simple Models

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

Results from recent molecular dynamics simulations of virus capsid self-assembly are described. The model is based on rigid trapezoidal particles designed to form polyhedral shells of size 60, together with an atomistic solvent. The underlying bonding process is fully reversible. More extensive computations are required than in previous work on icosahedral shells built from triangular particles, but the outcome is a high yield of closed shells. Intermediate clusters have a variety of forms, and bond counts provide a useful classification scheme

Interleaved concatenated codes: new perspectives on approaching the Shannon limit.

PubMed

Viterbi, A J; Viterbi, A M; Sindhushayana, N T

1997-09-02

The last few years have witnessed a significant decrease in the gap between the Shannon channel capacity limit and what is practically achievable. Progress has resulted from novel extensions of previously known coding techniques involving interleaved concatenated codes. A considerable body of simulation results is now available, supported by an important but limited theoretical basis. This paper presents a computational technique which further ties simulation results to the known theory and reveals a considerable reduction in the complexity required to approach the Shannon limit.

A Simple and Efficient Computational Approach to Chafed Cable Time-Domain Reflectometry Signature Prediction

NASA Technical Reports Server (NTRS)

Kowalski, Marc Edward

2009-01-01

A method for the prediction of time-domain signatures of chafed coaxial cables is presented. The method is quasi-static in nature, and is thus efficient enough to be included in inference and inversion routines. Unlike previous models proposed, no restriction on the geometry or size of the chafe is required in the present approach. The model is validated and its speed is illustrated via comparison to simulations from a commercial, three-dimensional electromagnetic simulator.

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

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

Computational open-channel hydraulics for movable-bed problems

USGS Publications Warehouse

Lai, Chintu; ,

1990-01-01

As a major branch of computational hydraulics, notable advances have been made in numerical modeling of unsteady open-channel flow since the beginning of the computer age. According to the broader definition and scope of 'computational hydraulics,' the basic concepts and technology of modeling unsteady open-channel flow have been systematically studied previously. As a natural extension, computational open-channel hydraulics for movable-bed problems are addressed in this paper. The introduction of the multimode method of characteristics (MMOC) has made the modeling of this class of unsteady flows both practical and effective. New modeling techniques are developed, thereby shedding light on several aspects of computational hydraulics. Some special features of movable-bed channel-flow simulation are discussed here in the same order as given by the author in the fixed-bed case.

Transport and collision dynamics in periodic asymmetric obstacle arrays: Rational design of microfluidic rare-cell immunocapture devices

NASA Astrophysics Data System (ADS)

Gleghorn, Jason P.; Smith, James P.; Kirby, Brian J.

2013-09-01

Microfluidic obstacle arrays have been used in numerous applications, and their ability to sort particles or capture rare cells from complex samples has broad and impactful applications in biology and medicine. We have investigated the transport and collision dynamics of particles in periodic obstacle arrays to guide the design of convective, rather than diffusive, transport-based immunocapture microdevices. Ballistic and full computational fluid dynamics simulations are used to understand the collision modes that evolve in cylindrical obstacle arrays with various geometries. We identify previously unrecognized collision mode structures and differential size-based collision frequencies that emerge from these arrays. Previous descriptions of transverse displacements that assume unidirectional flow in these obstacle arrays cannot capture mode transitions properly as these descriptions fail to capture the dependence of the mode transitions on column spacing and the attendant change in the flow field. Using these analytical and computational simulations, we elucidate design parameters that induce high collision rates for all particles larger than a threshold size or selectively increase collision frequencies for a narrow range of particle sizes within a polydisperse population. Furthermore, we investigate how the particle Péclet number affects collision dynamics and mode transitions and demonstrate that experimental observations from various obstacle array geometries are well described by our computational model.

Hierarchical neural network model of the visual system determining figure/ground relation

NASA Astrophysics Data System (ADS)

Kikuchi, Masayuki

2017-07-01

One of the most important functions of the visual perception in the brain is figure/ground interpretation from input images. Figural region in 2D image corresponding to object in 3D space are distinguished from background region extended behind the object. Previously the author proposed a neural network model of figure/ground separation constructed on the standpoint that local geometric features such as curvatures and outer angles at corners are extracted and propagated along input contour in a single layer network (Kikuchi & Akashi, 2001). However, such a processing principle has the defect that signal propagation requires manyiterations despite the fact that actual visual system determines figure/ground relation within the short period (Zhou et al., 2000). In order to attain speed-up for determining figure/ground, this study incorporates hierarchical architecture into the previous model. This study confirmed the effect of the hierarchization as for the computation time by simulation. As the number of layers increased, the required computation time reduced. However, such speed-up effect was saturatedas the layers increased to some extent. This study attempted to explain this saturation effect by the notion of average distance between vertices in the area of complex network, and succeeded to mimic the saturation effect by computer simulation.

Code Modernization of VPIC

NASA Astrophysics Data System (ADS)

Bird, Robert; Nystrom, David; Albright, Brian

2017-10-01

The ability of scientific simulations to effectively deliver performant computation is increasingly being challenged by successive generations of high-performance computing architectures. Code development to support efficient computation on these modern architectures is both expensive, and highly complex; if it is approached without due care, it may also not be directly transferable between subsequent hardware generations. Previous works have discussed techniques to support the process of adapting a legacy code for modern hardware generations, but despite the breakthroughs in the areas of mini-app development, portable-performance, and cache oblivious algorithms the problem still remains largely unsolved. In this work we demonstrate how a focus on platform agnostic modern code-development can be applied to Particle-in-Cell (PIC) simulations to facilitate effective scientific delivery. This work builds directly on our previous work optimizing VPIC, in which we replaced intrinsic based vectorisation with compile generated auto-vectorization to improve the performance and portability of VPIC. In this work we present the use of a specialized SIMD queue for processing some particle operations, and also preview a GPU capable OpenMP variant of VPIC. Finally we include a lessons learnt. Work performed under the auspices of the U.S. Dept. of Energy by the Los Alamos National Security, LLC Los Alamos National Laboratory under contract DE-AC52-06NA25396 and supported by the LANL LDRD program.

Digital-computer normal shock position and restart control of a Mach 2.5 axisymmetric mixed-compression inlet

NASA Technical Reports Server (NTRS)

Neiner, G. H.; Cole, G. L.; Arpasi, D. J.

1972-01-01

Digital computer control of a mixed-compression inlet is discussed. The inlet was terminated with a choked orifice at the compressor face station to dynamically simulate a turbojet engine. Inlet diffuser exit airflow disturbances were used. A digital version of a previously tested analog control system was used for both normal shock and restart control. Digital computer algorithms were derived using z-transform and finite difference methods. Using a sample rate of 1000 samples per second, the digital normal shock and restart controls essentially duplicated the inlet analog computer control results. At a sample rate of 100 samples per second, the control system performed adequately but was less stable.

Appendices to the user's manual for a computer program for the emulation/simulation of a space station environmental control and life support system

NASA Technical Reports Server (NTRS)

Yanosy, James L.

1988-01-01

A user's Manual for the Emulation Simulation Computer Model was published previously. The model consisted of a detailed model (emulation) of a SAWD CO2 removal subsystem which operated with much less detailed (simulation) models of a cabin, crew, and condensing and sensible heat exchangers. The purpose was to explore the utility of such an emulation/simulation combination in the design, development, and test of a piece of ARS hardware - SAWD. Extensions to this original effort are presented. The first extension is an update of the model to reflect changes in the SAWD control logic which resulted from the test. In addition, slight changes were also made to the SAWD model to permit restarting and to improve the iteration technique. The second extension is the development of simulation models for more pieces of air and water processing equipment. Models are presented for: EDC, Molecular Sieve, Bosch, Sabatier, a new condensing heat exchanger, SPE, SFWES, Catalytic Oxidizer, and multifiltration. The third extension is to create two system simulations using these models. The first system presented consists of one air and one water processing system, the second a potential Space Station air revitalization system.

Simulating the x-ray image contrast to setup techniques with desired flaw detectability

NASA Astrophysics Data System (ADS)

Koshti, Ajay M.

2015-04-01

The paper provides simulation data of previous work by the author in developing a model for estimating detectability of crack-like flaws in radiography. The methodology is developed to help in implementation of NASA Special x-ray radiography qualification, but is generically applicable to radiography. The paper describes a method for characterizing the detector resolution. Applicability of ASTM E 2737 resolution requirements to the model are also discussed. The paper describes a model for simulating the detector resolution. A computer calculator application, discussed here, also performs predicted contrast and signal-to-noise ratio calculations. Results of various simulation runs in calculating x-ray flaw size parameter and image contrast for varying input parameters such as crack depth, crack width, part thickness, x-ray angle, part-to-detector distance, part-to-source distance, source sizes, and detector sensitivity and resolution are given as 3D surfaces. These results demonstrate effect of the input parameters on the flaw size parameter and the simulated image contrast of the crack. These simulations demonstrate utility of the flaw size parameter model in setting up x-ray techniques that provide desired flaw detectability in radiography. The method is applicable to film radiography, computed radiography, and digital radiography.

Biased ART: a neural architecture that shifts attention toward previously disregarded features following an incorrect prediction.

PubMed

Carpenter, Gail A; Gaddam, Sai Chaitanya

2010-04-01

Memories in Adaptive Resonance Theory (ART) networks are based on matched patterns that focus attention on those portions of bottom-up inputs that match active top-down expectations. While this learning strategy has proved successful for both brain models and applications, computational examples show that attention to early critical features may later distort memory representations during online fast learning. For supervised learning, biased ARTMAP (bARTMAP) solves the problem of over-emphasis on early critical features by directing attention away from previously attended features after the system makes a predictive error. Small-scale, hand-computed analog and binary examples illustrate key model dynamics. Two-dimensional simulation examples demonstrate the evolution of bARTMAP memories as they are learned online. Benchmark simulations show that featural biasing also improves performance on large-scale examples. One example, which predicts movie genres and is based, in part, on the Netflix Prize database, was developed for this project. Both first principles and consistent performance improvements on all simulation studies suggest that featural biasing should be incorporated by default in all ARTMAP systems. Benchmark datasets and bARTMAP code are available from the CNS Technology Lab Website: http://techlab.bu.edu/bART/. Copyright 2009 Elsevier Ltd. All rights reserved.

Documenting the NASA Armstrong Flight Research Center Oblate Earth Simulation Equations of Motion and Integration Algorithm

NASA Technical Reports Server (NTRS)

Clarke, R.; Lintereur, L.; Bahm, C.

2016-01-01

A desire for more complete documentation of the National Aeronautics and Space Administration (NASA) Armstrong Flight Research Center (AFRC), Edwards, California legacy code used in the core simulation has led to this e ort to fully document the oblate Earth six-degree-of-freedom equations of motion and integration algorithm. The authors of this report have taken much of the earlier work of the simulation engineering group and used it as a jumping-o point for this report. The largest addition this report makes is that each element of the equations of motion is traced back to first principles and at no point is the reader forced to take an equation on faith alone. There are no discoveries of previously unknown principles contained in this report; this report is a collection and presentation of textbook principles. The value of this report is that those textbook principles are herein documented in standard nomenclature that matches the form of the computer code DERIVC. Previous handwritten notes are much of the backbone of this work, however, in almost every area, derivations are explicitly shown to assure the reader that the equations which make up the oblate Earth version of the computer routine, DERIVC, are correct.

The numerical modelling of falling film thickness flow on horizontal tubes

NASA Astrophysics Data System (ADS)

Hassan, I. A.; Sadikin, A.; Isa, N. Mat

2017-04-01

This paper presents a computational modelling of water falling film flowing over horizontal tubes. The objective of this study is to use numerical predictions for comparing the film thickness along circumferential direction of tube on 2-D CFD models. The results are then validated with a theoretical result in previous literatures. A comprehensive design of 2-D models have been developed according to the real application and actual configuration of the falling film evaporator as well as previous experimental parameters. A computational modelling of the water falling film is presented with the aid of Ansys Fluent software. The Volume of Fluid (VOF) technique is adapted in this analysis since its capabilities of determining the film thickness on tubes surface is highly reliable. The numerical analysis is carried out under influence of ambient pressures at temperature of 27 °C. Three types of CFD numerical models were analyzed in this simulation with inter tube spacing of 30 mm, 20 mm and 10 mm respectively. The use of a numerical simulation tool on water falling film has resulted in a detailed investigation of film thickness. Based on the numerical simulated results, it is found that the average values of water film thickness for each model are 0.53 mm, 0.58 mm, and 0.63 mm.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Computing in Hydraulic Engineering Education

NASA Astrophysics Data System (ADS)

Duan, J. G.

2011-12-01

Civil engineers, pioneers of our civilization, are rarely perceived as leaders and innovators in modern society because of retardations in technology innovation. This crisis has resulted in the decline of the prestige of civil engineering profession, reduction of federal funding on deteriorating infrastructures, and problems with attracting the most talented high-school students. Infusion of cutting-edge computer technology and stimulating creativity and innovation therefore are the critical challenge to civil engineering education. To better prepare our graduates to innovate, this paper discussed the adaption of problem-based collaborative learning technique and integration of civil engineering computing into a traditional civil engineering curriculum. Three interconnected courses: Open Channel Flow, Computational Hydraulics, and Sedimentation Engineering, were developed with emphasis on computational simulations. In Open Channel flow, the focuses are principles of free surface flow and the application of computational models. This prepares students to the 2nd course, Computational Hydraulics, that introduce the fundamental principles of computational hydraulics, including finite difference and finite element methods. This course complements the Open Channel Flow class to provide students with in-depth understandings of computational methods. The 3rd course, Sedimentation Engineering, covers the fundamentals of sediment transport and river engineering, so students can apply the knowledge and programming skills gained from previous courses to develop computational models for simulating sediment transport. These courses effectively equipped students with important skills and knowledge to complete thesis and dissertation research.

The impact of supercomputers on experimentation: A view from a national laboratory

NASA Technical Reports Server (NTRS)

Peterson, V. L.; Arnold, J. O.

1985-01-01

The relative roles of large scale scientific computers and physical experiments in several science and engineering disciplines are discussed. Increasing dependence on computers is shown to be motivated both by the rapid growth in computer speed and memory, which permits accurate numerical simulation of complex physical phenomena, and by the rapid reduction in the cost of performing a calculation, which makes computation an increasingly attractive complement to experimentation. Computer speed and memory requirements are presented for selected areas of such disciplines as fluid dynamics, aerodynamics, aerothermodynamics, chemistry, atmospheric sciences, astronomy, and astrophysics, together with some examples of the complementary nature of computation and experiment. Finally, the impact of the emerging role of computers in the technical disciplines is discussed in terms of both the requirements for experimentation and the attainment of previously inaccessible information on physical processes.

Computing and Visualizing the Complex Dynamics of Earthquake Fault Systems: Towards Ensemble Earthquake Forecasting

NASA Astrophysics Data System (ADS)

Rundle, J.; Rundle, P.; Donnellan, A.; Li, P.

2003-12-01

We consider the problem of the complex dynamics of earthquake fault systems, and whether numerical simulations can be used to define an ensemble forecasting technology similar to that used in weather and climate research. To effectively carry out such a program, we need 1) a topological realistic model to simulate the fault system; 2) data sets to constrain the model parameters through a systematic program of data assimilation; 3) a computational technology making use of modern paradigms of high performance and parallel computing systems; and 4) software to visualize and analyze the results. In particular, we focus attention of a new version of our code Virtual California (version 2001) in which we model all of the major strike slip faults extending throughout California, from the Mexico-California border to the Mendocino Triple Junction. We use the historic data set of earthquakes larger than magnitude M > 6 to define the frictional properties of all 654 fault segments (degrees of freedom) in the model. Previous versions of Virtual California had used only 215 fault segments to model the strike slip faults in southern California. To compute the dynamics and the associated surface deformation, we use message passing as implemented in the MPICH standard distribution on a small Beowulf cluster consisting of 10 cpus. We are also planning to run the code on significantly larger machines so that we can begin to examine much finer spatial scales of resolution, and to assess scaling properties of the code. We present results of simulations both as static images and as mpeg movies, so that the dynamical aspects of the computation can be assessed by the viewer. We also compute a variety of statistics from the simulations, including magnitude-frequency relations, and compare these with data from real fault systems.

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

NASA Astrophysics Data System (ADS)

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

2018-07-01

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

Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC).

PubMed

Cockrell, Robert Chase; Christley, Scott; Chang, Eugene; An, Gary

2015-01-01

Perhaps the greatest challenge currently facing the biomedical research community is the ability to integrate highly detailed cellular and molecular mechanisms to represent clinical disease states as a pathway to engineer effective therapeutics. This is particularly evident in the representation of organ-level pathophysiology in terms of abnormal tissue structure, which, through histology, remains a mainstay in disease diagnosis and staging. As such, being able to generate anatomic scale simulations is a highly desirable goal. While computational limitations have previously constrained the size and scope of multi-scale computational models, advances in the capacity and availability of high-performance computing (HPC) resources have greatly expanded the ability of computational models of biological systems to achieve anatomic, clinically relevant scale. Diseases of the intestinal tract are exemplary examples of pathophysiological processes that manifest at multiple scales of spatial resolution, with structural abnormalities present at the microscopic, macroscopic and organ-levels. In this paper, we describe a novel, massively parallel computational model of the gut, the Spatially Explicitly General-purpose Model of Enteric Tissue_HPC (SEGMEnT_HPC), which extends an existing model of the gut epithelium, SEGMEnT, in order to create cell-for-cell anatomic scale simulations. We present an example implementation of SEGMEnT_HPC that simulates the pathogenesis of ileal pouchitis, and important clinical entity that affects patients following remedial surgery for ulcerative colitis.

Genetic demographic networks: Mathematical model and applications.

PubMed

Kimmel, Marek; Wojdyła, Tomasz

2016-10-01

Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans. Copyright © 2016 Elsevier Inc. All rights reserved.

Strong scaling and speedup to 16,384 processors in cardiac electro-mechanical simulations.

PubMed

Reumann, Matthias; Fitch, Blake G; Rayshubskiy, Aleksandr; Keller, David U J; Seemann, Gunnar; Dossel, Olaf; Pitman, Michael C; Rice, John J

2009-01-01

High performance computing is required to make feasible simulations of whole organ models of the heart with biophysically detailed cellular models in a clinical setting. Increasing model detail by simulating electrophysiology and mechanical models increases computation demands. We present scaling results of an electro - mechanical cardiac model of two ventricles and compare them to our previously published results using an electrophysiological model only. The anatomical data-set was given by both ventricles of the Visible Female data-set in a 0.2 mm resolution. Fiber orientation was included. Data decomposition for the distribution onto the distributed memory system was carried out by orthogonal recursive bisection. Load weight ratios for non-tissue vs. tissue elements used in the data decomposition were 1:1, 1:2, 1:5, 1:10, 1:25, 1:38.85, 1:50 and 1:100. The ten Tusscher et al. (2004) electrophysiological cell model was used and the Rice et al. (1999) model for the computation of the calcium transient dependent force. Scaling results for 512, 1024, 2048, 4096, 8192 and 16,384 processors were obtained for 1 ms simulation time. The simulations were carried out on an IBM Blue Gene/L supercomputer. The results show linear scaling from 512 to 16,384 processors with speedup factors between 1.82 and 2.14 between partitions. The most optimal load ratio was 1:25 for on all partitions. However, a shift towards load ratios with higher weight for the tissue elements can be recognized as can be expected when adding computational complexity to the model while keeping the same communication setup. This work demonstrates that it is potentially possible to run simulations of 0.5 s using the presented electro-mechanical cardiac model within 1.5 hours.

Investigation of non-uniform airflow signal oscillation during high frequency chest compression

PubMed Central

Sohn, Kiwon; Warwick, Warren J; Lee, Yong W; Lee, Jongwon; Holte, James E

2005-01-01

Background High frequency chest compression (HFCC) is a useful and popular therapy for clearing bronchial airways of excessive or thicker mucus. Our observation of respiratory airflow of a subject during use of HFCC showed the airflow oscillation by HFCC was strongly influenced by the nonlinearity of the respiratory system. We used a computational model-based approach to analyse the respiratory airflow during use of HFCC. Methods The computational model, which is based on previous physiological studies and represented by an electrical circuit analogue, was used for simulation of in vivo protocol that shows the nonlinearity of the respiratory system. Besides, airflow was measured during use of HFCC. We compared the simulation results to either the measured data or the previous research, to understand and explain the observations. Results and discussion We could observe two important phenomena during respiration pertaining to the airflow signal oscillation generated by HFCC. The amplitudes of HFCC airflow signals varied depending on spontaneous airflow signals. We used the simulation results to investigate how the nonlinearity of airway resistance, lung capacitance, and inertance of air characterized the respiratory airflow. The simulation results indicated that lung capacitance or the inertance of air is also not a factor in the non-uniformity of HFCC airflow signals. Although not perfect, our circuit analogue model allows us to effectively simulate the nonlinear characteristics of the respiratory system. Conclusion We found that the amplitudes of HFCC airflow signals behave as a function of spontaneous airflow signals. This is due to the nonlinearity of the respiratory system, particularly variations in airway resistance. PMID:15904523

Parallelisation study of a three-dimensional environmental flow model

NASA Astrophysics Data System (ADS)

O'Donncha, Fearghal; Ragnoli, Emanuele; Suits, Frank

2014-03-01

There are many simulation codes in the geosciences that are serial and cannot take advantage of the parallel computational resources commonly available today. One model important for our work in coastal ocean current modelling is EFDC, a Fortran 77 code configured for optimal deployment on vector computers. In order to take advantage of our cache-based, blade computing system we restructured EFDC from serial to parallel, thereby allowing us to run existing models more quickly, and to simulate larger and more detailed models that were previously impractical. Since the source code for EFDC is extensive and involves detailed computation, it is important to do such a port in a manner that limits changes to the files, while achieving the desired speedup. We describe a parallelisation strategy involving surgical changes to the source files to minimise error-prone alteration of the underlying computations, while allowing load-balanced domain decomposition for efficient execution on a commodity cluster. The use of conjugate gradient posed particular challenges due to implicit non-local communication posing a hindrance to standard domain partitioning schemes; a number of techniques are discussed to address this in a feasible, computationally efficient manner. The parallel implementation demonstrates good scalability in combination with a novel domain partitioning scheme that specifically handles mixed water/land regions commonly found in coastal simulations. The approach presented here represents a practical methodology to rejuvenate legacy code on a commodity blade cluster with reasonable effort; our solution has direct application to other similar codes in the geosciences.

Rotating shell eggs immersed in hot water for the purpose of pasteurization

USDA-ARS?s Scientific Manuscript database

Pasteurization of shell eggs for inactivation of Salmonella using hot water immersion can be used to improve their safety. The rotation of a shell egg immersed in hot water has previously been simulated by computational fluid dynamics (CFD); however, experimental data to verify the results do not ex...

What Influences College Students to Continue Using Business Simulation Games? The Taiwan Experience

ERIC Educational Resources Information Center

Tao, Yu-Hui; Cheng, Chieh-Jen; Sun, Szu-Yuan

2009-01-01

Previous studies have pointed out that computer games could improve students' motivation to learn, but these studies have mostly targeted teachers or students in elementary and secondary education and are without user adoption models. Because business and management institutions in higher education have been increasingly using educational…

Using Interval-Based Systems to Measure Behavior in Early Childhood Special Education and Early Intervention

ERIC Educational Resources Information Center

Lane, Justin D.; Ledford, Jennifer R.

2014-01-01

The purpose of this article is to summarize the current literature on the accuracy and reliability of interval systems using data from previously published experimental studies that used either human observations of behavior or computer simulations. Although multiple comparison studies provided mathematical adjustments or modifications to interval…

Irradiation-driven Mass Transfer Cycles in Compact Binaries

NASA Astrophysics Data System (ADS)

Büning, A.; Ritter, H.

2005-08-01

We elaborate on the analytical model of Ritter, Zhang, & Kolb (2000) which describes the basic physics of irradiation-driven mass transfer cycles in semi-detached compact binary systems. In particular, we take into account a contribution to the thermal relaxation of the donor star which is unrelated to irradiation and which was neglected in previous studies. We present results of simulations of the evolution of compact binaries undergoing mass transfer cycles, in particular also of systems with a nuclear evolved donor star. These computations have been carried out with a stellar evolution code which computes mass transfer implicitly and models irradiation of the donor star in a point source approximation, thereby allowing for much more realistic simulations than were hitherto possible. We find that low-mass X-ray binaries (LMXBs) and cataclysmic variables (CVs) with orbital periods ⪉ 6hr can undergo mass transfer cycles only for low angular momentum loss rates. CVs containing a giant donor or one near the terminal age main sequence are more stable than previously thought, but can possibly also undergo mass transfer cycles.

Bubble nucleation in simple and molecular liquids via the largest spherical cavity method

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

Gonzalez, Miguel A., E-mail: m.gonzalez12@imperial.ac.uk; Department of Chemistry, Imperial College London, London SW7 2AZ; Abascal, José L. F.

2015-04-21

In this work, we propose a methodology to compute bubble nucleation free energy barriers using trajectories generated via molecular dynamics simulations. We follow the bubble nucleation process by means of a local order parameter, defined by the volume of the largest spherical cavity (LSC) formed in the nucleating trajectories. This order parameter simplifies considerably the monitoring of the nucleation events, as compared with the previous approaches which require ad hoc criteria to classify the atoms and molecules as liquid or vapor. The combination of the LSC and the mean first passage time technique can then be used to obtain themore » free energy curves. Upon computation of the cavity distribution function the nucleation rate and free-energy barrier can then be computed. We test our method against recent computations of bubble nucleation in simple liquids and water at negative pressures. We obtain free-energy barriers in good agreement with the previous works. The LSC method provides a versatile and computationally efficient route to estimate the volume of critical bubbles the nucleation rate and to compute bubble nucleation free-energies in both simple and molecular liquids.« less

A Gaussian mixture model based adaptive classifier for fNIRS brain-computer interfaces and its testing via simulation

NASA Astrophysics Data System (ADS)

Li, Zheng; Jiang, Yi-han; Duan, Lian; Zhu, Chao-zhe

2017-08-01

Objective. Functional near infra-red spectroscopy (fNIRS) is a promising brain imaging technology for brain-computer interfaces (BCI). Future clinical uses of fNIRS will likely require operation over long time spans, during which neural activation patterns may change. However, current decoders for fNIRS signals are not designed to handle changing activation patterns. The objective of this study is to test via simulations a new adaptive decoder for fNIRS signals, the Gaussian mixture model adaptive classifier (GMMAC). Approach. GMMAC can simultaneously classify and track activation pattern changes without the need for ground-truth labels. This adaptive classifier uses computationally efficient variational Bayesian inference to label new data points and update mixture model parameters, using the previous model parameters as priors. We test GMMAC in simulations in which neural activation patterns change over time and compare to static decoders and unsupervised adaptive linear discriminant analysis classifiers. Main results. Our simulation experiments show GMMAC can accurately decode under time-varying activation patterns: shifts of activation region, expansions of activation region, and combined contractions and shifts of activation region. Furthermore, the experiments show the proposed method can track the changing shape of the activation region. Compared to prior work, GMMAC performed significantly better than the other unsupervised adaptive classifiers on a difficult activation pattern change simulation: 99% versus  <54% in two-choice classification accuracy. Significance. We believe GMMAC will be useful for clinical fNIRS-based brain-computer interfaces, including neurofeedback training systems, where operation over long time spans is required.

Experimental evaluation of the effect of a modified port-location mode on the performance of a three-zone simulated moving-bed process for the separation of valine and isoleucine.

PubMed

Park, Chanhun; Nam, Hee-Geun; Kim, Pung-Ho; Mun, Sungyong

2014-06-01

The removal of isoleucine from valine has been a key issue in the stage of valine crystallization, which is the final step in the valine production process in industry. To address this issue, a three-zone simulated moving-bed (SMB) process for the separation of valine and isoleucine has been developed previously. However, the previous process, which was based on a classical port-location mode, had some limitations in throughput and valine product concentration. In this study, a three-zone SMB process based on a modified port-location mode was applied to the separation of valine and isoleucine for the purpose of making a marked improvement in throughput and valine product concentration. Computer simulations and a lab-scale process experiment showed that the modified three-zone SMB for valine separation led to >65% higher throughput and >160% higher valine concentration compared to the previous three-zone SMB for the same separation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Estimation of whole-body radiation exposure from brachytherapy for oral cancer using a Monte Carlo simulation

PubMed Central

Ozaki, Y.; Kaida, A.; Miura, M.; Nakagawa, K.; Toda, K.; Yoshimura, R.; Sumi, Y.; Kurabayashi, T.

2017-01-01

Abstract Early stage oral cancer can be cured with oral brachytherapy, but whole-body radiation exposure status has not been previously studied. Recently, the International Commission on Radiological Protection Committee (ICRP) recommended the use of ICRP phantoms to estimate radiation exposure from external and internal radiation sources. In this study, we used a Monte Carlo simulation with ICRP phantoms to estimate whole-body exposure from oral brachytherapy. We used a Particle and Heavy Ion Transport code System (PHITS) to model oral brachytherapy with 192Ir hairpins and 198Au grains and to perform a Monte Carlo simulation on the ICRP adult reference computational phantoms. To confirm the simulations, we also computed local dose distributions from these small sources, and compared them with the results from Oncentra manual Low Dose Rate Treatment Planning (mLDR) software which is used in day-to-day clinical practice. We successfully obtained data on absorbed dose for each organ in males and females. Sex-averaged equivalent doses were 0.547 and 0.710 Sv with 192Ir hairpins and 198Au grains, respectively. Simulation with PHITS was reliable when compared with an alternative computational technique using mLDR software. We concluded that the absorbed dose for each organ and whole-body exposure from oral brachytherapy can be estimated with Monte Carlo simulation using PHITS on ICRP reference phantoms. Effective doses for patients with oral cancer were obtained. PMID:28339846

Application of classical simulations for the computation of vibrational properties of free molecules.

PubMed

Tikhonov, Denis S; Sharapa, Dmitry I; Schwabedissen, Jan; Rybkin, Vladimir V

2016-10-12

In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS 2 , benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I 2 -1,2-closo-C 2 B 10 H 10 . The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.

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

PubMed

Heath, Anna; Manolopoulou, Ioanna; Baio, Gianluca

2018-02-01

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

Electron Nuclear Dynamics Simulations of Proton Cancer Therapy Reactions: Water Radiolysis and Proton- and Electron-Induced DNA Damage in Computational Prototypes.

PubMed

Teixeira, Erico S; Uppulury, Karthik; Privett, Austin J; Stopera, Christopher; McLaurin, Patrick M; Morales, Jorge A

2018-05-06

Proton cancer therapy (PCT) utilizes high-energy proton projectiles to obliterate cancerous tumors with low damage to healthy tissues and without the side effects of X-ray therapy. The healing action of the protons results from their damage on cancerous cell DNA. Despite established clinical use, the chemical mechanisms of PCT reactions at the molecular level remain elusive. This situation prevents a rational design of PCT that can maximize its therapeutic power and minimize its side effects. The incomplete characterization of PCT reactions is partially due to the health risks associated with experimental/clinical techniques applied to human subjects. To overcome this situation, we are conducting time-dependent and non-adiabatic computer simulations of PCT reactions with the electron nuclear dynamics (END) method. Herein, we present a review of our previous and new END research on three fundamental types of PCT reactions: water radiolysis reactions, proton-induced DNA damage and electron-induced DNA damage. These studies are performed on the computational prototypes: proton + H₂O clusters, proton + DNA/RNA bases and + cytosine nucleotide, and electron + cytosine nucleotide + H₂O. These simulations provide chemical mechanisms and dynamical properties of the selected PCT reactions in comparison with available experimental and alternative computational results.

Plant-Level Modeling and Simulation of Used Nuclear Fuel Dissolution

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

de Almeida, Valmor F.

2012-09-07

Plant-level modeling and simulation of a used nuclear fuel prototype dissolver is presented. Emphasis is given in developing a modeling and simulation approach to be explored by other processes involved in the recycle of used fuel. The commonality concepts presented in a previous communication were used to create a model and realize its software module. An initial model was established based on a theory of chemical thermomechanical network transport outlined previously. A software module prototype was developed with the required external behavior and internal mathematical structure. Results obtained demonstrate the generality of the design approach and establish an extensible mathematicalmore » model with its corresponding software module for a wide range of dissolvers. Scale up numerical tests were made varying the type of used fuel (breeder and light-water reactors) and the capacity of dissolution (0.5 t/d to 1.7 t/d). These tests were motivated by user requirements in the area of nuclear materials safeguards. A computer module written in high-level programing languages (MATLAB and Octave) was developed, tested, and provided as open-source code (MATLAB) for integration into the Separations and Safeguards Performance Model application in development at Sandia National Laboratories. The modeling approach presented here is intended to serve as a template for a rational modeling of all plant-level modules. This will facilitate the practical application of the commonality features underlying the unifying network transport theory proposed recently. In addition, by example, this model describes, explicitly, the needed data from sub-scale models, and logical extensions for future model development. For example, from thermodynamics, an off-line simulation of molecular dynamics could quantify partial molar volumes for the species in the liquid phase; this simulation is currently at reach for high-performance computing. From fluid mechanics, a hold-up capacity function is needed for the dissolver device; this simulation is currently at reach for computational fluid mechanics given the existing CAD geometry. From chemical transport phenomena, a simulation of the particle-scale dissolution front is needed to derive an improved solid dissolution kinetics law by predicting the local surface area change; an example was provided in this report. In addition, the associated reaction mechanisms for dissolution are presently largely untested and simplified, hence even a parallel experimental program in reaction kinetics is needed to support modeling and simulation efforts. Last but not least, a simple account of finite rates of solid feed and transfer can be readily introduced via a coupled delayed model. These are some of the theoretical benefits of a rational plant-level modeling approach which guides the development of smaller length and time scale modeling. Practical, and other theoretical benefits have been presented on a previous report.« less

Cosmological neutrino simulations at extreme scale

DOE PAGES

Emberson, J. D.; Yu, Hao-Ran; Inman, Derek; ...

2017-08-01

Constraining neutrino mass remains an elusive challenge in modern physics. Precision measurements are expected from several upcoming cosmological probes of large-scale structure. Achieving this goal relies on an equal level of precision from theoretical predictions of neutrino clustering. Numerical simulations of the non-linear evolution of cold dark matter and neutrinos play a pivotal role in this process. We incorporate neutrinos into the cosmological N-body code CUBEP3M and discuss the challenges associated with pushing to the extreme scales demanded by the neutrino problem. We highlight code optimizations made to exploit modern high performance computing architectures and present a novel method ofmore » data compression that reduces the phase-space particle footprint from 24 bytes in single precision to roughly 9 bytes. We scale the neutrino problem to the Tianhe-2 supercomputer and provide details of our production run, named TianNu, which uses 86% of the machine (13,824 compute nodes). With a total of 2.97 trillion particles, TianNu is currently the world’s largest cosmological N-body simulation and improves upon previous neutrino simulations by two orders of magnitude in scale. We finish with a discussion of the unanticipated computational challenges that were encountered during the TianNu runtime.« less

Computing elastic‐rebound‐motivated rarthquake probabilities in unsegmented fault models: a new methodology supported by physics‐based simulators

USGS Publications Warehouse

Field, Edward H.

2015-01-01

A methodology is presented for computing elastic‐rebound‐based probabilities in an unsegmented fault or fault system, which involves computing along‐fault averages of renewal‐model parameters. The approach is less biased and more self‐consistent than a logical extension of that applied most recently for multisegment ruptures in California. It also enables the application of magnitude‐dependent aperiodicity values, which the previous approach does not. Monte Carlo simulations are used to analyze long‐term system behavior, which is generally found to be consistent with that of physics‐based earthquake simulators. Results cast doubt that recurrence‐interval distributions at points on faults look anything like traditionally applied renewal models, a fact that should be considered when interpreting paleoseismic data. We avoid such assumptions by changing the "probability of what" question (from offset at a point to the occurrence of a rupture, assuming it is the next event to occur). The new methodology is simple, although not perfect in terms of recovering long‐term rates in Monte Carlo simulations. It represents a reasonable, improved way to represent first‐order elastic‐rebound predictability, assuming it is there in the first place, and for a system that clearly exhibits other unmodeled complexities, such as aftershock triggering.

Interactive physically-based sound simulation

NASA Astrophysics Data System (ADS)

Raghuvanshi, Nikunj

The realization of interactive, immersive virtual worlds requires the ability to present a realistic audio experience that convincingly compliments their visual rendering. Physical simulation is a natural way to achieve such realism, enabling deeply immersive virtual worlds. However, physically-based sound simulation is very computationally expensive owing to the high-frequency, transient oscillations underlying audible sounds. The increasing computational power of desktop computers has served to reduce the gap between required and available computation, and it has become possible to bridge this gap further by using a combination of algorithmic improvements that exploit the physical, as well as perceptual properties of audible sounds. My thesis is a step in this direction. My dissertation concentrates on developing real-time techniques for both sub-problems of sound simulation: synthesis and propagation. Sound synthesis is concerned with generating the sounds produced by objects due to elastic surface vibrations upon interaction with the environment, such as collisions. I present novel techniques that exploit human auditory perception to simulate scenes with hundreds of sounding objects undergoing impact and rolling in real time. Sound propagation is the complementary problem of modeling the high-order scattering and diffraction of sound in an environment as it travels from source to listener. I discuss my work on a novel numerical acoustic simulator (ARD) that is hundred times faster and consumes ten times less memory than a high-accuracy finite-difference technique, allowing acoustic simulations on previously-intractable spaces, such as a cathedral, on a desktop computer. Lastly, I present my work on interactive sound propagation that leverages my ARD simulator to render the acoustics of arbitrary static scenes for multiple moving sources and listener in real time, while accounting for scene-dependent effects such as low-pass filtering and smooth attenuation behind obstructions, reverberation, scattering from complex geometry and sound focusing. This is enabled by a novel compact representation that takes a thousand times less memory than a direct scheme, thus reducing memory footprints to fit within available main memory. To the best of my knowledge, this is the only technique and system in existence to demonstrate auralization of physical wave-based effects in real-time on large, complex 3D scenes.

A computational fluid dynamics simulation framework for ventricular catheter design optimization.

PubMed

Weisenberg, Sofy H; TerMaath, Stephanie C; Barbier, Charlotte N; Hill, Judith C; Killeffer, James A

2017-11-10

OBJECTIVE Cerebrospinal fluid (CSF) shunts are the primary treatment for patients suffering from hydrocephalus. While proven effective in symptom relief, these shunt systems are plagued by high failure rates and often require repeated revision surgeries to replace malfunctioning components. One of the leading causes of CSF shunt failure is obstruction of the ventricular catheter by aggregations of cells, proteins, blood clots, or fronds of choroid plexus that occlude the catheter's small inlet holes or even the full internal catheter lumen. Such obstructions can disrupt CSF diversion out of the ventricular system or impede it entirely. Previous studies have suggested that altering the catheter's fluid dynamics may help to reduce the likelihood of complete ventricular catheter failure caused by obstruction. However, systematic correlation between a ventricular catheter's design parameters and its performance, specifically its likelihood to become occluded, still remains unknown. Therefore, an automated, open-source computational fluid dynamics (CFD) simulation framework was developed for use in the medical community to determine optimized ventricular catheter designs and to rapidly explore parameter influence for a given flow objective. METHODS The computational framework was developed by coupling a 3D CFD solver and an iterative optimization algorithm and was implemented in a high-performance computing environment. The capabilities of the framework were demonstrated by computing an optimized ventricular catheter design that provides uniform flow rates through the catheter's inlet holes, a common design objective in the literature. The baseline computational model was validated using 3D nuclear imaging to provide flow velocities at the inlet holes and through the catheter. RESULTS The optimized catheter design achieved through use of the automated simulation framework improved significantly on previous attempts to reach a uniform inlet flow rate distribution using the standard catheter hole configuration as a baseline. While the standard ventricular catheter design featuring uniform inlet hole diameters and hole spacing has a standard deviation of 14.27% for the inlet flow rates, the optimized design has a standard deviation of 0.30%. CONCLUSIONS This customizable framework, paired with high-performance computing, provides a rapid method of design testing to solve complex flow problems. While a relatively simplified ventricular catheter model was used to demonstrate the framework, the computational approach is applicable to any baseline catheter model, and it is easily adapted to optimize catheters for the unique needs of different patients as well as for other fluid-based medical devices.

Design, Modeling, Fabrication, and Evaluation of the Air Amplifier for Improved Detection of Biomolecules by Electrospray Ionization Mass Spectrometry

PubMed Central

Robichaud, Guillaume; Dixon, R. Brent; Potturi, Amarnatha S.; Cassidy, Dan; Edwards, Jack R.; Sohn, Alex; Dow, Thomas A.; Muddiman, David C.

2010-01-01

Through a multi-disciplinary approach, the air amplifier is being evolved as a highly engineered device to improve detection limits of biomolecules when using electrospray ionization. Several key aspects have driven the modifications to the device through experimentation and simulations. We have developed a computer simulation that accurately portrays actual conditions and the results from these simulations are corroborated by the experimental data. These computer simulations can be used to predict outcomes from future designs resulting in a design process that is efficient in terms of financial cost and time. We have fabricated a new device with annular gap control over a range of 50 to 70 μm using piezoelectric actuators. This has enabled us to obtain better aerodynamic performance when compared to the previous design (2× more vacuum) and also more reproducible results. This is allowing us to study a broader experimental space than the previous design which is critical in guiding future directions. This work also presents and explains the principles behind a fractional factorial design of experiments methodology for testing a large number of experimental parameters in an orderly and efficient manner to understand and optimize the critical parameters that lead to obtain improved detection limits while minimizing the number of experiments performed. Preliminary results showed that several folds of improvements could be obtained for certain condition of operations (up to 34 folds). PMID:21499524

Numerical study of transient evolution of lifted jet flames: partially premixed flame propagation and influence of physical dimensions

NASA Astrophysics Data System (ADS)

Chen, Zhi; Ruan, Shaohong; Swaminathan, Nedunchezhian

2016-07-01

Three-dimensional (3D) unsteady Reynolds-averaged Navier-Stokes simulations of a spark-ignited turbulent methane/air jet flame evolving from ignition to stabilisation are conducted for different jet velocities. A partially premixed combustion model is used involving a correlated joint probability density function and both premixed and non-premixed combustion mode contributions. The 3D simulation results for the temporal evolution of the flame's leading edge are compared with previous two-dimensional (2D) results and experimental data. The comparison shows that the final stabilised flame lift-off height is well predicted by both 2D and 3D computations. However, the transient evolution of the flame's leading edge computed from 3D simulation agrees reasonably well with experiment, whereas evident discrepancies were found in the previous 2D study. This difference suggests that the third physical dimension plays an important role during the flame transient evolution process. The flame brush's leading edge displacement speed resulting from reaction, normal and tangential diffusion processes are studied at different typical stages after ignition in order to understand the effect of the third physical dimension further. Substantial differences are found for the reaction and normal diffusion components between 2D and 3D simulations especially in the initial propagation stage. The evolution of reaction progress variable scalar gradients and its interaction with the flow and mixing field in the 3D physical space have an important effect on the flame's leading edge propagation.

Final Report for ALCC Allocation: Predictive Simulation of Complex Flow in Wind Farms

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

Barone, Matthew F.; Ananthan, Shreyas; Churchfield, Matt

This report documents work performed using ALCC computing resources granted under a proposal submitted in February 2016, with the resource allocation period spanning the period July 2016 through June 2017. The award allocation was 10.7 million processor-hours at the National Energy Research Scientific Computing Center. The simulations performed were in support of two projects: the Atmosphere to Electrons (A2e) project, supported by the DOE EERE office; and the Exascale Computing Project (ECP), supported by the DOE Office of Science. The project team for both efforts consists of staff scientists and postdocs from Sandia National Laboratories and the National Renewable Energymore » Laboratory. At the heart of these projects is the open-source computational-fluid-dynamics (CFD) code, Nalu. Nalu solves the low-Mach-number Navier-Stokes equations using an unstructured- grid discretization. Nalu leverages the open-source Trilinos solver library and the Sierra Toolkit (STK) for parallelization and I/O. This report documents baseline computational performance of the Nalu code on problems of direct relevance to the wind plant physics application - namely, Large Eddy Simulation (LES) of an atmospheric boundary layer (ABL) flow and wall-modeled LES of a flow past a static wind turbine rotor blade. Parallel performance of Nalu and its constituent solver routines residing in the Trilinos library has been assessed previously under various campaigns. However, both Nalu and Trilinos have been, and remain, in active development and resources have not been available previously to rigorously track code performance over time. With the initiation of the ECP, it is important to establish and document baseline code performance on the problems of interest. This will allow the project team to identify and target any deficiencies in performance, as well as highlight any performance bottlenecks as we exercise the code on a greater variety of platforms and at larger scales. The current study is rather modest in scale, examining performance on problem sizes of O(100 million) elements and core counts up to 8k cores. This will be expanded as more computational resources become available to the projects.« less

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers.

PubMed

Bennett, W F Drew; Hong, Chun Kit; Wang, Yi; Tieleman, D Peter

2016-09-13

Due to antimicrobial resistance, the development of new drugs to combat bacterial and fungal infections is an important area of research. Nature uses short, charged, and amphipathic peptides for antimicrobial defense, many of which disrupt the lipid membrane in addition to other possible targets inside the cell. Computer simulations have revealed atomistic details for the interactions of antimicrobial peptides and cell-penetrating peptides with lipid bilayers. Strong interactions between the polar interface and the charged peptides can induce bilayer deformations - including membrane rupture and peptide stabilization of a hydrophilic pore. Here, we performed microsecond-long simulations of the antimicrobial peptide CM15 in a POPC bilayer expecting to observe pore formation (based on previous molecular dynamics simulations). We show that caution is needed when interpreting results of equilibrium peptide-membrane simulations, given the length of time single trajectories can dwell in local energy minima for 100's of ns to microseconds. While we did record significant membrane perturbations from the CM15 peptide, pores were not observed. We explain this discrepancy by computing the free energy for pore formation with different force fields. Our results show a large difference in the free energy barrier (ca. 40 kJ/mol) against pore formation predicted by the different force fields that would result in orders of magnitude differences in the simulation time required to observe spontaneous pore formation. This explains why previous simulations using the Berger lipid parameters reported pores induced by charged peptides, while with CHARMM based models pores were not observed in our long time-scale simulations. We reconcile some of the differences in the distance dependent free energies by shifting the free energy profiles to account for thickness differences between force fields. The shifted curves show that all the models describe small defects in lipid bilayers in a consistent manner, suggesting a common physical basis.

Bypassing the malfunction junction in warm dense matter simulations

NASA Astrophysics Data System (ADS)

Cangi, Attila; Pribram-Jones, Aurora

2015-03-01

Simulation of warm dense matter requires computational methods that capture both quantum and classical behavior efficiently under high-temperature and high-density conditions. The state-of-the-art approach to model electrons and ions under those conditions is density functional theory molecular dynamics, but this method's computational cost skyrockets as temperatures and densities increase. We propose finite-temperature potential functional theory as an in-principle-exact alternative that suffers no such drawback. In analogy to the zero-temperature theory developed previously, we derive an orbital-free free energy approximation through a coupling-constant formalism. Our density approximation and its associated free energy approximation demonstrate the method's accuracy and efficiency. A.C. has been partially supported by NSF Grant CHE-1112442. A.P.J. is supported by DOE Grant DE-FG02-97ER25308.

Lattice QCD static potentials of the meson-meson and tetraquark systems computed with both quenched and full QCD

NASA Astrophysics Data System (ADS)

Bicudo, P.; Cardoso, M.; Oliveira, O.; Silva, P. J.

2017-10-01

We revisit the static potential for the Q Q Q ¯Q ¯ system using SU(3) lattice simulations, studying both the color singlets' ground state and first excited state. We consider geometries where the two static quarks and the two antiquarks are at the corners of rectangles of different sizes. We analyze the transition between a tetraquark system and a two-meson system with a two by two correlator matrix. We compare the potentials computed with quenched QCD and with dynamical quarks. We also compare our simulations with the results of previous studies and analyze quantitatively fits of our results with Ansätze inspired in the string flip-flop model and in its possible color excitations.

Large-scale dynamo action precedes turbulence in shearing box simulations of the magnetorotational instability

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

Bhat, Pallavi; Ebrahimi, Fatima; Blackman, Eric G.

Here, we study the dynamo generation (exponential growth) of large-scale (planar averaged) fields in unstratified shearing box simulations of the magnetorotational instability (MRI). In contrast to previous studies restricted to horizontal (x–y) averaging, we also demonstrate the presence of large-scale fields when vertical (y–z) averaging is employed instead. By computing space–time planar averaged fields and power spectra, we find large-scale dynamo action in the early MRI growth phase – a previously unidentified feature. Non-axisymmetric linear MRI modes with low horizontal wavenumbers and vertical wavenumbers near that of expected maximal growth, amplify the large-scale fields exponentially before turbulence and high wavenumbermore » fluctuations arise. Thus the large-scale dynamo requires only linear fluctuations but not non-linear turbulence (as defined by mode–mode coupling). Vertical averaging also allows for monitoring the evolution of the large-scale vertical field and we find that a feedback from horizontal low wavenumber MRI modes provides a clue as to why the large-scale vertical field sustains against turbulent diffusion in the non-linear saturation regime. We compute the terms in the mean field equations to identify the individual contributions to large-scale field growth for both types of averaging. The large-scale fields obtained from vertical averaging are found to compare well with global simulations and quasi-linear analytical analysis from a previous study by Ebrahimi & Blackman. We discuss the potential implications of these new results for understanding the large-scale MRI dynamo saturation and turbulence.« less

Large-scale dynamo action precedes turbulence in shearing box simulations of the magnetorotational instability

DOE PAGES

Bhat, Pallavi; Ebrahimi, Fatima; Blackman, Eric G.

2016-07-06

Here, we study the dynamo generation (exponential growth) of large-scale (planar averaged) fields in unstratified shearing box simulations of the magnetorotational instability (MRI). In contrast to previous studies restricted to horizontal (x–y) averaging, we also demonstrate the presence of large-scale fields when vertical (y–z) averaging is employed instead. By computing space–time planar averaged fields and power spectra, we find large-scale dynamo action in the early MRI growth phase – a previously unidentified feature. Non-axisymmetric linear MRI modes with low horizontal wavenumbers and vertical wavenumbers near that of expected maximal growth, amplify the large-scale fields exponentially before turbulence and high wavenumbermore » fluctuations arise. Thus the large-scale dynamo requires only linear fluctuations but not non-linear turbulence (as defined by mode–mode coupling). Vertical averaging also allows for monitoring the evolution of the large-scale vertical field and we find that a feedback from horizontal low wavenumber MRI modes provides a clue as to why the large-scale vertical field sustains against turbulent diffusion in the non-linear saturation regime. We compute the terms in the mean field equations to identify the individual contributions to large-scale field growth for both types of averaging. The large-scale fields obtained from vertical averaging are found to compare well with global simulations and quasi-linear analytical analysis from a previous study by Ebrahimi & Blackman. We discuss the potential implications of these new results for understanding the large-scale MRI dynamo saturation and turbulence.« less

Spaceborne computer executive routine functional design specification. Volume 2: Computer executive design for space station/base

NASA Technical Reports Server (NTRS)

Kennedy, J. R.; Fitzpatrick, W. S.

1971-01-01

The computer executive functional system design concepts derived from study of the Space Station/Base are presented. Information Management System hardware configuration as directly influencing the executive design is reviewed. The hardware configuration and generic executive design requirements are considered in detail in a previous report (System Configuration and Executive Requirements Specifications for Reusable Shuttle and Space Station/Base, 9/25/70). This report defines basic system primitives and delineates processes and process control. Supervisor states are considered for describing basic multiprogramming and multiprocessing systems. A high-level computer executive including control of scheduling, allocation of resources, system interactions, and real-time supervisory functions is defined. The description is oriented to provide a baseline for a functional simulation of the computer executive system.

On the use of inexact, pruned hardware in atmospheric modelling

PubMed Central

Düben, Peter D.; Joven, Jaume; Lingamneni, Avinash; McNamara, Hugh; De Micheli, Giovanni; Palem, Krishna V.; Palmer, T. N.

2014-01-01

Inexact hardware design, which advocates trading the accuracy of computations in exchange for significant savings in area, power and/or performance of computing hardware, has received increasing prominence in several error-tolerant application domains, particularly those involving perceptual or statistical end-users. In this paper, we evaluate inexact hardware for its applicability in weather and climate modelling. We expand previous studies on inexact techniques, in particular probabilistic pruning, to floating point arithmetic units and derive several simulated set-ups of pruned hardware with reasonable levels of error for applications in atmospheric modelling. The set-up is tested on the Lorenz ‘96 model, a toy model for atmospheric dynamics, using software emulation for the proposed hardware. The results show that large parts of the computation tolerate the use of pruned hardware blocks without major changes in the quality of short- and long-time diagnostics, such as forecast errors and probability density functions. This could open the door to significant savings in computational cost and to higher resolution simulations with weather and climate models. PMID:24842031

Molecular dynamics simulations of the dielectric properties of fructose aqueous solutions

NASA Astrophysics Data System (ADS)

Sonoda, Milton T.; Elola, M. Dolores; Skaf, Munir S.

2016-10-01

The static dielectric permittivity and dielectric relaxation properties of fructose aqueous solutions of different concentrations ranging from 1.0 to 4.0 mol l-1 are investigated by means of molecular dynamics simulations. The contributions from intra- and interspecies molecular correlations were computed individually for both the static and frequency-dependent dielectric properties, and the results were compared with the available experimental data. Simulation results in the time- and frequency-domains were analyzed and indicate that the presence of fructose has little effect on the position of the fast, high-frequency (>500 cm-1) components of the dielectric response spectrum. The low-frequency (<0.1 cm-1) components, however, are markedly influenced by sugar concentration. Our analysis indicates that fructose-fructose and fructose-water interactions strongly affect the rotational-diffusion regime of molecular motions in the solutions. Increasing fructose concentration not only enhances sugar-sugar and sugar-water low frequency contributions to the dielectric loss spectrum but also slows down the reorientational dynamics of water molecules. These results are consistent with previous computer simulations carried out for other disaccharide aqueous solutions.

A stochastic Markov chain approach for tennis: Monte Carlo simulation and modeling

NASA Astrophysics Data System (ADS)

Aslam, Kamran

This dissertation describes the computational formulation of probability density functions (pdfs) that facilitate head-to-head match simulations in tennis along with ranking systems developed from their use. A background on the statistical method used to develop the pdfs , the Monte Carlo method, and the resulting rankings are included along with a discussion on ranking methods currently being used both in professional sports and in other applications. Using an analytical theory developed by Newton and Keller in [34] that defines a tennis player's probability of winning a game, set, match and single elimination tournament, a computational simulation has been developed in Matlab that allows further modeling not previously possible with the analytical theory alone. Such experimentation consists of the exploration of non-iid effects, considers the concept the varying importance of points in a match and allows an unlimited number of matches to be simulated between unlikely opponents. The results of these studies have provided pdfs that accurately model an individual tennis player's ability along with a realistic, fair and mathematically sound platform for ranking them.

Three Dimensional Simulation of the Baneberry Nuclear Event

NASA Astrophysics Data System (ADS)

Lomov, Ilya N.; Antoun, Tarabay H.; Wagoner, Jeff; Rambo, John T.

2004-07-01

Baneberry, a 10-kiloton nuclear event, was detonated at a depth of 278 m at the Nevada Test Site on December 18, 1970. Shortly after detonation, radioactive gases emanating from the cavity were released into the atmosphere through a shock-induced fissure near surface ground zero. Extensive geophysical investigations, coupled with a series of 1D and 2D computational studies were used to reconstruct the sequence of events that led to the catastrophic failure. However, the geological profile of the Baneberry site is complex and inherently three-dimensional, which meant that some geological features had to be simplified or ignored in the 2D simulations. This left open the possibility that features unaccounted for in the 2D simulations could have had an important influence on the eventual containment failure of the Baneberry event. This paper presents results from a high-fidelity 3D Baneberry simulation based on the most accurate geologic and geophysical data available. The results are compared with available data, and contrasted against the results of the previous 2D computational studies.

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

PubMed

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

2013-09-10

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

Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

PubMed

Frembgen-Kesner, Tamara; Elcock, Adrian H

2010-11-03

Theory and computation have long been used to rationalize the experimental association rate constants of protein-protein complexes, and Brownian dynamics (BD) simulations, in particular, have been successful in reproducing the relative rate constants of wild-type and mutant protein pairs. Missing from previous BD studies of association kinetics, however, has been the description of hydrodynamic interactions (HIs) between, and within, the diffusing proteins. Here we address this issue by rigorously including HIs in BD simulations of the barnase-barstar association reaction. We first show that even very simplified representations of the proteins--involving approximately one pseudoatom for every three residues in the protein--can provide excellent reproduction of the absolute association rate constants of wild-type and mutant protein pairs. We then show that simulations that include intermolecular HIs also produce excellent estimates of association rate constants, but, for a given reaction criterion, yield values that are decreased by ∼35-80% relative to those obtained in the absence of intermolecular HIs. The neglect of intermolecular HIs in previous BD simulation studies, therefore, is likely to have contributed to the somewhat overestimated absolute rate constants previously obtained. Consequently, intermolecular HIs could be an important component to include in accurate modeling of the kinetics of macromolecular association events. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Flame-Vortex Studies to Quantify Markstein Numbers Needed to Model Flame Extinction Limits

NASA Technical Reports Server (NTRS)

Driscoll, James F.; Feikema, Douglas A.

2003-01-01

This has quantified a database of Markstein numbers for unsteady flames; future work will quantify a database of flame extinction limits for unsteady conditions. Unsteady extinction limits have not been documented previously; both a stretch rate and a residence time must be measured, since extinction requires that the stretch rate be sufficiently large for a sufficiently long residence time. Ma was measured for an inwardly-propagating flame (IPF) that is negatively-stretched under microgravity conditions. Computations also were performed using RUN-1DL to explain the measurements. The Markstein number of an inwardly-propagating flame, for both the microgravity experiment and the computations, is significantly larger than that of an outwardy-propagating flame. The computed profiles of the various species within the flame suggest reasons. Computed hydrogen concentrations build up ahead of the IPF but not the OPF. Understanding was gained by running the computations for both simplified and full-chemistry conditions. Numerical Simulations. To explain the experimental findings, numerical simulations of both inwardly and outwardly propagating spherical flames (with complex chemistry) were generated using the RUN-1DL code, which includes 16 species and 46 reactions.

Vector computer memory bank contention

NASA Technical Reports Server (NTRS)

Bailey, D. H.

1985-01-01

A number of vector supercomputers feature very large memories. Unfortunately the large capacity memory chips that are used in these computers are much slower than the fast central processing unit (CPU) circuitry. As a result, memory bank reservation times (in CPU ticks) are much longer than on previous generations of computers. A consequence of these long reservation times is that memory bank contention is sharply increased, resulting in significantly lowered performance rates. The phenomenon of memory bank contention in vector computers is analyzed using both a Markov chain model and a Monte Carlo simulation program. The results of this analysis indicate that future generations of supercomputers must either employ much faster memory chips or else feature very large numbers of independent memory banks.

Robot computer problem solving system

NASA Technical Reports Server (NTRS)

Merriam, E. W.; Becker, J. D.

1973-01-01

A robot computer problem solving system which represents a robot exploration vehicle in a simulated Mars environment is described. The model exhibits changes and improvements made on a previously designed robot in a city environment. The Martian environment is modeled in Cartesian coordinates; objects are scattered about a plane; arbitrary restrictions on the robot's vision have been removed; and the robot's path contains arbitrary curves. New environmental features, particularly the visual occlusion of objects by other objects, were added to the model. Two different algorithms were developed for computing occlusion. Movement and vision capabilities of the robot were established in the Mars environment, using LISP/FORTRAN interface for computational efficiency. The graphical display program was redesigned to reflect the change to the Mars-like environment.

Provable classically intractable sampling with measurement-based computation in constant time

NASA Astrophysics Data System (ADS)

Sanders, Stephen; Miller, Jacob; Miyake, Akimasa

We present a constant-time measurement-based quantum computation (MQC) protocol to perform a classically intractable sampling problem. We sample from the output probability distribution of a subclass of the instantaneous quantum polynomial time circuits introduced by Bremner, Montanaro and Shepherd. In contrast with the usual circuit model, our MQC implementation includes additional randomness due to byproduct operators associated with the computation. Despite this additional randomness we show that our sampling task cannot be efficiently simulated by a classical computer. We extend previous results to verify the quantum supremacy of our sampling protocol efficiently using only single-qubit Pauli measurements. Center for Quantum Information and Control, Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA.

Vector computer memory bank contention

NASA Technical Reports Server (NTRS)

Bailey, David H.

1987-01-01

A number of vector supercomputers feature very large memories. Unfortunately the large capacity memory chips that are used in these computers are much slower than the fast central processing unit (CPU) circuitry. As a result, memory bank reservation times (in CPU ticks) are much longer than on previous generations of computers. A consequence of these long reservation times is that memory bank contention is sharply increased, resulting in significantly lowered performance rates. The phenomenon of memory bank contention in vector computers is analyzed using both a Markov chain model and a Monte Carlo simulation program. The results of this analysis indicate that future generations of supercomputers must either employ much faster memory chips or else feature very large numbers of independent memory banks.

GEANT4 Tuning For pCT Development

NASA Astrophysics Data System (ADS)

Yevseyeva, Olga; de Assis, Joaquim T.; Evseev, Ivan; Schelin, Hugo R.; Paschuk, Sergei A.; Milhoretto, Edney; Setti, João A. P.; Díaz, Katherin S.; Hormaza, Joel M.; Lopes, Ricardo T.

2011-08-01

Proton beams in medical applications deal with relatively thick targets like the human head or trunk. Thus, the fidelity of proton computed tomography (pCT) simulations as a tool for proton therapy planning depends in the general case on the accuracy of results obtained for the proton interaction with thick absorbers. GEANT4 simulations of proton energy spectra after passing thick absorbers do not agree well with existing experimental data, as showed previously. Moreover, the spectra simulated for the Bethe-Bloch domain showed an unexpected sensitivity to the choice of low-energy electromagnetic models during the code execution. These observations were done with the GEANT4 version 8.2 during our simulations for pCT. This work describes in more details the simulations of the proton passage through aluminum absorbers with varied thickness. The simulations were done by modifying only the geometry in the Hadrontherapy Example, and for all available choices of the Electromagnetic Physics Models. As the most probable reasons for these effects is some specific feature in the code, or some specific implicit parameters in the GEANT4 manual, we continued our study with version 9.2 of the code. Some improvements in comparison with our previous results were obtained. The simulations were performed considering further applications for pCT development.

A parallelization method for time periodic steady state in simulation of radio frequency sheath dynamics

NASA Astrophysics Data System (ADS)

Kwon, Deuk-Chul; Shin, Sung-Sik; Yu, Dong-Hun

2017-10-01

In order to reduce the computing time in simulation of radio frequency (rf) plasma sources, various numerical schemes were developed. It is well known that the upwind, exponential, and power-law schemes can efficiently overcome the limitation on the grid size for fluid transport simulations of high density plasma discharges. Also, the semi-implicit method is a well-known numerical scheme to overcome on the simulation time step. However, despite remarkable advances in numerical techniques and computing power over the last few decades, efficient multi-dimensional modeling of low temperature plasma discharges has remained a considerable challenge. In particular, there was a difficulty on parallelization in time for the time periodic steady state problems such as capacitively coupled plasma discharges and rf sheath dynamics because values of plasma parameters in previous time step are used to calculate new values each time step. Therefore, we present a parallelization method for the time periodic steady state problems by using period-slices. In order to evaluate the efficiency of the developed method, one-dimensional fluid simulations are conducted for describing rf sheath dynamics. The result shows that speedup can be achieved by using a multithreading method.

SPH Simulations of Spherical Bondi Accretion: First Step of Implementing AGN Feedback in Galaxy Formation

NASA Astrophysics Data System (ADS)

Barai, Paramita; Proga, D.; Nagamine, K.

2011-01-01

Our motivation is to numerically test the assumption of Black Hole (BH) accretion (that the central massive BH of a galaxy accretes mass at the Bondi-Hoyle accretion rate, with ad-hoc choice of parameters), made in many previous galaxy formation studies including AGN feedback. We perform simulations of a spherical distribution of gas, within the radius range 0.1 - 200 pc, accreting onto a central supermassive black hole (the Bondi problem), using the 3D Smoothed Particle Hydrodynamics code Gadget. In our simulations we study the radial distribution of various gas properties (density, velocity, temperature, Mach number). We compute the central mass inflow rate at the inner boundary (0.1 pc), and investigate how different gas properties (initial density and velocity profiles) and computational parameters (simulation outer boundary, particle number) affect the central inflow. Radiative processes (namely heating by a central X-ray corona and gas cooling) have been included in our simulations. We study the thermal history of accreting gas, and identify the contribution of radiative and adiabatic terms in shaping the gas properties. We find that the current implementation of artificial viscosity in the Gadget code causes unwanted extra heating near the inner radius.

Vectorization of a particle simulation method for hypersonic rarefied flow

NASA Technical Reports Server (NTRS)

Mcdonald, Jeffrey D.; Baganoff, Donald

1988-01-01

An efficient particle simulation technique for hypersonic rarefied flows is presented at an algorithmic and implementation level. The implementation is for a vector computer architecture, specifically the Cray-2. The method models an ideal diatomic Maxwell molecule with three translational and two rotational degrees of freedom. Algorithms are designed specifically for compatibility with fine grain parallelism by reducing the number of data dependencies in the computation. By insisting on this compatibility, the method is capable of performing simulation on a much larger scale than previously possible. A two-dimensional simulation of supersonic flow over a wedge is carried out for the near-continuum limit where the gas is in equilibrium and the ideal solution can be used as a check on the accuracy of the gas model employed in the method. Also, a three-dimensional, Mach 8, rarefied flow about a finite-span flat plate at a 45 degree angle of attack was simulated. It utilized over 10 to the 7th particles carried through 400 discrete time steps in less than one hour of Cray-2 CPU time. This problem was chosen to exhibit the capability of the method in handling a large number of particles and a true three-dimensional geometry.

X-Ray Astronomy

NASA Technical Reports Server (NTRS)

Wu, S. T.

2000-01-01

Dr. S. N. Zhang has lead a seven member group (Dr. Yuxin Feng, Mr. XuejunSun, Mr. Yongzhong Chen, Mr. Jun Lin, Mr. Yangsen Yao, and Ms. Xiaoling Zhang). This group has carried out the following activities: continued data analysis from space astrophysical missions CGRO, RXTE, ASCA and Chandra. Significant scientific results have been produced as results of their work. They discovered the three-layered accretion disk structure around black holes in X-ray binaries; their paper on this discovery is to appear in the prestigious Science magazine. They have also developed a new method for energy spectral analysis of black hole X-ray binaries; four papers on this topics were presented at the most recent Atlanta AAS meeting. They have also carried Monte-Carlo simulations of X-ray detectors, in support to the hardware development efforts at Marshall Space Flight Center (MSFC). These computation-intensive simulations have been carried out entirely on the computers at UAH. They have also carried out extensive simulations for astrophysical applications, taking advantage of the Monte-Carlo simulation codes developed previously at MSFC and further improved at UAH for detector simulations. One refereed paper and one contribution to conference proceedings have been resulted from this effort.

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

Bailey, David H.

In a previous humorous note entitled 'Twelve Ways to Fool the Masses,' I outlined twelve common ways in which performance figures for technical computer systems can be distorted. In this paper and accompanying conference talk, I give a reprise of these twelve 'methods' and give some actual examples that have appeared in peer-reviewed literature in years past. I then propose guidelines for reporting performance, the adoption of which would raise the level of professionalism and reduce the level of confusion, not only in the world of device simulation but also in the larger arena of technical computing.

Physical analysis and second-order modelling of an unsteady turbulent flow - The oscillating boundary layer on a flat plate

NASA Technical Reports Server (NTRS)

Ha Minh, H.; Viegas, J. R.; Rubesin, M. W.; Spalart, P.; Vandromme, D. D.

1989-01-01

The turbulent boundary layer under a freestream whose velocity varies sinusoidally in time around a zero mean is computed using two second order turbulence closure models. The time or phase dependent behavior of the Reynolds stresses are analyzed and results are compared to those of a previous SPALART-BALDWIN direct simulation. Comparisons show that the second order modeling is quite satisfactory for almost all phase angles, except in the relaminarization period where the computations lead to a relatively high wall shear stress.

Analysis of computer images in the presence of metals

NASA Astrophysics Data System (ADS)

Buzmakov, Alexey; Ingacheva, Anastasia; Prun, Victor; Nikolaev, Dmitry; Chukalina, Marina; Ferrero, Claudio; Asadchikov, Victor

2018-04-01

Artifacts caused by intensely absorbing inclusions are encountered in computed tomography via polychromatic scanning and may obscure or simulate pathologies in medical applications. To improve the quality of reconstruction if high-Z inclusions in presence, previously we proposed and tested with synthetic data an iterative technique with soft penalty mimicking linear inequalities on the photon-starved rays. This note reports a test at the tomographic laboratory set-up at the Institute of Crystallography FSRC "Crystallography and Photonics" RAS in which tomographic scans were successfully made of temporary tooth without inclusion and with Pb inclusion.

LAMPS software

NASA Technical Reports Server (NTRS)

Perkey, D. J.; Kreitzberg, C. W.

1984-01-01

The dynamic prediction model along with its macro-processor capability and data flow system from the Drexel Limited-Area and Mesoscale Prediction System (LAMPS) were converted and recorded for the Perkin-Elmer 3220. The previous version of this model was written for Control Data Corporation 7600 and CRAY-1a computer environment which existed until recently at the National Center for Atmospheric Research. The purpose of this conversion was to prepare LAMPS for porting to computer environments other than that encountered at NCAR. The emphasis was shifted from programming tasks to model simulation and evaluation tests.

Maintenance of ventricular fibrillation in heterogeneous ventricle.

PubMed

Arevalo, Hamenegild J; Trayanova, Natalia A

2006-01-01

Although ventricular fibrillation (VF) is the prevalent cause of sudden cardiac death, the mechanisms that underlie VF remain elusive. One possible explanation is that VF is driven by a single robust rotor that is the source of wavefronts that break-up due to functional heterogeneities. Previous 2D computer simulations have proposed that a heterogeneity in background potassium current (IK1) can serve as the substrate for the formation of mother rotor activity. This study incorporates IK1 heterogeneity between the left and right ventricle in a realistic 3D rabbit ventricle model to examine its effects on the organization of VF. Computer simulations show that the IK1 heterogeneity contributes to the initiation and maintenance of VF by providing regions of different refractoriness which serves as sites of wave break and rotor formation. A single rotor that drives the fibrillatory activity in the ventricle is not found in this study. Instead, multiple sites of reentry are recorded throughout the ventricle. Calculation of dominant frequencies for each myocardial node yields no significant difference between the dominant frequency of the LV and the RV. The 3D computer simulations suggest that IK1 spatial heterogeneity alone can not lead to the formation of a stable rotor.

Identification of a Novel Class of BRD4 Inhibitors by Computational Screening and Binding Simulations

PubMed Central

2017-01-01

Computational screening is a method to prioritize small-molecule compounds based on the structural and biochemical attributes built from ligand and target information. Previously, we have developed a scalable virtual screening workflow to identify novel multitarget kinase/bromodomain inhibitors. In the current study, we identified several novel N-[3-(2-oxo-pyrrolidinyl)phenyl]-benzenesulfonamide derivatives that scored highly in our ensemble docking protocol. We quantified the binding affinity of these compounds for BRD4(BD1) biochemically and generated cocrystal structures, which were deposited in the Protein Data Bank. As the docking poses obtained in the virtual screening pipeline did not align with the experimental cocrystal structures, we evaluated the predictions of their precise binding modes by performing molecular dynamics (MD) simulations. The MD simulations closely reproduced the experimentally observed protein–ligand cocrystal binding conformations and interactions for all compounds. These results suggest a computational workflow to generate experimental-quality protein–ligand binding models, overcoming limitations of docking results due to receptor flexibility and incomplete sampling, as a useful starting point for the structure-based lead optimization of novel BRD4(BD1) inhibitors. PMID:28884163

An earth imaging camera simulation using wide-scale construction of reflectance surfaces

NASA Astrophysics Data System (ADS)

Murthy, Kiran; Chau, Alexandra H.; Amin, Minesh B.; Robinson, M. Dirk

2013-10-01

Developing and testing advanced ground-based image processing systems for earth-observing remote sensing applications presents a unique challenge that requires advanced imagery simulation capabilities. This paper presents an earth-imaging multispectral framing camera simulation system called PayloadSim (PaySim) capable of generating terabytes of photorealistic simulated imagery. PaySim leverages previous work in 3-D scene-based image simulation, adding a novel method for automatically and efficiently constructing 3-D reflectance scenes by draping tiled orthorectified imagery over a geo-registered Digital Elevation Map (DEM). PaySim's modeling chain is presented in detail, with emphasis given to the techniques used to achieve computational efficiency. These techniques as well as cluster deployment of the simulator have enabled tuning and robust testing of image processing algorithms, and production of realistic sample data for customer-driven image product development. Examples of simulated imagery of Skybox's first imaging satellite are shown.

Fabrication and evaluation of novel rabbit model cardiovascular simulator with 3D printer

NASA Astrophysics Data System (ADS)

Jang, Min; Lee, Min-Woo; Seo, See-Yoon; Shin, Sang-Hoon

2017-03-01

Simulators allow researchers to study the hemodynamics of the cardiovascular system in a reproducible way without using complicated equations. Previous simulators focused on heart functions. However, a detailed model of the vessels is required to replicate the pulse wave of the arterial system. A computer simulation was used to simplify the arterial branch because producing every small artery is neither possible nor necessary. A 3D-printed zig was used to make a hand-made arterial tree. The simulator that was developed was evaluated by comparing its results to in-vivo data, in terms of the hemodynamic parameters (waveform, augmentation index, impedance, etc.) that were measured at three points: the ascending aorta, the thoracic aorta, and the brachiocephalic artery. The results from the simulator showed good agreement with the in-vivo data. Therefore, this simulator can be used as a research tool for the cardiovascular study of animal models, specifically rabbits.

Surface order in cold liquids: X-ray reflectivity studies of dielectric liquids and comparison to liquid metals

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

Chattopadhyay, S.; Ehrlich, S.; Uysal, A.

2010-05-17

Oscillatory surface-density profiles layers have previously been reported in several metallic liquids, one dielectric liquid, and in computer simulations of dielectric liquids. We have now seen surface layers in two other dielectric liquids, pentaphenyl trimethyl trisiloxane, and pentavinyl pentamethyl cyclopentasiloxane. These layers appear below T?285 K and T?130 K, respectively; both thresholds correspond to T/Tc?0.2 where Tc is the liquid-gas critical temperature. All metallic and dielectric liquid surfaces previously studied are also consistent with the existence of this T/Tc threshold, first indicated by the simulations of Chacon et al. The layer width parameters, determined using a distorted-crystal fitting model, followmore » common trends as functions of Tc for both metallic and dielectric liquids.« less

Translational and rotational dynamics of monosaccharide solutions.

PubMed

Lelong, Gérald; Howells, W Spencer; Brady, John W; Talón, César; Price, David L; Saboungi, Marie-Louise

2009-10-01

Molecular dynamics computer simulations have been carried out on aqueous solutions of glucose at concentrations bracketing those previously measured with quasi-elastic neutron scattering (QENS), in order to investigate the motions and interactions of the sugar and water molecules. In addition, QENS measurements have been carried out on fructose solutions to determine whether the effects previously observed for glucose apply to monosaccharide solutions. The simulations indicate a dynamical analogy between higher solute concentration and lower temperature that could provide a key explanation of the bioprotective phenomena observed in many living organisms. The experimental results on fructose solutions show qualitatively similar behavior to the glucose solutions. The dynamics of the water molecules are essentially the same, while the translational diffusion of the sugar molecules is slightly faster in the fructose solutions.

Interleaved concatenated codes: New perspectives on approaching the Shannon limit

PubMed Central

Viterbi, A. J.; Viterbi, A. M.; Sindhushayana, N. T.

1997-01-01

The last few years have witnessed a significant decrease in the gap between the Shannon channel capacity limit and what is practically achievable. Progress has resulted from novel extensions of previously known coding techniques involving interleaved concatenated codes. A considerable body of simulation results is now available, supported by an important but limited theoretical basis. This paper presents a computational technique which further ties simulation results to the known theory and reveals a considerable reduction in the complexity required to approach the Shannon limit. PMID:11038568

Nucleation and growth in one dimension. I. The generalized Kolmogorov-Johnson-Mehl-Avrami model

NASA Astrophysics Data System (ADS)

Jun, Suckjoon; Zhang, Haiyang; Bechhoefer, John

2005-01-01

Motivated by a recent application of the Kolmogorov-Johnson-Mehl-Avrami (KJMA) model to the study of DNA replication, we consider the one-dimensional (1D) version of this model. We generalize previous work to the case where the nucleation rate is an arbitrary function I(t) and obtain analytical results for the time-dependent distributions of various quantities (such as the island distribution). We also present improved computer simulation algorithms to study the 1D KJMA model. The analytical results and simulations are in excellent agreement.

Large Eddy Simulation Study for Fluid Disintegration and Mixing

NASA Technical Reports Server (NTRS)

Bellan, Josette; Taskinoglu, Ezgi

2011-01-01

A new modeling approach is based on the concept of large eddy simulation (LES) within which the large scales are computed and the small scales are modeled. The new approach is expected to retain the fidelity of the physics while also being computationally efficient. Typically, only models for the small-scale fluxes of momentum, species, and enthalpy are used to reintroduce in the simulation the physics lost because the computation only resolves the large scales. These models are called subgrid (SGS) models because they operate at a scale smaller than the LES grid. In a previous study of thermodynamically supercritical fluid disintegration and mixing, additional small-scale terms, one in the momentum and one in the energy conservation equations, were identified as requiring modeling. These additional terms were due to the tight coupling between dynamics and real-gas thermodynamics. It was inferred that if these terms would not be modeled, the high density-gradient magnitude regions, experimentally identified as a characteristic feature of these flows, would not be accurately predicted without the additional term in the momentum equation; these high density-gradient magnitude regions were experimentally shown to redistribute turbulence in the flow. And it was also inferred that without the additional term in the energy equation, the heat flux magnitude could not be accurately predicted; the heat flux to the wall of combustion devices is a crucial quantity that determined necessary wall material properties. The present work involves situations where only the term in the momentum equation is important. Without this additional term in the momentum equation, neither the SGS-flux constant-coefficient Smagorinsky model nor the SGS-flux constant-coefficient Gradient model could reproduce in LES the pressure field or the high density-gradient magnitude regions; the SGS-flux constant- coefficient Scale-Similarity model was the most successful in this endeavor although not totally satisfactory. With a model for the additional term in the momentum equation, the predictions of the constant-coefficient Smagorinsky and constant-coefficient Scale-Similarity models were improved to a certain extent; however, most of the improvement was obtained for the Gradient model. The previously derived model and a newly developed model for the additional term in the momentum equation were both tested, with the new model proving even more successful than the previous model at reproducing the high density-gradient magnitude regions. Several dynamic SGS-flux models, in which the SGS-flux model coefficient is computed as part of the simulation, were tested in conjunction with the new model for this additional term in the momentum equation. The most successful dynamic model was a "mixed" model combining the Smagorinsky and Gradient models. This work is directly applicable to simulations of gas turbine engines (aeronautics) and rocket engines (astronautics).

Ab initio MD simulations of Mg2SiO4 liquid at high pressures and temperatures relevant to the Earth's mantle

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2010-12-01

Computational studies implementing Density Functional Theory (DFT) methods have become very popular in the Materials Sciences in recent years. DFT codes are now used routinely to simulate properties of geomaterials—mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only 100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it would be useful to be able to compute larger systems especially for extracting transport properties and coordination statistics. Previous studies have used codes such as VASP where CPU time increases as N2, making calculations on systems of more than 100 atoms computationally very taxing. SIESTA (Soler, et al. 2002) is a an order-N (linear-scaling) DFT code that enables electronic structure and MD computations on larger systems (N 1000) by making approximations such as localized numerical orbitals. Here we test the applicability of SIESTA to simulate geosilicates in the liquid and glass state. We have used SIESTA for MD simulations of liquid Mg2SiO4 at various state points pertinent to the Earth’s mantle and congruous with those calculated in a previous DFT study using the VASP code (DeKoker, et al. 2008). The core electronic wave functions of Mg, Si, and O were approximated using pseudopotentials with a core cutoff radius of 1.38, 1.0, and 0.61 Angstroms respectively. The Ceperly-Alder parameterization of the Local Density Approximation (LDA) was used as the exchange-correlation functional. Known systematic overbinding of LDA was corrected with the addition of a pressure term, P 1.6 GPa, which is the pressure calculated by SIESTA at the experimental zero-pressure volume of forsterite under static conditions (Stixrude and Lithgow-Bertollini 2005). Results are reported here that show SIESTA calculations of T and P on densities in the range of 2.7 - 5.0 g/cc of liquid Mg2SiO4 are similar to the VASP calculations of DeKoker et al. (2008), which used the same functional. This opens the possibility of conducting fast /emph{ab initio} MD simulations of geomaterials with a hundreds of atoms.

Quantum computation based on photonic systems with two degrees of freedom assisted by the weak cross-Kerr nonlinearity

PubMed Central

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

2016-01-01

Most of previous quantum computations only take use of one degree of freedom (DoF) of photons. An experimental system may possess various DoFs simultaneously. In this paper, with the weak cross-Kerr nonlinearity, we investigate the parallel quantum computation dependent on photonic systems with two DoFs. We construct nearly deterministic controlled-not (CNOT) gates operating on the polarization spatial DoFs of the two-photon or one-photon system. These CNOT gates show that two photonic DoFs can be encoded as independent qubits without auxiliary DoF in theory. Only the coherent states are required. Thus one half of quantum simulation resources may be saved in quantum applications if more complicated circuits are involved. Hence, one may trade off the implementation complexity and simulation resources by using different photonic systems. These CNOT gates are also used to complete various applications including the quantum teleportation and quantum superdense coding. PMID:27424767

Quantum computation based on photonic systems with two degrees of freedom assisted by the weak cross-Kerr nonlinearity.

PubMed

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

2016-07-18

Most of previous quantum computations only take use of one degree of freedom (DoF) of photons. An experimental system may possess various DoFs simultaneously. In this paper, with the weak cross-Kerr nonlinearity, we investigate the parallel quantum computation dependent on photonic systems with two DoFs. We construct nearly deterministic controlled-not (CNOT) gates operating on the polarization spatial DoFs of the two-photon or one-photon system. These CNOT gates show that two photonic DoFs can be encoded as independent qubits without auxiliary DoF in theory. Only the coherent states are required. Thus one half of quantum simulation resources may be saved in quantum applications if more complicated circuits are involved. Hence, one may trade off the implementation complexity and simulation resources by using different photonic systems. These CNOT gates are also used to complete various applications including the quantum teleportation and quantum superdense coding.

Effects of Geometric Details on Slat Noise Generation and Propagation

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Lockard, David P.

2006-01-01

The relevance of geometric details to the generation and propagation of noise from leading-edge slats is considered. Typically, such details are omitted in computational simulations and model-scale experiments thereby creating ambiguities in comparisons with acoustic results from flight tests. The current study uses two-dimensional, computational simulations in conjunction with a Ffowcs Williams-Hawkings (FW-H) solver to investigate the effects of previously neglected slat "bulb" and "blade" seals on the local flow field and the associated acoustic radiation. The computations clearly show that the presence of the "blade" seal at the cusp significantly changes the slat cove flow dynamics, reduces the amplitudes of the radiated sound, and to a lesser extent, alters the directivity beneath the airfoil. Furthermore, it is demonstrated that a modest extension of the baseline "blade" seal further enhances the suppression of slat noise. As a side issue, the utility and equivalence of FW-H methodology for calculating far-field noise as opposed to a more direct approach is examined and demonstrated.

A Computational Framework for Realistic Retina Modeling.

PubMed

Martínez-Cañada, Pablo; Morillas, Christian; Pino, Begoña; Ros, Eduardo; Pelayo, Francisco

2016-11-01

Computational simulations of the retina have led to valuable insights about the biophysics of its neuronal activity and processing principles. A great number of retina models have been proposed to reproduce the behavioral diversity of the different visual processing pathways. While many of these models share common computational stages, previous efforts have been more focused on fitting specific retina functions rather than generalizing them beyond a particular model. Here, we define a set of computational retinal microcircuits that can be used as basic building blocks for the modeling of different retina mechanisms. To validate the hypothesis that similar processing structures may be repeatedly found in different retina functions, we implemented a series of retina models simply by combining these computational retinal microcircuits. Accuracy of the retina models for capturing neural behavior was assessed by fitting published electrophysiological recordings that characterize some of the best-known phenomena observed in the retina: adaptation to the mean light intensity and temporal contrast, and differential motion sensitivity. The retinal microcircuits are part of a new software platform for efficient computational retina modeling from single-cell to large-scale levels. It includes an interface with spiking neural networks that allows simulation of the spiking response of ganglion cells and integration with models of higher visual areas.

Structured water in polyelectrolyte dendrimers: Understanding small angle neutron scattering results through atomistic simulation

NASA Astrophysics Data System (ADS)

Wu, Bin; Kerkeni, Boutheïna; Egami, Takeshi; Do, Changwoo; Liu, Yun; Wang, Yongmei; Porcar, Lionel; Hong, Kunlun; Smith, Sean C.; Liu, Emily L.; Smith, Gregory S.; Chen, Wei-Ren

2012-04-01

Based on atomistic molecular dynamics (MD) simulations, the small angle neutron scattering (SANS) intensity behavior of a single generation-4 polyelectrolyte polyamidoamine starburst dendrimer is investigated at different levels of molecular protonation. The SANS form factor, P(Q), and Debye autocorrelation function, γ(r), are calculated from the equilibrium MD trajectory based on a mathematical approach proposed in this work. The consistency found in comparison against previously published experimental findings (W.-R. Chen, L. Porcar, Y. Liu, P. D. Butler, and L. J. Magid, Macromolecules 40, 5887 (2007)) leads to a link between the neutron scattering experiment and MD computation, and fresh perspectives. The simulations enable scattering calculations of not only the hydrocarbons but also the contribution from the scattering length density fluctuations caused by structured, confined water within the dendrimer. Based on our computational results, we explore the validity of using radius of gyration RG for microstructure characterization of a polyelectrolyte dendrimer from the scattering perspective.

DES Prediction of Cavitation Erosion and Its Validation for a Ship Scale Propeller

NASA Astrophysics Data System (ADS)

Ponkratov, Dmitriy, Dr

2015-12-01

Lloyd's Register Technical Investigation Department (LR TID) have developed numerical functions for the prediction of cavitation erosion aggressiveness within Computational Fluid Dynamics (CFD) simulations. These functions were previously validated for a model scale hydrofoil and ship scale rudder [1]. For the current study the functions were applied to a cargo ship's full scale propeller, on which the severe cavitation erosion was reported. The performed Detach Eddy Simulation (DES) required a fine computational mesh (approximately 22 million cells), together with a very small time step (2.0E-4 s). As the cavitation for this type of vessel is primarily caused by a highly non-uniform wake, the hull was also included in the simulation. The applied method under predicted the cavitation extent and did not fully resolve the tip vortex; however, the areas of cavitation collapse were captured successfully. Consequently, the developed functions showed a very good prediction of erosion areas, as confirmed by comparison with underwater propeller inspection results.

Homogeneous nucleation and microstructure evolution in million-atom molecular dynamics simulation

PubMed Central

Shibuta, Yasushi; Oguchi, Kanae; Takaki, Tomohiro; Ohno, Munekazu

2015-01-01

Homogeneous nucleation from an undercooled iron melt is investigated by the statistical sampling of million-atom molecular dynamics (MD) simulations performed on a graphics processing unit (GPU). Fifty independent instances of isothermal MD calculations with one million atoms in a quasi-two-dimensional cell over a nanosecond reveal that the nucleation rate and the incubation time of nucleation as functions of temperature have characteristic shapes with a nose at the critical temperature. This indicates that thermally activated homogeneous nucleation occurs spontaneously in MD simulations without any inducing factor, whereas most previous studies have employed factors such as pressure, surface effect, and continuous cooling to induce nucleation. Moreover, further calculations over ten nanoseconds capture the microstructure evolution on the order of tens of nanometers from the atomistic viewpoint and the grain growth exponent is directly estimated. Our novel approach based on the concept of “melting pots in a supercomputer” is opening a new phase in computational metallurgy with the aid of rapid advances in computational environments. PMID:26311304

Numerical investigation of the vortex-induced vibration of an elastically mounted circular cylinder at high Reynolds number (Re = 104) and low mass ratio using the RANS code.

PubMed

Khan, Niaz Bahadur; Ibrahim, Zainah; Nguyen, Linh Tuan The; Javed, Muhammad Faisal; Jameel, Mohammed

2017-01-01

This study numerically investigates the vortex-induced vibration (VIV) of an elastically mounted rigid cylinder by using Reynolds-averaged Navier-Stokes (RANS) equations with computational fluid dynamic (CFD) tools. CFD analysis is performed for a fixed-cylinder case with Reynolds number (Re) = 104 and for a cylinder that is free to oscillate in the transverse direction and possesses a low mass-damping ratio and Re = 104. Previously, similar studies have been performed with 3-dimensional and comparatively expensive turbulent models. In the current study, the capability and accuracy of the RANS model are validated, and the results of this model are compared with those of detached eddy simulation, direct numerical simulation, and large eddy simulation models. All three response branches and the maximum amplitude are well captured. The 2-dimensional case with the RANS shear-stress transport k-w model, which involves minimal computational cost, is reliable and appropriate for analyzing the characteristics of VIV.

Intrinsic frame transport for a model of nematic liquid crystal

NASA Astrophysics Data System (ADS)

Cozzini, S.; Rull, L. F.; Ciccotti, G.; Paolini, G. V.

1997-02-01

We present a computer simulation study of the dynamical properties of a nematic liquid crystal model. The diffusional motion of the nematic director is taken into account in our calculations in order to give a proper estimate of the transport coefficients. Differently from other groups we do not attempt to stabilize the director through rigid constraints or applied external fields. We instead define an intrinsic frame which moves along with the director at each step of the simulation. The transport coefficients computed in the intrinsic frame are then compared against the ones calculated in the fixed laboratory frame, to show the inadequacy of the latter for systems with less than 500 molecules. Using this general scheme on the Gay-Berne liquid crystal model, we evidence the natural motion of the director and attempt to quantify its intrinsic time scale and size dependence. Through extended simulations of systems of different size we calculate the diffusion and viscosity coefficients of this model and compare our results with values previously obtained with fixed director.

A Simple Memristor Model for Circuit Simulations

NASA Astrophysics Data System (ADS)

Fullerton, Farrah-Amoy; Joe, Aaleyah; Gergel-Hackett, Nadine; Department of Chemistry; Physics Team

This work describes the development of a model for the memristor, a novel nanoelectronic technology. The model was designed to replicate the real-world electrical characteristics of previously fabricated memristor devices, but was constructed with basic circuit elements using a free widely available circuit simulator, LT Spice. The modeled memrsistors were then used to construct a circuit that performs material implication. Material implication is a digital logic that can be used to perform all of the same basic functions as traditional CMOS gates, but with fewer nanoelectronic devices. This memristor-based digital logic could enable memristors' use in new paradigms of computer architecture with advantages in size, speed, and power over traditional computing circuits. Additionally, the ability to model the real-world electrical characteristics of memristors in a free circuit simulator using its standard library of elements could enable not only the development of memristor material implication, but also the development of a virtually unlimited array of other memristor-based circuits.

Dynamic VMs placement for energy efficiency by PSO in cloud computing

NASA Astrophysics Data System (ADS)

Dashti, Seyed Ebrahim; Rahmani, Amir Masoud

2016-03-01

Recently, cloud computing is growing fast and helps to realise other high technologies. In this paper, we propose a hieratical architecture to satisfy both providers' and consumers' requirements in these technologies. We design a new service in the PaaS layer for scheduling consumer tasks. In the providers' perspective, incompatibility between specification of physical machine and user requests in cloud leads to problems such as energy-performance trade-off and large power consumption so that profits are decreased. To guarantee Quality of service of users' tasks, and reduce energy efficiency, we proposed to modify Particle Swarm Optimisation to reallocate migrated virtual machines in the overloaded host. We also dynamically consolidate the under-loaded host which provides power saving. Simulation results in CloudSim demonstrated that whatever simulation condition is near to the real environment, our method is able to save as much as 14% more energy and the number of migrations and simulation time significantly reduces compared with the previous works.

Brian hears: online auditory processing using vectorization over channels.

PubMed

Fontaine, Bertrand; Goodman, Dan F M; Benichoux, Victor; Brette, Romain

2011-01-01

The human cochlea includes about 3000 inner hair cells which filter sounds at frequencies between 20 Hz and 20 kHz. This massively parallel frequency analysis is reflected in models of auditory processing, which are often based on banks of filters. However, existing implementations do not exploit this parallelism. Here we propose algorithms to simulate these models by vectorizing computation over frequency channels, which are implemented in "Brian Hears," a library for the spiking neural network simulator package "Brian." This approach allows us to use high-level programming languages such as Python, because with vectorized operations, the computational cost of interpretation represents a small fraction of the total cost. This makes it possible to define and simulate complex models in a simple way, while all previous implementations were model-specific. In addition, we show that these algorithms can be naturally parallelized using graphics processing units, yielding substantial speed improvements. We demonstrate these algorithms with several state-of-the-art cochlear models, and show that they compare favorably with existing, less flexible, implementations.

Numerical validation of selected computer programs in nonlinear analysis of steel frame exposed to fire

NASA Astrophysics Data System (ADS)

Maślak, Mariusz; Pazdanowski, Michał; Woźniczka, Piotr

2018-01-01

Validation of fire resistance for the same steel frame bearing structure is performed here using three different numerical models, i.e. a bar one prepared in the SAFIR environment, and two 3D models developed within the framework of Autodesk Simulation Mechanical (ASM) and an alternative one developed in the environment of the Abaqus code. The results of the computer simulations performed are compared with the experimental results obtained previously, in a laboratory fire test, on a structure having the same characteristics and subjected to the same heating regimen. Comparison of the experimental and numerically determined displacement evolution paths for selected nodes of the considered frame during the simulated fire exposure constitutes the basic criterion applied to evaluate the validity of the numerical results obtained. The experimental and numerically determined estimates of critical temperature specific to the considered frame and related to the limit state of bearing capacity in fire have been verified as well.

Instabilities and Turbulence Generation by Pick-Up Ion Distributions in the Outer Heliosheath

NASA Astrophysics Data System (ADS)

Weichman, K.; Roytershteyn, V.; Delzanno, G. L.; Pogorelov, N.

2017-12-01

Pick-up ions (PUIs) play a significant role in the dynamics of the heliosphere. One problem that has attracted significant attention is the stability of ring-like distributions of PUIs and the electromagnetic fluctuations that could be generated by PUI distributions. For example, PUI stability is relevant to theories attempting to identify the origins of the IBEX ribbon. PUIs have previously been investigated by linear stability analysis of model (e.g. Gaussian) rings and corresponding computer simulations. The majority of these simulations utilized particle-in-cell methods which suffer from accuracy limitations imposed by the statistical noise associated with representing the plasma by a relatively small number of computational particles. In this work, we utilize highly accurate spectral Vlasov simulations conducted using the fully kinetic implicit code SPS (Spectral Plasma Solver) to investigate the PUI distributions inferred from a global heliospheric model (Heerikhuisen et al., 2016). Results are compared with those obtained by hybrid and fully kinetic particle-in-cell methods.

Multibody Parachute Flight Simulations for Planetary Entry Trajectories Using "Equilibrium Points"

NASA Technical Reports Server (NTRS)

Raiszadeh, Ben

2003-01-01

A method has been developed to reduce numerical stiffness and computer CPU requirements of high fidelity multibody flight simulations involving parachutes for planetary entry trajectories. Typical parachute entry configurations consist of entry bodies suspended from a parachute, connected by flexible lines. To accurately calculate line forces and moments, the simulations need to keep track of the point where the flexible lines meet (confluence point). In previous multibody parachute flight simulations, the confluence point has been modeled as a point mass. Using a point mass for the confluence point tends to make the simulation numerically stiff, because its mass is typically much less that than the main rigid body masses. One solution for stiff differential equations is to use a very small integration time step. However, this results in large computer CPU requirements. In the method described in the paper, the need for using a mass as the confluence point has been eliminated. Instead, the confluence point is modeled using an "equilibrium point". This point is calculated at every integration step as the point at which sum of all line forces is zero (static equilibrium). The use of this "equilibrium point" has the advantage of both reducing the numerical stiffness of the simulations, and eliminating the dynamical equations associated with vibration of a lumped mass on a high-tension string.

Simulating the X-Ray Image Contrast to Set-Up Techniques with Desired Flaw Detectability

NASA Technical Reports Server (NTRS)

Koshti, Ajay M.

2015-01-01

The paper provides simulation data of previous work by the author in developing a model for estimating detectability of crack-like flaws in radiography. The methodology is being developed to help in implementation of NASA Special x-ray radiography qualification, but is generically applicable to radiography. The paper describes a method for characterizing X-ray detector resolution for crack detection. Applicability of ASTM E 2737 resolution requirements to the model are also discussed. The paper describes a model for simulating the detector resolution. A computer calculator application, discussed here, also performs predicted contrast and signal-to-noise ratio calculations. Results of various simulation runs in calculating x-ray flaw size parameter and image contrast for varying input parameters such as crack depth, crack width, part thickness, x-ray angle, part-to-detector distance, part-to-source distance, source sizes, and detector sensitivity and resolution are given as 3D surfaces. These results demonstrate effect of the input parameters on the flaw size parameter and the simulated image contrast of the crack. These simulations demonstrate utility of the flaw size parameter model in setting up x-ray techniques that provide desired flaw detectability in radiography. The method is applicable to film radiography, computed radiography, and digital radiography.

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

NASA Astrophysics Data System (ADS)

Araki, Samuel J.

2016-11-01

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

The joint effect of mesoscale and microscale roughness on perceived gloss.

PubMed

Qi, Lin; Chantler, Mike J; Siebert, J Paul; Dong, Junyu

2015-10-01

Computer simulated stimuli can provide a flexible method for creating artificial scenes in the study of visual perception of material surface properties. Previous work based on this approach reported that the properties of surface roughness and glossiness are mutually interdependent and therefore, perception of one affects the perception of the other. In this case roughness was limited to a surface property termed bumpiness. This paper reports a study into how perceived gloss varies with two model parameters related to surface roughness in computer simulations: the mesoscale roughness parameter in a surface geometry model and the microscale roughness parameter in a surface reflectance model. We used a real-world environment map to provide complex illumination and a physically-based path tracer for rendering the stimuli. Eight observers took part in a 2AFC experiment, and the results were tested against conjoint measurement models. We found that although both of the above roughness parameters significantly affect perceived gloss, the additive model does not adequately describe their mutually interactive and nonlinear influence, which is at variance with previous findings. We investigated five image properties used to quantify specular highlights, and found that perceived gloss is well predicted using a linear model. Our findings provide computational support to the 'statistical appearance models' proposed recently for material perception. Copyright © 2015 Elsevier Ltd. All rights reserved.

Discriminating between stabilizing and destabilizing protein design mutations via recombination and simulation.

PubMed

Johnson, Lucas B; Gintner, Lucas P; Park, Sehoo; Snow, Christopher D

2015-08-01

Accuracy of current computational protein design (CPD) methods is limited by inherent approximations in energy potentials and sampling. These limitations are often used to qualitatively explain design failures; however, relatively few studies provide specific examples or quantitative details that can be used to improve future CPD methods. Expanding the design method to include a library of sequences provides data that is well suited for discriminating between stabilizing and destabilizing design elements. Using thermophilic endoglucanase E1 from Acidothermus cellulolyticus as a model enzyme, we computationally designed a sequence with 60 mutations. The design sequence was rationally divided into structural blocks and recombined with the wild-type sequence. Resulting chimeras were assessed for activity and thermostability. Surprisingly, unlike previous chimera libraries, regression analysis based on one- and two-body effects was not sufficient for predicting chimera stability. Analysis of molecular dynamics simulations proved helpful in distinguishing stabilizing and destabilizing mutations. Reverting to the wild-type amino acid at destabilized sites partially regained design stability, and introducing predicted stabilizing mutations in wild-type E1 significantly enhanced thermostability. The ability to isolate stabilizing and destabilizing elements in computational design offers an opportunity to interpret previous design failures and improve future CPD methods. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Simulation of Mach Probes in Non-Uniform Magnetized Plasmas: the Influence of a Background Density Gradient

NASA Astrophysics Data System (ADS)

Haakonsen, Christian Bernt; Hutchinson, Ian H.

2013-10-01

Mach probes can be used to measure transverse flow in magnetized plasmas, but what they actually measure in strongly non-uniform plasmas has not been definitively established. A fluid treatment in previous work has suggested that the diamagnetic drifts associated with background density and temperature gradients affect transverse flow measurements, but detailed computational study is required to validate and elaborate on those results; it is really a kinetic problem, since the probe deforms and introduces voids in the ion and electron distribution functions. A new code, the Plasma-Object Simulator with Iterated Trajectories (POSIT) has been developed to self-consistently compute the steady-state six-dimensional ion and electron distribution functions in the perturbed plasma. Particle trajectories are integrated backwards in time to the domain boundary, where arbitrary background distribution functions can be specified. This allows POSIT to compute the ion and electron density at each node of its unstructured mesh, update the potential based on those densities, and then iterate until convergence. POSIT is used to study the impact of a background density gradient on transverse Mach probe measurements, and the results compared to the previous fluid theory. C.B. Haakonsen was supported in part by NSF/DOE Grant No. DE-FG02-06ER54512, and in part by an SCGF award administered by ORISE under DOE Contract No. DE-AC05-06OR23100.

Ocean-Atmosphere Coupled Model Simulations of Precipitation in the Central Andes

NASA Technical Reports Server (NTRS)

Nicholls, Stephen D.; Mohr, Karen I.

2015-01-01

The meridional extent and complex orography of the South American continent contributes to a wide diversity of climate regimes ranging from hyper-arid deserts to tropical rainforests to sub-polar highland regions. In addition, South American meteorology and climate are also made further complicated by ENSO, a powerful coupled ocean-atmosphere phenomenon. Modelling studies in this region have typically resorted to either atmospheric mesoscale or atmosphere-ocean coupled global climate models. The latter offers full physics and high spatial resolution, but it is computationally inefficient typically lack an interactive ocean, whereas the former offers high computational efficiency and ocean-atmosphere coupling, but it lacks adequate spatial and temporal resolution to adequate resolve the complex orography and explicitly simulate precipitation. Explicit simulation of precipitation is vital in the Central Andes where rainfall rates are light (0.5-5 mm hr-1), there is strong seasonality, and most precipitation is associated with weak mesoscale-organized convection. Recent increases in both computational power and model development have led to the advent of coupled ocean-atmosphere mesoscale models for both weather and climate study applications. These modelling systems, while computationally expensive, include two-way ocean-atmosphere coupling, high resolution, and explicit simulation of precipitation. In this study, we use the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST), a fully-coupled mesoscale atmosphere-ocean modeling system. Previous work has shown COAWST to reasonably simulate the entire 2003-2004 wet season (Dec-Feb) as validated against both satellite and model analysis data when ECMWF interim analysis data were used for boundary conditions on a 27-9-km grid configuration (Outer grid extent: 60.4S to 17.7N and 118.6W to 17.4W).

Towards pattern generation and chaotic series prediction with photonic reservoir computers

NASA Astrophysics Data System (ADS)

Antonik, Piotr; Hermans, Michiel; Duport, François; Haelterman, Marc; Massar, Serge

2016-03-01

Reservoir Computing is a bio-inspired computing paradigm for processing time dependent signals that is particularly well suited for analog implementations. Our team has demonstrated several photonic reservoir computers with performance comparable to digital algorithms on a series of benchmark tasks such as channel equalisation and speech recognition. Recently, we showed that our opto-electronic reservoir computer could be trained online with a simple gradient descent algorithm programmed on an FPGA chip. This setup makes it in principle possible to feed the output signal back into the reservoir, and thus highly enrich the dynamics of the system. This will allow to tackle complex prediction tasks in hardware, such as pattern generation and chaotic and financial series prediction, which have so far only been studied in digital implementations. Here we report simulation results of our opto-electronic setup with an FPGA chip and output feedback applied to pattern generation and Mackey-Glass chaotic series prediction. The simulations take into account the major aspects of our experimental setup. We find that pattern generation can be easily implemented on the current setup with very good results. The Mackey-Glass series prediction task is more complex and requires a large reservoir and more elaborate training algorithm. With these adjustments promising result are obtained, and we now know what improvements are needed to match previously reported numerical results. These simulation results will serve as basis of comparison for experiments we will carry out in the coming months.

Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT_HPC)

PubMed Central

Cockrell, Robert Chase; Christley, Scott; Chang, Eugene; An, Gary

2015-01-01

Perhaps the greatest challenge currently facing the biomedical research community is the ability to integrate highly detailed cellular and molecular mechanisms to represent clinical disease states as a pathway to engineer effective therapeutics. This is particularly evident in the representation of organ-level pathophysiology in terms of abnormal tissue structure, which, through histology, remains a mainstay in disease diagnosis and staging. As such, being able to generate anatomic scale simulations is a highly desirable goal. While computational limitations have previously constrained the size and scope of multi-scale computational models, advances in the capacity and availability of high-performance computing (HPC) resources have greatly expanded the ability of computational models of biological systems to achieve anatomic, clinically relevant scale. Diseases of the intestinal tract are exemplary examples of pathophysiological processes that manifest at multiple scales of spatial resolution, with structural abnormalities present at the microscopic, macroscopic and organ-levels. In this paper, we describe a novel, massively parallel computational model of the gut, the Spatially Explicitly General-purpose Model of Enteric Tissue_HPC (SEGMEnT_HPC), which extends an existing model of the gut epithelium, SEGMEnT, in order to create cell-for-cell anatomic scale simulations. We present an example implementation of SEGMEnT_HPC that simulates the pathogenesis of ileal pouchitis, and important clinical entity that affects patients following remedial surgery for ulcerative colitis. PMID:25806784

Cloud computing and validation of expandable in silico livers.

PubMed

Ropella, Glen E P; Hunt, C Anthony

2010-12-03

In Silico Livers (ISLs) are works in progress. They are used to challenge multilevel, multi-attribute, mechanistic hypotheses about the hepatic disposition of xenobiotics coupled with hepatic responses. To enhance ISL-to-liver mappings, we added discrete time metabolism, biliary elimination, and bolus dosing features to a previously validated ISL and initiated re-validated experiments that required scaling experiments to use more simulated lobules than previously, more than could be achieved using the local cluster technology. Rather than dramatically increasing the size of our local cluster we undertook the re-validation experiments using the Amazon EC2 cloud platform. So doing required demonstrating the efficacy of scaling a simulation to use more cluster nodes and assessing the scientific equivalence of local cluster validation experiments with those executed using the cloud platform. The local cluster technology was duplicated in the Amazon EC2 cloud platform. Synthetic modeling protocols were followed to identify a successful parameterization. Experiment sample sizes (number of simulated lobules) on both platforms were 49, 70, 84, and 152 (cloud only). Experimental indistinguishability was demonstrated for ISL outflow profiles of diltiazem using both platforms for experiments consisting of 84 or more samples. The process was analogous to demonstration of results equivalency from two different wet-labs. The results provide additional evidence that disposition simulations using ISLs can cover the behavior space of liver experiments in distinct experimental contexts (there is in silico-to-wet-lab phenotype similarity). The scientific value of experimenting with multiscale biomedical models has been limited to research groups with access to computer clusters. The availability of cloud technology coupled with the evidence of scientific equivalency has lowered the barrier and will greatly facilitate model sharing as well as provide straightforward tools for scaling simulations to encompass greater detail with no extra investment in hardware.

An improved cellular automaton method to model multispecies biofilms.

PubMed

Tang, Youneng; Valocchi, Albert J

2013-10-01

Biomass-spreading rules used in previous cellular automaton methods to simulate multispecies biofilm introduced extensive mixing between different biomass species or resulted in spatially discontinuous biomass concentration and distribution; this caused results based on the cellular automaton methods to deviate from experimental results and those from the more computationally intensive continuous method. To overcome the problems, we propose new biomass-spreading rules in this work: Excess biomass spreads by pushing a line of grid cells that are on the shortest path from the source grid cell to the destination grid cell, and the fractions of different biomass species in the grid cells on the path change due to the spreading. To evaluate the new rules, three two-dimensional simulation examples are used to compare the biomass distribution computed using the continuous method and three cellular automaton methods, one based on the new rules and the other two based on rules presented in two previous studies. The relationship between the biomass species is syntrophic in one example and competitive in the other two examples. Simulation results generated using the cellular automaton method based on the new rules agree much better with the continuous method than do results using the other two cellular automaton methods. The new biomass-spreading rules are no more complex to implement than the existing rules. Copyright © 2013 Elsevier Ltd. All rights reserved.

Numerical Simulation of the Diffusion Processes in Nanoelectrode Arrays Using an Axial Neighbor Symmetry Approximation.

PubMed

Peinetti, Ana Sol; Gilardoni, Rodrigo S; Mizrahi, Martín; Requejo, Felix G; González, Graciela A; Battaglini, Fernando

2016-06-07

Nanoelectrode arrays have introduced a complete new battery of devices with fascinating electrocatalytic, sensitivity, and selectivity properties. To understand and predict the electrochemical response of these arrays, a theoretical framework is needed. Cyclic voltammetry is a well-fitted experimental technique to understand the undergoing diffusion and kinetics processes. Previous works describing microelectrode arrays have exploited the interelectrode distance to simulate its behavior as the summation of individual electrodes. This approach becomes limited when the size of the electrodes decreases to the nanometer scale due to their strong radial effect with the consequent overlapping of the diffusional fields. In this work, we present a computational model able to simulate the electrochemical behavior of arrays working either as the summation of individual electrodes or being affected by the overlapping of the diffusional fields without previous considerations. Our computational model relays in dividing a regular electrode array in cells. In each of them, there is a central electrode surrounded by neighbor electrodes; these neighbor electrodes are transformed in a ring maintaining the same active electrode area than the summation of the closest neighbor electrodes. Using this axial neighbor symmetry approximation, the problem acquires a cylindrical symmetry, being applicable to any diffusion pattern. The model is validated against micro- and nanoelectrode arrays showing its ability to predict their behavior and therefore to be used as a designing tool.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

Computer simulations of disordering kinetics in irradiated intermetallic compounds

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

Spaczer, M.; Caro, A.; Victoria, M.

1994-11-01

Molecular-dynamics computer simulations of collision cascades in intermetallic Cu[sub 3]Au, Ni[sub 3]Al, and NiAl have been performed to study the nature of the disordering processes in the collision cascade. The choice of these systems was suggested by the quite accurate description of the thermodynamic properties obtained using embedded-atom-type potentials. Since melting occurs in the core of the cascades, interesting effects appear as a result of the superposition of the loss (and subsequent recovery) of the crystalline order and the evolution of the chemical order, both processes being developed on different time scales. In our previous simulations on Ni[sub 3]Al andmore » Cu[sub 3]Au [T. Diaz de la Rubia, A. Caro, and M. Spaczer, Phys. Rev. B 47, 11 483 (1993)] we found a significant difference between the time evolution of the chemical short-range order (SRO) and the crystalline order in the cascade core for both alloys, namely the complete loss of the crystalline structure but only partial chemical disordering. Recent computer simulations in NiAl show the same phenomena. To understand these features we study the liquid phase of these three alloys and present simulation results concerning the dynamical melting of small samples, examining the atomic mobility, the relaxation time, and the saturation value of the chemical short-range order. An analytic model for the time evolution of the SRO is given.« less

Estimation of whole-body radiation exposure from brachytherapy for oral cancer using a Monte Carlo simulation.

PubMed

Ozaki, Y; Watanabe, H; Kaida, A; Miura, M; Nakagawa, K; Toda, K; Yoshimura, R; Sumi, Y; Kurabayashi, T

2017-07-01

Early stage oral cancer can be cured with oral brachytherapy, but whole-body radiation exposure status has not been previously studied. Recently, the International Commission on Radiological Protection Committee (ICRP) recommended the use of ICRP phantoms to estimate radiation exposure from external and internal radiation sources. In this study, we used a Monte Carlo simulation with ICRP phantoms to estimate whole-body exposure from oral brachytherapy. We used a Particle and Heavy Ion Transport code System (PHITS) to model oral brachytherapy with 192Ir hairpins and 198Au grains and to perform a Monte Carlo simulation on the ICRP adult reference computational phantoms. To confirm the simulations, we also computed local dose distributions from these small sources, and compared them with the results from Oncentra manual Low Dose Rate Treatment Planning (mLDR) software which is used in day-to-day clinical practice. We successfully obtained data on absorbed dose for each organ in males and females. Sex-averaged equivalent doses were 0.547 and 0.710 Sv with 192Ir hairpins and 198Au grains, respectively. Simulation with PHITS was reliable when compared with an alternative computational technique using mLDR software. We concluded that the absorbed dose for each organ and whole-body exposure from oral brachytherapy can be estimated with Monte Carlo simulation using PHITS on ICRP reference phantoms. Effective doses for patients with oral cancer were obtained. © The Author 2017. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

A comparative research of different ensemble surrogate models based on set pair analysis for the DNAPL-contaminated aquifer remediation strategy optimization.

PubMed

Hou, Zeyu; Lu, Wenxi; Xue, Haibo; Lin, Jin

2017-08-01

Surrogate-based simulation-optimization technique is an effective approach for optimizing the surfactant enhanced aquifer remediation (SEAR) strategy for clearing DNAPLs. The performance of the surrogate model, which is used to replace the simulation model for the aim of reducing computation burden, is the key of corresponding researches. However, previous researches are generally based on a stand-alone surrogate model, and rarely make efforts to improve the approximation accuracy of the surrogate model to the simulation model sufficiently by combining various methods. In this regard, we present set pair analysis (SPA) as a new method to build ensemble surrogate (ES) model, and conducted a comparative research to select a better ES modeling pattern for the SEAR strategy optimization problems. Surrogate models were developed using radial basis function artificial neural network (RBFANN), support vector regression (SVR), and Kriging. One ES model is assembling RBFANN model, SVR model, and Kriging model using set pair weights according their performance, and the other is assembling several Kriging (the best surrogate modeling method of three) models built with different training sample datasets. Finally, an optimization model, in which the ES model was embedded, was established to obtain the optimal remediation strategy. The results showed the residuals of the outputs between the best ES model and simulation model for 100 testing samples were lower than 1.5%. Using an ES model instead of the simulation model was critical for considerably reducing the computation time of simulation-optimization process and maintaining high computation accuracy simultaneously. Copyright © 2017 Elsevier B.V. All rights reserved.

Identifying secondary-school students' difficulties when reading visual representations displayed in physics simulations

NASA Astrophysics Data System (ADS)

López, Víctor; Pintó, Roser

2017-07-01

Computer simulations are often considered effective educational tools, since their visual and communicative power enable students to better understand physical systems and phenomena. However, previous studies have found that when students read visual representations some reading difficulties can arise, especially when these are complex or dynamic representations. We have analyzed how secondary-school students read the visual representations displayed in two PhET simulations (one addressing the friction-heating at microscopic level, and the other addressing the electromagnetic induction), and different typologies of reading difficulties have been identified: when reading the compositional structure of the representation, when giving appropriate relevance and semantic meaning to each visual element, and also when dealing with multiple representations and dynamic information. All students experienced at least one of these difficulties, and very similar difficulties appeared in the two groups of students, despite the different scientific content of the simulations. In conclusion, visualisation does not imply a full comprehension of the content of scientific simulations per se, and an effective reading process requires a set of reading skills, previous knowledge, attention, and external supports. Science teachers should bear in mind these issues in order to help students read images to take benefit of their educational potential.

Automated Knowledge Discovery From Simulators

NASA Technical Reports Server (NTRS)

Burl, Michael; DeCoste, Dennis; Mazzoni, Dominic; Scharenbroich, Lucas; Enke, Brian; Merline, William

2007-01-01

A computational method, SimLearn, has been devised to facilitate efficient knowledge discovery from simulators. Simulators are complex computer programs used in science and engineering to model diverse phenomena such as fluid flow, gravitational interactions, coupled mechanical systems, and nuclear, chemical, and biological processes. SimLearn uses active-learning techniques to efficiently address the "landscape characterization problem." In particular, SimLearn tries to determine which regions in "input space" lead to a given output from the simulator, where "input space" refers to an abstraction of all the variables going into the simulator, e.g., initial conditions, parameters, and interaction equations. Landscape characterization can be viewed as an attempt to invert the forward mapping of the simulator and recover the inputs that produce a particular output. Given that a single simulation run can take days or weeks to complete even on a large computing cluster, SimLearn attempts to reduce costs by reducing the number of simulations needed to effect discoveries. Unlike conventional data-mining methods that are applied to static predefined datasets, SimLearn involves an iterative process in which a most informative dataset is constructed dynamically by using the simulator as an oracle. On each iteration, the algorithm models the knowledge it has gained through previous simulation trials and then chooses which simulation trials to run next. Running these trials through the simulator produces new data in the form of input-output pairs. The overall process is embodied in an algorithm that combines support vector machines (SVMs) with active learning. SVMs use learning from examples (the examples are the input-output pairs generated by running the simulator) and a principle called maximum margin to derive predictors that generalize well to new inputs. In SimLearn, the SVM plays the role of modeling the knowledge that has been gained through previous simulation trials. Active learning is used to determine which new input points would be most informative if their output were known. The selected input points are run through the simulator to generate new information that can be used to refine the SVM. The process is then repeated. SimLearn carefully balances exploration (semi-randomly searching around the input space) versus exploitation (using the current state of knowledge to conduct a tightly focused search). During each iteration, SimLearn uses not one, but an ensemble of SVMs. Each SVM in the ensemble is characterized by different hyper-parameters that control various aspects of the learned predictor - for example, whether the predictor is constrained to be very smooth (nearby points in input space lead to similar output predictions) or whether the predictor is allowed to be "bumpy." The various SVMs will have different preferences about which input points they would like to run through the simulator next. SimLearn includes a formal mechanism for balancing the ensemble SVM preferences so that a single choice can be made for the next set of trials.

Optical signal processing using photonic reservoir computing

NASA Astrophysics Data System (ADS)

Salehi, Mohammad Reza; Dehyadegari, Louiza

2014-10-01

As a new approach to recognition and classification problems, photonic reservoir computing has such advantages as parallel information processing, power efficient and high speed. In this paper, a photonic structure has been proposed for reservoir computing which is investigated using a simple, yet, non-partial noisy time series prediction task. This study includes the application of a suitable topology with self-feedbacks in a network of SOA's - which lends the system a strong memory - and leads to adjusting adequate parameters resulting in perfect recognition accuracy (100%) for noise-free time series, which shows a 3% improvement over previous results. For the classification of noisy time series, the rate of accuracy showed a 4% increase and amounted to 96%. Furthermore, an analytical approach was suggested to solve rate equations which led to a substantial decrease in the simulation time, which is an important parameter in classification of large signals such as speech recognition, and better results came up compared with previous works.

High performance ultrasonic field simulation on complex geometries

NASA Astrophysics Data System (ADS)

Chouh, H.; Rougeron, G.; Chatillon, S.; Iehl, J. C.; Farrugia, J. P.; Ostromoukhov, V.

2016-02-01

Ultrasonic field simulation is a key ingredient for the design of new testing methods as well as a crucial step for NDT inspection simulation. As presented in a previous paper [1], CEA-LIST has worked on the acceleration of these simulations focusing on simple geometries (planar interfaces, isotropic materials). In this context, significant accelerations were achieved on multicore processors and GPUs (Graphics Processing Units), bringing the execution time of realistic computations in the 0.1 s range. In this paper, we present recent works that aim at similar performances on a wider range of configurations. We adapted the physical model used by the CIVA platform to design and implement a new algorithm providing a fast ultrasonic field simulation that yields nearly interactive results for complex cases. The improvements over the CIVA pencil-tracing method include adaptive strategies for pencil subdivisions to achieve a good refinement of the sensor geometry while keeping a reasonable number of ray-tracing operations. Also, interpolation of the times of flight was used to avoid time consuming computations in the impulse response reconstruction stage. To achieve the best performance, our algorithm runs on multi-core superscalar CPUs and uses high performance specialized libraries such as Intel Embree for ray-tracing, Intel MKL for signal processing and Intel TBB for parallelization. We validated the simulation results by comparing them to the ones produced by CIVA on identical test configurations including mono-element and multiple-element transducers, homogeneous, meshed 3D CAD specimens, isotropic and anisotropic materials and wave paths that can involve several interactions with interfaces. We show performance results on complete simulations that achieve computation times in the 1s range.

Accelerating Wright–Fisher Forward Simulations on the Graphics Processing Unit

PubMed Central

Lawrie, David S.

2017-01-01

Forward Wright–Fisher simulations are powerful in their ability to model complex demography and selection scenarios, but suffer from slow execution on the Central Processor Unit (CPU), thus limiting their usefulness. However, the single-locus Wright–Fisher forward algorithm is exceedingly parallelizable, with many steps that are so-called “embarrassingly parallel,” consisting of a vast number of individual computations that are all independent of each other and thus capable of being performed concurrently. The rise of modern Graphics Processing Units (GPUs) and programming languages designed to leverage the inherent parallel nature of these processors have allowed researchers to dramatically speed up many programs that have such high arithmetic intensity and intrinsic concurrency. The presented GPU Optimized Wright–Fisher simulation, or “GO Fish” for short, can be used to simulate arbitrary selection and demographic scenarios while running over 250-fold faster than its serial counterpart on the CPU. Even modest GPU hardware can achieve an impressive speedup of over two orders of magnitude. With simulations so accelerated, one can not only do quick parametric bootstrapping of previously estimated parameters, but also use simulated results to calculate the likelihoods and summary statistics of demographic and selection models against real polymorphism data, all without restricting the demographic and selection scenarios that can be modeled or requiring approximations to the single-locus forward algorithm for efficiency. Further, as many of the parallel programming techniques used in this simulation can be applied to other computationally intensive algorithms important in population genetics, GO Fish serves as an exciting template for future research into accelerating computation in evolution. GO Fish is part of the Parallel PopGen Package available at: http://dl42.github.io/ParallelPopGen/. PMID:28768689

Three-Dimensional Liver Surgery Simulation: Computer-Assisted Surgical Planning with Three-Dimensional Simulation Software and Three-Dimensional Printing^.

PubMed

Oshiro, Yukio; Ohkohchi, Nobuhiro

2017-06-01

To perform accurate hepatectomy without injury, it is necessary to understand the anatomical relationship among the branches of Glisson's sheath, hepatic veins, and tumor. In Japan, three-dimensional (3D) preoperative simulation for liver surgery is becoming increasingly common, and liver 3D modeling and 3D hepatectomy simulation by 3D analysis software for liver surgery have been covered by universal healthcare insurance since 2012. Herein, we review the history of virtual hepatectomy using computer-assisted surgery (CAS) and our research to date, and we discuss the future prospects of CAS. We have used the SYNAPSE VINCENT medical imaging system (Fujifilm Medical, Tokyo, Japan) for 3D visualization and virtual resection of the liver since 2010. We developed a novel fusion imaging technique combining 3D computed tomography (CT) with magnetic resonance imaging (MRI). The fusion image enables us to easily visualize anatomic relationships among the hepatic arteries, portal veins, bile duct, and tumor in the hepatic hilum. In 2013, we developed an original software, called Liversim, which enables real-time deformation of the liver using physical simulation, and a randomized control trial has recently been conducted to evaluate the use of Liversim and SYNAPSE VINCENT for preoperative simulation and planning. Furthermore, we developed a novel hollow 3D-printed liver model whose surface is covered with frames. This model is useful for safe liver resection, has better visibility, and the production cost is reduced to one-third of a previous model. Preoperative simulation and navigation with CAS in liver resection are expected to help planning and conducting a surgery and surgical education. Thus, a novel CAS system will contribute to not only the performance of reliable hepatectomy but also to surgical education.

Efficient computation of the Grünwald-Letnikov fractional diffusion derivative using adaptive time step memory

NASA Astrophysics Data System (ADS)

MacDonald, Christopher L.; Bhattacharya, Nirupama; Sprouse, Brian P.; Silva, Gabriel A.

2015-09-01

Computing numerical solutions to fractional differential equations can be computationally intensive due to the effect of non-local derivatives in which all previous time points contribute to the current iteration. In general, numerical approaches that depend on truncating part of the system history while efficient, can suffer from high degrees of error and inaccuracy. Here we present an adaptive time step memory method for smooth functions applied to the Grünwald-Letnikov fractional diffusion derivative. This method is computationally efficient and results in smaller errors during numerical simulations. Sampled points along the system's history at progressively longer intervals are assumed to reflect the values of neighboring time points. By including progressively fewer points backward in time, a temporally 'weighted' history is computed that includes contributions from the entire past of the system, maintaining accuracy, but with fewer points actually calculated, greatly improving computational efficiency.

A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes.

PubMed

Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando

2015-07-21

We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke's law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.

A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes

NASA Astrophysics Data System (ADS)

Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando

2015-07-01

We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke's law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.

High performance computation of radiative transfer equation using the finite element method

NASA Astrophysics Data System (ADS)

Badri, M. A.; Jolivet, P.; Rousseau, B.; Favennec, Y.

2018-05-01

This article deals with an efficient strategy for numerically simulating radiative transfer phenomena using distributed computing. The finite element method alongside the discrete ordinate method is used for spatio-angular discretization of the monochromatic steady-state radiative transfer equation in an anisotropically scattering media. Two very different methods of parallelization, angular and spatial decomposition methods, are presented. To do so, the finite element method is used in a vectorial way. A detailed comparison of scalability, performance, and efficiency on thousands of processors is established for two- and three-dimensional heterogeneous test cases. Timings show that both algorithms scale well when using proper preconditioners. It is also observed that our angular decomposition scheme outperforms our domain decomposition method. Overall, we perform numerical simulations at scales that were previously unattainable by standard radiative transfer equation solvers.

Multiscale atomistic simulation of metal-oxygen surface interactions: Methodological development, theoretical investigation, and correlation with experiment

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

Yang, Judith C.

The purpose of this grant is to develop the multi-scale theoretical methods to describe the nanoscale oxidation of metal thin films, as the PI (Yang) extensive previous experience in the experimental elucidation of the initial stages of Cu oxidation by primarily in situ transmission electron microscopy methods. Through the use and development of computational tools at varying length (and time) scales, from atomistic quantum mechanical calculation, force field mesoscale simulations, to large scale Kinetic Monte Carlo (KMC) modeling, the fundamental underpinings of the initial stages of Cu oxidation have been elucidated. The development of computational modeling tools allows for acceleratedmore » materials discovery. The theoretical tools developed from this program impact a wide range of technologies that depend on surface reactions, including corrosion, catalysis, and nanomaterials fabrication.« less

Discrete Adjoint-Based Design Optimization of Unsteady Turbulent Flows on Dynamic Unstructured Grids

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Diskin, Boris; Yamaleev, Nail K.

2009-01-01

An adjoint-based methodology for design optimization of unsteady turbulent flows on dynamic unstructured grids is described. The implementation relies on an existing unsteady three-dimensional unstructured grid solver capable of dynamic mesh simulations and discrete adjoint capabilities previously developed for steady flows. The discrete equations for the primal and adjoint systems are presented for the backward-difference family of time-integration schemes on both static and dynamic grids. The consistency of sensitivity derivatives is established via comparisons with complex-variable computations. The current work is believed to be the first verified implementation of an adjoint-based optimization methodology for the true time-dependent formulation of the Navier-Stokes equations in a practical computational code. Large-scale shape optimizations are demonstrated for turbulent flows over a tiltrotor geometry and a simulated aeroelastic motion of a fighter jet.

Experimental and computational investigation of lateral gauge response in polycarbonate

NASA Astrophysics Data System (ADS)

Eliot, Jim; Harris, Ernst; Hazell, Paul; Appleby-Thomas, Gareth; Winter, Ronald; Wood, David; Owen, Gareth

2011-06-01

Polycarbonate's use in personal armour systems means its high strain-rate response has been extensively studied. Interestingly, embedded lateral manganin stress gauges in polycarbonate have shown gradients behind incident shocks, suggestive of increasing shear strength. However, such gauges need to be embedded in a central (typically) epoxy interlayer - an inherently invasive approach. Recently, research has suggested that in such metal systems interlayer/target impedance may contribute to observed gradients in lateral stress. Here, experimental T-gauge (Vishay Micro-Measurements® type J2M-SS-580SF-025) traces from polycarbonate targets are compared to computational simulations. This work extends previous efforts such that similar impedance exists between the interlayer and matrix (target) interface. Further, experiments and simulations are presented investigating the effects of a ``dry joint'' in polycarbonate, in which no encapsulating medium is employed.

Solution of the one-dimensional consolidation theory equation with a pseudospectral method

USGS Publications Warehouse

Sepulveda, N.; ,

1991-01-01

The one-dimensional consolidation theory equation is solved for an aquifer system using a pseudospectral method. The spatial derivatives are computed using Fast Fourier Transforms and the time derivative is solved using a fourth-order Runge-Kutta scheme. The computer model calculates compaction based on the void ratio changes accumulated during the simulated periods of time. Compactions and expansions resulting from groundwater withdrawals and recharges are simulated for two observation wells in Santa Clara Valley and two in San Joaquin Valley, California. Field data previously published are used to obtain mean values for the soil grain density and the compression index and to generate depth-dependent profiles for hydraulic conductivity and initial void ratio. The water-level plots for the wells studied were digitized and used to obtain the time dependent profiles of effective stress.

Examination of the nature of lattice matched III V semiconductor interfaces using computer simulated molecular beam epitaxial growth I. AC/BC interfaces

NASA Astrophysics Data System (ADS)

Thomsen, M.; Ghaisas, S. V.; Madhukar, A.

1987-07-01

A previously developed computer simulation of molecular beam epitaxial growth of III-V semiconductors based on the configuration dependent reactive incorporation (CDRI) model is extended to allow for two different cation species. Attention is focussed on examining the nature of interfaces formed in lattice matched quantum well structures of the form AC/BC/AC(100). We consider cation species with substantially different effective diffusion lengths, as is the case with Al and Ga during the growth of their respective As compounds. The degree of intermixing occuring at the interface is seen to be dependent upon, among other growth parameters, the pressure of the group V species during growth. Examination of an intraplanar order parameter at the interfaces reveals the existence of short range clustering of the cation species.

Documentation of a computer program to simulate aquifer-system compaction using the modular finite-difference ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Prudic, David E.

1991-01-01

Removal of ground water by pumping from aquifers may result in compaction of compressible fine-grained beds that are within or adjacent to the aquifers. Compaction of the sediments and resulting land subsidence may be permanent if the head declines result in vertical stresses beyond the previous maximum stress. The process of permanent compaction is not routinely included in simulations of ground-water flow. To simulate storage changes from both elastic and inelastic compaction, a computer program was written for use with the U.S. Geological Survey modular finite-difference ground- water flow model. The new program, the Interbed-Storage Package, is designed to be incorporated into this model. In the Interbed-Storage Package, elastic compaction or expansion is assumed to be proportional to change in head. The constant of proportionality is the product of the skeletal component of elastic specific storage and the thickness of the sediments. Similarly, inelastic compaction is assumed to be proportional to decline in head. The constant of proportionality is the product of the skeletal component of inelastic specific storage and the thickness of the sediments. Storage changes are incorporated into the ground-water flow model by adding an additional term to the right-hand side of the flow equation. Within a model time step, the package appropriately apportions storage changes between elastic and inelastic components on the basis of the relation of simulated head to the previous minimum (preconsolidation) head. Two tests were performed to verify that the package works correctly. The first test compared model-calculated storage and compaction changes to hand-calculated values for a three-dimensional simulation. Model and hand-calculated values were essentially equal. The second test was performed to compare the results of the Interbed-Storage Package with results of the one-dimensional Helm compaction model. This test problem simulated compaction in doubly draining confining beds stressed by head changes in adjacent aquifers. The Interbed-Storage Package and the Helm model computed essentially equal values of compaction. Documentation of the Interbed-Storage Package includes data input instructions, flow charts, narratives, and listings for each of the five modules included in the package. The documentation also includes an appendix describing input instructions and a listing of a computer program for time-variant specified-head boundaries. That package was developed to reduce the amount of data input and output associated with one of the Interbed-Storage Package test problems.

Computational simulation of extravehicular activity dynamics during a satellite capture attempt.

PubMed

Schaffner, G; Newman, D J; Robinson, S K

2000-01-01

A more quantitative approach to the analysis of astronaut extravehicular activity (EVA) tasks is needed because of their increasing complexity, particularly in preparation for the on-orbit assembly of the International Space Station. Existing useful EVA computer analyses produce either high-resolution three-dimensional computer images based on anthropometric representations or empirically derived predictions of astronaut strength based on lean body mass and the position and velocity of body joints but do not provide multibody dynamic analysis of EVA tasks. Our physics-based methodology helps fill the current gap in quantitative analysis of astronaut EVA by providing a multisegment human model and solving the equations of motion in a high-fidelity simulation of the system dynamics. The simulation work described here improves on the realism of previous efforts by including three-dimensional astronaut motion, incorporating joint stops to account for the physiological limits of range of motion, and incorporating use of constraint forces to model interaction with objects. To demonstrate the utility of this approach, the simulation is modeled on an actual EVA task, namely, the attempted capture of a spinning Intelsat VI satellite during STS-49 in May 1992. Repeated capture attempts by an EVA crewmember were unsuccessful because the capture bar could not be held in contact with the satellite long enough for the capture latches to fire and successfully retrieve the satellite.

Noise in Neuronal and Electronic Circuits: A General Modeling Framework and Non-Monte Carlo Simulation Techniques.

PubMed

Kilinc, Deniz; Demir, Alper

2017-08-01

The brain is extremely energy efficient and remarkably robust in what it does despite the considerable variability and noise caused by the stochastic mechanisms in neurons and synapses. Computational modeling is a powerful tool that can help us gain insight into this important aspect of brain mechanism. A deep understanding and computational design tools can help develop robust neuromorphic electronic circuits and hybrid neuroelectronic systems. In this paper, we present a general modeling framework for biological neuronal circuits that systematically captures the nonstationary stochastic behavior of ion channels and synaptic processes. In this framework, fine-grained, discrete-state, continuous-time Markov chain models of both ion channels and synaptic processes are treated in a unified manner. Our modeling framework features a mechanism for the automatic generation of the corresponding coarse-grained, continuous-state, continuous-time stochastic differential equation models for neuronal variability and noise. Furthermore, we repurpose non-Monte Carlo noise analysis techniques, which were previously developed for analog electronic circuits, for the stochastic characterization of neuronal circuits both in time and frequency domain. We verify that the fast non-Monte Carlo analysis methods produce results with the same accuracy as computationally expensive Monte Carlo simulations. We have implemented the proposed techniques in a prototype simulator, where both biological neuronal and analog electronic circuits can be simulated together in a coupled manner.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Monte Carlo simulations of adult and pediatric computed tomography exams: Validation studies of organ doses with physical phantoms

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

Long, Daniel J.; Lee, Choonsik; Tien, Christopher

2013-01-15

Purpose: To validate the accuracy of a Monte Carlo source model of the Siemens SOMATOM Sensation 16 CT scanner using organ doses measured in physical anthropomorphic phantoms. Methods: The x-ray output of the Siemens SOMATOM Sensation 16 multidetector CT scanner was simulated within the Monte Carlo radiation transport code, MCNPX version 2.6. The resulting source model was able to perform various simulated axial and helical computed tomographic (CT) scans of varying scan parameters, including beam energy, filtration, pitch, and beam collimation. Two custom-built anthropomorphic phantoms were used to take dose measurements on the CT scanner: an adult male and amore » 9-month-old. The adult male is a physical replica of University of Florida reference adult male hybrid computational phantom, while the 9-month-old is a replica of University of Florida Series B 9-month-old voxel computational phantom. Each phantom underwent a series of axial and helical CT scans, during which organ doses were measured using fiber-optic coupled plastic scintillator dosimeters developed at University of Florida. The physical setup was reproduced and simulated in MCNPX using the CT source model and the computational phantoms upon which the anthropomorphic phantoms were constructed. Average organ doses were then calculated based upon these MCNPX results. Results: For all CT scans, good agreement was seen between measured and simulated organ doses. For the adult male, the percent differences were within 16% for axial scans, and within 18% for helical scans. For the 9-month-old, the percent differences were all within 15% for both the axial and helical scans. These results are comparable to previously published validation studies using GE scanners and commercially available anthropomorphic phantoms. Conclusions: Overall results of this study show that the Monte Carlo source model can be used to accurately and reliably calculate organ doses for patients undergoing a variety of axial or helical CT examinations on the Siemens SOMATOM Sensation 16 scanner.« less

A Probabilistic Framework for the Validation and Certification of Computer Simulations

NASA Technical Reports Server (NTRS)

Ghanem, Roger; Knio, Omar

2000-01-01

The paper presents a methodology for quantifying, propagating, and managing the uncertainty in the data required to initialize computer simulations of complex phenomena. The purpose of the methodology is to permit the quantitative assessment of a certification level to be associated with the predictions from the simulations, as well as the design of a data acquisition strategy to achieve a target level of certification. The value of a methodology that can address the above issues is obvious, specially in light of the trend in the availability of computational resources, as well as the trend in sensor technology. These two trends make it possible to probe physical phenomena both with physical sensors, as well as with complex models, at previously inconceivable levels. With these new abilities arises the need to develop the knowledge to integrate the information from sensors and computer simulations. This is achieved in the present work by tracing both activities back to a level of abstraction that highlights their commonalities, thus allowing them to be manipulated in a mathematically consistent fashion. In particular, the mathematical theory underlying computer simulations has long been associated with partial differential equations and functional analysis concepts such as Hilbert spares and orthogonal projections. By relying on a probabilistic framework for the modeling of data, a Hilbert space framework emerges that permits the modeling of coefficients in the governing equations as random variables, or equivalently, as elements in a Hilbert space. This permits the development of an approximation theory for probabilistic problems that parallels that of deterministic approximation theory. According to this formalism, the solution of the problem is identified by its projection on a basis in the Hilbert space of random variables, as opposed to more traditional techniques where the solution is approximated by its first or second-order statistics. The present representation, in addition to capturing significantly more information than the traditional approach, facilitates the linkage between different interacting stochastic systems as is typically observed in real-life situations.

Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution

NASA Astrophysics Data System (ADS)

Chodera, John D.; Noé, Frank

2010-09-01

Discrete-state Markov (or master equation) models provide a useful simplified representation for characterizing the long-time statistical evolution of biomolecules in a manner that allows direct comparison with experiments as well as the elucidation of mechanistic pathways for an inherently stochastic process. A vital part of meaningful comparison with experiment is the characterization of the statistical uncertainty in the predicted experimental measurement, which may take the form of an equilibrium measurement of some spectroscopic signal, the time-evolution of this signal following a perturbation, or the observation of some statistic (such as the correlation function) of the equilibrium dynamics of a single molecule. Without meaningful error bars (which arise from both approximation and statistical error), there is no way to determine whether the deviations between model and experiment are statistically meaningful. Previous work has demonstrated that a Bayesian method that enforces microscopic reversibility can be used to characterize the statistical component of correlated uncertainties in state-to-state transition probabilities (and functions thereof) for a model inferred from molecular simulation data. Here, we extend this approach to include the uncertainty in observables that are functions of molecular conformation (such as surrogate spectroscopic signals) characterizing each state, permitting the full statistical uncertainty in computed spectroscopic experiments to be assessed. We test the approach in a simple model system to demonstrate that the computed uncertainties provide a useful indicator of statistical variation, and then apply it to the computation of the fluorescence autocorrelation function measured for a dye-labeled peptide previously studied by both experiment and simulation.

A Lagrangian subgrid-scale model with dynamic estimation of Lagrangian time scale for large eddy simulation of complex flows

NASA Astrophysics Data System (ADS)

Verma, Aman; Mahesh, Krishnan

2012-08-01

The dynamic Lagrangian averaging approach for the dynamic Smagorinsky model for large eddy simulation is extended to an unstructured grid framework and applied to complex flows. The Lagrangian time scale is dynamically computed from the solution and does not need any adjustable parameter. The time scale used in the standard Lagrangian model contains an adjustable parameter θ. The dynamic time scale is computed based on a "surrogate-correlation" of the Germano-identity error (GIE). Also, a simple material derivative relation is used to approximate GIE at different events along a pathline instead of Lagrangian tracking or multi-linear interpolation. Previously, the time scale for homogeneous flows was computed by averaging along directions of homogeneity. The present work proposes modifications for inhomogeneous flows. This development allows the Lagrangian averaged dynamic model to be applied to inhomogeneous flows without any adjustable parameter. The proposed model is applied to LES of turbulent channel flow on unstructured zonal grids at various Reynolds numbers. Improvement is observed when compared to other averaging procedures for the dynamic Smagorinsky model, especially at coarse resolutions. The model is also applied to flow over a cylinder at two Reynolds numbers and good agreement with previous computations and experiments is obtained. Noticeable improvement is obtained using the proposed model over the standard Lagrangian model. The improvement is attributed to a physically consistent Lagrangian time scale. The model also shows good performance when applied to flow past a marine propeller in an off-design condition; it regularizes the eddy viscosity and adjusts locally to the dominant flow features.

Monte Carlo simulations of liquid tetrahydrofuran including pseudorotationa)

NASA Astrophysics Data System (ADS)

Chandrasekhar, Jayaraman; Jorgensen, William L.

1982-11-01

Monte Carlo statistical mechanics simulations have been carried out for liquid tetrahydrofuran (THF) with and without pseudorotation at 1 atm and 25 °C. The intermolecular potential functions consisted of Lennard-Jones and Coulomb terms in the TIPS format reported previously for ethers. Pseudorotation of the ring was described using the generalized coordinates defined by Cremer and Pople, viz., the puckering amplitude and the phase angle of the ring. The corresponding intramolecular potential function was derived from molecular mechanics (MM2) calculations. Compared to the gas phase, the rings tend to be more flat and the population of the C2 twist geometry is slightly higher in liquid THF. However, pseudorotation has negligible effect on the calculated intermolecular structure and thermodynamic properties. The computed density, heat of vaporization, and heat capacity are in good agreement with experiment. The results are also compared with those from previous simulations of acyclic ethers. The present study provides the foundation for investigations of the solvating ability of THF.

A stochastic optimization model under modeling uncertainty and parameter certainty for groundwater remediation design--part I. Model development.

PubMed

He, L; Huang, G H; Lu, H W

2010-04-15

Solving groundwater remediation optimization problems based on proxy simulators can usually yield optimal solutions differing from the "true" ones of the problem. This study presents a new stochastic optimization model under modeling uncertainty and parameter certainty (SOMUM) and the associated solution method for simultaneously addressing modeling uncertainty associated with simulator residuals and optimizing groundwater remediation processes. This is a new attempt different from the previous modeling efforts. The previous ones focused on addressing uncertainty in physical parameters (i.e. soil porosity) while this one aims to deal with uncertainty in mathematical simulator (arising from model residuals). Compared to the existing modeling approaches (i.e. only parameter uncertainty is considered), the model has the advantages of providing mean-variance analysis for contaminant concentrations, mitigating the effects of modeling uncertainties on optimal remediation strategies, offering confidence level of optimal remediation strategies to system designers, and reducing computational cost in optimization processes. 2009 Elsevier B.V. All rights reserved.

The ShakeOut earthquake source and ground motion simulations

USGS Publications Warehouse

Graves, R.W.; Houston, Douglas B.; Hudnut, K.W.

2011-01-01

The ShakeOut Scenario is premised upon the detailed description of a hypothetical Mw 7.8 earthquake on the southern San Andreas Fault and the associated simulated ground motions. The main features of the scenario, such as its endpoints, magnitude, and gross slip distribution, were defined through expert opinion and incorporated information from many previous studies. Slip at smaller length scales, rupture speed, and rise time were constrained using empirical relationships and experience gained from previous strong-motion modeling. Using this rupture description and a 3-D model of the crust, broadband ground motions were computed over a large region of Southern California. The largest simulated peak ground acceleration (PGA) and peak ground velocity (PGV) generally range from 0.5 to 1.0 g and 100 to 250 cm/s, respectively, with the waveforms exhibiting strong directivity and basin effects. Use of a slip-predictable model results in a high static stress drop event and produces ground motions somewhat higher than median level predictions from NGA ground motion prediction equations (GMPEs).

Uranus: a rapid prototyping tool for FPGA embedded computer vision

NASA Astrophysics Data System (ADS)

Rosales-Hernández, Victor; Castillo-Jimenez, Liz; Viveros-Velez, Gilberto; Zuñiga-Grajeda, Virgilio; Treviño Torres, Abel; Arias-Estrada, M.

2007-01-01

The starting point for all successful system development is the simulation. Performing high level simulation of a system can help to identify, insolate and fix design problems. This work presents Uranus, a software tool for simulation and evaluation of image processing algorithms with support to migrate them to an FPGA environment for algorithm acceleration and embedded processes purposes. The tool includes an integrated library of previous coded operators in software and provides the necessary support to read and display image sequences as well as video files. The user can use the previous compiled soft-operators in a high level process chain, and code his own operators. Additional to the prototyping tool, Uranus offers FPGA-based hardware architecture with the same organization as the software prototyping part. The hardware architecture contains a library of FPGA IP cores for image processing that are connected with a PowerPC based system. The Uranus environment is intended for rapid prototyping of machine vision and the migration to FPGA accelerator platform, and it is distributed for academic purposes.

Wang-Landau sampling: Saving CPU time

NASA Astrophysics Data System (ADS)

Ferreira, L. S.; Jorge, L. N.; Leão, S. A.; Caparica, A. A.

2018-04-01

In this work we propose an improvement to the Wang-Landau (WL) method that allows an economy in CPU time of about 60% leading to the same results with the same accuracy. We used the 2D Ising model to show that one can initiate all WL simulations using the outputs of an advanced WL level from a previous simulation. We showed that up to the seventh WL level (f6) the simulations are not biased yet and can proceed to any value that the simulation from the very beginning would reach. As a result the initial WL levels can be simulated just once. It was also observed that the saving in CPU time is larger for larger lattice sizes, exactly where the computational cost is considerable. We carried out high-resolution simulations beginning initially from the first WL level (f0) and another beginning from the eighth WL level (f7) using all the data at the end of the previous level and showed that the results for the critical temperature Tc and the critical static exponents β and γ coincide within the error bars. Finally we applied the same procedure to the 1/2-spin Baxter-Wu model and the economy in CPU time was of about 64%.

Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation

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

Schnell, Sondre K.; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720; Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim

2014-10-14

We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtainedmore » with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation.« less

A method for simulating a flux-locked DC SQUID

NASA Technical Reports Server (NTRS)

Gutt, G. M.; Kasdin, N. J.; Condron, M. R., II; Muhlfelder, B.; Lockhart, J. M.; Cromar, M. W.

1993-01-01

The authors describe a computationally efficient and accurate method for simulating a dc SQUID's V-Phi (voltage-flux) and I-V characteristics which has proven valuable in evaluating and improving various SQUID readout methods. The simulation of the SQUID is based on fitting of previously acquired data from either a real or a modeled device using the Fourier transform of the V-Phi curve. This method does not predict SQUID behavior, but rather is a way of replicating a known behavior efficiently with portability into various simulation programs such as SPICE. The authors discuss the methods used to simulate the SQUID and the flux-locking control electronics, and present specific examples of this approach. Results include an estimate of the slew rate and linearity of a simple flux-locked loop using a characterized dc SQUID.

Enforcing dust mass conservation in 3D simulations of tightly coupled grains with the PHANTOM SPH code

NASA Astrophysics Data System (ADS)

Ballabio, G.; Dipierro, G.; Veronesi, B.; Lodato, G.; Hutchison, M.; Laibe, G.; Price, D. J.

2018-06-01

We describe a new implementation of the one-fluid method in the SPH code PHANTOM to simulate the dynamics of dust grains in gas protoplanetary discs. We revise and extend previously developed algorithms by computing the evolution of a new fluid quantity that produces a more accurate and numerically controlled evolution of the dust dynamics. Moreover, by limiting the stopping time of uncoupled grains that violate the assumptions of the terminal velocity approximation, we avoid fatal numerical errors in mass conservation. We test and validate our new algorithm by running 3D SPH simulations of a large range of disc models with tightly and marginally coupled grains.

A computational study suggests that replacing PEG with PMOZ may increase exposure of hydrophobic targeting moiety.

PubMed

Magarkar, Aniket; Róg, Tomasz; Bunker, Alex

2017-05-30

In a previous study we showed that the cause of failure of a new, proposed, targeting ligand, the AETP moiety, when attached to a PEGylated liposome, was occlusion by the poly(ethylene glycol) (PEG) layer due to its hydrophobic nature, given that PEG is not entirely hydrophilic. At the time we proposed that possible replacement with a more hydrophilic protective polymer could alleviate this problem. In this study we have used computational molecular dynamics modelling, using a model with all atom resolution, to suggest that a specific alternative protective polymer, poly(2-methyloxazoline) (PMOZ), would perform exactly this function. Our results show that when PEG is replaced by PMOZ the relative exposure to the solvent of AETP is increased to a level even greater than that we found in previous simulations for the RGD peptide, a targeting moiety that has previously been used successfully in PEGylated liposome based therapies. While the AETP moiety itself is no longer under consideration, the results of this computational study have broader significance: the use of PMOZ as an alternative polymer coating to PEG could be efficacious in the context of more hydrophobic targeting ligands. In addition to PMOZ we studied another polyoxazoline, poly(2-ethyloxazoline) (PEOZ), that has also been mooted as a possible alternate protective polymer. It was also found that the RDG peptide occlusion was significantly greater for the case of both oxazolines as opposed to PEG and that, unlike PEG, neither oxazoline entered the membrane. As far as we are aware this is the first time that polyoxazolines have been studied using molecular dynamics simulation with all atom resolution. Copyright © 2017 Elsevier B.V. All rights reserved.

Star Identification Without Attitude Knowledge: Testing with X-Ray Timing Experiment Data

NASA Technical Reports Server (NTRS)

Ketchum, Eleanor

1997-01-01

As the budget for the scientific exploration of space shrinks, the need for more autonomous spacecraft increases. For a spacecraft with a star tracker, the ability to determinate attitude from a lost in space state autonomously requires the capability to identify the stars in the field of view of the tracker. Although there have been efforts to produce autonomous star trackers which perform this function internally, many programs cannot afford these sensors. The author previously presented a method for identifying stars without a priori attitude knowledge specifically targeted for onboard computers as it minimizes the necessary computer storage. The method has previously been tested with simulated data. This paper provides results of star identification without a priori attitude knowledge using flight data from two 8 by 8 degree charge coupled device star trackers onboard the X-Ray Timing Experiment.

Computer simulation on the collision-sticking dynamics of two colloidal particles in an optical trap.

PubMed

Xu, Shenghua; Sun, Zhiwei

2007-04-14

Collisions of a particle pair induced by optical tweezers have been employed to study colloidal stability. In order to deepen insights regarding the collision-sticking dynamics of a particle pair in the optical trap that were observed in experimental approaches at the particle level, the authors carry out a Brownian dynamics simulation. In the simulation, various contributing factors, including the Derjaguin-Landau-Verwey-Overbeek interaction of particles, hydrodynamic interactions, optical trapping forces on the two particles, and the Brownian motion, were all taken into account. The simulation reproduces the tendencies of the accumulated sticking probability during the trapping duration for the trapped particle pair described in our previous study and provides an explanation for why the two entangled particles in the trap experience two different statuses.

Normal Brain-Skull Development with Hybrid Deformable VR Models Simulation.

PubMed

Jin, Jing; De Ribaupierre, Sandrine; Eagleson, Roy

2016-01-01

This paper describes a simulation framework for a clinical application involving skull-brain co-development in infants, leading to a platform for craniosynostosis modeling. Craniosynostosis occurs when one or more sutures are fused early in life, resulting in an abnormal skull shape. Surgery is required to reopen the suture and reduce intracranial pressure, but is difficult without any predictive model to assist surgical planning. We aim to study normal brain-skull growth by computer simulation, which requires a head model and appropriate mathematical methods for brain and skull growth respectively. On the basis of our previous model, we further specified suture model into fibrous and cartilaginous sutures and develop algorithm for skull extension. We evaluate the resulting simulation by comparison with datasets of cases and normal growth.

Surface order in cold liquids: X-ray reflectivity studies of dielectric liquids and comparison to liquid metals

NASA Astrophysics Data System (ADS)

Chattopadhyay, Sudeshna; Uysal, Ahmet; Stripe, Benjamin; Ehrlich, Steven; Karapetrova, Evguenia A.; Dutta, Pulak

2010-05-01

Oscillatory surface-density profiles (layers) have previously been reported in several metallic liquids, one dielectric liquid, and in computer simulations of dielectric liquids. We have now seen surface layers in two other dielectric liquids, pentaphenyl trimethyl trisiloxane, and pentavinyl pentamethyl cyclopentasiloxane. These layers appear below T˜285K and T˜130K , respectively; both thresholds correspond to T/Tc˜0.2 where Tc is the liquid-gas critical temperature. All metallic and dielectric liquid surfaces previously studied are also consistent with the existence of this T/Tc threshold, first indicated by the simulations of Chacón [Phys. Rev. Lett. 87, 166101 (2001)]. The layer width parameters, determined using a distorted-crystal fitting model, follow common trends as functions of Tc for both metallic and dielectric liquids.

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

PubMed

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

2018-05-04

Nowadays, most of the efforts in NMR applied to porous media are dedicated to studying the molecular fluid dynamics within and among the pores. These analyses have a higher complexity due to morphology and chemical composition of rocks, besides dynamic effects as restricted diffusion, diffusional coupling, and exchange processes. Since the translational nuclear spin diffusion in a confined geometry (e.g. pores and fractures) requires specific boundary conditions, the theoretical solutions are restricted to some special problems and, in many cases, computational methods are required. The Random Walk Method is a classic way to simulate self-diffusion along a Digital Porous Medium. Bergman model considers the magnetic relaxation process of the fluid molecules by including a probability rate of magnetization survival under surface interactions. Here we propose a statistical approach to correlate surface magnetic relaxivity with the computational method applied to the NMR relaxation in order to elucidate the relationship between simulated relaxation time and pore size of the Digital Porous Medium. The proposed computational method simulates one- and two-dimensional NMR techniques reproducing, for example, longitudinal and transverse relaxation times (T 1 and T 2 , respectively), diffusion coefficients (D), as well as their correlations. For a good approximation between the numerical and experimental results, it is necessary to preserve the complexity of translational diffusion through the microstructures in the digital rocks. Therefore, we use Digital Porous Media obtained by 3D X-ray microtomography. To validate the method, relaxation times of ideal spherical pores were obtained and compared with the previous determinations by the Brownstein-Tarr model, as well as the computational approach proposed by Bergman. Furthermore, simulated and experimental results of synthetic porous media are compared. These results make evident the potential of computational physics in the analysis of the NMR data for complex porous materials. Copyright © 2018 Elsevier Inc. All rights reserved.

Modeling parameterized geometry in GPU-based Monte Carlo particle transport simulation for radiotherapy.

PubMed

Chi, Yujie; Tian, Zhen; Jia, Xun

2016-08-07

Monte Carlo (MC) particle transport simulation on a graphics-processing unit (GPU) platform has been extensively studied recently due to the efficiency advantage achieved via massive parallelization. Almost all of the existing GPU-based MC packages were developed for voxelized geometry. This limited application scope of these packages. The purpose of this paper is to develop a module to model parametric geometry and integrate it in GPU-based MC simulations. In our module, each continuous region was defined by its bounding surfaces that were parameterized by quadratic functions. Particle navigation functions in this geometry were developed. The module was incorporated to two previously developed GPU-based MC packages and was tested in two example problems: (1) low energy photon transport simulation in a brachytherapy case with a shielded cylinder applicator and (2) MeV coupled photon/electron transport simulation in a phantom containing several inserts of different shapes. In both cases, the calculated dose distributions agreed well with those calculated in the corresponding voxelized geometry. The averaged dose differences were 1.03% and 0.29%, respectively. We also used the developed package to perform simulations of a Varian VS 2000 brachytherapy source and generated a phase-space file. The computation time under the parameterized geometry depended on the memory location storing the geometry data. When the data was stored in GPU's shared memory, the highest computational speed was achieved. Incorporation of parameterized geometry yielded a computation time that was ~3 times of that in the corresponding voxelized geometry. We also developed a strategy to use an auxiliary index array to reduce frequency of geometry calculations and hence improve efficiency. With this strategy, the computational time ranged in 1.75-2.03 times of the voxelized geometry for coupled photon/electron transport depending on the voxel dimension of the auxiliary index array, and in 0.69-1.23 times for photon only transport.

Extending rule-based methods to model molecular geometry and 3D model resolution.

PubMed

Hoard, Brittany; Jacobson, Bruna; Manavi, Kasra; Tapia, Lydia

2016-08-01

Computational modeling is an important tool for the study of complex biochemical processes associated with cell signaling networks. However, it is challenging to simulate processes that involve hundreds of large molecules due to the high computational cost of such simulations. Rule-based modeling is a method that can be used to simulate these processes with reasonably low computational cost, but traditional rule-based modeling approaches do not include details of molecular geometry. The incorporation of geometry into biochemical models can more accurately capture details of these processes, and may lead to insights into how geometry affects the products that form. Furthermore, geometric rule-based modeling can be used to complement other computational methods that explicitly represent molecular geometry in order to quantify binding site accessibility and steric effects. We propose a novel implementation of rule-based modeling that encodes details of molecular geometry into the rules and binding rates. We demonstrate how rules are constructed according to the molecular curvature. We then perform a study of antigen-antibody aggregation using our proposed method. We simulate the binding of antibody complexes to binding regions of the shrimp allergen Pen a 1 using a previously developed 3D rigid-body Monte Carlo simulation, and we analyze the aggregate sizes. Then, using our novel approach, we optimize a rule-based model according to the geometry of the Pen a 1 molecule and the data from the Monte Carlo simulation. We use the distances between the binding regions of Pen a 1 to optimize the rules and binding rates. We perform this procedure for multiple conformations of Pen a 1 and analyze the impact of conformation and resolution on the optimal rule-based model. We find that the optimized rule-based models provide information about the average steric hindrance between binding regions and the probability that antibodies will bind to these regions. These optimized models quantify the variation in aggregate size that results from differences in molecular geometry and from model resolution.

User's Guide for TOUGH2-MP - A Massively Parallel Version of the TOUGH2 Code

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

Earth Sciences Division; Zhang, Keni; Zhang, Keni

TOUGH2-MP is a massively parallel (MP) version of the TOUGH2 code, designed for computationally efficient parallel simulation of isothermal and nonisothermal flows of multicomponent, multiphase fluids in one, two, and three-dimensional porous and fractured media. In recent years, computational requirements have become increasingly intensive in large or highly nonlinear problems for applications in areas such as radioactive waste disposal, CO2 geological sequestration, environmental assessment and remediation, reservoir engineering, and groundwater hydrology. The primary objective of developing the parallel-simulation capability is to significantly improve the computational performance of the TOUGH2 family of codes. The particular goal for the parallel simulator ismore » to achieve orders-of-magnitude improvement in computational time for models with ever-increasing complexity. TOUGH2-MP is designed to perform parallel simulation on multi-CPU computational platforms. An earlier version of TOUGH2-MP (V1.0) was based on the TOUGH2 Version 1.4 with EOS3, EOS9, and T2R3D modules, a software previously qualified for applications in the Yucca Mountain project, and was designed for execution on CRAY T3E and IBM SP supercomputers. The current version of TOUGH2-MP (V2.0) includes all fluid property modules of the standard version TOUGH2 V2.0. It provides computationally efficient capabilities using supercomputers, Linux clusters, or multi-core PCs, and also offers many user-friendly features. The parallel simulator inherits all process capabilities from V2.0 together with additional capabilities for handling fractured media from V1.4. This report provides a quick starting guide on how to set up and run the TOUGH2-MP program for users with a basic knowledge of running the (standard) version TOUGH2 code, The report also gives a brief technical description of the code, including a discussion of parallel methodology, code structure, as well as mathematical and numerical methods used. To familiarize users with the parallel code, illustrative sample problems are presented.« less

Supplemental computational phantoms to estimate out-of-field absorbed dose in photon radiotherapy

NASA Astrophysics Data System (ADS)

Gallagher, Kyle J.; Tannous, Jaad; Nabha, Racile; Feghali, Joelle Ann; Ayoub, Zeina; Jalbout, Wassim; Youssef, Bassem; Taddei, Phillip J.

2018-01-01

The purpose of this study was to develop a straightforward method of supplementing patient anatomy and estimating out-of-field absorbed dose for a cohort of pediatric radiotherapy patients with limited recorded anatomy. A cohort of nine children, aged 2-14 years, who received 3D conformal radiotherapy for low-grade localized brain tumors (LBTs), were randomly selected for this study. The extent of these patients’ computed tomography simulation image sets were cranial only. To approximate their missing anatomy, we supplemented the LBT patients’ image sets with computed tomography images of patients in a previous study with larger extents of matched sex, height, and mass and for whom contours of organs at risk for radiogenic cancer had already been delineated. Rigid fusion was performed between the LBT patients’ data and that of the supplemental computational phantoms using commercial software and in-house codes. In-field dose was calculated with a clinically commissioned treatment planning system, and out-of-field dose was estimated with a previously developed analytical model that was re-fit with parameters based on new measurements for intracranial radiotherapy. Mean doses greater than 1 Gy were found in the red bone marrow, remainder, thyroid, and skin of the patients in this study. Mean organ doses between 150 mGy and 1 Gy were observed in the breast tissue of the girls and lungs of all patients. Distant organs, i.e. prostate, bladder, uterus, and colon, received mean organ doses less than 150 mGy. The mean organ doses of the younger, smaller LBT patients (0-4 years old) were a factor of 2.4 greater than those of the older, larger patients (8-12 years old). Our findings demonstrated the feasibility of a straightforward method of applying supplemental computational phantoms and dose-calculation models to estimate absorbed dose for a set of children of various ages who received radiotherapy and for whom anatomies were largely missing in their original computed tomography simulations.

GPU accelerated Monte-Carlo simulation of SEM images for metrology

NASA Astrophysics Data System (ADS)

Verduin, T.; Lokhorst, S. R.; Hagen, C. W.

2016-03-01

In this work we address the computation times of numerical studies in dimensional metrology. In particular, full Monte-Carlo simulation programs for scanning electron microscopy (SEM) image acquisition are known to be notoriously slow. Our quest in reducing the computation time of SEM image simulation has led us to investigate the use of graphics processing units (GPUs) for metrology. We have succeeded in creating a full Monte-Carlo simulation program for SEM images, which runs entirely on a GPU. The physical scattering models of this GPU simulator are identical to a previous CPU-based simulator, which includes the dielectric function model for inelastic scattering and also refinements for low-voltage SEM applications. As a case study for the performance, we considered the simulated exposure of a complex feature: an isolated silicon line with rough sidewalls located on a at silicon substrate. The surface of the rough feature is decomposed into 408 012 triangles. We have used an exposure dose of 6 mC/cm2, which corresponds to 6 553 600 primary electrons on average (Poisson distributed). We repeat the simulation for various primary electron energies, 300 eV, 500 eV, 800 eV, 1 keV, 3 keV and 5 keV. At first we run the simulation on a GeForce GTX480 from NVIDIA. The very same simulation is duplicated on our CPU-based program, for which we have used an Intel Xeon X5650. Apart from statistics in the simulation, no difference is found between the CPU and GPU simulated results. The GTX480 generates the images (depending on the primary electron energy) 350 to 425 times faster than a single threaded Intel X5650 CPU. Although this is a tremendous speedup, we actually have not reached the maximum throughput because of the limited amount of available memory on the GTX480. Nevertheless, the speedup enables the fast acquisition of simulated SEM images for metrology. We now have the potential to investigate case studies in CD-SEM metrology, which otherwise would take unreasonable amounts of computation time.

Provenance-aware optimization of workload for distributed data production

NASA Astrophysics Data System (ADS)

Makatun, Dzmitry; Lauret, Jérôme; Rudová, Hana; Šumbera, Michal

2017-10-01

Distributed data processing in High Energy and Nuclear Physics (HENP) is a prominent example of big data analysis. Having petabytes of data being processed at tens of computational sites with thousands of CPUs, standard job scheduling approaches either do not address well the problem complexity or are dedicated to one specific aspect of the problem only (CPU, network or storage). Previously we have developed a new job scheduling approach dedicated to distributed data production - an essential part of data processing in HENP (preprocessing in big data terminology). In this contribution, we discuss the load balancing with multiple data sources and data replication, present recent improvements made to our planner and provide results of simulations which demonstrate the advantage against standard scheduling policies for the new use case. Multi-source or provenance is common in computing models of many applications whereas the data may be copied to several destinations. The initial input data set would hence be already partially replicated to multiple locations and the task of the scheduler is to maximize overall computational throughput considering possible data movements and CPU allocation. The studies have shown that our approach can provide a significant gain in overall computational performance in a wide scope of simulations considering realistic size of computational Grid and various input data distribution.

Simulation of an Isolated Tiltrotor in Hover with an Unstructured Overset-Grid RANS Solver

NASA Technical Reports Server (NTRS)

Lee-Rausch, Elizabeth M.; Biedron, Robert T.

2009-01-01

An unstructured overset-grid Reynolds Averaged Navier-Stokes (RANS) solver, FUN3D, is used to simulate an isolated tiltrotor in hover. An overview of the computational method is presented as well as the details of the overset-grid systems. Steady-state computations within a noninertial reference frame define the performance trends of the rotor across a range of the experimental collective settings. Results are presented to show the effects of off-body grid refinement and blade grid refinement. The computed performance and blade loading trends show good agreement with experimental results and previously published structured overset-grid computations. Off-body flow features indicate a significant improvement in the resolution of the first perpendicular blade vortex interaction with background grid refinement across the collective range. Considering experimental data uncertainty and effects of transition, the prediction of figure of merit on the baseline and refined grid is reasonable at the higher collective range- within 3 percent of the measured values. At the lower collective settings, the computed figure of merit is approximately 6 percent lower than the experimental data. A comparison of steady and unsteady results show that with temporal refinement, the dynamic results closely match the steady-state noninertial results which gives confidence in the accuracy of the dynamic overset-grid approach.

Simulating coupled dynamics of a rigid-flexible multibody system and compressible fluid

NASA Astrophysics Data System (ADS)

Hu, Wei; Tian, Qiang; Hu, HaiYan

2018-04-01

As a subsequent work of previous studies of authors, a new parallel computation approach is proposed to simulate the coupled dynamics of a rigid-flexible multibody system and compressible fluid. In this approach, the smoothed particle hydrodynamics (SPH) method is used to model the compressible fluid, the natural coordinate formulation (NCF) and absolute nodal coordinate formulation (ANCF) are used to model the rigid and flexible bodies, respectively. In order to model the compressible fluid properly and efficiently via SPH method, three measures are taken as follows. The first is to use the Riemann solver to cope with the fluid compressibility, the second is to define virtual particles of SPH to model the dynamic interaction between the fluid and the multibody system, and the third is to impose the boundary conditions of periodical inflow and outflow to reduce the number of SPH particles involved in the computation process. Afterwards, a parallel computation strategy is proposed based on the graphics processing unit (GPU) to detect the neighboring SPH particles and to solve the dynamic equations of SPH particles in order to improve the computation efficiency. Meanwhile, the generalized-alpha algorithm is used to solve the dynamic equations of the multibody system. Finally, four case studies are given to validate the proposed parallel computation approach.

Formulation and implementation of a practical algorithm for parameter estimation with process and measurement noise

NASA Technical Reports Server (NTRS)

Maine, R. E.; Iliff, K. W.

1980-01-01

A new formulation is proposed for the problem of parameter estimation of dynamic systems with both process and measurement noise. The formulation gives estimates that are maximum likelihood asymptotically in time. The means used to overcome the difficulties encountered by previous formulations are discussed. It is then shown how the proposed formulation can be efficiently implemented in a computer program. A computer program using the proposed formulation is available in a form suitable for routine application. Examples with simulated and real data are given to illustrate that the program works well.

A new method for computing the gyrocenter orbit in the tokamak configuration

NASA Astrophysics Data System (ADS)

Xu, Yingfeng

2013-10-01

Gyrokinetic theory is an important tool for studying the long-time behavior of magnetized plasmas in Tokamaks. The gyrocenter trajectory determined by the gyrocenter equations of motion can be computed by using a special kind of the Lie-transform perturbation method. The corresponding Lie-transform called I-transform makes that the transformed equations of motion have the same form as the unperturbed ones. The gyrocenter trajectory in short time is divided into two parts. One is along the unperturbed orbit. The other one, which is related to perturbation, is determined by the I-transform generating vector. The numerical gyrocenter orbit code based on this new method has been developed in the tokamak configuration and benchmarked with the other orbit code in some simple cases. Furthermore, it is clearly demonstrated that this new method for computing gyrocenter orbit is equivalent to the gyrocenter Hamilton equations of motion up to the second order in timestep. The new method can be applied to the gyrokinetic simulation. The gyrocenter orbit of the unperturbed part determined by the equilibrium fields can be computed previously in the gyrokinetic simulation, and the corresponding time consumption is neglectable.

Using Computational Modeling to Assess the Impact of Clinical Decision Support on Cancer Screening within Community Health Centers

PubMed Central

Carney, Timothy Jay; Morgan, Geoffrey P.; Jones, Josette; McDaniel, Anna M.; Weaver, Michael; Weiner, Bryan; Haggstrom, David A.

2014-01-01

Our conceptual model demonstrates our goal to investigate the impact of clinical decision support (CDS) utilization on cancer screening improvement strategies in the community health care (CHC) setting. We employed a dual modeling technique using both statistical and computational modeling to evaluate impact. Our statistical model used the Spearman’s Rho test to evaluate the strength of relationship between our proximal outcome measures (CDS utilization) against our distal outcome measure (provider self-reported cancer screening improvement). Our computational model relied on network evolution theory and made use of a tool called Construct-TM to model the use of CDS measured by the rate of organizational learning. We employed the use of previously collected survey data from community health centers Cancer Health Disparities Collaborative (HDCC). Our intent is to demonstrate the added valued gained by using a computational modeling tool in conjunction with a statistical analysis when evaluating the impact a health information technology, in the form of CDS, on health care quality process outcomes such as facility-level screening improvement. Significant simulated disparities in organizational learning over time were observed between community health centers beginning the simulation with high and low clinical decision support capability. PMID:24953241

Numerical Modelling of Tsunami Generated by Deformable Submarine Slides: Parameterisation of Slide Dynamics for Coupling to Tsunami Propagation Model

NASA Astrophysics Data System (ADS)

Smith, R. C.; Collins, G. S.; Hill, J.; Piggott, M. D.; Mouradian, S. L.

2015-12-01

Numerical modelling informs risk assessment of tsunami generated by submarine slides; however, for large-scale slides modelling can be complex and computationally challenging. Many previous numerical studies have approximated slides as rigid blocks that moved according to prescribed motion. However, wave characteristics are strongly dependent on the motion of the slide and previous work has recommended that more accurate representation of slide dynamics is needed. We have used the finite-element, adaptive-mesh CFD model Fluidity, to perform multi-material simulations of deformable submarine slide-generated waves at real world scales for a 2D scenario in the Gulf of Mexico. Our high-resolution approach represents slide dynamics with good accuracy, compared to other numerical simulations of this scenario, but precludes tracking of wave propagation over large distances. To enable efficient modelling of further propagation of the waves, we investigate an approach to extract information about the slide evolution from our multi-material simulations in order to drive a single-layer wave propagation model, also using Fluidity, which is much less computationally expensive. The extracted submarine slide geometry and position as a function of time are parameterised using simple polynomial functions. The polynomial functions are used to inform a prescribed velocity boundary condition in a single-layer simulation, mimicking the effect the submarine slide motion has on the water column. The approach is verified by successful comparison of wave generation in the single-layer model with that recorded in the multi-material, multi-layer simulations. We then extend this approach to 3D for further validation of this methodology (using the Gulf of Mexico scenario proposed by Horrillo et al., 2013) and to consider the effect of lateral spreading. This methodology is then used to simulate a series of hypothetical submarine slide events in the Arctic Ocean (based on evidence of historic slides) and examine the hazard posed to the UK coast.

Timing and Mode of Landscape Response to Glacial-Interglacial Climate Forcing From Fluvial Fill Terrace Sediments: Humahuaca Basin, E Cordillera, NW Argentina

NASA Astrophysics Data System (ADS)

Schildgen, T. F.; Robinson, R. A. J.; Savi, S.; Bookhagen, B.; Tofelde, S.; Strecker, M. R.

2014-12-01

Numerical modelling informs risk assessment of tsunami generated by submarine slides; however, for large-scale slides modelling can be complex and computationally challenging. Many previous numerical studies have approximated slides as rigid blocks that moved according to prescribed motion. However, wave characteristics are strongly dependent on the motion of the slide and previous work has recommended that more accurate representation of slide dynamics is needed. We have used the finite-element, adaptive-mesh CFD model Fluidity, to perform multi-material simulations of deformable submarine slide-generated waves at real world scales for a 2D scenario in the Gulf of Mexico. Our high-resolution approach represents slide dynamics with good accuracy, compared to other numerical simulations of this scenario, but precludes tracking of wave propagation over large distances. To enable efficient modelling of further propagation of the waves, we investigate an approach to extract information about the slide evolution from our multi-material simulations in order to drive a single-layer wave propagation model, also using Fluidity, which is much less computationally expensive. The extracted submarine slide geometry and position as a function of time are parameterised using simple polynomial functions. The polynomial functions are used to inform a prescribed velocity boundary condition in a single-layer simulation, mimicking the effect the submarine slide motion has on the water column. The approach is verified by successful comparison of wave generation in the single-layer model with that recorded in the multi-material, multi-layer simulations. We then extend this approach to 3D for further validation of this methodology (using the Gulf of Mexico scenario proposed by Horrillo et al., 2013) and to consider the effect of lateral spreading. This methodology is then used to simulate a series of hypothetical submarine slide events in the Arctic Ocean (based on evidence of historic slides) and examine the hazard posed to the UK coast.

An underwater light attenuation scheme for marine ecosystem models.

PubMed

Penta, Bradley; Lee, Zhongping; Kudela, Raphael M; Palacios, Sherry L; Gray, Deric J; Jolliff, Jason K; Shulman, Igor G

2008-10-13

Simulation of underwater light is essential for modeling marine ecosystems. A new model of underwater light attenuation is presented and compared with previous models. In situ data collected in Monterey Bay, CA. during September 2006 are used for validation. It is demonstrated that while the new light model is computationally simple and efficient it maintains accuracy and flexibility. When this light model is incorporated into an ecosystem model, the correlation between modeled and observed coastal chlorophyll is improved over an eight-year time period. While the simulation of a deep chlorophyll maximum demonstrates the effect of the new model at depth.

The Plasma Simulation Code: A modern particle-in-cell code with patch-based load-balancing

NASA Astrophysics Data System (ADS)

Germaschewski, Kai; Fox, William; Abbott, Stephen; Ahmadi, Narges; Maynard, Kristofor; Wang, Liang; Ruhl, Hartmut; Bhattacharjee, Amitava

2016-08-01

This work describes the Plasma Simulation Code (PSC), an explicit, electromagnetic particle-in-cell code with support for different order particle shape functions. We review the basic components of the particle-in-cell method as well as the computational architecture of the PSC code that allows support for modular algorithms and data structure in the code. We then describe and analyze in detail a distinguishing feature of PSC: patch-based load balancing using space-filling curves which is shown to lead to major efficiency gains over unbalanced methods and a previously used simpler balancing method.

Application of a BOSS – Gaussian Interface for QM/MM Simulations of Henry and Methyl Transfer Reactions

PubMed Central

Vilseck, Jonah Z.; Kostal, Jakub; Tirado-Rives, Julian; Jorgensen, William L.

2015-01-01

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with quantum mechanics alone. For several decades, semi-empirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the inter-program communication. The BOSS–Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS–Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations employing semiempirical methods. PMID:26311531

Documentation of a computer program to simulate aquifer-system compaction using the modular finite-difference ground-water flow model

USGS Publications Warehouse

Leake, S.A.; Prudic, David E.

1988-01-01

The process of permanent compaction is not routinely included in simulations of groundwater flow. To simulate storage changes from both elastic and inelastic compaction, a computer program was written for use with the U. S. Geological Survey modular finite-difference groundwater flow model. The new program is called the Interbed-Storage Package. In the Interbed-Storage Package, elastic compaction or expansion is assumed to be proportional to change in head. The constant of proportionality is the product of skeletal component of elastic specific storage and thickness of the sediments. Similarly, inelastic compaction is assumed to be proportional to decline in head. The constant of proportionality is the product of the skeletal component of inelastic specific storage and the thickness of the sediments. Storage changes are incorporated into the groundwater flow model by adding an additional term to the flow equation. Within a model time step, the package appropriately apportions storage changes between elastic and inelastic components on the basis of the relation of simulated head to the previous minimum head. Another package that allows for a time-varying specified-head boundary is also documented. This package was written to reduce the data requirements for test simulations of the Interbed-Storage Package. (USGS)

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

PubMed

Vilseck, Jonah Z; Kostal, Jakub; Tirado-Rives, Julian; Jorgensen, William L

2015-10-15

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods. © 2015 Wiley Periodicals, Inc.

Application of the finite-element method and the eigenmode expansion method to investigate the periodic and spectral characteristic of discrete phase-shift fiber Bragg grating

NASA Astrophysics Data System (ADS)

He, Yue-Jing; Hung, Wei-Chih; Syu, Cheng-Jyun

2017-12-01

The finite-element method (FEM) and eigenmode expansion method (EEM) were adopted to analyze the guided modes and spectrum of phase-shift fiber Bragg grating at five phase-shift degrees (including zero, 1/4π, 1/2π, 3/4π, and π). In previous studies on optical fiber grating, conventional coupled-mode theory was crucial. This theory contains abstruse knowledge about physics and complex computational processes, and thus is challenging for users. Therefore, a numerical simulation method was coupled with a simple and rigorous design procedure to help beginners and users to overcome difficulty in entering the field; in addition, graphical simulation results were presented. To reduce the difference between the simulated context and the actual context, a perfectly matched layer and perfectly reflecting boundary were added to the FEM and the EEM. When the FEM was used for grid cutting, the object meshing method and the boundary meshing method proposed in this study were used to effectively enhance computational accuracy and substantially reduce the time required for simulation. In summary, users can use the simulation results in this study to easily and rapidly design an optical fiber communication system and optical sensors with spectral characteristics.

Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation.

PubMed

Lee, Juyong; Kim, Yang-Gyun; Kim, Kyeong Kyu; Seok, Chaok

2010-08-05

Canonical, right-handed B-DNA can be transformed into noncanonical, left-handed Z-DNA in vitro at high salt concentrations or in vivo under physiological conditions. The molecular mechanism of this drastic conformational transition is still unknown despite numerous studies. Inspired by the crystal structure of a B-Z junction and the previous zipper model, we show here, with the aid of molecular dynamics simulations, that a stepwise propagation of a B-Z junction is a highly probable pathway for the B-Z transition. In this paper, the movement of a B-Z junction by a two-base-pair step in a double-strand nonamer, [d(GpCpGpCpGpCpGpCpG)](2), is considered. Targeted molecular dynamics simulations and umbrella sampling for this transition resulted in a transition pathway with a free energy barrier of 13 kcal/mol. This barrier is much more favorable than those obtained from previous atomistic simulations that lead to concerted transitions of the whole strands. The free energy difference between B-DNA and Z-DNA evaluated from our simulation is 0.9 kcal/mol per dinucleotide unit, which is consistent with previous experiments. The current computation thus strongly supports the proposal that the B-Z transition involves a relatively fast extension of B-DNA or Z-DNA by sequential propagation of B-Z junctions once nucleation of junctions is established.

Interventional radiology virtual simulator for liver biopsy.

PubMed

Villard, P F; Vidal, F P; ap Cenydd, L; Holbrey, R; Pisharody, S; Johnson, S; Bulpitt, A; John, N W; Bello, F; Gould, D

2014-03-01

Training in Interventional Radiology currently uses the apprenticeship model, where clinical and technical skills of invasive procedures are learnt during practice in patients. This apprenticeship training method is increasingly limited by regulatory restrictions on working hours, concerns over patient risk through trainees' inexperience and the variable exposure to case mix and emergencies during training. To address this, we have developed a computer-based simulation of visceral needle puncture procedures. A real-time framework has been built that includes: segmentation, physically based modelling, haptics rendering, pseudo-ultrasound generation and the concept of a physical mannequin. It is the result of a close collaboration between different universities, involving computer scientists, clinicians, clinical engineers and occupational psychologists. The technical implementation of the framework is a robust and real-time simulation environment combining a physical platform and an immersive computerized virtual environment. The face, content and construct validation have been previously assessed, showing the reliability and effectiveness of this framework, as well as its potential for teaching visceral needle puncture. A simulator for ultrasound-guided liver biopsy has been developed. It includes functionalities and metrics extracted from cognitive task analysis. This framework can be useful during training, particularly given the known difficulties in gaining significant practice of core skills in patients.

Faster and exact implementation of the continuous cellular automaton for anisotropic etching simulations

NASA Astrophysics Data System (ADS)

Ferrando, N.; Gosálvez, M. A.; Cerdá, J.; Gadea, R.; Sato, K.

2011-02-01

The current success of the continuous cellular automata for the simulation of anisotropic wet chemical etching of silicon in microengineering applications is based on a relatively fast, approximate, constant time stepping implementation (CTS), whose accuracy against the exact algorithm—a computationally slow, variable time stepping implementation (VTS)—has not been previously analyzed in detail. In this study we show that the CTS implementation can generate moderately wrong etch rates and overall etching fronts, thus justifying the presentation of a novel, exact reformulation of the VTS implementation based on a new state variable, referred to as the predicted removal time (PRT), and the use of a self-balanced binary search tree that enables storage and efficient access to the PRT values in each time step in order to quickly remove the corresponding surface atom/s. The proposed PRT method reduces the simulation cost of the exact implementation from {O}(N^{5/3}) to {O}(N^{3/2} log N) without introducing any model simplifications. This enables more precise simulations (only limited by numerical precision errors) with affordable computational times that are similar to the less precise CTS implementation and even faster for low reactivity systems.

Computational Investigation of In-Flight Temperature in Shaped Charge Jets and Explosively Formed Penetrators

NASA Astrophysics Data System (ADS)

Sable, Peter; Helminiak, Nathaniel; Harstad, Eric; Gullerud, Arne; Hollenshead, Jeromy; Hertel, Eugene; Sandia National Laboratories Collaboration; Marquette University Collaboration

2017-06-01

With the increasing use of hydrocodes in modeling and system design, experimental benchmarking of software has never been more important. While this has been a large area of focus since the inception of computational design, comparisons with temperature data are sparse due to experimental limitations. A novel temperature measurement technique, magnetic diffusion analysis, has enabled the acquisition of in-flight temperature measurements of hyper velocity projectiles. Using this, an AC-14 bare shaped charge and an LX-14 EFP, both with copper linings, were simulated using CTH to benchmark temperature against experimental results. Particular attention was given to the slug temperature profiles after separation, and the effect of varying equation-of-state and strength models. Simulations are in agreement with experimental, attaining better than 2% error between observed shaped charge temperatures. This varied notably depending on the strength model used. Similar observations were made simulating the EFP case, with a minimum 4% deviation. Jet structures compare well with radiographic images and are consistent with ALEGRA simulations previously conducted. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Hybrid Monte Carlo/Deterministic Methods for Accelerating Active Interrogation Modeling

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

Peplow, Douglas E.; Miller, Thomas Martin; Patton, Bruce W

2013-01-01

The potential for smuggling special nuclear material (SNM) into the United States is a major concern to homeland security, so federal agencies are investigating a variety of preventive measures, including detection and interdiction of SNM during transport. One approach for SNM detection, called active interrogation, uses a radiation source, such as a beam of neutrons or photons, to scan cargo containers and detect the products of induced fissions. In realistic cargo transport scenarios, the process of inducing and detecting fissions in SNM is difficult due to the presence of various and potentially thick materials between the radiation source and themore » SNM, and the practical limitations on radiation source strength and detection capabilities. Therefore, computer simulations are being used, along with experimental measurements, in efforts to design effective active interrogation detection systems. The computer simulations mostly consist of simulating radiation transport from the source to the detector region(s). Although the Monte Carlo method is predominantly used for these simulations, difficulties persist related to calculating statistically meaningful detector responses in practical computing times, thereby limiting their usefulness for design and evaluation of practical active interrogation systems. In previous work, the benefits of hybrid methods that use the results of approximate deterministic transport calculations to accelerate high-fidelity Monte Carlo simulations have been demonstrated for source-detector type problems. In this work, the hybrid methods are applied and evaluated for three example active interrogation problems. Additionally, a new approach is presented that uses multiple goal-based importance functions depending on a particle s relevance to the ultimate goal of the simulation. Results from the examples demonstrate that the application of hybrid methods to active interrogation problems dramatically increases their calculational efficiency.« less

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

NASA Astrophysics Data System (ADS)

Dednam, W.; Botha, A. E.

2015-01-01

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

Eulerian-Lagrangian CFD modelling of pesticide dust emissions from maize planters

NASA Astrophysics Data System (ADS)

Devarrewaere, Wouter; Foqué, Dieter; Nicolai, Bart; Nuyttens, David; Verboven, Pieter

2018-07-01

An Eulerian-Lagrangian 3D computational fluid dynamics (CFD) model of pesticide dust drift from precision vacuum planters in field conditions was developed. Tractor and planter models were positioned in an atmospheric computational domain, representing the field and its edges. Physicochemical properties of dust abraded from maize seeds (particle size, shape, porosity, density, a.i. content), dust emission rates and exhaust air velocity values at the planter fan outlets were measured experimentally and implemented in the model. The wind profile, the airflow pattern around the machines and the dust dispersion were computed. Various maize sowing scenarios with different wind conditions, dust properties, planter designs and vacuum pressures were simulated. Dust particle trajectories were calculated by means of Lagrangian particle tracking, considering nonspherical particle drag, gravity and turbulent dispersion. The dust dispersion model was previously validated with wind tunnel data. In this study, simulated pesticide concentrations in the air and on the soil in the different sowing scenarios were compared and discussed. The model predictions were similar to experimental literature data in terms of concentrations and drift distance. Pesticide exposure levels to bees during flight and foraging were estimated from the simulated concentrations. The proposed CFD model can be used in risk assessment studies and in the evaluation of dust drift mitigation measures.

Development of Three-Dimensional Flow Code Package to Predict Performance and Stability of Aircraft with Leading Edge Ice Contamination

NASA Technical Reports Server (NTRS)

Strash, D. J.; Summa, J. M.

1996-01-01

In the work reported herein, a simplified, uncoupled, zonal procedure is utilized to assess the capability of numerically simulating icing effects on a Boeing 727-200 aircraft. The computational approach combines potential flow plus boundary layer simulations by VSAERO for the un-iced aircraft forces and moments with Navier-Stokes simulations by NPARC for the incremental forces and moments due to iced components. These are compared with wind tunnel force and moment data, supplied by the Boeing Company, examining longitudinal flight characteristics. Grid refinement improved the local flow features over previously reported work with no appreciable difference in the incremental ice effect. The computed lift curve slope with and without empennage ice matches the experimental value to within 1%, and the zero lift angle agrees to within 0.2 of a degree. The computed slope of the un-iced and iced aircraft longitudinal stability curve is within about 2% of the test data. This work demonstrates the feasibility of a zonal method for the icing analysis of complete aircraft or isolated components within the linear angle of attack range. In fact, this zonal technique has allowed for the viscous analysis of a complete aircraft with ice which is currently not otherwise considered tractable.

A new computer-aided simulation model for polycrystalline silicon film resistors

NASA Astrophysics Data System (ADS)

Ching-Yuan Wu; Weng-Dah Ken

1983-07-01

A general transport theory for the I-V characteristics of a polycrystalline film resistor has been derived by including the effects of carrier degeneracy, majority-carrier thermionic-diffusion across the space charge regions produced by carrier trapping in the grain boundaries, and quantum mechanical tunneling through the grain boundaries. Based on the derived transport theory, a new conduction model for the electrical resistivity of polycrystalline film resitors has been developed by incorporating the effects of carrier trapping and dopant segregation in the grain boundaries. Moreover, an empirical formula for the coefficient of the dopant-segregation effects has been proposed, which enables us to predict the dependence of the electrical resistivity of phosphorus-and arsenic-doped polycrystalline silicon films on thermal annealing temperature. Phosphorus-doped polycrystalline silicon resistors have been fabricated by using ion-implantation with doses ranged from 1.6 × 10 11 to 5 × 10 15/cm 2. The dependence of the electrical resistivity on doping concentration and temperature have been measured and shown to be in good agreement with the results of computer simulations. In addition, computer simulations for boron-and arsenic-doped polycrystalline silicon resistors have also been performed and shown to be consistent with the experimental results published by previous authors.

Electronic Circular Dichroism of [16]Helicene With Simplified TD-DFT: Beyond the Single Structure Approach.

PubMed

Bannwarth, Christoph; Seibert, Jakob; Grimme, Stefan

2016-05-01

The electronic circular dichroism (ECD) spectrum of the recently synthesized [16]helicene and a derivative comprising two triisopropylsilyloxy protection groups was computed by means of the very efficient simplified time-dependent density functional theory (sTD-DFT) approach. Different from many previous ECD studies of helicenes, nonequilibrium structure effects were accounted for by computing ECD spectra on "snapshots" obtained from a molecular dynamics (MD) simulation including solvent molecules. The trajectories are based on a molecule specific classical potential as obtained from the recently developed quantum chemically derived force field (QMDFF) scheme. The reduced computational cost in the MD simulation due to the use of the QMDFF (compared to ab-initio MD) as well as the sTD-DFT approach make realistic spectral simulations feasible for these compounds that comprise more than 100 atoms. While the ECD spectra of [16]helicene and its derivative computed vertically on the respective gas phase, equilibrium geometries show noticeable differences, these are "washed" out when nonequilibrium structures are taken into account. The computed spectra with two recommended density functionals (ωB97X and BHLYP) and extended basis sets compare very well with the experimental one. In addition we provide an estimate for the missing absolute intensities of the latter. The approach presented here could also be used in future studies to capture nonequilibrium effects, but also to systematically average ECD spectra over different conformations in more flexible molecules. Chirality 28:365-369, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Exhaustively sampling peptide adsorption with metadynamics.

PubMed

Deighan, Michael; Pfaendtner, Jim

2013-06-25

Simulating the adsorption of a peptide or protein and obtaining quantitative estimates of thermodynamic observables remains challenging for many reasons. One reason is the dearth of molecular scale experimental data available for validating such computational models. We also lack simulation methodologies that effectively address the dual challenges of simulating protein adsorption: overcoming strong surface binding and sampling conformational changes. Unbiased classical simulations do not address either of these challenges. Previous attempts that apply enhanced sampling generally focus on only one of the two issues, leaving the other to chance or brute force computing. To improve our ability to accurately resolve adsorbed protein orientation and conformational states, we have applied the Parallel Tempering Metadynamics in the Well-Tempered Ensemble (PTMetaD-WTE) method to several explicitly solvated protein/surface systems. We simulated the adsorption behavior of two peptides, LKα14 and LKβ15, onto two self-assembled monolayer (SAM) surfaces with carboxyl and methyl terminal functionalities. PTMetaD-WTE proved effective at achieving rapid convergence of the simulations, whose results elucidated different aspects of peptide adsorption including: binding free energies, side chain orientations, and preferred conformations. We investigated how specific molecular features of the surface/protein interface change the shape of the multidimensional peptide binding free energy landscape. Additionally, we compared our enhanced sampling technique with umbrella sampling and also evaluated three commonly used molecular dynamics force fields.

Student Workshops for Severe Weather Warning Decision Making using AWIPS-2 at the University of Oklahoma

NASA Astrophysics Data System (ADS)

Zwink, A. B.; Morris, D.; Ware, P. J.; Ernst, S.; Holcomb, B.; Riley, S.; Hardy, J.; Mullens, S.; Bowlan, M.; Payne, C.; Bates, A.; Williams, B.

2016-12-01

For several years, employees at the Cooperative Institute of Mesoscale Meteorological Studies at the University of Oklahoma (OU) that are affiliated with Warning Decision Training Division (WDTD) of the National Weather Service (NWS) provided training simulations to students from OU's School of Meteorology (SoM). These simulations focused on warning decision making using Dual-Pol radar data products in an AWIPS-1 environment. Building on these previous experiences, CIMMS/WDTD recently continued the collaboration with the SoM Oklahoma Weather Lab (OWL) by holding a warning decision workshop simulating a NWS Weather Forecast Office (WFO) experience. The workshop took place in the WDTD AWIPS-2 computer laboratory with 25 AWIPS-2 workstations and the WES-2 Bridge (Weather Event Simulator) software which replayed AWIPS-2 data. Using the WES-2 Bridge and the WESSL-2 (WES Scripting Language) event display, this computer lab has the state-of-the-art ability to simulate severe weather events and recreate WFO warning operations. OWL Student forecasters attending the workshop worked in teams in a multi-player simulation of the Hastings, Nebraska WFO on May 6th, 2015, where thunderstorms across the service area produced large hail, damaging winds, and multiple tornadoes. This paper will discuss the design and goals of the WDTD/OWL workshop, as well as plans for holding similar workshops in the future.

Exploring biological interaction networks with tailored weighted quasi-bicliques

PubMed Central

2012-01-01

Background Biological networks provide fundamental insights into the functional characterization of genes and their products, the characterization of DNA-protein interactions, the identification of regulatory mechanisms, and other biological tasks. Due to the experimental and biological complexity, their computational exploitation faces many algorithmic challenges. Results We introduce novel weighted quasi-biclique problems to identify functional modules in biological networks when represented by bipartite graphs. In difference to previous quasi-biclique problems, we include biological interaction levels by using edge-weighted quasi-bicliques. While we prove that our problems are NP-hard, we also describe IP formulations to compute exact solutions for moderately sized networks. Conclusions We verify the effectiveness of our IP solutions using both simulation and empirical data. The simulation shows high quasi-biclique recall rates, and the empirical data corroborate the abilities of our weighted quasi-bicliques in extracting features and recovering missing interactions from biological networks. PMID:22759421

Criticality of the random field Ising model in and out of equilibrium: A nonperturbative functional renormalization group description

NASA Astrophysics Data System (ADS)

Balog, Ivan; Tarjus, Gilles; Tissier, Matthieu

2018-03-01

We show that, contrary to previous suggestions based on computer simulations or erroneous theoretical treatments, the critical points of the random-field Ising model out of equilibrium, when quasistatically changing the applied source at zero temperature, and in equilibrium are not in the same universality class below some critical dimension dD R≈5.1 . We demonstrate this by implementing a nonperturbative functional renormalization group for the associated dynamical field theory. Above dD R, the avalanches, which characterize the evolution of the system at zero temperature, become irrelevant at large distance, and hysteresis and equilibrium critical points are then controlled by the same fixed point. We explain how to use computer simulation and finite-size scaling to check the correspondence between in and out of equilibrium criticality in a far less ambiguous way than done so far.

KONFIG and REKONFIG: Two interactive preprocessing to the Navy/NASA Engine Program (NNEP)

NASA Technical Reports Server (NTRS)

Fishbach, L. H.

1981-01-01

The NNEP is a computer program that is currently being used to simulate the thermodynamic cycle performance of almost all types of turbine engines by many government, industry, and university personnel. The NNEP uses arrays of input data to set up the engine simulation and component matching method as well as to describe the characteristics of the components. A preprocessing program (KONFIG) is described in which the user at a terminal on a time shared computer can interactively prepare the arrays of data required. It is intended to make it easier for the occasional or new user to operate NNEP. Another preprocessing program (REKONFIG) in which the user can modify the component specifications of a previously configured NNEP dataset is also described. It is intended to aid in preparing data for parametric studies and/or studies of similar engines such a mixed flow turbofans, turboshafts, etc.

A 2D electrostatic PIC code for the Mark III Hypercube

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

Ferraro, R.D.; Liewer, P.C.; Decyk, V.K.

We have implemented a 2D electrostastic plasma particle in cell (PIC) simulation code on the Caltech/JPL Mark IIIfp Hypercube. The code simulates plasma effects by evolving in time the trajectories of thousands to millions of charged particles subject to their self-consistent fields. Each particle`s position and velocity is advanced in time using a leap frog method for integrating Newton`s equations of motion in electric and magnetic fields. The electric field due to these moving charged particles is calculated on a spatial grid at each time by solving Poisson`s equation in Fourier space. These two tasks represent the largest part ofmore » the computation. To obtain efficient operation on a distributed memory parallel computer, we are using the General Concurrent PIC (GCPIC) algorithm previously developed for a 1D parallel PIC code.« less

Computer simulation of the effects of shoe cushioning on internal and external loading during running impacts.

PubMed

Miller, Ross H; Hamill, Joseph

2009-08-01

Biomechanical aspects of running injuries are often inferred from external loading measurements. However, previous research has suggested that relationships between external loading and potential injury-inducing internal loads can be complex and nonintuitive. Further, the loading response to training interventions can vary widely between subjects. In this study, we use a subject-specific computer simulation approach to estimate internal and external loading of the distal tibia during the impact phase for two runners when running in shoes with different midsole cushioning parameters. The results suggest that: (1) changes in tibial loading induced by footwear are not reflected by changes in ground reaction force (GRF) magnitudes; (2) the GRF loading rate is a better surrogate measure of tibial loading and stress fracture risk than the GRF magnitude; and (3) averaging results across groups may potentially mask differential responses to training interventions between individuals.

Cerebral aneurysms: relations between geometry, hemodynamics and aneurysm location in the cerebral vasculature

NASA Astrophysics Data System (ADS)

Passerini, Tiziano; Veneziani, Alessandro; Sangalli, Laura; Secchi, Piercesare; Vantini, Simone

2010-11-01

In cerebral blood circulation, the interplay of arterial geometrical features and flow dynamics is thought to play a significant role in the development of aneurysms. In the framework of the Aneurisk project, patient-specific morphology reconstructions were conducted with the open-source software VMTK (www.vmtk.org) on a set of computational angiography images provided by Ospedale Niguarda (Milano, Italy). Computational fluid dynamics (CFD) simulations were performed with a software based on the library LifeV (www.lifev.org). The joint statistical analysis of geometries and simulations highlights the possible association of certain spatial patterns of radius, curvature and shear load along the Internal Carotid Artery (ICA) with the presence, position and previous event of rupture of an aneurysm in the entire cerebral vasculature. Moreover, some possible landmarks are identified to be monitored for the assessment of a Potential Rupture Risk Index.

Computer-based simulation training to improve learning outcomes in mannequin-based simulation exercises.

PubMed

Curtin, Lindsay B; Finn, Laura A; Czosnowski, Quinn A; Whitman, Craig B; Cawley, Michael J

2011-08-10

To assess the impact of computer-based simulation on the achievement of student learning outcomes during mannequin-based simulation. Participants were randomly assigned to rapid response teams of 5-6 students and then teams were randomly assigned to either a group that completed either computer-based or mannequin-based simulation cases first. In both simulations, students used their critical thinking skills and selected interventions independent of facilitator input. A predetermined rubric was used to record and assess students' performance in the mannequin-based simulations. Feedback and student performance scores were generated by the software in the computer-based simulations. More of the teams in the group that completed the computer-based simulation before completing the mannequin-based simulation achieved the primary outcome for the exercise, which was survival of the simulated patient (41.2% vs. 5.6%). The majority of students (>90%) recommended the continuation of simulation exercises in the course. Students in both groups felt the computer-based simulation should be completed prior to the mannequin-based simulation. The use of computer-based simulation prior to mannequin-based simulation improved the achievement of learning goals and outcomes. In addition to improving participants' skills, completing the computer-based simulation first may improve participants' confidence during the more real-life setting achieved in the mannequin-based simulation.

Fast Whole-Engine Stirling Analysis

NASA Technical Reports Server (NTRS)

Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.; Demko, Rikako

2005-01-01

An experimentally validated approach is described for fast axisymmetric Stirling engine simulations. These simulations include the entire displacer interior and demonstrate it is possible to model a complete engine cycle in less than an hour. The focus of this effort was to demonstrate it is possible to produce useful Stirling engine performance results in a time-frame short enough to impact design decisions. The combination of utilizing the latest 64-bit Opteron computer processors, fiber-optical Myrinet communications, dynamic meshing, and across zone partitioning has enabled solution times at least 240 times faster than previous attempts at simulating the axisymmetric Stirling engine. A comparison of the multidimensional results, calibrated one-dimensional results, and known experimental results is shown. This preliminary comparison demonstrates that axisymmetric simulations can be very accurate, but more work remains to improve the simulations through such means as modifying the thermal equilibrium regenerator models, adding fluid-structure interactions, including radiation effects, and incorporating mechanodynamics.

Modelling blood flow and metabolism in the piglet brain during hypoxia-ischaemia: simulating brain energetics.

PubMed

Moroz, Tracy; Hapuarachchi, Tharindi; Bainbridge, Alan; Price, David; Cady, Ernest; Baer, Ether; Broad, Kevin; Ezzati, Mojgan; Thomas, David; Golay, Xavier; Robertson, Nicola J; Cooper, Chris E; Tachtsidis, Ilias

2013-01-01

We have developed a computational model to simulate hypoxia-ischaemia (HI) in the neonatal piglet brain. It has been extended from a previous model by adding the simulation of carotid artery occlusion and including pH changes in the cytoplasm. Here, simulations from the model are compared with near-infrared spectroscopy (NIRS) and phosphorus magnetic resonance spectroscopy (MRS) measurements from two piglets during HI and short-term recovery. One of these piglets showed incomplete recovery after HI, and this is modelled by considering some of the cells to be dead. This is consistent with the results from MRS and the redox state of cytochrome-c-oxidase as measured by NIRS. However, the simulations do not match the NIRS haemoglobin measurements. The model therefore predicts that further physiological changes must also be taking place if the hypothesis of dead cells is correct.

Fast Whole-Engine Stirling Analysis

NASA Technical Reports Server (NTRS)

Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.; Demko, Rikako

2007-01-01

An experimentally validated approach is described for fast axisymmetric Stirling engine simulations. These simulations include the entire displacer interior and demonstrate it is possible to model a complete engine cycle in less than an hour. The focus of this effort was to demonstrate it is possible to produce useful Stirling engine performance results in a time-frame short enough to impact design decisions. The combination of utilizing the latest 64-bit Opteron computer processors, fiber-optical Myrinet communications, dynamic meshing, and across zone partitioning has enabled solution times at least 240 times faster than previous attempts at simulating the axisymmetric Stirling engine. A comparison of the multidimensional results, calibrated one-dimensional results, and known experimental results is shown. This preliminary comparison demonstrates that axisymmetric simulations can be very accurate, but more work remains to improve the simulations through such means as modifying the thermal equilibrium regenerator models, adding fluid-structure interactions, including radiation effects, and incorporating mechanodynamics.

Self-consistent radiation-based simulation of electric arcs: II. Application to gas circuit breakers

NASA Astrophysics Data System (ADS)

Iordanidis, A. A.; Franck, C. M.

2008-07-01

An accurate and robust method for radiative heat transfer simulation for arc applications was presented in the previous paper (part I). In this paper a self-consistent mathematical model based on computational fluid dynamics and a rigorous radiative heat transfer model is described. The model is applied to simulate switching arcs in high voltage gas circuit breakers. The accuracy of the model is proven by comparison with experimental data for all arc modes. The ablation-controlled arc model is used to simulate high current PTFE arcs burning in cylindrical tubes. Model accuracy for the lower current arcs is evaluated using experimental data on the axially blown SF6 arc in steady state and arc resistance measurements close to current zero. The complete switching process with the arc going through all three phases is also simulated and compared with the experimental data from an industrial circuit breaker switching test.

Adjusting for cross-cultural differences in computer-adaptive tests of quality of life.

PubMed

Gibbons, C J; Skevington, S M

2018-04-01

Previous studies using the WHOQOL measures have demonstrated that the relationship between individual items and the underlying quality of life (QoL) construct may differ between cultures. If unaccounted for, these differing relationships can lead to measurement bias which, in turn, can undermine the reliability of results. We used item response theory (IRT) to assess differential item functioning (DIF) in WHOQOL data from diverse language versions collected in UK, Zimbabwe, Russia, and India (total N = 1332). Data were fitted to the partial credit 'Rasch' model. We used four item banks previously derived from the WHOQOL-100 measure, which provided excellent measurement for physical, psychological, social, and environmental quality of life domains (40 items overall). Cross-cultural differential item functioning was assessed using analysis of variance for item residuals and post hoc Tukey tests. Simulated computer-adaptive tests (CATs) were conducted to assess the efficiency and precision of the four items banks. Splitting item parameters by DIF results in four linked item banks without DIF or other breaches of IRT model assumptions. Simulated CATs were more precise and efficient than longer paper-based alternatives. Assessing differential item functioning using item response theory can identify measurement invariance between cultures which, if uncontrolled, may undermine accurate comparisons in computer-adaptive testing assessments of QoL. We demonstrate how compensating for DIF using item anchoring allowed data from all four countries to be compared on a common metric, thus facilitating assessments which were both sensitive to cultural nuance and comparable between countries.

Study on the CFD simulation of refrigerated container

NASA Astrophysics Data System (ADS)

Arif Budiyanto, Muhammad; Shinoda, Takeshi; Nasruddin

2017-10-01

The objective this study is to performed Computational Fluid Dynamic (CFD) simulation of refrigerated container in the container port. Refrigerated container is a thermal cargo container constructed from an insulation wall to carry kind of perishable goods. CFD simulation was carried out use cross sectional of container walls to predict surface temperatures of refrigerated container and to estimate its cooling load. The simulation model is based on the solution of the partial differential equations governing the fluid flow and heat transfer processes. The physical model of heat-transfer processes considered in this simulation are consist of solar radiation from the sun, heat conduction on the container walls, heat convection on the container surfaces and thermal radiation among the solid surfaces. The validation of simulation model was assessed uses surface temperatures at center points on each container walls obtained from the measurement experimentation in the previous study. The results shows the surface temperatures of simulation model has good agreement with the measurement data on all container walls.

Deployable reflector antenna performance optimization using automated surface correction and array-feed compensation

NASA Technical Reports Server (NTRS)

Schroeder, Lyle C.; Bailey, M. C.; Mitchell, John L.

1992-01-01

Methods for increasing the electromagnetic (EM) performance of reflectors with rough surfaces were tested and evaluated. First, one quadrant of the 15-meter hoop-column antenna was retrofitted with computer-driven and controlled motors to allow automated adjustment of the reflector surface. The surface errors, measured with metric photogrammetry, were used in a previously verified computer code to calculate control motor adjustments. With this system, a rough antenna surface (rms of approximately 0.180 inch) was corrected in two iterations to approximately the structural surface smoothness limit of 0.060 inch rms. The antenna pattern and gain improved significantly as a result of these surface adjustments. The EM performance was evaluated with a computer program for distorted reflector antennas which had been previously verified with experimental data. Next, the effects of the surface distortions were compensated for in computer simulations by superimposing excitation from an array feed to maximize antenna performance relative to an undistorted reflector. Results showed that a 61-element array could produce EM performance improvements equal to surface adjustments. When both mechanical surface adjustment and feed compensation techniques were applied, the equivalent operating frequency increased from approximately 6 to 18 GHz.

Adaptive two-regime method: Application to front propagation

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

Robinson, Martin, E-mail: martin.robinson@maths.ox.ac.uk; Erban, Radek, E-mail: erban@maths.ox.ac.uk; Flegg, Mark, E-mail: mark.flegg@monash.edu

2014-03-28

The Adaptive Two-Regime Method (ATRM) is developed for hybrid (multiscale) stochastic simulation of reaction-diffusion problems. It efficiently couples detailed Brownian dynamics simulations with coarser lattice-based models. The ATRM is a generalization of the previously developed Two-Regime Method [Flegg et al., J. R. Soc., Interface 9, 859 (2012)] to multiscale problems which require a dynamic selection of regions where detailed Brownian dynamics simulation is used. Typical applications include a front propagation or spatio-temporal oscillations. In this paper, the ATRM is used for an in-depth study of front propagation in a stochastic reaction-diffusion system which has its mean-field model given in termsmore » of the Fisher equation [R. Fisher, Ann. Eugen. 7, 355 (1937)]. It exhibits a travelling reaction front which is sensitive to stochastic fluctuations at the leading edge of the wavefront. Previous studies into stochastic effects on the Fisher wave propagation speed have focused on lattice-based models, but there has been limited progress using off-lattice (Brownian dynamics) models, which suffer due to their high computational cost, particularly at the high molecular numbers that are necessary to approach the Fisher mean-field model. By modelling only the wavefront itself with the off-lattice model, it is shown that the ATRM leads to the same Fisher wave results as purely off-lattice models, but at a fraction of the computational cost. The error analysis of the ATRM is also presented for a morphogen gradient model.« less

GPU accelerated FDTD solver and its application in MRI.

PubMed

Chi, J; Liu, F; Jin, J; Mason, D G; Crozier, S

2010-01-01

The finite difference time domain (FDTD) method is a popular technique for computational electromagnetics (CEM). The large computational power often required, however, has been a limiting factor for its applications. In this paper, we will present a graphics processing unit (GPU)-based parallel FDTD solver and its successful application to the investigation of a novel B1 shimming scheme for high-field magnetic resonance imaging (MRI). The optimized shimming scheme exhibits considerably improved transmit B(1) profiles. The GPU implementation dramatically shortened the runtime of FDTD simulation of electromagnetic field compared with its CPU counterpart. The acceleration in runtime has made such investigation possible, and will pave the way for other studies of large-scale computational electromagnetic problems in modern MRI which were previously impractical.

Quantum simulator review

NASA Astrophysics Data System (ADS)

Bednar, Earl; Drager, Steven L.

2007-04-01

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

Illumination discrimination in real and simulated scenes

PubMed Central

Radonjić, Ana; Pearce, Bradley; Aston, Stacey; Krieger, Avery; Dubin, Hilary; Cottaris, Nicolas P.; Brainard, David H.; Hurlbert, Anya C.

2016-01-01

Characterizing humans' ability to discriminate changes in illumination provides information about the visual system's representation of the distal stimulus. We have previously shown that humans are able to discriminate illumination changes and that sensitivity to such changes depends on their chromatic direction. Probing illumination discrimination further would be facilitated by the use of computer-graphics simulations, which would, in practice, enable a wider range of stimulus manipulations. There is no a priori guarantee, however, that results obtained with simulated scenes generalize to real illuminated scenes. To investigate this question, we measured illumination discrimination in real and simulated scenes that were well-matched in mean chromaticity and scene geometry. Illumination discrimination thresholds were essentially identical for the two stimulus types. As in our previous work, these thresholds varied with illumination change direction. We exploited the flexibility offered by the use of graphics simulations to investigate whether the differences across direction are preserved when the surfaces in the scene are varied. We show that varying the scene's surface ensemble in a manner that also changes mean scene chromaticity modulates the relative sensitivity to illumination changes along different chromatic directions. Thus, any characterization of sensitivity to changes in illumination must be defined relative to the set of surfaces in the scene. PMID:28558392

Grid Sensitivity Study for Slat Noise Simulations

NASA Technical Reports Server (NTRS)

Lockard, David P.; Choudhari, Meelan M.; Buning, Pieter G.

2014-01-01

The slat noise from the 30P/30N high-lift system is being investigated through computational fluid dynamics simulations in conjunction with a Ffowcs Williams-Hawkings acoustics solver. Many previous simulations have been performed for the configuration, and the case was introduced as a new category for the Second AIAA workshop on Benchmark problems for Airframe Noise Configurations (BANC-II). However, the cost of the simulations has restricted the study of grid resolution effects to a baseline grid and coarser meshes. In the present study, two different approaches are being used to investigate the effect of finer resolution of near-field unsteady structures. First, a standard grid refinement by a factor of two is used, and the calculations are performed by using the same CFL3D solver employed in the majority of the previous simulations. Second, the OVERFLOW code is applied to the baseline grid, but with a 5th-order upwind spatial discretization as compared with the second-order discretization used in the CFL3D simulations. In general, the fine grid CFL3D simulation and OVERFLOW calculation are in very good agreement and exhibit the lowest levels of both surface pressure fluctuations and radiated noise. Although the smaller scales resolved by these simulations increase the velocity fluctuation levels, they appear to mitigate the influence of the larger scales on the surface pressure. These new simulations are used to investigate the influence of the grid on unsteady high-lift simulations and to gain a better understanding of the physics responsible for the noise generation and radiation.

Modeling laser velocimeter signals as triply stochastic Poisson processes

NASA Technical Reports Server (NTRS)

Mayo, W. T., Jr.

1976-01-01

Previous models of laser Doppler velocimeter (LDV) systems have not adequately described dual-scatter signals in a manner useful for analysis and simulation of low-level photon-limited signals. At low photon rates, an LDV signal at the output of a photomultiplier tube is a compound nonhomogeneous filtered Poisson process, whose intensity function is another (slower) Poisson process with the nonstationary rate and frequency parameters controlled by a random flow (slowest) process. In the present paper, generalized Poisson shot noise models are developed for low-level LDV signals. Theoretical results useful in detection error analysis and simulation are presented, along with measurements of burst amplitude statistics. Computer generated simulations illustrate the difference between Gaussian and Poisson models of low-level signals.

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

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

Sarkar, Avik; Sun, Xin; Sundaresan, Sankaran

2014-04-23

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

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

Dang, Liem X.; Vo, Quynh N.; Nilsson, Mikael

We report one of the first simulations using a classical rate theory approach to predict the mechanism of the exchange process between water and aqueous uranyl ions. Using our water and ion-water polarizable force fields and molecular dynamics techniques, we computed the potentials of mean force for the uranyl ion-water pair as the function of pressures at ambient temperature. Subsequently, these simulated potentials of mean force were used to calculate rate constants using the transition rate theory; the time dependent transmission coefficients were also examined using the reactive flux method and Grote-Hynes treatments of the dynamic response of the solvent.more » The computed activation volumes using transition rate theory and the corrected rate constants are positive, thus the mechanism of this particular water-exchange is a dissociative process. We discuss our rate theory results and compare them with previously studies in which non-polarizable force fields were used. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Using distributed partial memories to improve self-organizing collective movements.

PubMed

Winder, Ransom; Reggia, James A

2004-08-01

Past self-organizing models of collectively moving "particles" (simulated bird flocks, fish schools, etc.) have typically been based on purely reflexive agents that have no significant memory of past movements. We hypothesized that giving such individual particles a limited distributed memory of past obstacles they encountered could lead to significantly faster travel between goal destinations. Systematic computational experiments using six terrains that had different arrangements of obstacles demonstrated that, at least in some domains, this conjecture is true. Furthermore, these experiments demonstrated that improved performance over time came not only from the avoidance of previously seen obstacles, but also (surprisingly) immediately after first encountering obstacles due to decreased delays in circumventing those obstacles. Simulations also showed that, of the four strategies we tested for removal of remembered obstacles when memory was full and a new obstacle was to be saved, none was better than random selection. These results may be useful in interpreting future experimental research on group movements in biological populations, and in improving existing methodologies for control of collective movements in computer graphics, robotic teams, particle swarm optimization, and computer games.

A computational investigation of the finite-time blow-up of the 3D incompressible Euler equations based on the Voigt regularization

DOE PAGES

Larios, Adam; Petersen, Mark R.; Titi, Edriss S.; ...

2017-04-29

We report the results of a computational investigation of two blow-up criteria for the 3D incompressible Euler equations. One criterion was proven in a previous work, and a related criterion is proved here. These criteria are based on an inviscid regularization of the Euler equations known as the 3D Euler-Voigt equations, which are known to be globally well-posed. Moreover, simulations of the 3D Euler-Voigt equations also require less resolution than simulations of the 3D Euler equations for xed values of the regularization parameter α > 0. Therefore, the new blow-up criteria allow one to gain information about possible singularity formationmore » in the 3D Euler equations indirectly; namely, by simulating the better-behaved 3D Euler-Voigt equations. The new criteria are only known to be suficient for blow-up. Therefore, to test the robustness of the inviscid-regularization approach, we also investigate analogous criteria for blow-up of the 1D Burgers equation, where blow-up is well-known to occur.« less

Development of a computational model on the neural activity patterns of a visual working memory in a hierarchical feedforward Network

NASA Astrophysics Data System (ADS)

An, Soyoung; Choi, Woochul; Paik, Se-Bum

2015-11-01

Understanding the mechanism of information processing in the human brain remains a unique challenge because the nonlinear interactions between the neurons in the network are extremely complex and because controlling every relevant parameter during an experiment is difficult. Therefore, a simulation using simplified computational models may be an effective approach. In the present study, we developed a general model of neural networks that can simulate nonlinear activity patterns in the hierarchical structure of a neural network system. To test our model, we first examined whether our simulation could match the previously-observed nonlinear features of neural activity patterns. Next, we performed a psychophysics experiment for a simple visual working memory task to evaluate whether the model could predict the performance of human subjects. Our studies show that the model is capable of reproducing the relationship between memory load and performance and may contribute, in part, to our understanding of how the structure of neural circuits can determine the nonlinear neural activity patterns in the human brain.

Direct numerical simulation of turbulent plane Couette flow under neutral and stable stratification

NASA Astrophysics Data System (ADS)

Mortikov, Evgeny

2017-11-01

Direct numerical simulation (DNS) approach was used to study turbulence dynamics in plane Couette flow under conditions ranging from neutral stability to the case of extreme stable stratification, where intermittency is observed. Simulations were performed for Reynolds numbers, based on the channel height and relative wall speed, up to 2 ×105 . Using DNS data, which covers a wide range of stability conditions, parameterizations of pressure correlation terms used in second-order closure turbulence models are discussed. Particular attention is also paid to the sustainment of intermittent turbulence under strong stratification. Intermittent regime is found to be associated with the formation of secondary large-scale structures elongated in the spanwise direction, which define spatially confined alternating regions of laminar and turbulent flow. The spanwise length of this structures increases with the increase in the bulk Richardson number and defines and additional constraint on the computational box size. In this work DNS results are presented in extended computational domains, where the intermittent turbulence is sustained for sufficiently higher Richardson numbers than previously reported.

Numerical investigation of the vortex-induced vibration of an elastically mounted circular cylinder at high Reynolds number (Re = 104) and low mass ratio using the RANS code

PubMed Central

2017-01-01

This study numerically investigates the vortex-induced vibration (VIV) of an elastically mounted rigid cylinder by using Reynolds-averaged Navier–Stokes (RANS) equations with computational fluid dynamic (CFD) tools. CFD analysis is performed for a fixed-cylinder case with Reynolds number (Re) = 104 and for a cylinder that is free to oscillate in the transverse direction and possesses a low mass-damping ratio and Re = 104. Previously, similar studies have been performed with 3-dimensional and comparatively expensive turbulent models. In the current study, the capability and accuracy of the RANS model are validated, and the results of this model are compared with those of detached eddy simulation, direct numerical simulation, and large eddy simulation models. All three response branches and the maximum amplitude are well captured. The 2-dimensional case with the RANS shear–stress transport k-w model, which involves minimal computational cost, is reliable and appropriate for analyzing the characteristics of VIV. PMID:28982172

LBM-EP: Lattice-Boltzmann method for fast cardiac electrophysiology simulation from 3D images.

PubMed

Rapaka, S; Mansi, T; Georgescu, B; Pop, M; Wright, G A; Kamen, A; Comaniciu, Dorin

2012-01-01

Current treatments of heart rhythm troubles require careful planning and guidance for optimal outcomes. Computational models of cardiac electrophysiology are being proposed for therapy planning but current approaches are either too simplified or too computationally intensive for patient-specific simulations in clinical practice. This paper presents a novel approach, LBM-EP, to solve any type of mono-domain cardiac electrophysiology models at near real-time that is especially tailored for patient-specific simulations. The domain is discretized on a Cartesian grid with a level-set representation of patient's heart geometry, previously estimated from images automatically. The cell model is calculated node-wise, while the transmembrane potential is diffused using Lattice-Boltzmann method within the domain defined by the level-set. Experiments on synthetic cases, on a data set from CESC'10 and on one patient with myocardium scar showed that LBM-EP provides results comparable to an FEM implementation, while being 10 - 45 times faster. Fast, accurate, scalable and requiring no specific meshing, LBM-EP paves the way to efficient and detailed models of cardiac electrophysiology for therapy planning.

A computational investigation of the finite-time blow-up of the 3D incompressible Euler equations based on the Voigt regularization

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

Larios, Adam; Petersen, Mark R.; Titi, Edriss S.

We report the results of a computational investigation of two blow-up criteria for the 3D incompressible Euler equations. One criterion was proven in a previous work, and a related criterion is proved here. These criteria are based on an inviscid regularization of the Euler equations known as the 3D Euler-Voigt equations, which are known to be globally well-posed. Moreover, simulations of the 3D Euler-Voigt equations also require less resolution than simulations of the 3D Euler equations for xed values of the regularization parameter α > 0. Therefore, the new blow-up criteria allow one to gain information about possible singularity formationmore » in the 3D Euler equations indirectly; namely, by simulating the better-behaved 3D Euler-Voigt equations. The new criteria are only known to be suficient for blow-up. Therefore, to test the robustness of the inviscid-regularization approach, we also investigate analogous criteria for blow-up of the 1D Burgers equation, where blow-up is well-known to occur.« less

Directable weathering of concave rock using curvature estimation.

PubMed

Jones, Michael D; Farley, McKay; Butler, Joseph; Beardall, Matthew

2010-01-01

We address the problem of directable weathering of exposed concave rock for use in computer-generated animation or games. Previous weathering models that admit concave surfaces are computationally inefficient and difficult to control. In nature, the spheroidal and cavernous weathering rates depend on the surface curvature. Spheroidal weathering is fastest in areas with large positive mean curvature and cavernous weathering is fastest in areas with large negative mean curvature. We simulate both processes using an approximation of mean curvature on a voxel grid. Both weathering rates are also influenced by rock durability. The user controls rock durability by editing a durability graph before and during weathering simulation. Simulations of rockfall and colluvium deposition further improve realism. The profile of the final weathered rock matches the shape of the durability graph up to the effects of weathering and colluvium deposition. We demonstrate the top-down directability and visual plausibility of the resulting model through a series of screenshots and rendered images. The results include the weathering of a cube into a sphere and of a sheltered inside corner into a cavern as predicted by the underlying geomorphological models.

The incompressibility assumption in computational simulations of nasal airflow.

PubMed

Cal, Ismael R; Cercos-Pita, Jose Luis; Duque, Daniel

2017-06-01

Most of the computational works on nasal airflow up to date have assumed incompressibility, given the low Mach number of these flows. However, for high temperature gradients, the incompressibility assumption could lead to a loss of accuracy, due to the temperature dependence of air density and viscosity. In this article we aim to shed some light on the influence of this assumption in a model of calm breathing in an Asian nasal cavity, by solving the fluid flow equations in compressible and incompressible formulation for different ambient air temperatures using the OpenFOAM package. At low flow rates and warm climatological conditions, similar results were obtained from both approaches, showing that density variations need not be taken into account to obtain a good prediction of all flow features, at least for usual breathing conditions. This agrees with most of the simulations previously reported, at least as far as the incompressibility assumption is concerned. However, parameters like nasal resistance and wall shear stress distribution differ for air temperatures below [Formula: see text]C approximately. Therefore, density variations should be considered for simulations at such low temperatures.

Brian Hears: Online Auditory Processing Using Vectorization Over Channels

PubMed Central

Fontaine, Bertrand; Goodman, Dan F. M.; Benichoux, Victor; Brette, Romain

2011-01-01

The human cochlea includes about 3000 inner hair cells which filter sounds at frequencies between 20 Hz and 20 kHz. This massively parallel frequency analysis is reflected in models of auditory processing, which are often based on banks of filters. However, existing implementations do not exploit this parallelism. Here we propose algorithms to simulate these models by vectorizing computation over frequency channels, which are implemented in “Brian Hears,” a library for the spiking neural network simulator package “Brian.” This approach allows us to use high-level programming languages such as Python, because with vectorized operations, the computational cost of interpretation represents a small fraction of the total cost. This makes it possible to define and simulate complex models in a simple way, while all previous implementations were model-specific. In addition, we show that these algorithms can be naturally parallelized using graphics processing units, yielding substantial speed improvements. We demonstrate these algorithms with several state-of-the-art cochlear models, and show that they compare favorably with existing, less flexible, implementations. PMID:21811453

Unfolding of Proteins: Thermal and Mechanical Unfolding

NASA Technical Reports Server (NTRS)

Hur, Joe S.; Darve, Eric

2004-01-01

We have employed a Hamiltonian model based on a self-consistent Gaussian appoximation to examine the unfolding process of proteins in external - both mechanical and thermal - force elds. The motivation was to investigate the unfolding pathways of proteins by including only the essence of the important interactions of the native-state topology. Furthermore, if such a model can indeed correctly predict the physics of protein unfolding, it can complement more computationally expensive simulations and theoretical work. The self-consistent Gaussian approximation by Micheletti et al. has been incorporated in our model to make the model mathematically tractable by signi cantly reducing the computational cost. All thermodynamic properties and pair contact probabilities are calculated by simply evaluating the values of a series of Incomplete Gamma functions in an iterative manner. We have compared our results to previous molecular dynamics simulation and experimental data for the mechanical unfolding of the giant muscle protein Titin (1TIT). Our model, especially in light of its simplicity and excellent agreement with experiment and simulation, demonstrates the basic physical elements necessary to capture the mechanism of protein unfolding in an external force field.

Water immersion and its computer simulation as analogs of weightlessness

NASA Technical Reports Server (NTRS)

Leonard, J. I.

1982-01-01

Experimental studies and computer simulations of water immersion are summarized and discussed with regard to their utility as analogs of weightlessness. Emphasis is placed on describing and interpreting the renal, endocrine, fluid, and circulatory changes that take place during immersion. A mathematical model, based on concepts of fluid volume regulation, is shown to be well suited to simulate the dynamic responses to water immersion. Further, it is shown that such a model provides a means to study specific mechanisms and pathways involved in the immersion response. A number of hypotheses are evaluated with the model related to the effects of dehydration, venous pressure disturbances, the control of ADH, and changes in plasma-interstitial volume. By inference, it is suggested that most of the model's responses to water immersion are plausible predictions of the acute changes expected, but not yet measured, during space flight. One important prediction of the model is that previous attempts to measure a diuresis during space flight failed because astronauts may have been dehydrated and urine samples were pooled over 24-hour periods.

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

PubMed

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

2010-05-01

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

Optimization of refractive liquid crystal lenses using an efficient multigrid simulation.

PubMed

Milton, Harry; Brimicombe, Paul; Morgan, Philip; Gleeson, Helen; Clamp, John

2012-05-07

A multigrid computational model has been developed to assess the performance of refractive liquid crystal lenses, which is up to 40 times faster than previous techniques. Using this model, the optimum geometries producing an ideal parabolic voltage distribution were deduced for refractive liquid crystal lenses with diameters from 1 to 9 mm. The ratio of insulation thickness to lens diameter was determined to be 1:2 for small diameter lenses, tending to 1:3 for larger lenses. The model is used to propose a new method of lens operation with lower operating voltages needed to induce specific optical powers. The operating voltages are calculated for the induction of optical powers between + 1.00 D and + 3.00 D in a 3 mm diameter lens, with the speed of the simulation facilitating the optimization of the refractive index profile. We demonstrate that the relationship between additional applied voltage and optical power is approximately linear for optical powers under + 3.00 D. The versatility of the computational simulation has also been demonstrated by modeling of in-plane electrode liquid crystal devices.

Critical behaviour and vapour-liquid coexistence of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide ionic liquids via Monte Carlo simulations.

PubMed

Rai, Neeraj; Maginn, Edward J

2012-01-01

Atomistic Monte Carlo simulations are used to compute vapour-liquid coexistence properties of a homologous series of [C(n)mim][NTf2] ionic liquids, with n = 1, 2, 4, 6. Estimates of the critical temperatures range from 1190 K to 1257 K, with longer cation alkyl chains serving to lower the critical temperature. Other quantities such as critical density, critical pressure, normal boiling point, and accentric factor are determined from the simulations. Vapour pressure curves and the temperature dependence of the enthalpy of vapourisation are computed and found to have a weak dependence on the length of the cation alkyl chain. The ions in the vapour phase are predominately in single ion pairs, although a significant number of ions are found in neutral clusters of larger sizes as temperature is increased. It is found that previous estimates of the critical point obtained from extrapolating experimental surface tension data agree reasonably well with the predictions obtained here, but group contribution methods and primitive models of ionic liquids do not capture many of the trends observed in the present study

NASCAP simulation of PIX 2 experiments

NASA Technical Reports Server (NTRS)

Roche, J. C.; Mandell, M. J.

1985-01-01

The latest version of the NASCAP/LEO digital computer code used to simulate the PIX 2 experiment is discussed. NASCAP is a finite-element code and previous versions were restricted to a single fixed mesh size. As a consequence the resolution was dictated by the largest physical dimension to be modeled. The latest version of NASCAP/LEO can subdivide selected regions. This permitted the modeling of the overall Delta launch vehicle in the primary computational grid at a coarse resolution, with subdivided regions at finer resolution being used to pick up the details of the experiment module configuration. Langmuir probe data from the flight were used to estimate the space plasma density and temperature and the Delta ground potential relative to the space plasma. This information is needed for input to NASCAP. Because of the uncertainty or variability in the values of these parameters, it was necessary to explore a range around the nominal value in order to determine the variation in current collection. The flight data from PIX 2 were also compared with the results of the NASCAP simulation.

A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes

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

Chacón, Enrique, E-mail: echacon@icmm.csic.es; Tarazona, Pedro, E-mail: pedro.tarazona@uam.es; Bresme, Fernando, E-mail: f.bresme@imperial.ac.uk

We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributionsmore » related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke’s law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.« less

Computational Fluid Dynamics Investigation of Human Aspiration in Low Velocity Air: Orientation Effects on Nose-Breathing Simulations

PubMed Central

Anderson, Kimberly R.; Anthony, T. Renée

2014-01-01

An understanding of how particles are inhaled into the human nose is important for developing samplers that measure biologically relevant estimates of exposure in the workplace. While previous computational mouth-breathing investigations of particle aspiration have been conducted in slow moving air, nose breathing still required exploration. Computational fluid dynamics was used to estimate nasal aspiration efficiency for an inhaling humanoid form in low velocity wind speeds (0.1–0.4 m s−1). Breathing was simplified as continuous inhalation through the nose. Fluid flow and particle trajectories were simulated over seven discrete orientations relative to the oncoming wind (0, 15, 30, 60, 90, 135, 180°). Sensitivities of the model simplification and methods were assessed, particularly the placement of the recessed nostril surface and the size of the nose. Simulations identified higher aspiration (13% on average) when compared to published experimental wind tunnel data. Significant differences in aspiration were identified between nose geometry, with the smaller nose aspirating an average of 8.6% more than the larger nose. Differences in fluid flow solution methods accounted for 2% average differences, on the order of methodological uncertainty. Similar trends to mouth-breathing simulations were observed including increasing aspiration efficiency with decreasing freestream velocity and decreasing aspiration with increasing rotation away from the oncoming wind. These models indicate nasal aspiration in slow moving air occurs only for particles <100 µm. PMID:24665111

An assessment of the potential of PFEM-2 for solving long real-time industrial applications

NASA Astrophysics Data System (ADS)

Gimenez, Juan M.; Ramajo, Damián E.; Márquez Damián, Santiago; Nigro, Norberto M.; Idelsohn, Sergio R.

2017-07-01

The latest generation of the particle finite element method (PFEM-2) is a numerical method based on the Lagrangian formulation of the equations, which presents advantages in terms of robustness and efficiency over classical Eulerian methodologies when certain kind of flows are simulated, especially those where convection plays an important role. These situations are often encountered in real engineering problems, where very complex geometries and operating conditions require very large and long computations. The advantages that the parallelism introduced in the computational fluid dynamics making affordable computations with very fine spatial discretizations are well known. However, it is not possible to have the time parallelized, despite the effort that is being dedicated to use space-time formulations. In this sense, PFEM-2 adds a valuable feature in that its strong stability with little loss of accuracy provides an interesting way of satisfying the real-life computation needs. After having already demonstrated in previous publications its ability to achieve academic-based solutions with a good compromise between accuracy and efficiency, in this work, the method is revisited and employed to solve several nonacademic problems of technological interest, which fall into that category. Simulations concerning oil-water separation, waste-water treatment, metallurgical foundries, and safety assessment are presented. These cases are selected due to their particular requirements of long simulation times and or intensive interface treatment. Thus, large time-steps may be employed with PFEM-2 without compromising the accuracy and robustness of the simulation, as occurs with Eulerian alternatives, showing the potentiality of the methodology for solving not only academic tests but also real engineering problems.

Development of a high resolution voxelised head phantom for medical physics applications.

PubMed

Giacometti, V; Guatelli, S; Bazalova-Carter, M; Rosenfeld, A B; Schulte, R W

2017-01-01

Computational anthropomorphic phantoms have become an important investigation tool for medical imaging and dosimetry for radiotherapy and radiation protection. The development of computational phantoms with realistic anatomical features contribute significantly to the development of novel methods in medical physics. For many applications, it is desirable that such computational phantoms have a real-world physical counterpart in order to verify the obtained results. In this work, we report the development of a voxelised phantom, the HIGH_RES_HEAD, modelling a paediatric head based on the commercial phantom 715-HN (CIRS). HIGH_RES_HEAD is unique for its anatomical details and high spatial resolution (0.18×0.18mm 2 pixel size). The development of such a phantom was required to investigate the performance of a new proton computed tomography (pCT) system, in terms of detector technology and image reconstruction algorithms. The HIGH_RES_HEAD was used in an ad-hoc Geant4 simulation modelling the pCT system. The simulation application was previously validated with respect to experimental results. When compared to a standard spatial resolution voxelised phantom of the same paediatric head, it was shown that in pCT reconstruction studies, the use of the HIGH_RES_HEAD translates into a reduction from 2% to 0.7% of the average relative stopping power difference between experimental and simulated results thus improving the overall quality of the head phantom simulation. The HIGH_RES_HEAD can also be used for other medical physics applications such as treatment planning studies. A second version of the voxelised phantom was created that contains a prototypic base of skull tumour and surrounding organs at risk. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Percutaneous spinal fixation simulation with virtual reality and haptics.

PubMed

Luciano, Cristian J; Banerjee, P Pat; Sorenson, Jeffery M; Foley, Kevin T; Ansari, Sameer A; Rizzi, Silvio; Germanwala, Anand V; Kranzler, Leonard; Chittiboina, Prashant; Roitberg, Ben Z

2013-01-01

In this study, we evaluated the use of a part-task simulator with 3-dimensional and haptic feedback as a training tool for percutaneous spinal needle placement. To evaluate the learning effectiveness in terms of entry point/target point accuracy of percutaneous spinal needle placement on a high-performance augmented-reality and haptic technology workstation with the ability to control the duration of computer-simulated fluoroscopic exposure, thereby simulating an actual situation. Sixty-three fellows and residents performed needle placement on the simulator. A virtual needle was percutaneously inserted into a virtual patient's thoracic spine derived from an actual patient computed tomography data set. Ten of 126 needle placement attempts by 63 participants ended in failure for a failure rate of 7.93%. From all 126 needle insertions, the average error (15.69 vs 13.91), average fluoroscopy exposure (4.6 vs 3.92), and average individual performance score (32.39 vs 30.71) improved from the first to the second attempt. Performance accuracy yielded P = .04 from a 2-sample t test in which the rejected null hypothesis assumes no improvement in performance accuracy from the first to second attempt in the test session. The experiments showed evidence (P = .04) of performance accuracy improvement from the first to the second percutaneous needle placement attempt. This result, combined with previous learning retention and/or face validity results of using the simulator for open thoracic pedicle screw placement and ventriculostomy catheter placement, supports the efficacy of augmented reality and haptics simulation as a learning tool.

Simulation of automatic precision departures and missed approaches using the microwave landing system

NASA Technical Reports Server (NTRS)

Feather, J. B.

1987-01-01

Results of simulated precision departures and missed approaches using MLS guidance concepts are presented. The study was conducted under the Terminal Configured Vehicle (TCV) Program, and is an extension of previous work by DAC under the Advanced Transport Operating System (ATOPS) Technology Studies Program. The study model included simulation of an MD-80 aircraft, an autopilot, and a MLS guidance computer that provided lateral and vertical steering commands. Precision departures were evaluated using a noise abatement procedure. Several curved path departures were simulated with MLS noise and under various environmental conditions. Missed approaches were considered for the same runway, where lateral MLS guidance maintained the aircraft along the extended runway centerline. In both the departures and the missed approach cases, pitch autopilot takeoff and go-around modes of operation were used in conjunction with MLS lateral guidance.

Numerical study of rotating detonation engine with an array of injection holes

NASA Astrophysics Data System (ADS)

Yao, S.; Han, X.; Liu, Y.; Wang, J.

2017-05-01

This paper aims to adopt the method of injection via an array of holes in three-dimensional numerical simulations of a rotating detonation engine (RDE). The calculation is based on the Euler equations coupled with a one-step Arrhenius chemistry model. A pre-mixed stoichiometric hydrogen-air mixture is used. The present study uses a more practical fuel injection method in RDE simulations, injection via an array of holes, which is different from the previous conventional simulations where a relatively simple full injection method is usually adopted. The computational results capture some important experimental observations and a transient period after initiation. These phenomena are usually absent in conventional RDE simulations due to the use of an idealistic injection approximation. The results are compared with those obtained from other numerical studies and experiments with RDEs.

On Fast Post-Processing of Global Positioning System Simulator Truth Data and Receiver Measurements and Solutions Data

NASA Technical Reports Server (NTRS)

Kizhner, Semion; Day, John H. (Technical Monitor)

2000-01-01

Post-Processing of data related to a Global Positioning System (GPS) simulation is an important activity in qualification of a GPS receiver for space flight. Because a GPS simulator is a critical resource it is desirable to move off the pertinent simulation data from the simulator as soon as a test is completed. The simulator data files are usually moved to a Personal Computer (PC), where the post-processing of the receiver logged measurements and solutions data and simulated data is performed. Typically post-processing is accomplished using PC-based commercial software languages and tools. Because of commercial software systems generality their general-purpose functions are notoriously slow and more than often are the bottleneck problem even for short duration experiments. For example, it may take 8 hours to post-process data from a 6-hour simulation. There is a need to do post-processing faster, especially in order to use the previous test results as feedback for a next simulation setup. This paper demonstrates that a fast software linear interpolation algorithm is applicable to a large class of engineering problems, like GPS simulation data post-processing, where computational time is a critical resource and is one of the most important considerations. An approach is developed that allows to speed-up post-processing by an order of magnitude. It is based on improving the post-processing bottleneck interpolation algorithm using apriori information that is specific to the GPS simulation application. The presented post-processing scheme was used in support of a few successful space flight missions carrying GPS receivers. A future approach to solving the post-processing performance problem using Field Programmable Gate Array (FPGA) technology is described.

An attempt of modelling debris flows characterised by strong inertial effects through Cellular Automata

NASA Astrophysics Data System (ADS)

Iovine, G.; D'Ambrosio, D.

2003-04-01

Cellular Automata models do represent a valid method for the simulation of complex phenomena, when these latter can be described in "a-centric" terms - i.e. through local interactions within a discrete time-space. In particular, flow-type landslides (such as debris flows) can be viewed as a-centric dynamical system. SCIDDICA S4b, the last release of a family of two-dimensional hexagonal Cellular Automata models, has recently been developed for simulating debris flows characterised by strong inertial effects. It has been derived by progressively enriching an initial simplified CA model, originally derived for simulating very simple cases of slow-moving flow-type landslides. In S4b, by applying an empirical strategy, the inertial characters of the flowing mass have been translated into CA terms. In the transition function of the model, the distribution of landslide debris among the cells is computed by considering the momentum of the debris which move among the cells of the neighbourhood, and privileging the flow direction. By properly setting the value of one of the global parameters of the model (the "inertial factor"), the mechanism of distribution of the landslide debris among the cells can be influenced in order to emphasise the inertial effects, according to the energy of the flowing mass. Moreover, the high complexity of both the model and of the phenomena to be simulated (e.g. debris flows characterised by severe erosion along their path, and by strong inertial effects) suggested to employ an automated technique of evaluation, for the determination of the best set of global parameters. Accordingly, the calibration of the model has been performed through Genetic Algorithms, by considering several real cases of study: these latter have been selected among the population of landslides triggered in Campania (Southern Italy) in May 1998 and December 1999. Obtained results are satisfying: errors computed by comparing the simulations with the map of the real landslides are smaller than those previously obtained either through previous releases of the same model or without Genetic Algorithms. Nevertheless, results are still only preliminary, as the experiments have been realised in sequential computing environment. A more efficient calibration of the model would certainly be possible by adopting a parallel environment of computing, as a great number of tests could be performed in reasonable times; moreover, the parameters' optimisation could be realised in wider ranges, and in greater detail.

Accelerated Enveloping Distribution Sampling: Enabling Sampling of Multiple End States while Preserving Local Energy Minima.

PubMed

Perthold, Jan Walther; Oostenbrink, Chris

2018-05-17

Enveloping distribution sampling (EDS) is an efficient approach to calculate multiple free-energy differences from a single molecular dynamics (MD) simulation. However, the construction of an appropriate reference-state Hamiltonian that samples all states efficiently is not straightforward. We propose a novel approach for the construction of the EDS reference-state Hamiltonian, related to a previously described procedure to smoothen energy landscapes. In contrast to previously suggested EDS approaches, our reference-state Hamiltonian preserves local energy minima of the combined end-states. Moreover, we propose an intuitive, robust and efficient parameter optimization scheme to tune EDS Hamiltonian parameters. We demonstrate the proposed method with established and novel test systems and conclude that our approach allows for the automated calculation of multiple free-energy differences from a single simulation. Accelerated EDS promises to be a robust and user-friendly method to compute free-energy differences based on solid statistical mechanics.

A breakthrough for experiencing and understanding simulated physics

NASA Technical Reports Server (NTRS)

Watson, Val

1988-01-01

The use of computer simulation in physics research is discussed, focusing on improvements to graphic workstations. Simulation capabilities and applications of enhanced visualization tools are outlined. The elements of an ideal computer simulation are presented and the potential for improving various simulation elements is examined. The interface between the human and the computer and simulation models are considered. Recommendations are made for changes in computer simulation practices and applications of simulation technology in education.

MaMiCo: Transient multi-instance molecular-continuum flow simulation on supercomputers

NASA Astrophysics Data System (ADS)

Neumann, Philipp; Bian, Xin

2017-11-01

We present extensions of the macro-micro-coupling tool MaMiCo, which was designed to couple continuum fluid dynamics solvers with discrete particle dynamics. To enable local extraction of smooth flow field quantities especially on rather short time scales, sampling over an ensemble of molecular dynamics simulations is introduced. We provide details on these extensions including the transient coupling algorithm, open boundary forcing, and multi-instance sampling. Furthermore, we validate the coupling in Couette flow using different particle simulation software packages and particle models, i.e. molecular dynamics and dissipative particle dynamics. Finally, we demonstrate the parallel scalability of the molecular-continuum simulations by using up to 65 536 compute cores of the supercomputer Shaheen II located at KAUST. Program Files doi:http://dx.doi.org/10.17632/w7rgdrhb85.1 Licensing provisions: BSD 3-clause Programming language: C, C++ External routines/libraries: For compiling: SCons, MPI (optional) Subprograms used: ESPResSo, LAMMPS, ls1 mardyn, waLBerla For installation procedures of the MaMiCo interfaces, see the README files in the respective code directories located in coupling/interface/impl. Journal reference of previous version: P. Neumann, H. Flohr, R. Arora, P. Jarmatz, N. Tchipev, H.-J. Bungartz. MaMiCo: Software design for parallel molecular-continuum flow simulations, Computer Physics Communications 200: 324-335, 2016 Does the new version supersede the previous version?: Yes. The functionality of the previous version is completely retained in the new version. Nature of problem: Coupled molecular-continuum simulation for multi-resolution fluid dynamics: parts of the domain are resolved by molecular dynamics or another particle-based solver whereas large parts are covered by a mesh-based CFD solver, e.g. a lattice Boltzmann automaton. Solution method: We couple existing MD and CFD solvers via MaMiCo (macro-micro coupling tool). Data exchange and coupling algorithmics are abstracted and incorporated in MaMiCo. Once an algorithm is set up in MaMiCo, it can be used and extended, even if other solvers are used (as soon as the respective interfaces are implemented/available). Reasons for the new version: We have incorporated a new algorithm to simulate transient molecular-continuum systems and to automatically sample data over multiple MD runs that can be executed simultaneously (on, e.g., a compute cluster). MaMiCo has further been extended by an interface to incorporate boundary forcing to account for open molecular dynamics boundaries. Besides support for coupling with various MD and CFD frameworks, the new version contains a test case that allows to run molecular-continuum Couette flow simulations out-of-the-box. No external tools or simulation codes are required anymore. However, the user is free to switch from the included MD simulation package to LAMMPS. For details on how to run the transient Couette problem, see the file README in the folder coupling/tests, Remark on MaMiCo V1.1. Summary of revisions: Open boundary forcing; Multi-instance MD sampling; support for transient molecular-continuum systems Restrictions: Currently, only single-centered systems are supported. For access to the LAMMPS-based implementation of DPD boundary forcing, please contact Xin Bian, xin.bian@tum.de. Additional comments: Please see file license_mamico.txt for further details regarding distribution and advertising of this software.

Symplectic molecular dynamics simulations on specially designed parallel computers.

PubMed

Borstnik, Urban; Janezic, Dusanka

2005-01-01

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

Cortical circuitry implementing graphical models.

PubMed

Litvak, Shai; Ullman, Shimon

2009-11-01

In this letter, we develop and simulate a large-scale network of spiking neurons that approximates the inference computations performed by graphical models. Unlike previous related schemes, which used sum and product operations in either the log or linear domains, the current model uses an inference scheme based on the sum and maximization operations in the log domain. Simulations show that using these operations, a large-scale circuit, which combines populations of spiking neurons as basic building blocks, is capable of finding close approximations to the full mathematical computations performed by graphical models within a few hundred milliseconds. The circuit is general in the sense that it can be wired for any graph structure, it supports multistate variables, and it uses standard leaky integrate-and-fire neuronal units. Following previous work, which proposed relations between graphical models and the large-scale cortical anatomy, we focus on the cortical microcircuitry and propose how anatomical and physiological aspects of the local circuitry may map onto elements of the graphical model implementation. We discuss in particular the roles of three major types of inhibitory neurons (small fast-spiking basket cells, large layer 2/3 basket cells, and double-bouquet neurons), subpopulations of strongly interconnected neurons with their unique connectivity patterns in different cortical layers, and the possible role of minicolumns in the realization of the population-based maximum operation.

Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution.

PubMed

Abolfath, Ramin M; Biswas, P K; Rajnarayanam, R; Brabec, Thomas; Kodym, Reinhard; Papiez, Lech

2012-04-19

Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic-spin-dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid quantum mechanical-molecular mechanical simulation to study the interaction of OH radicals with a guanine-deoxyribose-phosphate DNA molecular unit in the presence of water, where all of the water molecules and the deoxyribose-phosphate fragment are treated with the simplistic classical molecular mechanical scheme. Our result illustrates that the presence of water strongly alters the hydrogen-abstraction reaction as the hydrogen bonding of OH radicals with water restricts the relative orientation of the OH radicals with respect to the DNA base (here, guanine). This results in an angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen-abstraction mechanisms than previously anticipated for identical systems in vacuum. The method can easily be extended to single- and double-stranded DNA without any appreciable computational cost as these molecular units can be treated in the classical subsystem, as has been demonstrated here. © 2012 American Chemical Society

Computational investigation of potential dosing schedules for a switch of medication from warfarin to rivaroxaban—an oral, direct Factor Xa inhibitor

PubMed Central

Burghaus, Rolf; Coboeken, Katrin; Gaub, Thomas; Niederalt, Christoph; Sensse, Anke; Siegmund, Hans-Ulrich; Weiss, Wolfgang; Mueck, Wolfgang; Tanigawa, Takahiko; Lippert, Jörg

2014-01-01

The long-lasting anticoagulant effect of vitamin K antagonists can be problematic in cases of adverse drug reactions or when patients are switched to another anticoagulant therapy. The objective of this study was to examine in silico the anticoagulant effect of rivaroxaban, an oral, direct Factor Xa inhibitor, combined with the residual effect of discontinued warfarin. Our simulations were based on the recommended anticoagulant dosing regimen for stroke prevention in patients with atrial fibrillation. The effects of the combination of discontinued warfarin plus rivaroxaban were simulated using an extended version of a previously validated blood coagulation computer model. A strong synergistic effect of the two distinct mechanisms of action was observed in the first 2–3 days after warfarin discontinuation; thereafter, the effect was close to additive. Nomograms for the introduction of rivaroxaban therapy after warfarin discontinuation were derived for Caucasian and Japanese patients using safety and efficacy criteria described previously, together with the coagulation model. The findings of our study provide a mechanistic pharmacologic rationale for dosing schedules during the therapy switch from warfarin to rivaroxaban and support the switching strategies as outlined in the Summary of Product Characteristics and Prescribing Information for rivaroxaban. PMID:25426077

Computational investigation of potential dosing schedules for a switch of medication from warfarin to rivaroxaban-an oral, direct Factor Xa inhibitor.

PubMed

Burghaus, Rolf; Coboeken, Katrin; Gaub, Thomas; Niederalt, Christoph; Sensse, Anke; Siegmund, Hans-Ulrich; Weiss, Wolfgang; Mueck, Wolfgang; Tanigawa, Takahiko; Lippert, Jörg

2014-01-01

The long-lasting anticoagulant effect of vitamin K antagonists can be problematic in cases of adverse drug reactions or when patients are switched to another anticoagulant therapy. The objective of this study was to examine in silico the anticoagulant effect of rivaroxaban, an oral, direct Factor Xa inhibitor, combined with the residual effect of discontinued warfarin. Our simulations were based on the recommended anticoagulant dosing regimen for stroke prevention in patients with atrial fibrillation. The effects of the combination of discontinued warfarin plus rivaroxaban were simulated using an extended version of a previously validated blood coagulation computer model. A strong synergistic effect of the two distinct mechanisms of action was observed in the first 2-3 days after warfarin discontinuation; thereafter, the effect was close to additive. Nomograms for the introduction of rivaroxaban therapy after warfarin discontinuation were derived for Caucasian and Japanese patients using safety and efficacy criteria described previously, together with the coagulation model. The findings of our study provide a mechanistic pharmacologic rationale for dosing schedules during the therapy switch from warfarin to rivaroxaban and support the switching strategies as outlined in the Summary of Product Characteristics and Prescribing Information for rivaroxaban.

Adapting to life: ocean biogeochemical modelling and adaptive remeshing

NASA Astrophysics Data System (ADS)

Hill, J.; Popova, E. E.; Ham, D. A.; Piggott, M. D.; Srokosz, M.

2014-05-01

An outstanding problem in biogeochemical modelling of the ocean is that many of the key processes occur intermittently at small scales, such as the sub-mesoscale, that are not well represented in global ocean models. This is partly due to their failure to resolve sub-mesoscale phenomena, which play a significant role in vertical nutrient supply. Simply increasing the resolution of the models may be an inefficient computational solution to this problem. An approach based on recent advances in adaptive mesh computational techniques may offer an alternative. Here the first steps in such an approach are described, using the example of a simple vertical column (quasi-1-D) ocean biogeochemical model. We present a novel method of simulating ocean biogeochemical behaviour on a vertically adaptive computational mesh, where the mesh changes in response to the biogeochemical and physical state of the system throughout the simulation. We show that the model reproduces the general physical and biological behaviour at three ocean stations (India, Papa and Bermuda) as compared to a high-resolution fixed mesh simulation and to observations. The use of an adaptive mesh does not increase the computational error, but reduces the number of mesh elements by a factor of 2-3. Unlike previous work the adaptivity metric used is flexible and we show that capturing the physical behaviour of the model is paramount to achieving a reasonable solution. Adding biological quantities to the adaptivity metric further refines the solution. We then show the potential of this method in two case studies where we change the adaptivity metric used to determine the varying mesh sizes in order to capture the dynamics of chlorophyll at Bermuda and sinking detritus at Papa. We therefore demonstrate that adaptive meshes may provide a suitable numerical technique for simulating seasonal or transient biogeochemical behaviour at high vertical resolution whilst minimising the number of elements in the mesh. More work is required to move this to fully 3-D simulations.

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

PubMed Central

Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

2013-01-01

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

Virtual geotechnical laboratory experiments using a simulator

NASA Astrophysics Data System (ADS)

Penumadu, Dayakar; Zhao, Rongda; Frost, David

2000-04-01

The details of a test simulator that provides a realistic environment for performing virtual laboratory experimentals in soil mechanics is presented. A computer program Geo-Sim that can be used to perform virtual experiments, and allow for real-time observations of material response is presented. The results of experiments, for a given set of input parameters, are obtained with the test simulator using well-trained artificial neural-network-based soil models for different soil types and stress paths. Multimedia capabilities are integrated in Geo-Sim, using software that links and controls a laser disc player with a real-time parallel processing ability. During the simulation of a virtual experiment, relevant portions of the video image of a previously recorded test on an actual soil specimen are dispalyed along with the graphical presentation of response from the feedforward ANN model predictions. The pilot simulator developed to date includes all aspects related to performing a triaxial test on cohesionless soil under undrained and drained conditions. The benefits of the test simulator are also presented.

Numerical simulation of controlled directional solidification under microgravity conditions

NASA Astrophysics Data System (ADS)

Holl, S.; Roos, D.; Wein, J.

The computer-assisted simulation of solidification processes influenced by gravity has gained increased importance during the previous years regarding ground-based as well as microgravity research. Depending on the specific needs of the investigator, the simulation model ideally covers a broad spectrum of applications. These primarily include the optimization of furnace design in interaction with selected process parameters to meet the desired crystallization conditions. Different approaches concerning the complexity of the simulation models as well as their dedicated applications will be discussed in this paper. Special emphasis will be put on the potential of software tools to increase the scientific quality and cost-efficiency of microgravity experimentation. The results gained so far in the context of TEXUS, FSLP, D-1 and D-2 (preparatory program) experiments, highlighting their simulation-supported preparation and evaluation will be discussed. An outlook will then be given on the possibilities to enhance the efficiency of pre-industrial research in the Columbus era through the incorporation of suitable simulation methods and tools.

Secure multiparty computation of a comparison problem.

PubMed

Liu, Xin; Li, Shundong; Liu, Jian; Chen, Xiubo; Xu, Gang

2016-01-01

Private comparison is fundamental to secure multiparty computation. In this study, we propose novel protocols to privately determine [Formula: see text], or [Formula: see text] in one execution. First, a 0-1-vector encoding method is introduced to encode a number into a vector, and the Goldwasser-Micali encryption scheme is used to compare integers privately. Then, we propose a protocol by using a geometric method to compare rational numbers privately, and the protocol is information-theoretical secure. Using the simulation paradigm, we prove the privacy-preserving property of our protocols in the semi-honest model. The complexity analysis shows that our protocols are more efficient than previous solutions.

Computer modeling of batteries from nonlinear circuit elements

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

Waaben, S.; Dyer, C.K.; Federico, J.

1985-06-01

Circuit analogs for a single battery cell have previously been composed of resistors, capacitors, and inductors. This work introduces a nonlinear circuit model for cell behavior. The circuit is configured around the PIN junction diode, whose charge-storage behavior has features similar to those of electrochemical cells. A user-friendly integrated circuit simulation computer program has reproduced a variety of complex cell responses including electrica isolation effects causing capacity loss, as well as potentiodynamic peaks and discharge phenomena hitherto thought to be thermodynamic in origin. However, in this work, they are shown to be simply due to spatial distribution of stored chargemore » within a practical electrode.« less

Development of a thermal storage module using modified anhydrous sodium hydroxide

NASA Technical Reports Server (NTRS)

Rice, R. E.; Rowny, P. E.

1980-01-01

The laboratory scale testing of a modified anhydrous NaOH latent heat storage concept for small solar thermal power systems such as total energy systems utilizing organic Rankine systems is discussed. A diagnostic test on the thermal energy storage module and an investigation of alternative heat transfer fluids and heat exchange concepts are specifically addressed. A previously developed computer simulation model is modified to predict the performance of the module in a solar total energy system environment. In addition, the computer model is expanded to investigate parametrically the incorporation of a second heat exchange inside the module which will vaporize and superheat the Rankine cycle power fluid.

A fast, parallel algorithm for distant-dependent calculation of crystal properties

NASA Astrophysics Data System (ADS)

Stein, Matthew

2017-12-01

A fast, parallel algorithm for distant-dependent calculation and simulation of crystal properties is presented along with speedup results and methods of application. An illustrative example is used to compute the Lennard-Jones lattice constants up to 32 significant figures for 4 ≤ p ≤ 30 in the simple cubic, face-centered cubic, body-centered cubic, hexagonal-close-pack, and diamond lattices. In most cases, the known precision of these constants is more than doubled, and in some cases, corrected from previously published figures. The tools and strategies to make this computation possible are detailed along with application to other potentials, including those that model defects.

FUN3D Airload Predictions for the Full-Scale UH-60A Airloads Rotor in a Wind Tunnel

NASA Technical Reports Server (NTRS)

Lee-Rausch, Elizabeth M.; Biedron, Robert T.

2013-01-01

An unsteady Reynolds-Averaged Navier-Stokes solver for unstructured grids, FUN3D, is used to compute the rotor performance and airloads of the UH-60A Airloads Rotor in the National Full-Scale Aerodynamic Complex (NFAC) 40- by 80-foot Wind Tunnel. The flow solver is loosely coupled to a rotorcraft comprehensive code, CAMRAD-II, to account for trim and aeroelastic deflections. Computations are made for the 1-g level flight speed-sweep test conditions with the airloads rotor installed on the NFAC Large Rotor Test Apparatus (LRTA) and in the 40- by 80-ft wind tunnel to determine the influence of the test stand and wind-tunnel walls on the rotor performance and airloads. Detailed comparisons are made between the results of the CFD/CSD simulations and the wind tunnel measurements. The computed trends in solidity-weighted propulsive force and power coefficient match the experimental trends over the range of advance ratios and are comparable to previously published results. Rotor performance and sectional airloads show little sensitivity to the modeling of the wind-tunnel walls, which indicates that the rotor shaft-angle correction adequately compensates for the wall influence up to an advance ratio of 0.37. Sensitivity of the rotor performance and sectional airloads to the modeling of the rotor with the LRTA body/hub increases with advance ratio. The inclusion of the LRTA in the simulation slightly improves the comparison of rotor propulsive force between the computation and wind tunnel data but does not resolve the difference in the rotor power predictions at mu = 0.37. Despite a more precise knowledge of the rotor trim loads and flight condition, the level of comparison between the computed and measured sectional airloads/pressures at an advance ratio of 0.37 is comparable to the results previously published for the high-speed flight test condition.

Theory, Image Simulation, and Data Analysis of Chemical Release Experiments

NASA Technical Reports Server (NTRS)

Wescott, Eugene M.

1994-01-01

The final phase of Grant NAG6-1 involved analysis of physics of chemical releases in the upper atmosphere and analysis of data obtained on previous NASA sponsored chemical release rocket experiments. Several lines of investigation of past chemical release experiments and computer simulations have been proceeding in parallel. This report summarizes the work performed and the resulting publications. The following topics are addressed: analysis of the 1987 Greenland rocket experiments; calculation of emission rates for barium, strontium, and calcium; the CRIT 1 and 2 experiments (Collisional Ionization Cross Section experiments); image calibration using background stars; rapid ray motions in ionospheric plasma clouds; and the NOONCUSP rocket experiments.

Optimal temperature ladders in replica exchange simulations

NASA Astrophysics Data System (ADS)

Denschlag, Robert; Lingenheil, Martin; Tavan, Paul

2009-04-01

In replica exchange simulations, a temperature ladder with N rungs spans a given temperature interval. Considering systems with heat capacities independent of the temperature, here we address the question of how large N should be chosen for an optimally fast diffusion of the replicas through the temperature space. Using a simple example we show that choosing average acceptance probabilities of about 45% and computing N accordingly maximizes the round trip rates r across the given temperature range. This result differs from previous analyses which suggested smaller average acceptance probabilities of about 23%. We show that the latter choice maximizes the ratio r/N instead of r.

Finite Larmor radius effects on the (m = 2, n = 1) cylindrical tearing mode

NASA Astrophysics Data System (ADS)

Chen, Y.; Chowdhury, J.; Parker, S. E.; Wan, W.

2015-04-01

New field solvers are developed in the gyrokinetic code GEM [Chen and Parker, J. Comput. Phys. 220, 839 (2007)] to simulate low-n modes. A novel discretization is developed for the ion polarization term in the gyrokinetic vorticity equation. An eigenmode analysis with finite Larmor radius effects is developed to study the linear resistive tearing mode. The mode growth rate is shown to scale with resistivity as γ ˜ η1/3, the same as the semi-collisional regime in previous kinetic treatments [Drake and Lee, Phys. Fluids 20, 1341 (1977)]. Tearing mode simulations with gyrokinetic ions are verified with the eigenmode calculation.

Cloud computing and validation of expandable in silico livers

PubMed Central

2010-01-01

Background In Silico Livers (ISLs) are works in progress. They are used to challenge multilevel, multi-attribute, mechanistic hypotheses about the hepatic disposition of xenobiotics coupled with hepatic responses. To enhance ISL-to-liver mappings, we added discrete time metabolism, biliary elimination, and bolus dosing features to a previously validated ISL and initiated re-validated experiments that required scaling experiments to use more simulated lobules than previously, more than could be achieved using the local cluster technology. Rather than dramatically increasing the size of our local cluster we undertook the re-validation experiments using the Amazon EC2 cloud platform. So doing required demonstrating the efficacy of scaling a simulation to use more cluster nodes and assessing the scientific equivalence of local cluster validation experiments with those executed using the cloud platform. Results The local cluster technology was duplicated in the Amazon EC2 cloud platform. Synthetic modeling protocols were followed to identify a successful parameterization. Experiment sample sizes (number of simulated lobules) on both platforms were 49, 70, 84, and 152 (cloud only). Experimental indistinguishability was demonstrated for ISL outflow profiles of diltiazem using both platforms for experiments consisting of 84 or more samples. The process was analogous to demonstration of results equivalency from two different wet-labs. Conclusions The results provide additional evidence that disposition simulations using ISLs can cover the behavior space of liver experiments in distinct experimental contexts (there is in silico-to-wet-lab phenotype similarity). The scientific value of experimenting with multiscale biomedical models has been limited to research groups with access to computer clusters. The availability of cloud technology coupled with the evidence of scientific equivalency has lowered the barrier and will greatly facilitate model sharing as well as provide straightforward tools for scaling simulations to encompass greater detail with no extra investment in hardware. PMID:21129207

GFDL's unified regional-global weather-climate modeling system with variable resolution capability for severe weather predictions and regional climate simulations

NASA Astrophysics Data System (ADS)

Lin, S. J.

2015-12-01

The NOAA/Geophysical Fluid Dynamics Laboratory has been developing a unified regional-global modeling system with variable resolution capabilities that can be used for severe weather predictions (e.g., tornado outbreak events and cat-5 hurricanes) and ultra-high-resolution (1-km) regional climate simulations within a consistent global modeling framework. The fundation of this flexible regional-global modeling system is the non-hydrostatic extension of the vertically Lagrangian dynamical core (Lin 2004, Monthly Weather Review) known in the community as FV3 (finite-volume on the cubed-sphere). Because of its flexability and computational efficiency, the FV3 is one of the final candidates of NOAA's Next Generation Global Prediction System (NGGPS). We have built into the modeling system a stretched (single) grid capability, a two-way (regional-global) multiple nested grid capability, and the combination of the stretched and two-way nests, so as to make convection-resolving regional climate simulation within a consistent global modeling system feasible using today's High Performance Computing System. One of our main scientific goals is to enable simulations of high impact weather phenomena (such as tornadoes, thunderstorms, category-5 hurricanes) within an IPCC-class climate modeling system previously regarded as impossible. In this presentation I will demonstrate that it is computationally feasible to simulate not only super-cell thunderstorms, but also the subsequent genesis of tornadoes using a global model that was originally designed for century long climate simulations. As a unified weather-climate modeling system, we evaluated the performance of the model with horizontal resolution ranging from 1 km to as low as 200 km. In particular, for downscaling studies, we have developed various tests to ensure that the large-scale circulation within the global varaible resolution system is well simulated while at the same time the small-scale can be accurately captured within the targeted high resolution region.

Development of Efficient Real-Fluid Model in Simulating Liquid Rocket Injector Flows

NASA Technical Reports Server (NTRS)

Cheng, Gary; Farmer, Richard

2003-01-01

The characteristics of propellant mixing near the injector have a profound effect on the liquid rocket engine performance. However, the flow features near the injector of liquid rocket engines are extremely complicated, for example supercritical-pressure spray, turbulent mixing, and chemical reactions are present. Previously, a homogeneous spray approach with a real-fluid property model was developed to account for the compressibility and evaporation effects such that thermodynamics properties of a mixture at a wide range of pressures and temperatures can be properly calculated, including liquid-phase, gas- phase, two-phase, and dense fluid regions. The developed homogeneous spray model demonstrated a good success in simulating uni- element shear coaxial injector spray combustion flows. However, the real-fluid model suffered a computational deficiency when applied to a pressure-based computational fluid dynamics (CFD) code. The deficiency is caused by the pressure and enthalpy being the independent variables in the solution procedure of a pressure-based code, whereas the real-fluid model utilizes density and temperature as independent variables. The objective of the present research work is to improve the computational efficiency of the real-fluid property model in computing thermal properties. The proposed approach is called an efficient real-fluid model, and the improvement of computational efficiency is achieved by using a combination of a liquid species and a gaseous species to represent a real-fluid species.

Space-Time Conservation Element and Solution Element Method Being Developed

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Holographic Reciprocity Law Failure, with Applications to the Three-Dimensional Display of Medical Data

NASA Astrophysics Data System (ADS)

Johnson, Kristina Mary

In 1973 the computerized tomography (CT) scanner revolutionized medical imaging. This machine can isolate and display in two-dimensional cross-sections, internal lesions and organs previously impossible to visualize. The possibility of three-dimensional imaging however is not yet exploited by present tomographic systems. Using multiple-exposure holography, three-dimensional displays can be synthesizing from two-dimensional CT cross -sections. A multiple-exposure hologram is an incoherent superposition of many individual holograms. Intuitively it is expected that holograms recorded with equal energy will reconstruct images with equal brightness. It is found however, that holograms recorded first are brighter than holograms recorded later in the superposition. This phenomena is called Holographic Reciprocity Law Failure (HRLF). Computer simulations of latent image formation in multiple-exposure holography are one of the methods used to investigate HRLF. These simulations indicate that it is the time between individual exposures in the multiple -exposure hologram that is responsible for HRLF. This physical parameter introduces an asymmetry into the latent image formation process that favors the signal of previously recorded holograms over holograms recorded later in the superposition. The origin of this asymmetry lies in the dynamics of latent image formation, and in particular in the decay of single-atom latent image specks, which have lifetimes that are short compared to typical times between exposures. An analytical model is developed for a double exposure hologram that predicts a decrease in the brightness of the second exposure as compared to the first exposure as the time between exposures increases. These results are consistent with the computer simulations. Experiments investigating the influence of this parameter on the diffraction efficiency of reconstructed images in a double exposure hologram are also found to be consistent with the computer simulations and analytical results. From this information, two techniques are presented that correct for HRLF, and succeed in reconstructing multiple holographic images of CT cross-sections with equal brightness. The multiple multiple-exposure hologram is a new hologram that increases the number of equally bright images that can be superimposed on one photographic plate.

Ion transfer from an atmospheric pressure ion funnel into a mass spectrometer with different interface options: Simulation-based optimization of ion transmission efficiency.

PubMed

Mayer, Thomas; Borsdorf, Helko

2016-02-15

We optimized an atmospheric pressure ion funnel (APIF) including different interface options (pinhole, capillary, and nozzle) regarding a maximal ion transmission. Previous computer simulations consider the ion funnel itself and do not include the geometry of the following components which can considerably influence the ion transmission into the vacuum stage. Initially, a three-dimensional computer-aided design (CAD) model of our setup was created using Autodesk Inventor. This model was imported to the Autodesk Simulation CFD program where the computational fluid dynamics (CFD) were calculated. The flow field was transferred to SIMION 8.1. Investigations of ion trajectories were carried out using the SDS (statistical diffusion simulation) tool of SIMION, which allowed us to evaluate the flow regime, pressure, and temperature values that we obtained. The simulation-based optimization of different interfaces between an atmospheric pressure ion funnel and the first vacuum stage of a mass spectrometer require the consideration of fluid dynamics. The use of a Venturi nozzle ensures the highest level of transmission efficiency in comparison to capillaries or pinholes. However, the application of radiofrequency (RF) voltage and an appropriate direct current (DC) field leads to process optimization and maximum ion transfer. The nozzle does not hinder the transfer of small ions. Our high-resolution SIMION model (0.01 mm grid unit(-1) ) under consideration of fluid dynamics is generally suitable for predicting the ion transmission through an atmospheric-vacuum system for mass spectrometry and enables the optimization of operational parameters. A Venturi nozzle inserted between the ion funnel and the mass spectrometer permits maximal ion transmission. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Uncertainty-based simulation-optimization using Gaussian process emulation: Application to coastal groundwater management

NASA Astrophysics Data System (ADS)

Rajabi, Mohammad Mahdi; Ketabchi, Hamed

2017-12-01

Combined simulation-optimization (S/O) schemes have long been recognized as a valuable tool in coastal groundwater management (CGM). However, previous applications have mostly relied on deterministic seawater intrusion (SWI) simulations. This is a questionable simplification, knowing that SWI models are inevitably prone to epistemic and aleatory uncertainty, and hence a management strategy obtained through S/O without consideration of uncertainty may result in significantly different real-world outcomes than expected. However, two key issues have hindered the use of uncertainty-based S/O schemes in CGM, which are addressed in this paper. The first issue is how to solve the computational challenges resulting from the need to perform massive numbers of simulations. The second issue is how the management problem is formulated in presence of uncertainty. We propose the use of Gaussian process (GP) emulation as a valuable tool in solving the computational challenges of uncertainty-based S/O in CGM. We apply GP emulation to the case study of Kish Island (located in the Persian Gulf) using an uncertainty-based S/O algorithm which relies on continuous ant colony optimization and Monte Carlo simulation. In doing so, we show that GP emulation can provide an acceptable level of accuracy, with no bias and low statistical dispersion, while tremendously reducing the computational time. Moreover, five new formulations for uncertainty-based S/O are presented based on concepts such as energy distances, prediction intervals and probabilities of SWI occurrence. We analyze the proposed formulations with respect to their resulting optimized solutions, the sensitivity of the solutions to the intended reliability levels, and the variations resulting from repeated optimization runs.

Computational simulation of biomolecules transport with multi-physics near microchannel surface for development of biomolecules-detection devices.

PubMed

Suzuki, Yuma; Shimizu, Tetsuhide; Yang, Ming

2017-01-01

The quantitative evaluation of the biomolecules transport with multi-physics in nano/micro scale is demanded in order to optimize the design of microfluidics device for the biomolecules detection with high detection sensitivity and rapid diagnosis. This paper aimed to investigate the effectivity of the computational simulation using the numerical model of the biomolecules transport with multi-physics near a microchannel surface on the development of biomolecules-detection devices. The biomolecules transport with fluid drag force, electric double layer (EDL) force, and van der Waals force was modeled by Newtonian Equation of motion. The model validity was verified in the influence of ion strength and flow velocity on biomolecules distribution near the surface compared with experimental results of previous studies. The influence of acting forces on its distribution near the surface was investigated by the simulation. The trend of its distribution to ion strength and flow velocity was agreement with the experimental result by the combination of all acting forces. Furthermore, EDL force dominantly influenced its distribution near its surface compared with fluid drag force except for the case of high velocity and low ion strength. The knowledges from the simulation might be useful for the design of biomolecules-detection devices and the simulation can be expected to be applied on its development as the design tool for high detection sensitivity and rapid diagnosis in the future.

Solubility of NaCl in water by molecular simulation revisited.

PubMed

Aragones, J L; Sanz, E; Vega, C

2012-06-28

In this paper, the solubility of NaCl in water is evaluated by using computer simulations for three different force fields. The condition of chemical equilibrium (i.e., equal chemical potential of the salt in the solid and in the solution) is obtained at room temperature and pressure to determine the solubility of the salt. We used the same methodology that was described in our previous work [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] although several modifications were introduced to improve the accuracy of the calculations. It is found that the predictions of the solubility are quite sensitive to the details of the force field used. Certain force fields underestimate the experimental solubility of NaCl in water by a factor of four, whereas the predictions of other force fields are within 20% of the experimental value. Direct coexistence molecular dynamic simulations were also performed to determine the solubility of the salt. Reasonable agreement was found between the solubility obtained from free energy calculations and that obtained from direct coexistence simulations. This work shows that the evaluation of the solubility of salts in water can now be performed in computer simulations. The solubility depends on the ion-ion, ion-water, and water-water interactions. For this reason, the prediction of the solubility can be quite useful in future work to develop force fields for ions in water.

Modeling Real-Time Coordination of Distributed Expertise and Event Response in NASA Mission Control Center Operations

NASA Astrophysics Data System (ADS)

Onken, Jeffrey

This dissertation introduces a multidisciplinary framework for the enabling of future research and analysis of alternatives for control centers for real-time operations of safety-critical systems. The multidisciplinary framework integrates functional and computational models that describe the dynamics in fundamental concepts of previously disparate engineering and psychology research disciplines, such as group performance and processes, supervisory control, situation awareness, events and delays, and expertise. The application in this dissertation is the real-time operations within the NASA Mission Control Center in Houston, TX. This dissertation operationalizes the framework into a model and simulation, which simulates the functional and computational models in the framework according to user-configured scenarios for a NASA human-spaceflight mission. The model and simulation generates data according to the effectiveness of the mission-control team in supporting the completion of mission objectives and detecting, isolating, and recovering from anomalies. Accompanying the multidisciplinary framework is a proof of concept, which demonstrates the feasibility of such a framework. The proof of concept demonstrates that variability occurs where expected based on the models. The proof of concept also demonstrates that the data generated from the model and simulation is useful for analyzing and comparing MCC configuration alternatives because an investigator can give a diverse set of scenarios to the simulation and the output compared in detail to inform decisions about the effect of MCC configurations on mission operations performance.

Quantum analogue computing.

PubMed

Kendon, Vivien M; Nemoto, Kae; Munro, William J

2010-08-13

We briefly review what a quantum computer is, what it promises to do for us and why it is so hard to build one. Among the first applications anticipated to bear fruit is the quantum simulation of quantum systems. While most quantum computation is an extension of classical digital computation, quantum simulation differs fundamentally in how the data are encoded in the quantum computer. To perform a quantum simulation, the Hilbert space of the system to be simulated is mapped directly onto the Hilbert space of the (logical) qubits in the quantum computer. This type of direct correspondence is how data are encoded in a classical analogue computer. There is no binary encoding, and increasing precision becomes exponentially costly: an extra bit of precision doubles the size of the computer. This has important consequences for both the precision and error-correction requirements of quantum simulation, and significant open questions remain about its practicality. It also means that the quantum version of analogue computers, continuous-variable quantum computers, becomes an equally efficient architecture for quantum simulation. Lessons from past use of classical analogue computers can help us to build better quantum simulators in future.

Student Ability, Confidence, and Attitudes Toward Incorporating a Computer into a Patient Interview.

PubMed

Ray, Sarah; Valdovinos, Katie

2015-05-25

To improve pharmacy students' ability to effectively incorporate a computer into a simulated patient encounter and to improve their awareness of barriers and attitudes towards and their confidence in using a computer during simulated patient encounters. Students completed a survey that assessed their awareness of, confidence in, and attitudes towards computer use during simulated patient encounters. Students were evaluated with a rubric on their ability to incorporate a computer into a simulated patient encounter. Students were resurveyed and reevaluated after instruction. Students improved in their ability to effectively incorporate computer usage into a simulated patient encounter. They also became more aware of and improved their attitudes toward barriers regarding such usage and gained more confidence in their ability to use a computer during simulated patient encounters. Instruction can improve pharmacy students' ability to incorporate a computer into simulated patient encounters. This skill is critical to developing efficiency while maintaining rapport with patients.

Geant4 Computing Performance Benchmarking and Monitoring

DOE PAGES

Dotti, Andrea; Elvira, V. Daniel; Folger, Gunter; ...

2015-12-23

Performance evaluation and analysis of large scale computing applications is essential for optimal use of resources. As detector simulation is one of the most compute intensive tasks and Geant4 is the simulation toolkit most widely used in contemporary high energy physics (HEP) experiments, it is important to monitor Geant4 through its development cycle for changes in computing performance and to identify problems and opportunities for code improvements. All Geant4 development and public releases are being profiled with a set of applications that utilize different input event samples, physics parameters, and detector configurations. Results from multiple benchmarking runs are compared tomore » previous public and development reference releases to monitor CPU and memory usage. Observed changes are evaluated and correlated with code modifications. Besides the full summary of call stack and memory footprint, a detailed call graph analysis is available to Geant4 developers for further analysis. The set of software tools used in the performance evaluation procedure, both in sequential and multi-threaded modes, include FAST, IgProf and Open|Speedshop. In conclusion, the scalability of the CPU time and memory performance in multi-threaded application is evaluated by measuring event throughput and memory gain as a function of the number of threads for selected event samples.« less

Software Aids Visualization of Computed Unsteady Flow

NASA Technical Reports Server (NTRS)

Kao, David; Kenwright, David

2003-01-01

Unsteady Flow Analysis Toolkit (UFAT) is a computer program that synthesizes motions of time-dependent flows represented by very large sets of data generated in computational fluid dynamics simulations. Prior to the development of UFAT, it was necessary to rely on static, single-snapshot depictions of time-dependent flows generated by flow-visualization software designed for steady flows. Whereas it typically takes weeks to analyze the results of a largescale unsteady-flow simulation by use of steady-flow visualization software, the analysis time is reduced to hours when UFAT is used. UFAT can be used to generate graphical objects of flow visualization results using multi-block curvilinear grids in the format of a previously developed NASA data-visualization program, PLOT3D. These graphical objects can be rendered using FAST, another popular flow visualization software developed at NASA. Flow-visualization techniques that can be exploited by use of UFAT include time-dependent tracking of particles, detection of vortex cores, extractions of stream ribbons and surfaces, and tetrahedral decomposition for optimal particle tracking. Unique computational features of UFAT include capabilities for automatic (batch) processing, restart, memory mapping, and parallel processing. These capabilities significantly reduce analysis time and storage requirements, relative to those of prior flow-visualization software. UFAT can be executed on a variety of supercomputers.

Continuous-Variable Instantaneous Quantum Computing is Hard to Sample.

PubMed

Douce, T; Markham, D; Kashefi, E; Diamanti, E; Coudreau, T; Milman, P; van Loock, P; Ferrini, G

2017-02-17

Instantaneous quantum computing is a subuniversal quantum complexity class, whose circuits have proven to be hard to simulate classically in the discrete-variable realm. We extend this proof to the continuous-variable (CV) domain by using squeezed states and homodyne detection, and by exploring the properties of postselected circuits. In order to treat postselection in CVs, we consider finitely resolved homodyne detectors, corresponding to a realistic scheme based on discrete probability distributions of the measurement outcomes. The unavoidable errors stemming from the use of finitely squeezed states are suppressed through a qubit-into-oscillator Gottesman-Kitaev-Preskill encoding of quantum information, which was previously shown to enable fault-tolerant CV quantum computation. Finally, we show that, in order to render postselected computational classes in CVs meaningful, a logarithmic scaling of the squeezing parameter with the circuit size is necessary, translating into a polynomial scaling of the input energy.

Micro-Ramp Flow Control for Oblique Shock Interactions: Comparisons of Computational and Experimental Data

NASA Technical Reports Server (NTRS)

Hirt, Stefanie M.; Reich, David B.; O'Connor, Michael B.

2010-01-01

Computational fluid dynamics was used to study the effectiveness of micro-ramp vortex generators to control oblique shock boundary layer interactions. Simulations were based on experiments previously conducted in the 15 x 15 cm supersonic wind tunnel at NASA Glenn Research Center. Four micro-ramp geometries were tested at Mach 2.0 varying the height, chord length, and spanwise spacing between micro-ramps. The overall flow field was examined. Additionally, key parameters such as boundary-layer displacement thickness, momentum thickness and incompressible shape factor were also examined. The computational results predicted the effects of the micro-ramps well, including the trends for the impact that the devices had on the shock boundary layer interaction. However, computing the shock boundary layer interaction itself proved to be problematic since the calculations predicted more pronounced adverse effects on the boundary layer due to the shock than were seen in the experiment.

Micro-Ramp Flow Control for Oblique Shock Interactions: Comparisons of Computational and Experimental Data

NASA Technical Reports Server (NTRS)

Hirt, Stephanie M.; Reich, David B.; O'Connor, Michael B.

2012-01-01

Computational fluid dynamics was used to study the effectiveness of micro-ramp vortex generators to control oblique shock boundary layer interactions. Simulations were based on experiments previously conducted in the 15- by 15-cm supersonic wind tunnel at the NASA Glenn Research Center. Four micro-ramp geometries were tested at Mach 2.0 varying the height, chord length, and spanwise spacing between micro-ramps. The overall flow field was examined. Additionally, key parameters such as boundary-layer displacement thickness, momentum thickness and incompressible shape factor were also examined. The computational results predicted the effects of the microramps well, including the trends for the impact that the devices had on the shock boundary layer interaction. However, computing the shock boundary layer interaction itself proved to be problematic since the calculations predicted more pronounced adverse effects on the boundary layer due to the shock than were seen in the experiment.

Effects of heat exchanger tubes on hydrodynamics and CO 2 capture of a sorbent-based fluidized bed reactor

DOE PAGES

Lai, Canhai; Xu, Zhijie; Li, Tingwen; ...

2017-08-05

In virtual design and scale up of pilot-scale carbon capture systems, the coupled reactive multiphase flow problem must be solved to predict the adsorber's performance and capture efficiency under various operation conditions. This paper focuses on the detailed computational fluid dynamics (CFD) modeling of a pilot-scale fluidized bed adsorber equipped with vertical cooling tubes. Multiphase Flow with Interphase eXchanges (MFiX), an open-source multiphase flow CFD solver, is used for the simulations with custom code to simulate the chemical reactions and filtered sub-grid models to capture the effect of the unresolved details in the coarser mesh for simulations with reasonable accuracymore » and manageable computational effort. Previously developed filtered models for horizontal cylinder drag, heat transfer, and reaction kinetics have been modified to derive the 2D filtered models representing vertical cylinders in the coarse-grid CFD simulations. The effects of the heat exchanger configurations (i.e., horizontal or vertical tubes) on the adsorber's hydrodynamics and CO 2 capture performance are then examined. A one-dimensional three-region process model is briefly introduced for comparison purpose. The CFD model matches reasonably well with the process model while provides additional information about the flow field that is not available with the process model.« less

Long-time dynamics through parallel trajectory splicing

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

Perez, Danny; Cubuk, Ekin D.; Waterland, Amos

2015-11-24

Simulating the atomistic evolution of materials over long time scales is a longstanding challenge, especially for complex systems where the distribution of barrier heights is very heterogeneous. Such systems are difficult to investigate using conventional long-time scale techniques, and the fact that they tend to remain trapped in small regions of configuration space for extended periods of time strongly limits the physical insights gained from short simulations. We introduce a novel simulation technique, Parallel Trajectory Splicing (ParSplice), that aims at addressing this problem through the timewise parallelization of long trajectories. The computational efficiency of ParSplice stems from a speculation strategymore » whereby predictions of the future evolution of the system are leveraged to increase the amount of work that can be concurrently performed at any one time, hence improving the scalability of the method. ParSplice is also able to accurately account for, and potentially reuse, a substantial fraction of the computational work invested in the simulation. We validate the method on a simple Ag surface system and demonstrate substantial increases in efficiency compared to previous methods. As a result, we then demonstrate the power of ParSplice through the study of topology changes in Ag 42Cu 13 core–shell nanoparticles.« less

Preferential Concentration Of Solid Particles In Turbulent Horizontal Circular Pipe Flow

NASA Astrophysics Data System (ADS)

Kim, Jaehee; Yang, Kyung-Soo

2017-11-01

In particle-laden turbulent pipe flow, turbophoresis can lead to a preferential concentration of particles near the wall. To investigate this phenomenon, one-way coupled Direct Numerical Simulation (DNS) has been performed. Fully-developed turbulent pipe flow of the carrier fluid (air) is at Reτ = 200 based on the pipe radius and the mean friction velocity, whereas the Stokes numbers of the particles (solid) are St+ = 0.1 , 1 , 10 based on the mean friction velocity and the kinematic viscosity of the fluid. The computational domain for particle simulation is extended along the axial direction by duplicating the domain of the fluid simulation. By doing so, particle statistics in the spatially developing region as well as in the fully-developed region can be obtained. Accumulation of particles has been noticed at St+ = 1 and 10 mostly in the viscous sublayer, more intensive in the latter case. Compared with other authors' previous results, our results suggest that drag force on the particles should be computed by using an empirical correlation and a higher-order interpolation scheme even in a low-Re regime in order to improve the accuracy of particle simulation. This work was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP) (No. 2015R1A2A2A01002981).

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

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Fares, Ehab

2016-01-01

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

Accelerating Approximate Bayesian Computation with Quantile Regression: application to cosmological redshift distributions

NASA Astrophysics Data System (ADS)

Kacprzak, T.; Herbel, J.; Amara, A.; Réfrégier, A.

2018-02-01

Approximate Bayesian Computation (ABC) is a method to obtain a posterior distribution without a likelihood function, using simulations and a set of distance metrics. For that reason, it has recently been gaining popularity as an analysis tool in cosmology and astrophysics. Its drawback, however, is a slow convergence rate. We propose a novel method, which we call qABC, to accelerate ABC with Quantile Regression. In this method, we create a model of quantiles of distance measure as a function of input parameters. This model is trained on a small number of simulations and estimates which regions of the prior space are likely to be accepted into the posterior. Other regions are then immediately rejected. This procedure is then repeated as more simulations are available. We apply it to the practical problem of estimation of redshift distribution of cosmological samples, using forward modelling developed in previous work. The qABC method converges to nearly same posterior as the basic ABC. It uses, however, only 20% of the number of simulations compared to basic ABC, achieving a fivefold gain in execution time for our problem. For other problems the acceleration rate may vary; it depends on how close the prior is to the final posterior. We discuss possible improvements and extensions to this method.

Modelling of Dispersed Gas-Liquid Flow using LBGK and LPT Approach

NASA Astrophysics Data System (ADS)

Agarwal, Alankar; Prakash, Akshay; Ravindra, B.

2017-11-01

The dynamics of gas bubbles play a significant, if not crucial, role in a large variety of industrial process that involves using reactors. Many of these processes are still not well understood in terms of optimal scale-up strategies.An accurate modeling of bubbles and bubble swarms become important for high fidelity bioreactor simulations. This study is a part of the development of robust bubble fluid interaction modules for simulation of industrial-scale reactors. The work presents the simulation of a single bubble rising in a quiescent water tank using current models presented in the literature for bubble-fluid interaction. In this multiphase benchmark problem, the continuous phase (water) is discretized using the Lattice Bhatnagar-Gross and Krook (LBGK) model of Lattice Boltzmann Method (LBM), while the dispersed gas phase (i.e. air-bubble) modeled with the Lagrangian particle tracking (LPT) approach. The cheap clipped fourth order polynomial function is used to model the interaction between two phases. The model is validated by comparing the simulation results for terminal velocity of a bubble at varying bubble diameter and the influence of bubble motion in liquid velocity with the theoretical and previously available experimental data. This work is supported by the ``Centre for Development of Advanced Computing (C-DAC), Pune'' by providing the advanced computational facility in PARAM Yuva-II.

Asymmetric Uncertainty Expression for High Gradient Aerodynamics

NASA Technical Reports Server (NTRS)

Pinier, Jeremy T

2012-01-01

When the physics of the flow around an aircraft changes very abruptly either in time or space (e.g., flow separation/reattachment, boundary layer transition, unsteadiness, shocks, etc), the measurements that are performed in a simulated environment like a wind tunnel test or a computational simulation will most likely incorrectly predict the exact location of where (or when) the change in physics happens. There are many reasons for this, includ- ing the error introduced by simulating a real system at a smaller scale and at non-ideal conditions, or the error due to turbulence models in a computational simulation. The un- certainty analysis principles that have been developed and are being implemented today do not fully account for uncertainty in the knowledge of the location of abrupt physics changes or sharp gradients, leading to a potentially underestimated uncertainty in those areas. To address this problem, a new asymmetric aerodynamic uncertainty expression containing an extra term to account for a phase-uncertainty, the magnitude of which is emphasized in the high-gradient aerodynamic regions is proposed in this paper. Additionally, based on previous work, a method for dispersing aerodynamic data within asymmetric uncer- tainty bounds in a more realistic way has been developed for use within Monte Carlo-type analyses.

Quantification of Wear and Deformation in Different Configurations of Polyethylene Acetabular Cups Using Micro X-ray Computed Tomography

PubMed Central

Affatato, Saverio; Zanini, Filippo; Carmignato, Simone

2017-01-01

Wear is currently quantified as mass loss of the bearing materials measured using gravimetric methods. However, this method does not provide other information, such as volumetric loss or surface deviation. In this work, we validated a technique to quantify polyethylene wear in three different batches of ultrahigh-molecular-polyethylene acetabular cups used for hip implants using nondestructive microcomputed tomography. Three different configurations of polyethylene acetabular cups, previously tested under the ISO 14242 parameters, were tested on a hip simulator for an additional 2 million cycles using a modified ISO 14242 load waveform. In this context, a new approach was proposed in order to simulate, on a hip joint simulator, high-demand activities. In addition, the effects of these activities were analyzed in terms of wear and deformations of those polyethylenes by means of gravimetric method and micro X-ray computed tomography. In particular, while the gravimetric method was used for weight loss assessment, microcomputed tomography allowed for acquisition of additional quantitative information about the evolution of local wear and deformation through three-dimensional surface deviation maps for the entire cups’ surface. Experimental results showed that the wear and deformation behavior of these materials change according to different mechanical simulations. PMID:28772616

Postcollapse Evolution of Globular Clusters

NASA Astrophysics Data System (ADS)

Makino, Junichiro

1996-11-01

A number of globular clusters appear to have undergone core collapse, in the sense that their predicted collapse times are much shorter than their current ages. Simulations with gas models and the Fokker-Planck approximation have shown that the central density of a globular cluster after the collapse undergoes nonlinear oscillation with a large amplitude (gravothermal oscillation). However, the question whether such an oscillation actually takes place in real N-body systems has remained unsolved because an N-body simulation with a sufficiently high resolution would have required computing resources of the order of several GFLOPS-yr. In the present paper, we report the results of such a simulation performed on a dedicated special-purpose computer, GRAPE-4. We have simulated the evolution of isolated point-mass systems with up to 32,768 particles. The largest number of particles reported previously is 10,000. We confirm that gravothermal oscillation takes place in an N-body system. The expansion phase shows all the signatures that are considered to be evidence of the gravothermal nature of the oscillation. At the maximum expansion, the core radius is ˜1% of the half-mass radius for the run with 32,768 particles. The maximum core size, rc, depends on N as ∝ N-1/3.

Unsteady Analysis of Inlet-Compressor Acoustic Interactions Using Coupled 3-D and 1-D CFD Codes

NASA Technical Reports Server (NTRS)

Suresh, A.; Cole, G. L.

2000-01-01

It is well known that the dynamic response of a mixed compression supersonic inlet is very sensitive to the boundary condition imposed at the subsonic exit (engine face) of the inlet. In previous work, a 3-D computational fluid dynamics (CFD) inlet code (NPARC) was coupled at the engine face to a 3-D turbomachinery code (ADPAC) simulating an isolated rotor and the coupled simulation used to study the unsteady response of the inlet. The main problem with this approach is that the high fidelity turbomachinery simulation becomes prohibitively expensive as more stages are included in the simulation. In this paper, an alternative approach is explored, wherein the inlet code is coupled to a lesser fidelity 1-D transient compressor code (DYNTECC) which simulates the whole compressor. The specific application chosen for this evaluation is the collapsing bump experiment performed at the University of Cincinnati, wherein reflections of a large-amplitude acoustic pulse from a compressor were measured. The metrics for comparison are the pulse strength (time integral of the pulse amplitude) and wave form (shape). When the compressor is modeled by stage characteristics the computed strength is about ten percent greater than that for the experiment, but the wave shapes are in poor agreement. An alternate approach that uses a fixed rise in duct total pressure and temperature (so-called 'lossy' duct) to simulate a compressor gives good pulse shapes but the strength is about 30 percent low.

Wetting and interfacial properties of water nanodroplets in contact with graphene and monolayer boron-nitride sheets.

PubMed

Li, Hui; Zeng, Xiao Cheng

2012-03-27

Born-Oppenheim quantum molecular dynamics (QMD) simulations are performed to investigate wetting, diffusive, and interfacial properties of water nanodroplets in contact with a graphene sheet or a monolayer boron-nitride (BN) sheet. Contact angles of the water nanodroplets on the two sheets are computed for the first time using QMD simulations. Structural and dynamic properties of the water droplets near the graphene or BN sheet are also studied to gain insights into the interfacial interaction between the water droplet and the substrate. QMD simulation results are compared with those from previous classic MD simulations and with the experimental measurements. The QMD simulations show that the graphene sheet yields a contact angle of 87°, while the monolayer BN sheet gives rise to a contact angle of 86°. Hence, like graphene, the monolayer BN sheet is also weakly hydrophobic, even though the BN bonds entail a large local dipole moment. QMD simulations also show that the interfacial water can induce net positive charges on the contacting surface of the graphene and monolayer BN sheets, and such charge induction may affect electronic structure of the contacting graphene in view that graphene is a semimetal. Contact angles of nanodroplets of water in a supercooled state on the graphene are also computed. It is found that under the supercooled condition, water nanodroplets exhibit an appreciably larger contact angle than under the ambient condition. © 2012 American Chemical Society

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.

PubMed

Kasahara, Kota; Ma, Benson; Goto, Kota; Dasgupta, Bhaskar; Higo, Junichi; Fukuda, Ikuo; Mashimo, Tadaaki; Akiyama, Yutaka; Nakamura, Haruki

2016-01-01

Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named "myPresto/omegagene" that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods, e.g. , the virtual-system-coupled multi-canonical MD (V-McMD) method, replace a multi-process parallelized run with multiple independent runs to avoid inter-node communication overhead. In addition, adopting the non-Ewald-based zero-multipole summation method (ZMM) makes it possible to eliminate the Fourier space calculations altogether. The combination of these state-of-the-art techniques realizes efficient and accurate calculations of the conformational ensemble at an equilibrium state. By taking these advantages, myPresto/omegagene is specialized for the single process execution with Graphics Processing Unit (GPU). We performed benchmark simulations for the 20-mer peptide, Trp-cage, with explicit solvent. One of the most thermodynamically stable conformations generated by the V-McMD simulation is very similar to an experimentally solved native conformation. Furthermore, the computation speed is four-times faster than that of our previous simulation engine, myPresto/psygene-G. The new simulator, myPresto/omegagene, is freely available at the following URLs: http://www.protein.osaka-u.ac.jp/rcsfp/pi/omegagene/ and http://presto.protein.osaka-u.ac.jp/myPresto4/.

QDENSITY—A Mathematica quantum computer simulation

NASA Astrophysics Data System (ADS)

Juliá-Díaz, Bruno; Burdis, Joseph M.; Tabakin, Frank

2009-03-01

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. New version program summaryProgram title: QDENSITY 2.0 Catalogue identifier: ADXH_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v2_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.: 26 055 No. of bytes in distributed program, including test data, etc.: 227 540 Distribution format: tar.gz Programming language: Mathematica 6.0 Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4 Catalogue identifier of previous version: ADXH_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914 Classification: 4.15 Does the new version supersede the previous version?: Offers an alternative, more up to date, implementation Nature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters. Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed. Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0 Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0 Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.

Electron cloud simulations for the main ring of J-PARC

NASA Astrophysics Data System (ADS)

Yee-Rendon, Bruce; Muto, Ryotaro; Ohmi, Kazuhito; Satou, Kenichirou; Tomizawa, Masahito; Toyama, Takeshi

2017-07-01

The simulation of beam instabilities is a helpful tool to evaluate potential threats against the machine protection of the high intensity beams. At Main Ring (MR) of J-PARC, signals related to the electron cloud have been observed during the slow beam extraction mode. Hence, several studies were conducted to investigate the mechanism that produces it, the results confirmed a strong dependence on the beam intensity and the bunch structure in the formation of the electron cloud, however, the precise explanation of its trigger conditions remains incomplete. To shed light on the problem, electron cloud simulations were done using an updated version of the computational model developed from previous works at KEK. The code employed the signals of the measurements to reproduce the events seen during the surveys.

A Numerical Simulation and Statistical Modeling of High Intensity Radiated Fields Experiment Data

NASA Technical Reports Server (NTRS)

Smith, Laura J.

2004-01-01

Tests are conducted on a quad-redundant fault tolerant flight control computer to establish upset characteristics of an avionics system in an electromagnetic field. A numerical simulation and statistical model are described in this work to analyze the open loop experiment data collected in the reverberation chamber at NASA LaRC as a part of an effort to examine the effects of electromagnetic interference on fly-by-wire aircraft control systems. By comparing thousands of simulation and model outputs, the models that best describe the data are first identified and then a systematic statistical analysis is performed on the data. All of these efforts are combined which culminate in an extrapolation of values that are in turn used to support previous efforts used in evaluating the data.

A geometric initial guess for localized electronic orbitals in modular biological systems

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

Beckman, P. G.; Fattebert, J. L.; Lau, E. Y.

Recent first-principles molecular dynamics algorithms using localized electronic orbitals have achieved O(N) complexity and controlled accuracy in simulating systems with finite band gaps. However, accurately deter- mining the centers of these localized orbitals during simulation setup may require O(N 3) operations, which is computationally infeasible for many biological systems. We present an O(N) approach for approximating orbital centers in proteins, DNA, and RNA which uses non-localized solutions for a set of fixed-size subproblems to create a set of geometric maps applicable to larger systems. This scalable approach, used as an initial guess in the O(N) first-principles molecular dynamics code MGmol,more » facilitates first-principles simulations in biological systems of sizes which were previously impossible.« less

Simulations of Bluff Body Flow Interaction for Noise Source Modeling

NASA Technical Reports Server (NTRS)

Khorrami, Medi R.; Lockard David P.; Choudhari, Meelan M.; Jenkins, Luther N.; Neuhart, Dan H.; McGinley, Catherine B.

2006-01-01

The current study is a continuation of our effort to characterize the details of flow interaction between two cylinders in a tandem configuration. This configuration is viewed to possess many of the pertinent flow features of the highly interactive unsteady flow field associated with the main landing gear of large civil transports. The present effort extends our previous two-dimensional, unsteady, Reynolds Averaged Navier-Stokes computations to three dimensions using a quasilaminar, zonal approach, in conjunction with a two-equation turbulence model. Two distinct separation length-to-diameter ratios of L/D = 3.7 and 1.435, representing intermediate and short separation distances between the two cylinders, are simulated. The Mach 0.166 simulations are performed at a Reynolds number of Re = 1.66 105 to match the companion experiments at NASA Langley Research Center. Extensive comparisons with the measured steady and unsteady surface pressure and off-surface particle image velocimetry data show encouraging agreement. Both prominent and some of the more subtle trends in the mean and fluctuating flow fields are correctly predicted. Both computations and the measured data reveal a more robust and energetic shedding process at L/D = 3.7 in comparison with the weaker shedding in the shorter separation case of L/D = 1.435. The vortex shedding frequency based on the computed surface pressure spectra is in reasonable agreement with the measured Strouhal frequency.

A Computational Model for Aperture Control in Reach-to-Grasp Movement Based on Predictive Variability

PubMed Central

Takemura, Naohiro; Fukui, Takao; Inui, Toshio

2015-01-01

In human reach-to-grasp movement, visual occlusion of a target object leads to a larger peak grip aperture compared to conditions where online vision is available. However, no previous computational and neural network models for reach-to-grasp movement explain the mechanism of this effect. We simulated the effect of online vision on the reach-to-grasp movement by proposing a computational control model based on the hypothesis that the grip aperture is controlled to compensate for both motor variability and sensory uncertainty. In this model, the aperture is formed to achieve a target aperture size that is sufficiently large to accommodate the actual target; it also includes a margin to ensure proper grasping despite sensory and motor variability. To this end, the model considers: (i) the variability of the grip aperture, which is predicted by the Kalman filter, and (ii) the uncertainty of the object size, which is affected by visual noise. Using this model, we simulated experiments in which the effect of the duration of visual occlusion was investigated. The simulation replicated the experimental result wherein the peak grip aperture increased when the target object was occluded, especially in the early phase of the movement. Both predicted motor variability and sensory uncertainty play important roles in the online visuomotor process responsible for grip aperture control. PMID:26696874

Stabilized finite element methods to simulate the conductances of ion channels

NASA Astrophysics Data System (ADS)

Tu, Bin; Xie, Yan; Zhang, Linbo; Lu, Benzhuo

2015-03-01

We have previously developed a finite element simulator, ichannel, to simulate ion transport through three-dimensional ion channel systems via solving the Poisson-Nernst-Planck equations (PNP) and Size-modified Poisson-Nernst-Planck equations (SMPNP), and succeeded in simulating some ion channel systems. However, the iterative solution between the coupled Poisson equation and the Nernst-Planck equations has difficulty converging for some large systems. One reason we found is that the NP equations are advection-dominated diffusion equations, which causes troubles in the usual FE solution. The stabilized schemes have been applied to compute fluids flow in various research fields. However, they have not been studied in the simulation of ion transport through three-dimensional models based on experimentally determined ion channel structures. In this paper, two stabilized techniques, the SUPG and the Pseudo Residual-Free Bubble function (PRFB) are introduced to enhance the numerical robustness and convergence performance of the finite element algorithm in ichannel. The conductances of the voltage dependent anion channel (VDAC) and the anthrax toxin protective antigen pore (PA) are simulated to validate the stabilization techniques. Those two stabilized schemes give reasonable results for the two proteins, with decent agreement with both experimental data and Brownian dynamics (BD) simulations. For a variety of numerical tests, it is found that the simulator effectively avoids previous numerical instability after introducing the stabilization methods. Comparison based on our test data set between the two stabilized schemes indicates both SUPG and PRFB have similar performance (the latter is slightly more accurate and stable), while SUPG is relatively more convenient to implement.

Space environment and lunar surface processes

NASA Technical Reports Server (NTRS)

Comstock, G. M.

1979-01-01

The development of a general rock/soil model capable of simulating in a self consistent manner the mechanical and exposure history of an assemblage of solid and loose material from submicron to planetary size scales, applicable to lunar and other space exposed planetary surfaces is discussed. The model was incorporated into a computer code called MESS.2 (model for the evolution of space exposed surfaces). MESS.2, which represents a considerable increase in sophistication and scope over previous soil and rock surface models, is described. The capabilities of previous models for near surface soil and rock surfaces are compared with the rock/soil model, MESS.2.

Sinking bubbles in stout beers

NASA Astrophysics Data System (ADS)

Lee, W. T.; Kaar, S.; O'Brien, S. B. G.

2018-04-01

A surprising phenomenon witnessed by many is the sinking bubbles seen in a settling pint of stout beer. Bubbles are less dense than the surrounding fluid so how does this happen? Previous work has shown that the explanation lies in a circulation of fluid promoted by the tilted sides of the glass. However, this work has relied heavily on computational fluid dynamics (CFD) simulations. Here, we show that the phenomenon of sinking bubbles can be predicted using a simple analytic model. To make the model analytically tractable, we work in the limit of small bubbles and consider a simplified geometry. The model confirms both the existence of sinking bubbles and the previously proposed mechanism.

A dynamical systems analysis of the kinematics of time-periodic vortex shedding past a circular cylinder

NASA Technical Reports Server (NTRS)

Ottino, Julio M.

1991-01-01

Computer flow simulation aided by dynamical systems analysis is used to investigate the kinematics of time-periodic vortex shedding past a two-dimensional circular cylinder in the context of the following general questions: (1) Is a dynamical systems viewpoint useful in the understanding of this and similar problems involving time-periodic shedding behind bluff bodies; and (2) Is it indeed possible, by adopting such a point of view, to complement previous analyses or to understand kinematical aspects of the vortex shedding process that somehow remained hidden in previous approaches. We argue that the answers to these questions are positive. Results are described.

Detached Eddy Simulation of the UH-60 Rotor Wake Using Adaptive Mesh Refinement

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.; Ahmad, Jasim U.

2012-01-01

Time-dependent Navier-Stokes flow simulations have been carried out for a UH-60 rotor with simplified hub in forward flight and hover flight conditions. Flexible rotor blades and flight trim conditions are modeled and established by loosely coupling the OVERFLOW Computational Fluid Dynamics (CFD) code with the CAMRAD II helicopter comprehensive code. High order spatial differences, Adaptive Mesh Refinement (AMR), and Detached Eddy Simulation (DES) are used to obtain highly resolved vortex wakes, where the largest turbulent structures are captured. Special attention is directed towards ensuring the dual time accuracy is within the asymptotic range, and verifying the loose coupling convergence process using AMR. The AMR/DES simulation produced vortical worms for forward flight and hover conditions, similar to previous results obtained for the TRAM rotor in hover. AMR proved to be an efficient means to capture a rotor wake without a priori knowledge of the wake shape.

Comparison of three large-eddy simulations of shock-induced turbulent separation bubbles

NASA Astrophysics Data System (ADS)

Touber, Emile; Sandham, Neil D.

2009-12-01

Three different large-eddy simulation investigations of the interaction between an impinging oblique shock and a supersonic turbulent boundary layer are presented. All simulations made use of the same inflow technique, specifically aimed at avoiding possible low-frequency interferences with the shock/boundary-layer interaction system. All simulations were run on relatively wide computational domains and integrated over times greater than twenty five times the period of the most commonly reported low-frequency shock-oscillation, making comparisons at both time-averaged and low-frequency-dynamic levels possible. The results confirm previous experimental results which suggested a simple linear relation between the interaction length and the oblique-shock strength if scaled using the boundary-layer thickness and wall-shear stress. All the tested cases show evidences of significant low-frequency shock motions. At the wall, energetic low-frequency pressure fluctuations are observed, mainly in the initial part of interaction.

Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

PubMed Central

Wen, Bin; Peng, Junhui; Zuo, Xiaobing; Gong, Qingguo; Zhang, Zhiyong

2014-01-01

Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations. PMID:25140431

Classical simulation of quantum error correction in a Fibonacci anyon code

NASA Astrophysics Data System (ADS)

Burton, Simon; Brell, Courtney G.; Flammia, Steven T.

2017-02-01

Classically simulating the dynamics of anyonic excitations in two-dimensional quantum systems is likely intractable in general because such dynamics are sufficient to implement universal quantum computation. However, processes of interest for the study of quantum error correction in anyon systems are typically drawn from a restricted class that displays significant structure over a wide range of system parameters. We exploit this structure to classically simulate, and thereby demonstrate the success of, an error-correction protocol for a quantum memory based on the universal Fibonacci anyon model. We numerically simulate a phenomenological model of the system and noise processes on lattice sizes of up to 128 ×128 sites, and find a lower bound on the error-correction threshold of approximately 0.125 errors per edge, which is comparable to those previously known for Abelian and (nonuniversal) non-Abelian anyon models.

Rotor Airloads Prediction Using Unstructured Meshes and Loose CFD/CSD Coupling

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Lee-Rausch, Elizabeth M.

2008-01-01

The FUN3D unsteady Reynolds-averaged Navier-Stokes solver for unstructured grids has been modified to allow prediction of trimmed rotorcraft airloads. The trim of the rotorcraft and the aeroelastic deformation of the rotor blades are accounted for via loose coupling with the CAMRAD II rotorcraft computational structural dynamics code. The set of codes is used to analyze the HART-II Baseline, Minimum Noise and Minimum Vibration test conditions. The loose coupling approach is found to be stable and convergent for the cases considered. Comparison of the resulting airloads and structural deformations with experimentally measured data is presented. The effect of grid resolution and temporal accuracy is examined. Rotorcraft airloads prediction presents a very substantial challenge for Computational Fluid Dynamics (CFD). Not only must the unsteady nature of the flow be accurately modeled, but since most rotorcraft blades are not structurally stiff, an accurate simulation must account for the blade structural dynamics. In addition, trim of the rotorcraft to desired thrust and moment targets depends on both aerodynamic loads and structural deformation, and vice versa. Further, interaction of the fuselage with the rotor flow field can be important, so that relative motion between the blades and the fuselage must be accommodated. Thus a complete simulation requires coupled aerodynamics, structures and trim, with the ability to model geometrically complex configurations. NASA has recently initiated a Subsonic Rotary Wing (SRW) Project under the overall Fundamental Aeronautics Program. Within the context of SRW are efforts aimed at furthering the state of the art of high-fidelity rotorcraft flow simulations, using both structured and unstructured meshes. Structured-mesh solvers have an advantage in computation speed, but even though remarkably complex configurations may be accommodated using the overset grid approach, generation of complex structured-mesh systems can require months to set up. As a result, many rotorcraft simulations using structured-grid CFD neglect the fuselage. On the other hand, unstructured-mesh solvers are easily able to handle complex geometries, but suffer from slower execution speed. However, advances in both computer hardware and CFD algorithms have made previously state-of-the-art computations routine for unstructured-mesh solvers, so that rotorcraft simulations using unstructured grids are now viable. The aim of the present work is to develop a first principles rotorcraft simulation tool based on an unstructured CFD solver.

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.

Computational simulation of concurrent engineering for aerospace propulsion systems

NASA Technical Reports Server (NTRS)

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

1992-01-01

Results are summarized of an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulations methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties - fundamental in developing such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering for propulsion systems and systems in general. Benefits and facets needing early attention in the development are outlined.

Computational simulation for concurrent engineering of aerospace propulsion systems

NASA Technical Reports Server (NTRS)

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

1993-01-01

Results are summarized for an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulation methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties--fundamental to develop such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering of propulsion systems and systems in general. Benefits and issues needing early attention in the development are outlined.

Computational simulation for concurrent engineering of aerospace propulsion systems

NASA Astrophysics Data System (ADS)

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

1993-02-01

Results are summarized for an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulation methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties--fundamental to develop such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering of propulsion systems and systems in general. Benefits and issues needing early attention in the development are outlined.

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

NASA Technical Reports Server (NTRS)

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

2015-01-01

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

Step-by-step magic state encoding for efficient fault-tolerant quantum computation

PubMed Central

Goto, Hayato

2014-01-01

Quantum error correction allows one to make quantum computers fault-tolerant against unavoidable errors due to decoherence and imperfect physical gate operations. However, the fault-tolerant quantum computation requires impractically large computational resources for useful applications. This is a current major obstacle to the realization of a quantum computer. In particular, magic state distillation, which is a standard approach to universality, consumes the most resources in fault-tolerant quantum computation. For the resource problem, here we propose step-by-step magic state encoding for concatenated quantum codes, where magic states are encoded step by step from the physical level to the logical one. To manage errors during the encoding, we carefully use error detection. Since the sizes of intermediate codes are small, it is expected that the resource overheads will become lower than previous approaches based on the distillation at the logical level. Our simulation results suggest that the resource requirements for a logical magic state will become comparable to those for a single logical controlled-NOT gate. Thus, the present method opens a new possibility for efficient fault-tolerant quantum computation. PMID:25511387

Step-by-step magic state encoding for efficient fault-tolerant quantum computation.

PubMed

Goto, Hayato

2014-12-16

Quantum error correction allows one to make quantum computers fault-tolerant against unavoidable errors due to decoherence and imperfect physical gate operations. However, the fault-tolerant quantum computation requires impractically large computational resources for useful applications. This is a current major obstacle to the realization of a quantum computer. In particular, magic state distillation, which is a standard approach to universality, consumes the most resources in fault-tolerant quantum computation. For the resource problem, here we propose step-by-step magic state encoding for concatenated quantum codes, where magic states are encoded step by step from the physical level to the logical one. To manage errors during the encoding, we carefully use error detection. Since the sizes of intermediate codes are small, it is expected that the resource overheads will become lower than previous approaches based on the distillation at the logical level. Our simulation results suggest that the resource requirements for a logical magic state will become comparable to those for a single logical controlled-NOT gate. Thus, the present method opens a new possibility for efficient fault-tolerant quantum computation.

Modeling equine race surface vertical mechanical behaviors in a musculoskeletal modeling environment.

PubMed

Symons, Jennifer E; Fyhrie, David P; Hawkins, David A; Upadhyaya, Shrinivasa K; Stover, Susan M

2015-02-26

Race surfaces have been associated with the incidence of racehorse musculoskeletal injury, the leading cause of racehorse attrition. Optimal race surface mechanical behaviors that minimize injury risk are unknown. Computational models are an economical method to determine optimal mechanical behaviors. Previously developed equine musculoskeletal models utilized ground reaction floor models designed to simulate a stiff, smooth floor appropriate for a human gait laboratory. Our objective was to develop a computational race surface model (two force-displacement functions, one linear and one nonlinear) that reproduced experimental race surface mechanical behaviors for incorporation in equine musculoskeletal models. Soil impact tests were simulated in a musculoskeletal modeling environment and compared to experimental force and displacement data collected during initial and repeat impacts at two racetracks with differing race surfaces - (i) dirt and (ii) synthetic. Best-fit model coefficients (7 total) were compared between surface types and initial and repeat impacts using a mixed model ANCOVA. Model simulation results closely matched empirical force, displacement and velocity data (Mean R(2)=0.930-0.997). Many model coefficients were statistically different between surface types and impacts. Principal component analysis of model coefficients showed systematic differences based on surface type and impact. In the future, the race surface model may be used in conjunction with previously developed the equine musculoskeletal models to understand the effects of race surface mechanical behaviors on limb dynamics, and determine race surface mechanical behaviors that reduce the incidence of racehorse musculoskeletal injury through modulation of limb dynamics. Copyright © 2015 Elsevier Ltd. All rights reserved.