Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

PubMed

Romo, Tod D; Leioatts, Nicholas; Grossfield, Alan

2014-12-15

LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development. © 2014 Wiley Periodicals, Inc.

The Australian Computational Earth Systems Simulator

NASA Astrophysics Data System (ADS)

Mora, P.; Muhlhaus, H.; Lister, G.; Dyskin, A.; Place, D.; Appelbe, B.; Nimmervoll, N.; Abramson, D.

2001-12-01

Numerical simulation of the physics and dynamics of the entire earth system offers an outstanding opportunity for advancing earth system science and technology but represents a major challenge due to the range of scales and physical processes involved, as well as the magnitude of the software engineering effort required. However, new simulation and computer technologies are bringing this objective within reach. Under a special competitive national funding scheme to establish new Major National Research Facilities (MNRF), the Australian government together with a consortium of Universities and research institutions have funded construction of the Australian Computational Earth Systems Simulator (ACcESS). The Simulator or computational virtual earth will provide the research infrastructure to the Australian earth systems science community required for simulations of dynamical earth processes at scales ranging from microscopic to global. It will consist of thematic supercomputer infrastructure and an earth systems simulation software system. The Simulator models and software will be constructed over a five year period by a multi-disciplinary team of computational scientists, mathematicians, earth scientists, civil engineers and software engineers. The construction team will integrate numerical simulation models (3D discrete elements/lattice solid model, particle-in-cell large deformation finite-element method, stress reconstruction models, multi-scale continuum models etc) with geophysical, geological and tectonic models, through advanced software engineering and visualization technologies. When fully constructed, the Simulator aims to provide the software and hardware infrastructure needed to model solid earth phenomena including global scale dynamics and mineralisation processes, crustal scale processes including plate tectonics, mountain building, interacting fault system dynamics, and micro-scale processes that control the geological, physical and dynamic behaviour of earth systems. ACcESS represents a part of Australia's contribution to the APEC Cooperation for Earthquake Simulation (ACES) international initiative. Together with other national earth systems science initiatives including the Japanese Earth Simulator and US General Earthquake Model projects, ACcESS aims to provide a driver for scientific advancement and technological breakthroughs including: quantum leaps in understanding of earth evolution at global, crustal, regional and microscopic scales; new knowledge of the physics of crustal fault systems required to underpin the grand challenge of earthquake prediction; new understanding and predictive capabilities of geological processes such as tectonics and mineralisation.

Determination and Control of Optical and X-Ray Wave Fronts

NASA Technical Reports Server (NTRS)

Kim, Young K.

1997-01-01

A successful design of a space-based or ground optical system requires an iterative procedure which includes the kinematics and dynamics of the system in operating environment, control synthesis and verification. To facilitate the task of designing optical wave front control systems being developed at NASA/MSFC, a multi-discipline dynamics and control tool has been developed by utilizing TREETOPS, a multi-body dynamics and control simulation, NASTRAN and MATLAB. Dynamics and control models of STABLE and ARIS were developed for TREETOPS simulation, and their simulation results are documented in this report.

Real-time electron dynamics for massively parallel excited-state simulations

NASA Astrophysics Data System (ADS)

Andrade, Xavier

The simulation of the real-time dynamics of electrons, based on time dependent density functional theory (TDDFT), is a powerful approach to study electronic excited states in molecular and crystalline systems. What makes the method attractive is its flexibility to simulate different kinds of phenomena beyond the linear-response regime, including strongly-perturbed electronic systems and non-adiabatic electron-ion dynamics. Electron-dynamics simulations are also attractive from a computational point of view. They can run efficiently on massively parallel architectures due to the low communication requirements. Our implementations of electron dynamics, based on the codes Octopus (real-space) and Qball (plane-waves), allow us to simulate systems composed of thousands of atoms and to obtain good parallel scaling up to 1.6 million processor cores. Due to the versatility of real-time electron dynamics and its parallel performance, we expect it to become the method of choice to apply the capabilities of exascale supercomputers for the simulation of electronic excited states.

Rupture Dynamics and Seismic Radiation on Rough Faults for Simulation-Based PSHA

NASA Astrophysics Data System (ADS)

Mai, P. M.; Galis, M.; Thingbaijam, K. K. S.; Vyas, J. C.; Dunham, E. M.

2017-12-01

Simulation-based ground-motion predictions may augment PSHA studies in data-poor regions or provide additional shaking estimations, incl. seismic waveforms, for critical facilities. Validation and calibration of such simulation approaches, based on observations and GMPE's, is important for engineering applications, while seismologists push to include the precise physics of the earthquake rupture process and seismic wave propagation in 3D heterogeneous Earth. Geological faults comprise both large-scale segmentation and small-scale roughness that determine the dynamics of the earthquake rupture process and its radiated seismic wavefield. We investigate how different parameterizations of fractal fault roughness affect the rupture evolution and resulting near-fault ground motions. Rupture incoherence induced by fault roughness generates realistic ω-2 decay for high-frequency displacement amplitude spectra. Waveform characteristics and GMPE-based comparisons corroborate that these rough-fault rupture simulations generate realistic synthetic seismogram for subsequent engineering application. Since dynamic rupture simulations are computationally expensive, we develop kinematic approximations that emulate the observed dynamics. Simplifying the rough-fault geometry, we find that perturbations in local moment tensor orientation are important, while perturbations in local source location are not. Thus, a planar fault can be assumed if the local strike, dip, and rake are maintained. The dynamic rake angle variations are anti-correlated with local dip angles. Based on a dynamically consistent Yoffe source-time function, we show that the seismic wavefield of the approximated kinematic rupture well reproduces the seismic radiation of the full dynamic source process. Our findings provide an innovative pseudo-dynamic source characterization that captures fault roughness effects on rupture dynamics. Including the correlations between kinematic source parameters, we present a new pseudo-dynamic rupture modeling approach for computing broadband ground-motion time-histories for simulation-based PSHA

Code Samples Used for Complexity and Control

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

The following sections are included: * MathematicaⓇ Code * Generic Chaotic Simulator * Vector Differential Operators * NLS Explorer * 2C++ Code * C++ Lambda Functions for Real Calculus * Accelerometer Data Processor * Simple Predictor-Corrector Integrator * Solving the BVP with the Shooting Method * Linear Hyperbolic PDE Solver * Linear Elliptic PDE Solver * Method of Lines for a Set of the NLS Equations * C# Code * Iterative Equation Solver * Simulated Annealing: A Function Minimum * Simple Nonlinear Dynamics * Nonlinear Pendulum Simulator * Lagrangian Dynamics Simulator * Complex-Valued Crowd Attractor Dynamics * Freeform Fortran Code * Lorenz Attractor Simulator * Complex Lorenz Attractor * Simple SGE Soliton * Complex Signal Presentation * Gaussian Wave Packet * Hermitian Matrices * Euclidean L2-Norm * Vector/Matrix Operations * Plain C-Code: Levenberg-Marquardt Optimizer * Free Basic Code: 2D Crowd Dynamics with 3000 Agents

A simple dynamic engine model for use in a real-time aircraft simulation with thrust vectoring

NASA Technical Reports Server (NTRS)

Johnson, Steven A.

1990-01-01

A simple dynamic engine model was developed at the NASA Ames Research Center, Dryden Flight Research Facility, for use in thrust vectoring control law development and real-time aircraft simulation. The simple dynamic engine model of the F404-GE-400 engine (General Electric, Lynn, Massachusetts) operates within the aircraft simulator. It was developed using tabular data generated from a complete nonlinear dynamic engine model supplied by the manufacturer. Engine dynamics were simulated using a throttle rate limiter and low-pass filter. Included is a description of a method to account for axial thrust loss resulting from thrust vectoring. In addition, the development of the simple dynamic engine model and its incorporation into the F-18 high alpha research vehicle (HARV) thrust vectoring simulation. The simple dynamic engine model was evaluated at Mach 0.2, 35,000 ft altitude and at Mach 0.7, 35,000 ft altitude. The simple dynamic engine model is within 3 percent of the steady state response, and within 25 percent of the transient response of the complete nonlinear dynamic engine model.

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks.

PubMed

Salis, Howard; Kaznessis, Yiannis N

2005-12-01

Stochastic chemical kinetics more accurately describes the dynamics of "small" chemical systems, such as biological cells. Many real systems contain dynamical stiffness, which causes the exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend the majority of their time executing frequently occurring reaction events. Previous methods have successfully applied a type of probabilistic steady-state approximation by deriving an evolution equation, such as the chemical master equation, for the relaxed fast dynamics and using the solution of that equation to determine the slow dynamics. However, because the solution of the chemical master equation is limited to small, carefully selected, or linear reaction networks, an alternate equation-free method would be highly useful. We present a probabilistic steady-state approximation that separates the time scales of an arbitrary reaction network, detects the convergence of a marginal distribution to a quasi-steady-state, directly samples the underlying distribution, and uses those samples to accurately predict the state of the system, including the effects of the slow dynamics, at future times. The numerical method produces an accurate solution of both the fast and slow reaction dynamics while, for stiff systems, reducing the computational time by orders of magnitude. The developed theory makes no approximations on the shape or form of the underlying steady-state distribution and only assumes that it is ergodic. We demonstrate the accuracy and efficiency of the method using multiple interesting examples, including a highly nonlinear protein-protein interaction network. The developed theory may be applied to any type of kinetic Monte Carlo simulation to more efficiently simulate dynamically stiff systems, including existing exact, approximate, or hybrid stochastic simulation techniques.

Multiple shooting shadowing for sensitivity analysis of chaotic dynamical systems

NASA Astrophysics Data System (ADS)

Blonigan, Patrick J.; Wang, Qiqi

2018-02-01

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

Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.

PubMed

Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus

2015-05-01

The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

PubMed

Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

2014-09-01

Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

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.

A digital computer program for the dynamic interaction simulation of controls and structure (DISCOS), volume 1

NASA Technical Reports Server (NTRS)

Bodley, C. S.; Devers, A. D.; Park, A. C.; Frisch, H. P.

1978-01-01

A theoretical development and associated digital computer program system for the dynamic simulation and stability analysis of passive and actively controlled spacecraft are presented. The dynamic system (spacecraft) is modeled as an assembly of rigid and/or flexible bodies not necessarily in a topological tree configuration. The computer program system is used to investigate total system dynamic characteristics, including interaction effects between rigid and/or flexible bodies, control systems, and a wide range of environmental loadings. In addition, the program system is used for designing attitude control systems and for evaluating total dynamic system performance, including time domain response and frequency domain stability analyses.

Brownian dynamics simulation of rigid particles of arbitrary shape in external fields.

PubMed

Fernandes, Miguel X; de la Torre, José García

2002-12-01

We have developed a Brownian dynamics simulation algorithm to generate Brownian trajectories of an isolated, rigid particle of arbitrary shape in the presence of electric fields or any other external agents. Starting from the generalized diffusion tensor, which can be calculated with the existing HYDRO software, the new program BROWNRIG (including a case-specific subprogram for the external agent) carries out a simulation that is analyzed later to extract the observable dynamic properties. We provide a variety of examples of utilization of this method, which serve as tests of its performance, and also illustrate its applicability. Examples include free diffusion, transport in an electric field, and diffusion in a restricting environment.

HYTESS 2: A Hypothetical Turbofan Engine Simplified Simulation with multivariable control and sensor analytical redundancy

NASA Technical Reports Server (NTRS)

Merrill, W. C.

1986-01-01

A hypothetical turbofan engine simplified simulation with a multivariable control and sensor failure detection, isolation, and accommodation logic (HYTESS II) is presented. The digital program, written in FORTRAN, is self-contained, efficient, realistic and easily used. Simulated engine dynamics were developed from linearized operating point models. However, essential nonlinear effects are retained. The simulation is representative of the hypothetical, low bypass ratio turbofan engine with an advanced control and failure detection logic. Included is a description of the engine dynamics, the control algorithm, and the sensor failure detection logic. Details of the simulation including block diagrams, variable descriptions, common block definitions, subroutine descriptions, and input requirements are given. Example simulation results are also presented.

Liquid li structure and dynamics: A comparison between OFDFT and second nearest-neighbor embedded-atom method

DOE PAGES

Chen, Mohan; Vella, Joseph R.; Panagiotopoulos, Athanassios Z.; ...

2015-04-08

The structure and dynamics of liquid lithium are studied using two simulation methods: orbital-free (OF) first-principles molecular dynamics (MD), which employs OF density functional theory (DFT), and classical MD utilizing a second nearest-neighbor embedded-atom method potential. The properties we studied include the dynamic structure factor, the self-diffusion coefficient, the dispersion relation, the viscosity, and the bond angle distribution function. Our simulation results were compared to available experimental data when possible. Each method has distinct advantages and disadvantages. For example, OFDFT gives better agreement with experimental dynamic structure factors, yet is more computationally demanding than classical simulations. Classical simulations can accessmore » a broader temperature range and longer time scales. The combination of first-principles and classical simulations is a powerful tool for studying properties of liquid lithium.« less

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Kremer, Kurt; Potestio, Raffaello; Tuckerman, Mark E.

2017-12-01

Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties. To this end, we derive a new integration algorithm that also makes use of multiple time-stepping. The scheme is validated via adaptive classical-path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins.

The AgroEcoSystem (AgES) response-function model simulates layered soil water dynamics in semi-arid Colorado: sensitivity and calibration

USDA-ARS?s Scientific Manuscript database

Simulation of vertical soil hydrology is a critical component of simulating even more complex soil water dynamics in space and time, including land-atmosphere and subsurface interactions. The AgroEcoSystem (AgES) model is defined here as a single land unit implementation of the full AgES-W (Watershe...

Early Results from Solar Dynamic Space Power System Testing

NASA Technical Reports Server (NTRS)

Shaltens, Richard K.; Mason, Lee S.

1996-01-01

A government/industry team designed, built and tested a 2-kWe solar dynamic space power system in a large thermal vacuum facility with a simulated Sun at the NASA Lewis Research Center. The Lewis facility provides an accurate simulation of temperatures, high vacuum and solar flux as encountered in low-Earth orbit. The solar dynamic system includes a Brayton power conversion unit integrated with a solar receiver which is designed to store energy for continuous power operation during the eclipse phase of the orbit. This paper reviews the goals and status of the Solar Dynamic Ground Test Demonstration project and describes the initial testing, including both operational and performance data. System testing to date has accumulated over 365 hours of power operation (ranging from 400 watts to 2.0-W(sub e)), including 187 simulated orbits, 16 ambient starts and 2 hot restarts. Data are shown for an orbital startup, transient and steady-state orbital operation and shutdown. System testing with varying insolation levels and operating speeds is discussed. The solar dynamic ground test demonstration is providing the experience and confidence toward a successful flight demonstration of the solar dynamic technologies on the Space Station Mir in 1997.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

PubMed

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

Space station dynamics, attitude control and momentum management

NASA Technical Reports Server (NTRS)

Sunkel, John W.; Singh, Ramen P.; Vengopal, Ravi

1989-01-01

The Space Station Attitude Control System software test-bed provides a rigorous environment for the design, development and functional verification of GN and C algorithms and software. The approach taken for the simulation of the vehicle dynamics and environmental models using a computationally efficient algorithm is discussed. The simulation includes capabilities for docking/berthing dynamics, prescribed motion dynamics associated with the Mobile Remote Manipulator System (MRMS) and microgravity disturbances. The vehicle dynamics module interfaces with the test-bed through the central Communicator facility which is in turn driven by the Station Control Simulator (SCS) Executive. The Communicator addresses issues such as the interface between the discrete flight software and the continuous vehicle dynamics, and multi-programming aspects such as the complex flow of control in real-time programs. Combined with the flight software and redundancy management modules, the facility provides a flexible, user-oriented simulation platform.

Computational Methods for Structural Mechanics and Dynamics

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

1989-01-01

Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.

Dynamic extension of the Simulation Problem Analysis Kernel (SPANK)

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

Sowell, E.F.; Buhl, W.F.

1988-07-15

The Simulation Problem Analysis Kernel (SPANK) is an object-oriented simulation environment for general simulation purposes. Among its unique features is use of the directed graph as the primary data structure, rather than the matrix. This allows straightforward use of graph algorithms for matching variables and equations, and reducing the problem graph for efficient numerical solution. The original prototype implementation demonstrated the principles for systems of algebraic equations, allowing simulation of steady-state, nonlinear systems (Sowell 1986). This paper describes how the same principles can be extended to include dynamic objects, allowing simulation of general dynamic systems. The theory is developed andmore » an implementation is described. An example is taken from the field of building energy system simulation. 2 refs., 9 figs.« less

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

PubMed

Rapaport, D C

2009-04-01

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

Influence of ecohydrologic feedbacks from simulated crop growth on integrated regional hydrologic simulations under climate scenarios

NASA Astrophysics Data System (ADS)

van Walsum, P. E. V.; Supit, I.

2012-06-01

Hydrologic climate change modelling is hampered by climate-dependent model parameterizations. To reduce this dependency, we extended the regional hydrologic modelling framework SIMGRO to host a two-way coupling between the soil moisture model MetaSWAP and the crop growth simulation model WOFOST, accounting for ecohydrologic feedbacks in terms of radiation fraction that reaches the soil, crop coefficient, interception fraction of rainfall, interception storage capacity, and root zone depth. Except for the last, these feedbacks are dependent on the leaf area index (LAI). The influence of regional groundwater on crop growth is included via a coupling to MODFLOW. Two versions of the MetaSWAP-WOFOST coupling were set up: one with exogenous vegetation parameters, the "static" model, and one with endogenous crop growth simulation, the "dynamic" model. Parameterization of the static and dynamic models ensured that for the current climate the simulated long-term averages of actual evapotranspiration are the same for both models. Simulations were made for two climate scenarios and two crops: grass and potato. In the dynamic model, higher temperatures in a warm year under the current climate resulted in accelerated crop development, and in the case of potato a shorter growing season, thus partly avoiding the late summer heat. The static model has a higher potential transpiration; depending on the available soil moisture, this translates to a higher actual transpiration. This difference between static and dynamic models is enlarged by climate change in combination with higher CO2 concentrations. Including the dynamic crop simulation gives for potato (and other annual arable land crops) systematically higher effects on the predicted recharge change due to climate change. Crop yields from soils with poor water retention capacities strongly depend on capillary rise if moisture supply from other sources is limited. Thus, including a crop simulation model in an integrated hydrologic simulation provides a valuable addition for hydrologic modelling as well as for crop modelling.

Analyses of the dynamic docking test system for advanced mission docking system test programs. [Apollo Soyuz Test Project

NASA Technical Reports Server (NTRS)

Gates, R. M.; Williams, J. E.

1974-01-01

Results are given of analytical studies performed in support of the design, implementation, checkout and use of NASA's dynamic docking test system (DDTS). Included are analyses of simulator components, a list of detailed operational test procedures, a summary of simulator performance, and an analysis and comparison of docking dynamics and loads obtained by test and analysis.

Parallel processing for nonlinear dynamics simulations of structures including rotating bladed-disk assemblies

NASA Technical Reports Server (NTRS)

Hsieh, Shang-Hsien

1993-01-01

The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.

Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment

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

Pratihar, Subha; Barnes, George L.; Laskin, Julia

In this Perspective mass spectrometry experiments and chemical dynamics simulations are described which have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated surface-induced dissociation (SID) for which peptide-H+ fragments upon collision with the surface, peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). The simulations include QM+MM and QM/MM direct dynamics. For collisions with self-assembled monolayer (SAM) surfaces there is quite good agreement between experiment and simulation in the efficiency of energy transfer to the peptide-H+ ion’s internal degrees of freedom. Both themore » experiments and simulations show two mechanisms for peptide-H+ fragmentation, i.e. shattering and statistical, RRKM dynamics. Mechanisms for SL are probed in simulations of collisions of protonated dialanine with a perfluorinated SAM surface. RL has been studied experimentally for a number of peptide-H+ + surface systems, and qualitative agreement between simulation and experiment is found for two similar systems.« less

High Fidelity, “Faster than Real-Time” Simulator for Predicting Power System Dynamic Behavior - Final Technical Report

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

Flueck, Alex

The “High Fidelity, Faster than Real­Time Simulator for Predicting Power System Dynamic Behavior” was designed and developed by Illinois Institute of Technology with critical contributions from Electrocon International, Argonne National Laboratory, Alstom Grid and McCoy Energy. Also essential to the project were our two utility partners: Commonwealth Edison and AltaLink. The project was a success due to several major breakthroughs in the area of large­scale power system dynamics simulation, including (1) a validated faster than real­ time simulation of both stable and unstable transient dynamics in a large­scale positive sequence transmission grid model, (2) a three­phase unbalanced simulation platform formore » modeling new grid devices, such as independently controlled single­phase static var compensators (SVCs), (3) the world’s first high fidelity three­phase unbalanced dynamics and protection simulator based on Electrocon’s CAPE program, and (4) a first­of­its­ kind implementation of a single­phase induction motor model with stall capability. The simulator results will aid power grid operators in their true time of need, when there is a significant risk of cascading outages. The simulator will accelerate performance and enhance accuracy of dynamics simulations, enabling operators to maintain reliability and steer clear of blackouts. In the long­term, the simulator will form the backbone of the newly conceived hybrid real­time protection and control architecture that will coordinate local controls, wide­area measurements, wide­area controls and advanced real­time prediction capabilities. The nation’s citizens will benefit in several ways, including (1) less down time from power outages due to the faster­than­real­time simulator’s predictive capability, (2) higher levels of reliability due to the detailed dynamics plus protection simulation capability, and (3) more resiliency due to the three­ phase unbalanced simulator’s ability to model three­phase and single­ phase networks and devices.« less

Simulation of cooperating robot manipulators on a mobile platform

NASA Technical Reports Server (NTRS)

Murphy, Steve H.; Wen, John T.; Saridis, George N.

1990-01-01

The dynamic equations of motion for two manipulators holding a common object on a freely moving mobile platform are developed. The full dynamic interactions from arms to platform and arm-tip to arm-tip are included in the formulation. The development of the closed chain dynamics allows for the use of any solution for the open topological tree of base and manipulator links. In particular, because the system has 18 degrees of freedom, recursive solutions for the dynamic simulation become more promising for efficient calculations of the motion. Simulation of the system is accomplished through a MATLAB program, and the response is visualized graphically using the SILMA Cimstation.

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Two-Speed Gearbox Dynamic Simulation Predictions and Test Validation

NASA Technical Reports Server (NTRS)

Lewicki, David G.; DeSmidt, Hans; Smith, Edward C.; Bauman, Steven W.

2010-01-01

Dynamic simulations and experimental validation tests were performed on a two-stage, two-speed gearbox as part of the drive system research activities of the NASA Fundamental Aeronautics Subsonics Rotary Wing Project. The gearbox was driven by two electromagnetic motors and had two electromagnetic, multi-disk clutches to control output speed. A dynamic model of the system was created which included a direct current electric motor with proportional-integral-derivative (PID) speed control, a two-speed gearbox with dual electromagnetically actuated clutches, and an eddy current dynamometer. A six degree-of-freedom model of the gearbox accounted for the system torsional dynamics and included gear, clutch, shaft, and load inertias as well as shaft flexibilities and a dry clutch stick-slip friction model. Experimental validation tests were performed on the gearbox in the NASA Glenn gear noise test facility. Gearbox output speed and torque as well as drive motor speed and current were compared to those from the analytical predictions. The experiments correlate very well with the predictions, thus validating the dynamic simulation methodologies.

ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology.

PubMed

Bittig, Arne T; Uhrmacher, Adelinde M

2017-01-01

Spatio-temporal dynamics of cellular processes can be simulated at different levels of detail, from (deterministic) partial differential equations via the spatial Stochastic Simulation algorithm to tracking Brownian trajectories of individual particles. We present a spatial simulation approach for multi-level rule-based models, which includes dynamically hierarchically nested cellular compartments and entities. Our approach ML-Space combines discrete compartmental dynamics, stochastic spatial approaches in discrete space, and particles moving in continuous space. The rule-based specification language of ML-Space supports concise and compact descriptions of models and to adapt the spatial resolution of models easily.

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

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

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

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

Zitney, S.E.

This presentation will examine process systems engineering R&D needs for application to advanced fossil energy (FE) systems and highlight ongoing research activities at the National Energy Technology Laboratory (NETL) under the auspices of a recently launched Collaboratory for Process & Dynamic Systems Research. The three current technology focus areas include: 1) High-fidelity systems with NETL's award-winning Advanced Process Engineering Co-Simulator (APECS) technology for integrating process simulation with computational fluid dynamics (CFD) and virtual engineering concepts, 2) Dynamic systems with R&D on plant-wide IGCC dynamic simulation, control, and real-time training applications, and 3) Systems optimization including large-scale process optimization, stochastic simulationmore » for risk/uncertainty analysis, and cost estimation. Continued R&D aimed at these and other key process systems engineering models, methods, and tools will accelerate the development of advanced gasification-based FE systems and produce increasingly valuable outcomes for DOE and the Nation.« less

CO oxidation reaction on Pt(111) studied by the dynamic Monte Carlo method including lateral interactions of adsorbates.

PubMed

Nagasaka, Masanari; Kondoh, Hiroshi; Nakai, Ikuyo; Ohta, Toshiaki

2007-01-28

The dynamics of adsorbate structures during CO oxidation on Pt(111) surfaces and its effects on the reaction were studied by the dynamic Monte Carlo method including lateral interactions of adsorbates. The lateral interaction energies between adsorbed species were calculated by the density functional theory method. Dynamic Monte Carlo simulations were performed for the oxidation reaction over a mesoscopic scale, where the experimentally determined activation energies of elementary paths were altered by the calculated lateral interaction energies. The simulated results reproduced the characteristics of the microscopic and mesoscopic scale adsorbate structures formed during the reaction, and revealed that the complicated reaction kinetics is comprehensively explained by a single reaction path affected by the surrounding adsorbates. We also propose from the simulations that weakly adsorbed CO molecules at domain boundaries promote the island-periphery specific reaction.

Spatial simulation of forest succession and timber harvesting using LANDIS

Treesearch

Eric J. Gustafson; Stephen R. Shifley; David J. Mladenoff; Kevin K. Nimerfro; Hong S. He

2000-01-01

The LANDIS model simulates ecological dynamics, including forest succession, disturbance, seed dispersal and establishment, fire and wind disturbance, and their interactions. We describe the addition to LANDIS of capabilities to simulate forest vegetation management, including harvest. Stands (groups of cells) are prioritized for harvest using one of four ranking...

Formation and field-driven dynamics of nematic spheroids.

PubMed

Fu, Fred; Abukhdeir, Nasser Mohieddin

2017-07-19

Unlike the canonical application of liquid crystals (LCs), LC displays, emerging technologies based on LC materials are increasingly leveraging the presence of nanoscale defects. The inherent nanoscale characteristics of LC defects present both significant opportunities as well as barriers for the application of this fascinating class of materials. Simulation-based approaches to the study of the effects of confinement and interface anchoring conditions on LC domains has resulted in significant progress over the past decade, where simulations are now able to access experimentally-relevant length scales while simultaneously capturing nanoscale defect structures. In this work, continuum simulations were performed in order to study the dynamics of micron-scale nematic LC spheroids of varying shape. Nematic spheroids are one of the simplest inherently defect-containing LC structures and are relevant to polymer-dispersed LC-based "smart" window technology. Simulation results include nematic phase formation and external field-switching dynamics of nematic spheroids ranging in shape from oblate to prolate. Results include both qualitative and quantitative insight into the complex coupling of nanoscale defect dynamics and structure transitions to micron-scale reorientation. Dynamic mechanisms are presented and related to structural transitions in LC defects present in the nematic domain. Domain-averaged metrics including order parameters and response times are determined for a range of experimentally-accessible electric field strengths. These results have both fundamental and technological relevance, in that increased understanding of LC dynamics in the presence of defects is a key barrier to continued advancement in the field.

Predictions of Cockpit Simulator Experimental Outcome Using System Models

NASA Technical Reports Server (NTRS)

Sorensen, J. A.; Goka, T.

1984-01-01

This study involved predicting the outcome of a cockpit simulator experiment where pilots used cockpit displays of traffic information (CDTI) to establish and maintain in-trail spacing behind a lead aircraft during approach. The experiments were run on the NASA Ames Research Center multicab cockpit simulator facility. Prior to the experiments, a mathematical model of the pilot/aircraft/CDTI flight system was developed which included relative in-trail and vertical dynamics between aircraft in the approach string. This model was used to construct a digital simulation of the string dynamics including response to initial position errors. The model was then used to predict the outcome of the in-trail following cockpit simulator experiments. Outcome included performance and sensitivity to different separation criteria. The experimental results were then used to evaluate the model and its prediction accuracy. Lessons learned in this modeling and prediction study are noted.

How to assess the impact of a physical parameterization in simulations of moist convection?

NASA Astrophysics Data System (ADS)

Grabowski, Wojciech

2017-04-01

A numerical model capable in simulating moist convection (e.g., cloud-resolving model or large-eddy simulation model) consists of a fluid flow solver combined with required representations (i.e., parameterizations) of physical processes. The later typically include cloud microphysics, radiative transfer, and unresolved turbulent transport. Traditional approaches to investigate impacts of such parameterizations on convective dynamics involve parallel simulations with different parameterization schemes or with different scheme parameters. Such methodologies are not reliable because of the natural variability of a cloud field that is affected by the feedback between the physics and dynamics. For instance, changing the cloud microphysics typically leads to a different realization of the cloud-scale flow, and separating dynamical and microphysical impacts is difficult. This presentation will present a novel modeling methodology, the piggybacking, that allows studying the impact of a physical parameterization on cloud dynamics with confidence. The focus will be on the impact of cloud microphysics parameterization. Specific examples of the piggybacking approach will include simulations concerning the hypothesized deep convection invigoration in polluted environments, the validity of the saturation adjustment in modeling condensation in moist convection, and separation of physical impacts from statistical uncertainty in simulations applying particle-based Lagrangian microphysics, the super-droplet method.

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics

NASA Astrophysics Data System (ADS)

Tao, Xuecheng; Shushkov, Philip; Miller, Thomas F.

2018-03-01

We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation. An advantage of the isomorphic Hamiltonian is that it can easily be combined with existing mixed quantum-classical dynamics methods, such as surface hopping or Ehrenfest dynamics, to enable the simulation of electronically non-adiabatic processes with nuclear quantum effects. We present numerical applications of the isomorphic Hamiltonian to model two- and three-level systems, with encouraging results that include improvement upon a previously reported combination of RPMD with surface hopping in the deep-tunneling regime.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.

PubMed

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin

2014-10-14

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

The Dynamic Response Computation (DIRECT) computer program simulates vibrations induced in a complex structure by applied dynamic loads. Developed to enable rapid analysis of launch- and landing- induced vibrations and stresses in a space shuttle, DIRECT also can be used to analyze dynamic responses of other structures - for example, the response of a building to an earthquake, or the response of an oil-drilling platform and attached tanks to large ocean waves. For a space-shuttle simulation, the required input to DIRECT includes mathematical models of the space shuttle and its payloads, and a set of forcing functions that simulates launch and landing loads. DIRECT can accommodate multiple levels of payload attachment and substructure as well as nonlinear dynamic responses of structural interfaces. DIRECT combines the shuttle and payload models into a single structural model, to which the forcing functions are then applied. The resulting equations of motion are reduced to an optimum set and decoupled into a unique format for simulating dynamics. During the simulation, maximum vibrations, loads, and stresses are monitored and recorded for subsequent analysis to identify structural deficiencies in the shuttle and/or payloads.

MicroHH 1.0: a computational fluid dynamics code for direct numerical simulation and large-eddy simulation of atmospheric boundary layer flows

NASA Astrophysics Data System (ADS)

van Heerwaarden, Chiel C.; van Stratum, Bart J. H.; Heus, Thijs; Gibbs, Jeremy A.; Fedorovich, Evgeni; Mellado, Juan Pedro

2017-08-01

This paper describes MicroHH 1.0, a new and open-source (www.microhh.org) computational fluid dynamics code for the simulation of turbulent flows in the atmosphere. It is primarily made for direct numerical simulation but also supports large-eddy simulation (LES). The paper covers the description of the governing equations, their numerical implementation, and the parameterizations included in the code. Furthermore, the paper presents the validation of the dynamical core in the form of convergence and conservation tests, and comparison of simulations of channel flows and slope flows against well-established test cases. The full numerical model, including the associated parameterizations for LES, has been tested for a set of cases under stable and unstable conditions, under the Boussinesq and anelastic approximations, and with dry and moist convection under stationary and time-varying boundary conditions. The paper presents performance tests showing good scaling from 256 to 32 768 processes. The graphical processing unit (GPU)-enabled version of the code can reach a speedup of more than an order of magnitude for simulations that fit in the memory of a single GPU.

Simulation of FRET dyes allows quantitative comparison against experimental data

NASA Astrophysics Data System (ADS)

Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T.; Jacob, Christoph R.; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander

2018-03-01

Fully understanding biomolecular function requires detailed insight into the systems' structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

Force and Moment Approach for Achievable Dynamics Using Nonlinear Dynamic Inversion

NASA Technical Reports Server (NTRS)

Ostroff, Aaron J.; Bacon, Barton J.

1999-01-01

This paper describes a general form of nonlinear dynamic inversion control for use in a generic nonlinear simulation to evaluate candidate augmented aircraft dynamics. The implementation is specifically tailored to the task of quickly assessing an aircraft's control power requirements and defining the achievable dynamic set. The achievable set is evaluated while undergoing complex mission maneuvers, and perfect tracking will be accomplished when the desired dynamics are achievable. Variables are extracted directly from the simulation model each iteration, so robustness is not an issue. Included in this paper is a description of the implementation of the forces and moments from simulation variables, the calculation of control effectiveness coefficients, methods for implementing different types of aerodynamic and thrust vectoring controls, adjustments for control effector failures, and the allocation approach used. A few examples illustrate the perfect tracking results obtained.

The influence of fatty acids on the GpA dimer interface by coarse-grained molecular dynamics simulation.

PubMed

Flinner, Nadine; Mirus, Oliver; Schleiff, Enrico

2014-08-15

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA.

The Influence of Fatty Acids on the GpA Dimer Interface by Coarse-Grained Molecular Dynamics Simulation

PubMed Central

Flinner, Nadine; Mirus, Oliver; Schleiff, Enrico

2014-01-01

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA. PMID:25196522

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

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

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

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

A model of milk production in lactating dairy cows in relation to energy and nitrogen dynamics.

PubMed

Johnson, I R; France, J; Cullen, B R

2016-02-01

A generic daily time-step model of a dairy cow, designed to be included in whole-system pasture simulation models, is described that includes growth, milk production, and lactation in relation to energy and nitrogen dynamics. It is a development of a previously described animal growth and metabolism model that describes animal body composition in terms of protein, water, and fat, and energy dynamics in relation to growth requirements, resynthesis of degraded protein, and animal activity. This is further developed to include lactation and fetal growth. Intake is calculated in relation to stage of lactation, pasture availability, supplementary feed, and feed quality. Energy costs associated with urine N excretion and methane fermentation are accounted for. Milk production and fetal growth are then calculated in relation to the overall energy and nitrogen dynamics. The general behavior of the model is consistent with expected characteristics. Simulations using the model as part of a whole-system pasture simulation model (DairyMod) are compared with experimental data where good agreement between pasture, concentrate and forage intake, as well as milk production over 3 consecutive lactation cycles, is observed. The model is shown to be well suited for inclusion in large-scale system simulation models. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Transient Solid Dynamics Simulations on the Sandia/Intel Teraflop Computer

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

Attaway, S.; Brown, K.; Gardner, D.

1997-12-31

Transient solid dynamics simulations are among the most widely used engineering calculations. Industrial applications include vehicle crashworthiness studies, metal forging, and powder compaction prior to sintering. These calculations are also critical to defense applications including safety studies and weapons simulations. The practical importance of these calculations and their computational intensiveness make them natural candidates for parallelization. This has proved to be difficult, and existing implementations fail to scale to more than a few dozen processors. In this paper we describe our parallelization of PRONTO, Sandia`s transient solid dynamics code, via a novel algorithmic approach that utilizes multiple decompositions for differentmore » key segments of the computations, including the material contact calculation. This latter calculation is notoriously difficult to perform well in parallel, because it involves dynamically changing geometry, global searches for elements in contact, and unstructured communications among the compute nodes. Our approach scales to at least 3600 compute nodes of the Sandia/Intel Teraflop computer (the largest set of nodes to which we have had access to date) on problems involving millions of finite elements. On this machine we can simulate models using more than ten- million elements in a few tenths of a second per timestep, and solve problems more than 3000 times faster than a single processor Cray Jedi.« less

A mathematical simulation model of the CH-47B helicopter, volume 2

NASA Technical Reports Server (NTRS)

Weber, J. M.; Liu, T. Y.; Chung, W.

1984-01-01

A nonlinear simulation model of the CH-47B helicopter, was adapted for use in a simulation facility. The model represents the specific configuration of the variable stability CH-47B helicopter. Modeling of the helicopter uses a total force approach in six rigid body degrees of freedom. Rotor dynamics are simulated using the Wheatley-Bailey equations, steady state flapping dynamics and included in the model of the option for simulation of external suspension, slung load equations of motion. Validation of the model was accomplished by static and dynamic data from the original Boeing Vertol mathematical model and flight test data. The model is appropriate for use in real time piloted simulation and is implemented on the ARC Sigma IX computer where it may be operated with a digital cycle time of 0.03 sec.

A size-composition resolved aerosol model for simulating the dynamics of externally mixed particles: SCRAM (v 1.0)

NASA Astrophysics Data System (ADS)

Zhu, S.; Sartelet, K. N.; Seigneur, C.

2015-06-01

The Size-Composition Resolved Aerosol Model (SCRAM) for simulating the dynamics of externally mixed atmospheric particles is presented. This new model classifies aerosols by both composition and size, based on a comprehensive combination of all chemical species and their mass-fraction sections. All three main processes involved in aerosol dynamics (coagulation, condensation/evaporation and nucleation) are included. The model is first validated by comparison with a reference solution and with results of simulations using internally mixed particles. The degree of mixing of particles is investigated in a box model simulation using data representative of air pollution in Greater Paris. The relative influence on the mixing state of the different aerosol processes (condensation/evaporation, coagulation) and of the algorithm used to model condensation/evaporation (bulk equilibrium, dynamic) is studied.

Comparison of human driver dynamics in simulators with complex and simple visual displays and in an automobile on the road

NASA Technical Reports Server (NTRS)

Mcruer, D. T.; Klein, R. H.

1975-01-01

As part of a comprehensive program exploring driver/vehicle system response in lateral steering tasks, driver/vehicle system describing functions and other dynamic data have been gathered in several milieu. These include a simple fixed base simulator with an elementary roadway delineation only display; a fixed base statically operating automobile with a terrain model based, wide angle projection system display; and a full scale moving base automobile operating on the road. Dynamic data with the two fixed base simulators compared favorably, implying that the impoverished visual scene, lack of engine noise, and simplified steering wheel feel characteristics in the simple simulator did not induce significant driver dynamic behavior variations. The fixed base vs. moving base comparisons showed substantially greater crossover frequencies and phase margins on the road course.

Relating Standardized Visual Perception Measures to Simulator Visual System Performance

NASA Technical Reports Server (NTRS)

Kaiser, Mary K.; Sweet, Barbara T.

2013-01-01

Human vision is quantified through the use of standardized clinical vision measurements. These measurements typically include visual acuity (near and far), contrast sensitivity, color vision, stereopsis (a.k.a. stereo acuity), and visual field periphery. Simulator visual system performance is specified in terms such as brightness, contrast, color depth, color gamut, gamma, resolution, and field-of-view. How do these simulator performance characteristics relate to the perceptual experience of the pilot in the simulator? In this paper, visual acuity and contrast sensitivity will be related to simulator visual system resolution, contrast, and dynamic range; similarly, color vision will be related to color depth/color gamut. Finally, we will consider how some characteristics of human vision not typically included in current clinical assessments could be used to better inform simulator requirements (e.g., relating dynamic characteristics of human vision to update rate and other temporal display characteristics).

Simulating dynamic and mixed-severity fire regimes: a process-based fire extension for LANDIS-II

Treesearch

Brian R. Sturtevant; Robert M. Scheller; Brian R. Miranda; Douglas Shinneman; Alexandra Syphard

2009-01-01

Fire regimes result from reciprocal interactions between vegetation and fire that may be further affected by other disturbances, including climate, landform, and terrain. In this paper, we describe fire and fuel extensions for the forest landscape simulation model, LANDIS-II, that allow dynamic interactions among fire, vegetation, climate, and landscape structure, and...

Simulation of cooperating robot manipulators on a mobile platform

NASA Technical Reports Server (NTRS)

Murphy, Stephen H.; Wen, John Ting-Yung; Saridis, George N.

1991-01-01

The dynamic equations of motion are presented for two or more cooperating manipulators on a freely moving mobile platform. The system of cooperating robot manipulators forms a closed kinematic chain where the force of interaction must be included in the formulation of robot and platform dynamics. The formulation includes the full dynamic interactions from arms to platform and arm tip to arm tip, and the possible translation and rotation of the platform. The equations of motion are shown to be identical in structure to the fixed-platform cooperative manipulator dynamics. The number of DOFs of the system is sufficiently large to make recursive dynamic calculation methods potentially more efficient than closed-form solutions. A complete simulation with two 6-DOF manipulators of a free-floating platform is presented along a with a multiple-arm controller to position the common load.

Fully dynamical simulation of central nuclear collisions.

PubMed

van der Schee, Wilke; Romatschke, Paul; Pratt, Scott

2013-11-27

We present a fully dynamical simulation of central nuclear collisions around midrapidity at LHC energies. Unlike previous treatments, we simulate all phases of the collision, including the equilibration of the system. For the simulation, we use numerical relativity solutions to anti-de Sitter space/conformal field theory for the preequilibrium stage, viscous hydrodynamics for the plasma equilibrium stage, and kinetic theory for the low-density hadronic stage. Our preequilibrium stage provides initial conditions for hydrodynamics, resulting in sizable radial flow. The resulting light particle spectra reproduce the measurements from the ALICE experiment at all transverse momenta.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

NASA Astrophysics Data System (ADS)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

A suite of exercises for verifying dynamic earthquake rupture codes

USGS Publications Warehouse

Harris, Ruth A.; Barall, Michael; Aagaard, Brad T.; Ma, Shuo; Roten, Daniel; Olsen, Kim B.; Duan, Benchun; Liu, Dunyu; Luo, Bin; Bai, Kangchen; Ampuero, Jean-Paul; Kaneko, Yoshihiro; Gabriel, Alice-Agnes; Duru, Kenneth; Ulrich, Thomas; Wollherr, Stephanie; Shi, Zheqiang; Dunham, Eric; Bydlon, Sam; Zhang, Zhenguo; Chen, Xiaofei; Somala, Surendra N.; Pelties, Christian; Tago, Josue; Cruz-Atienza, Victor Manuel; Kozdon, Jeremy; Daub, Eric; Aslam, Khurram; Kase, Yuko; Withers, Kyle; Dalguer, Luis

2018-01-01

We describe a set of benchmark exercises that are designed to test if computer codes that simulate dynamic earthquake rupture are working as intended. These types of computer codes are often used to understand how earthquakes operate, and they produce simulation results that include earthquake size, amounts of fault slip, and the patterns of ground shaking and crustal deformation. The benchmark exercises examine a range of features that scientists incorporate in their dynamic earthquake rupture simulations. These include implementations of simple or complex fault geometry, off‐fault rock response to an earthquake, stress conditions, and a variety of formulations for fault friction. Many of the benchmarks were designed to investigate scientific problems at the forefronts of earthquake physics and strong ground motions research. The exercises are freely available on our website for use by the scientific community.

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

Hale, Richard Edward; Cetiner, Sacit M.; Fugate, David L.

The Small Modular Reactor (SMR) Dynamic System Modeling Tool project is in the third year of development. The project is designed to support collaborative modeling and study of various advanced SMR (non-light water cooled) concepts, including the use of multiple coupled reactors at a single site. The objective of the project is to provide a common simulation environment and baseline modeling resources to facilitate rapid development of dynamic advanced reactor SMR models, ensure consistency among research products within the Instrumentation, Controls, and Human-Machine Interface (ICHMI) technical area, and leverage cross-cutting capabilities while minimizing duplication of effort. The combined simulation environmentmore » and suite of models are identified as the Modular Dynamic SIMulation (MoDSIM) tool. The critical elements of this effort include (1) defining a standardized, common simulation environment that can be applied throughout the program, (2) developing a library of baseline component modules that can be assembled into full plant models using existing geometry and thermal-hydraulic data, (3) defining modeling conventions for interconnecting component models, and (4) establishing user interfaces and support tools to facilitate simulation development (i.e., configuration and parameterization), execution, and results display and capture.« less

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

PubMed

Hertig, Samuel; Latorraca, Naomi R; Dror, Ron O

2016-06-01

Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

Modeling and simulation of dust behaviors behind a moving vehicle

NASA Astrophysics Data System (ADS)

Wang, Jingfang

Simulation of physically realistic complex dust behaviors is a difficult and attractive problem in computer graphics. A fast, interactive and visually convincing model of dust behaviors behind moving vehicles is very useful in computer simulation, training, education, art, advertising, and entertainment. In my dissertation, an experimental interactive system has been implemented for the simulation of dust behaviors behind moving vehicles. The system includes physically-based models, particle systems, rendering engines and graphical user interface (GUI). I have employed several vehicle models including tanks, cars, and jeeps to test and simulate in different scenarios and conditions. Calm weather, winding condition, vehicle turning left or right, and vehicle simulation controlled by users from the GUI are all included. I have also tested the factors which play against the physical behaviors and graphics appearances of the dust particles through GUI or off-line scripts. The simulations are done on a Silicon Graphics Octane station. The animation of dust behaviors is achieved by physically-based modeling and simulation. The flow around a moving vehicle is modeled using computational fluid dynamics (CFD) techniques. I implement a primitive variable and pressure-correction approach to solve the three dimensional incompressible Navier Stokes equations in a volume covering the moving vehicle. An alternating- direction implicit (ADI) method is used for the solution of the momentum equations, with a successive-over- relaxation (SOR) method for the solution of the Poisson pressure equation. Boundary conditions are defined and simplified according to their dynamic properties. The dust particle dynamics is modeled using particle systems, statistics, and procedure modeling techniques. Graphics and real-time simulation techniques, such as dynamics synchronization, motion blur, blending, and clipping have been employed in the rendering to achieve realistic appearing dust behaviors. In addition, I introduce a temporal smoothing technique to eliminate the jagged effect caused by large simulation time. Several algorithms are used to speed up the simulation. For example, pre-calculated tables and display lists are created to replace some of the most commonly used functions, scripts and processes. The performance study shows that both time and space costs of the algorithms are linear in the number of particles in the system. On a Silicon Graphics Octane, three vehicles with 20,000 particles run at 6-8 frames per second on average. This speed does not include the extra calculations of convergence of the numerical integration for fluid dynamics which usually takes about 4-5 minutes to achieve steady state.

Development of Constraint Force Equation Methodology for Application to Multi-Body Dynamics Including Launch Vehicle Stage Seperation

NASA Technical Reports Server (NTRS)

Pamadi, Bandu N.; Toniolo, Matthew D.; Tartabini, Paul V.; Roithmayr, Carlos M.; Albertson, Cindy W.; Karlgaard, Christopher D.

2016-01-01

The objective of this report is to develop and implement a physics based method for analysis and simulation of multi-body dynamics including launch vehicle stage separation. The constraint force equation (CFE) methodology discussed in this report provides such a framework for modeling constraint forces and moments acting at joints when the vehicles are still connected. Several stand-alone test cases involving various types of joints were developed to validate the CFE methodology. The results were compared with ADAMS(Registered Trademark) and Autolev, two different industry standard benchmark codes for multi-body dynamic analysis and simulations. However, these two codes are not designed for aerospace flight trajectory simulations. After this validation exercise, the CFE algorithm was implemented in Program to Optimize Simulated Trajectories II (POST2) to provide a capability to simulate end-to-end trajectories of launch vehicles including stage separation. The POST2/CFE methodology was applied to the STS-1 Space Shuttle solid rocket booster (SRB) separation and Hyper-X Research Vehicle (HXRV) separation from the Pegasus booster as a further test and validation for its application to launch vehicle stage separation problems. Finally, to demonstrate end-to-end simulation capability, POST2/CFE was applied to the ascent, orbit insertion, and booster return of a reusable two-stage-to-orbit (TSTO) vehicle concept. With these validation exercises, POST2/CFE software can be used for performing conceptual level end-to-end simulations, including launch vehicle stage separation, for problems similar to those discussed in this report.

From force-fields to photons: MD simulations of dye-labeled nucleic acids and Monte Carlo modeling of FRET

NASA Astrophysics Data System (ADS)

Goldner, Lori

2012-02-01

Fluorescence resonance energy transfer (FRET) is a powerful technique for understanding the structural fluctuations and transformations of RNA, DNA and proteins. Molecular dynamics (MD) simulations provide a window into the nature of these fluctuations on a different, faster, time scale. We use Monte Carlo methods to model and compare FRET data from dye-labeled RNA with what might be predicted from the MD simulation. With a few notable exceptions, the contribution of fluorophore and linker dynamics to these FRET measurements has not been investigated. We include the dynamics of the ground state dyes and linkers in our study of a 16mer double-stranded RNA. Water is included explicitly in the simulation. Cyanine dyes are attached at either the 3' or 5' ends with a 3 carbon linker, and differences in labeling schemes are discussed.[4pt] Work done in collaboration with Peker Milas, Benjamin D. Gamari, and Louis Parrot.

Finding the Missing Physics: Simulating Polydisperse Polymer Melts

NASA Astrophysics Data System (ADS)

Rorrer, Nichoals; Dorgan, John

2014-03-01

A Monte Carlo algorithm has been developed to model polydisperse polymer melts. For the first time, this enables the specification of a predetermined molecular weight distribution for lattice based simulations. It is demonstrated how to map an arbitrary probability distributions onto a discrete number of chains residing on an fcc lattice. The resulting algorithm is able to simulate a wide variety of behaviors for polydisperse systems including confinement effects, shear flow, and parabolic flow. The dynamic version of the algorithm accurately captures Rouse dynamics for short polymer chains, and reptation-like dynamics for longer chain lengths.1 When polydispersity is introduced, smaller Rouse times and broadened the transition between different scaling regimes are observed. Rouse times also decrease under confinement for both polydisperse and monodisperse systems and chain length dependent migration effects are observed. The steady-state version of the algorithm enables the simulation of flow and when polydisperse systems are subject to parabolic (Poiseulle) flow, a migration phenomenon based on chain length is again present. These and other phenomena highlight the importance of including polydispersity in obtaining physically realistic simulations of polymeric melts. 1. Dorgan, J.R.; Rorrer, N.A.; Maupin, C.M., Macromolecules 2012, 45(21), 8833-8840. Work funded by the Fluid Dynamics program of the National Science Foundation under grant CBET-1067707.

Computational plasticity algorithm for particle dynamics simulations

NASA Astrophysics Data System (ADS)

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

2018-01-01

The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.

Parallel simulation today

NASA Technical Reports Server (NTRS)

Nicol, David; Fujimoto, Richard

1992-01-01

This paper surveys topics that presently define the state of the art in parallel simulation. Included in the tutorial are discussions on new protocols, mathematical performance analysis, time parallelism, hardware support for parallel simulation, load balancing algorithms, and dynamic memory management for optimistic synchronization.

Recent research and applications of numerical simulation for dynamic response of long-span bridges subjected to multiple loads.

PubMed

Chen, Zhiwei; Chen, Bo

2014-01-01

Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach is based on numerical simulation technologies. This paper provides a detailed review of key issues involved in dynamic response analysis of long-span multiload bridges based on numerical simulation technologies, including dynamic interactions between running trains and bridge, between running road vehicles and bridge, and between wind and bridge, and in the wind-vehicle-bridge coupled system. Then a comprehensive review is conducted for engineering applications of newly developed numerical simulation technologies to safety assessment of long-span bridges, such as assessment of fatigue damage and assessment under extreme events. Finally, the existing problems and promising research efforts for the numerical simulation technologies and their applications to assessment of long-span multiload bridges are explored.

Recent Research and Applications of Numerical Simulation for Dynamic Response of Long-Span Bridges Subjected to Multiple Loads

PubMed Central

Chen, Zhiwei; Chen, Bo

2014-01-01

Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach is based on numerical simulation technologies. This paper provides a detailed review of key issues involved in dynamic response analysis of long-span multiload bridges based on numerical simulation technologies, including dynamic interactions between running trains and bridge, between running road vehicles and bridge, and between wind and bridge, and in the wind-vehicle-bridge coupled system. Then a comprehensive review is conducted for engineering applications of newly developed numerical simulation technologies to safety assessment of long-span bridges, such as assessment of fatigue damage and assessment under extreme events. Finally, the existing problems and promising research efforts for the numerical simulation technologies and their applications to assessment of long-span multiload bridges are explored. PMID:25006597

Self-Organization of Metal Nanoparticles in Light: Electrodynamics-Molecular Dynamics Simulations and Optical Binding Experiments.

PubMed

McCormack, Patrick; Han, Fei; Yan, Zijie

2018-02-01

Light-driven self-organization of metal nanoparticles (NPs) can lead to unique optical matter systems, yet simulation of such self-organization (i.e., optical binding) is a complex computational problem that increases nonlinearly with system size. Here we show that a combined electrodynamics-molecular dynamics simulation technique can simulate the trajectories and predict stable configurations of silver NPs in optical fields. The simulated dynamic equilibrium of a two-NP system matches the probability density of oscillations for two optically bound NPs obtained experimentally. The predicted stable configurations for up to eight NPs are further compared to experimental observations of silver NP clusters formed by optical binding in a Bessel beam. All configurations are confirmed to form in real systems, including pentagonal clusters with five-fold symmetry. Our combined simulations and experiments have revealed a diverse optical matter system formed by anisotropic optical binding interactions, providing a new strategy to discover artificial materials.

Importance of vegetation distribution for future carbon balance

NASA Astrophysics Data System (ADS)

Ahlström, A.; Xia, J.; Arneth, A.; Luo, Y.; Smith, B.

2015-12-01

Projections of future terrestrial carbon uptake vary greatly between simulations. Net primary production (NPP), wild fires, vegetation dynamics (including biome shifts) and soil decomposition constitute the main processes governing the response of the terrestrial carbon cycle in a changing climate. While primary production and soil respiration are relatively well studied and implemented in all global ecosystem models used to project the future land sink of CO2, vegetation dynamics are less studied and not always represented in global models. Here we used a detailed second generation dynamic global vegetation model with advanced representation of vegetation growth and mortality and the associated turnover and proven skill in predicting vegetation distribution and succession. We apply an emulator that describes the carbon flows and pools exactly as in simulations with the full model. The emulator simulates ecosystem dynamics in response to 13 different climate or Earth system model simulations from the CMIP5 ensemble under RCP8.5 radiative forcing at year 2085. We exchanged carbon cycle processes between these 13 simulations and investigate the changes predicted by the emulator. This method allowed us to partition the entire ensemble carbon uptake uncertainty into individual processes. We found that NPP, vegetation dynamics (including biome shifts, wild fires and mortality) and soil decomposition rates explained 49%, 17% and 33% respectively of uncertainties in modeled global C-uptake. Uncertainty due to vegetation dynamics was further partitioned into stand-clearing disturbances (16%), wild fires (0%), stand dynamics (7%), reproduction (10%) and biome shifts (67%) globally. We conclude that while NPP and soil decomposition rates jointly account for 83% of future climate induced C-uptake uncertainties, vegetation turnover and structure, dominated by shifts in vegetation distribution, represent a significant fraction globally and regionally (tropical forests: 40%), strongly motivating their representation and analysis in future C-cycle studies.

OSSOS: X. How to use a Survey Simulator: Statistical Testing of Dynamical Models Against the Real Kuiper Belt

NASA Astrophysics Data System (ADS)

Lawler, Samantha M.; Kavelaars, J. J.; Alexandersen, Mike; Bannister, Michele T.; Gladman, Brett; Petit, Jean-Marc; Shankman, Cory

2018-05-01

All surveys include observational biases, which makes it impossible to directly compare properties of discovered trans-Neptunian Objects (TNOs) with dynamical models. However, by carefully keeping track of survey pointings on the sky, detection limits, tracking fractions, and rate cuts, the biases from a survey can be modelled in Survey Simulator software. A Survey Simulator takes an intrinsic orbital model (from, for example, the output of a dynamical Kuiper belt emplacement simulation) and applies the survey biases, so that the biased simulated objects can be directly compared with real discoveries. This methodology has been used with great success in the Outer Solar System Origins Survey (OSSOS) and its predecessor surveys. In this chapter, we give four examples of ways to use the OSSOS Survey Simulator to gain knowledge about the true structure of the Kuiper Belt. We demonstrate how to statistically compare different dynamical model outputs with real TNO discoveries, how to quantify detection biases within a TNO population, how to measure intrinsic population sizes, and how to use upper limits from non-detections. We hope this will provide a framework for dynamical modellers to statistically test the validity of their models.

Nonlinear dynamic simulation of single- and multi-spool core engines

NASA Technical Reports Server (NTRS)

Schobeiri, T.; Lippke, C.; Abouelkheir, M.

1993-01-01

In this paper a new computational method for accurate simulation of the nonlinear dynamic behavior of single- and multi-spool core engines, turbofan engines, and power generation gas turbine engines is presented. In order to perform the simulation, a modularly structured computer code has been developed which includes individual mathematical modules representing various engine components. The generic structure of the code enables the dynamic simulation of arbitrary engine configurations ranging from single-spool thrust generation to multi-spool thrust/power generation engines under adverse dynamic operating conditions. For precise simulation of turbine and compressor components, row-by-row calculation procedures were implemented that account for the specific turbine and compressor cascade and blade geometry and characteristics. The dynamic behavior of the subject engine is calculated by solving a number of systems of partial differential equations, which describe the unsteady behavior of the individual components. In order to ensure the capability, accuracy, robustness, and reliability of the code, comprehensive critical performance assessment and validation tests were performed. As representatives, three different transient cases with single- and multi-spool thrust and power generation engines were simulated. The transient cases range from operating with a prescribed fuel schedule, to extreme load changes, to generator and turbine shut down.

Mastodon

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

Coleman, Justin Leigh; Veeraraghavan, Swetha; Bolisetti, Chandrakanth

MASTODON has the capability to model stochastic nonlinear soil-structure interaction (NLSSI) in a dynamic probabilistic risk assessment framework. The NLSSI simulations include structural dynamics, time integration, dynamic porous media flow, nonlinear hysteretic soil constitutive models, geometric nonlinearities (gapping, sliding, and uplift). MASTODON is also the MOOSE based master application for dynamic PRA of external hazards.

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Butler, Jason E.; Shaqfeh, Eric S. G.

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions.

PubMed

Butler, Jason E; Shaqfeh, Eric S G

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions. (c) 2005 American Institute of Physics.

Modeling Common-Sense Decisions

NASA Astrophysics Data System (ADS)

Zak, Michail

This paper presents a methodology for efficient synthesis of dynamical model simulating a common-sense decision making process. The approach is based upon the extension of the physics' First Principles that includes behavior of living systems. The new architecture consists of motor dynamics simulating actual behavior of the object, and mental dynamics representing evolution of the corresponding knowledge-base and incorporating it in the form of information flows into the motor dynamics. The autonomy of the decision making process is achieved by a feedback from mental to motor dynamics. This feedback replaces unavailable external information by an internal knowledgebase stored in the mental model in the form of probability distributions.

Dynamical Scaling Relations and the Angular Momentum Problem in the FIRE Simulations

NASA Astrophysics Data System (ADS)

Schmitz, Denise; Hopkins, Philip F.; Quataert, Eliot; Keres, Dusan; Faucher-Giguere, Claude-Andre

2015-01-01

Simulations are an extremely important tool with which to study galaxy formation and evolution. However, even state-of-the-art simulations still fail to accurately predict important galaxy properties such as star formation rates and dynamical scaling relations. One possible explanation is the inadequacy of sub-grid models to capture the range of stellar feedback mechanisms which operate below the resolution limit of simulations. FIRE (Feedback in Realistic Environments) is a set of high-resolution cosmological galaxy simulations run using the code GIZMO. It includes more realistic models for various types of feedback including radiation pressure, supernovae, stellar winds, and photoionization and photoelectric heating. Recent FIRE results have demonstrated good agreement with the observed stellar mass-halo mass relation as well as more realistic star formation histories than previous simulations. We investigate the effects of FIRE's improved feedback prescriptions on the simulation "angular momentum problem," i.e., whether FIRE can reproduce observed scaling relations between galaxy stellar mass and rotational/dispersion velocities.

von Kármán–Howarth Equation for Hall Magnetohydrodynamics: Hybrid Simulations

NASA Astrophysics Data System (ADS)

Hellinger, Petr; Verdini, Andrea; Landi, Simone; Franci, Luca; Matteini, Lorenzo

2018-04-01

A dynamical vectorial equation for homogeneous incompressible Hall-magnetohydrodynamic (MHD) turbulence together with the exact scaling law for third-order correlation tensors, analogous to that for the incompressible MHD, is rederived and applied to the results of two-dimensional hybrid simulations of plasma turbulence. At large (MHD) scales the simulations exhibit a clear inertial range where the MHD dynamic law is valid. In the sub-ion range the cascade continues via the Hall term, but the dynamic law derived in the framework of incompressible Hall-MHD equations is obtained only in a low plasma beta simulation. For a higher beta plasma the cascade rate decreases in the sub-ion range and the change becomes more pronounced as the plasma beta increases. This break in the cascade flux can be ascribed to nonthermal (kinetic) features or to others terms in the dynamical equation that are not included in the Hall-MHD incompressible approximation.

Lean flammability limit of downward propagating hydrogen-air flames

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

1992-01-01

Detailed multidimensional numerical simulations that include the effects of wall heat losses have been performed to study the dynamics of downward flame propagation and extinguishment in lean hydrogen-air mixtures. The computational results show that a downward propagating flame in an isothermal channel has a flammability limit of around 9.75 percent. This is in excellent agreement with experimental results. Also in excellent agreement are the detailed observations of the flame behavior at the point of extinguishment. The primary conclusion of this work is that detailed numerical simulations that include wall heat losses and the effect of gravity can adequately simulate the dynamics of the extinguishment process in downward-propagating hydrogen-air flames. These simulations can be examined in detail to gain understanding of the actual extinction process.

V-SUIT Model Validation Using PLSS 1.0 Test Results

NASA Technical Reports Server (NTRS)

Olthoff, Claas

2015-01-01

The dynamic portable life support system (PLSS) simulation software Virtual Space Suit (V-SUIT) has been under development at the Technische Universitat Munchen since 2011 as a spin-off from the Virtual Habitat (V-HAB) project. The MATLAB(trademark)-based V-SUIT simulates space suit portable life support systems and their interaction with a detailed and also dynamic human model, as well as the dynamic external environment of a space suit moving on a planetary surface. To demonstrate the feasibility of a large, system level simulation like V-SUIT, a model of NASA's PLSS 1.0 prototype was created. This prototype was run through an extensive series of tests in 2011. Since the test setup was heavily instrumented, it produced a wealth of data making it ideal for model validation. The implemented model includes all components of the PLSS in both the ventilation and thermal loops. The major components are modeled in greater detail, while smaller and ancillary components are low fidelity black box models. The major components include the Rapid Cycle Amine (RCA) CO2 removal system, the Primary and Secondary Oxygen Assembly (POS/SOA), the Pressure Garment System Volume Simulator (PGSVS), the Human Metabolic Simulator (HMS), the heat exchanger between the ventilation and thermal loops, the Space Suit Water Membrane Evaporator (SWME) and finally the Liquid Cooling Garment Simulator (LCGS). Using the created model, dynamic simulations were performed using same test points also used during PLSS 1.0 testing. The results of the simulation were then compared to the test data with special focus on absolute values during the steady state phases and dynamic behavior during the transition between test points. Quantified simulation results are presented that demonstrate which areas of the V-SUIT model are in need of further refinement and those that are sufficiently close to the test results. Finally, lessons learned from the modelling and validation process are given in combination with implications for the future development of other PLSS models in V-SUIT.

Initial Development of a Quadcopter Simulation Environment for Auralization

NASA Technical Reports Server (NTRS)

Christian, Andrew; Lawrence, Joseph

2016-01-01

This paper describes a recently created computer simulation of quadcopter flight dynamics for the NASA DELIVER project. The goal of this effort is to produce a simulation that includes a number of physical effects that are not usually found in other dynamics simulations (e.g., those used for flight controller development). These effects will be shown to have a significant impact on the fidelity of auralizations - entirely synthetic time-domain predictions of sound - based on this simulation when compared to a recording. High-fidelity auralizations are an important precursor to human subject tests that seek to understand the impact of vehicle configurations on noise and annoyance.

Dynamic large eddy simulation: Stability via realizability

NASA Astrophysics Data System (ADS)

Mokhtarpoor, Reza; Heinz, Stefan

2017-10-01

The concept of dynamic large eddy simulation (LES) is highly attractive: such methods can dynamically adjust to changing flow conditions, which is known to be highly beneficial. For example, this avoids the use of empirical, case dependent approximations (like damping functions). Ideally, dynamic LES should be local in physical space (without involving artificial clipping parameters), and it should be stable for a wide range of simulation time steps, Reynolds numbers, and numerical schemes. These properties are not trivial, but dynamic LES suffers from such problems over decades. We address these questions by performing dynamic LES of periodic hill flow including separation at a high Reynolds number Re = 37 000. For the case considered, the main result of our studies is that it is possible to design LES that has the desired properties. It requires physical consistency: a PDF-realizable and stress-realizable LES model, which requires the inclusion of the turbulent kinetic energy in the LES calculation. LES models that do not honor such physical consistency can become unstable. We do not find support for the previous assumption that long-term correlations of negative dynamic model parameters are responsible for instability. Instead, we concluded that instability is caused by the stable spatial organization of significant unphysical states, which are represented by wall-type gradient streaks of the standard deviation of the dynamic model parameter. The applicability of our realizability stabilization to other dynamic models (including the dynamic Smagorinsky model) is discussed.

Simulation and experimental research of 1MWe solar tower power plant in China

NASA Astrophysics Data System (ADS)

Yu, Qiang; Wang, Zhifeng; Xu, Ershu

2016-05-01

The establishment of a reliable simulation system for a solar tower power plant can greatly increase the economic and safety performance of the whole system. In this paper, a dynamic model of the 1MWe Solar Tower Power Plant at Badaling in Beijing is developed based on the "STAR-90" simulation platform, including the heliostat field, the central receiver system (water/steam), etc. The dynamic behavior of the global CSP plant can be simulated. In order to verify the validity of simulation system, a complete experimental process was synchronously simulated by repeating the same operating steps based on the simulation platform, including the locations and number of heliostats, the mass flow of the feed water, etc. According to the simulation and experimental results, some important parameters are taken out to make a deep comparison. The results show that there is good alignment between the simulations and the experimental results and that the error range can be acceptable considering the error of the models. In the end, a comprehensive and deep analysis on the error source is carried out according to the comparative results.

Spacecraft boost and abort guidance and control systems requirement study, boost dynamics and control analysis study. Exhibit A: Boost dynamics and control anlaysis

NASA Technical Reports Server (NTRS)

Williams, F. E.; Price, J. B.; Lemon, R. S.

1972-01-01

The simulation developments for use in dynamics and control analysis during boost from liftoff to orbit insertion are reported. Also included are wind response studies of the NR-GD 161B/B9T delta wing booster/delta wing orbiter configuration, the MSC 036B/280 inch solid rocket motor configuration, the MSC 040A/L0X-propane liquid injection TVC configuration, the MSC 040C/dual solid rocket motor configuration, and the MSC 049/solid rocket motor configuration. All of the latest math models (rigid and flexible body) developed for the MSC/GD Space Shuttle Functional Simulator, are included.

Robotics On-Board Trainer (ROBoT)

NASA Technical Reports Server (NTRS)

Johnson, Genevieve; Alexander, Greg

2013-01-01

ROBoT is an on-orbit version of the ground-based Dynamics Skills Trainer (DST) that astronauts use for training on a frequent basis. This software consists of two primary software groups. The first series of components is responsible for displaying the graphical scenes. The remaining components are responsible for simulating the Mobile Servicing System (MSS), the Japanese Experiment Module Remote Manipulator System (JEMRMS), and the H-II Transfer Vehicle (HTV) Free Flyer Robotics Operations. The MSS simulation software includes: Robotic Workstation (RWS) simulation, a simulation of the Space Station Remote Manipulator System (SSRMS), a simulation of the ISS Command and Control System (CCS), and a portion of the Portable Computer System (PCS) software necessary for MSS operations. These components all run under the CentOS4.5 Linux operating system. The JEMRMS simulation software includes real-time, HIL, dynamics, manipulator multi-body dynamics, and a moving object contact model with Tricks discrete time scheduling. The JEMRMS DST will be used as a functional proficiency and skills trainer for flight crews. The HTV Free Flyer Robotics Operations simulation software adds a functional simulation of HTV vehicle controllers, sensors, and data to the MSS simulation software. These components are intended to support HTV ISS visiting vehicle analysis and training. The scene generation software will use DOUG (Dynamic On-orbit Ubiquitous Graphics) to render the graphical scenes. DOUG runs on a laptop running the CentOS4.5 Linux operating system. DOUG is an Open GL-based 3D computer graphics rendering package. It uses pre-built three-dimensional models of on-orbit ISS and space shuttle systems elements, and provides realtime views of various station and shuttle configurations.

Large eddy simulation of spanwise rotating turbulent channel flow with dynamic variants of eddy viscosity model

NASA Astrophysics Data System (ADS)

Jiang, Zhou; Xia, Zhenhua; Shi, Yipeng; Chen, Shiyi

2018-04-01

A fully developed spanwise rotating turbulent channel flow has been numerically investigated utilizing large-eddy simulation. Our focus is to assess the performances of the dynamic variants of eddy viscosity models, including dynamic Vreman's model (DVM), dynamic wall adapting local eddy viscosity (DWALE) model, dynamic σ (Dσ ) model, and the dynamic volumetric strain-stretching (DVSS) model, in this canonical flow. The results with dynamic Smagorinsky model (DSM) and direct numerical simulations (DNS) are used as references. Our results show that the DVM has a wrong asymptotic behavior in the near wall region, while the other three models can correctly predict it. In the high rotation case, the DWALE can get reliable mean velocity profile, but the turbulence intensities in the wall-normal and spanwise directions show clear deviations from DNS data. DVSS exhibits poor predictions on both the mean velocity profile and turbulence intensities. In all three cases, Dσ performs the best.

An intercomparison of GCM and RCM dynamical downscaling for characterizing the hydroclimatology of California and Nevada

NASA Astrophysics Data System (ADS)

Xu, Z.; Rhoades, A.; Johansen, H.; Ullrich, P. A.; Collins, W. D.

2017-12-01

Dynamical downscaling is widely used to properly characterize regional surface heterogeneities that shape the local hydroclimatology. However, the factors in dynamical downscaling, including the refinement of model horizontal resolution, large-scale forcing datasets and dynamical cores, have not been fully evaluated. Two cutting-edge global-to-regional downscaling methods are used to assess these, specifically the variable-resolution Community Earth System Model (VR-CESM) and the Weather Research & Forecasting (WRF) regional climate model, under different horizontal resolutions (28, 14, and 7 km). Two groups of WRF simulations are driven by either the NCEP reanalysis dataset (WRF_NCEP) or VR-CESM outputs (WRF_VRCESM) to evaluate the effects of the large-scale forcing datasets. The impacts of dynamical core are assessed by comparing the VR-CESM simulations to the coupled WRF_VRCESM simulations with the same physical parameterizations and similar grid domains. The simulated hydroclimatology (i.e., total precipitation, snow cover, snow water equivalent and surface temperature) are compared with the reference datasets. The large-scale forcing datasets are critical to the WRF simulations in more accurately simulating total precipitation, SWE and snow cover, but not surface temperature. Both the WRF and VR-CESM results highlight that no significant benefit is found in the simulated hydroclimatology by just increasing horizontal resolution refinement from 28 to 7 km. Simulated surface temperature is sensitive to the choice of dynamical core. WRF generally simulates higher temperatures than VR-CESM, alleviates the systematic cold bias of DJF temperatures over the California mountain region, but overestimates the JJA temperature in California's Central Valley.

A Collection of Nonlinear Aircraft Simulations in MATLAB

NASA Technical Reports Server (NTRS)

Garza, Frederico R.; Morelli, Eugene A.

2003-01-01

Nonlinear six degree-of-freedom simulations for a variety of aircraft were created using MATLAB. Data for aircraft geometry, aerodynamic characteristics, mass / inertia properties, and engine characteristics were obtained from open literature publications documenting wind tunnel experiments and flight tests. Each nonlinear simulation was implemented within a common framework in MATLAB, and includes an interface with another commercially-available program to read pilot inputs and produce a three-dimensional (3-D) display of the simulated airplane motion. Aircraft simulations include the General Dynamics F-16 Fighting Falcon, Convair F-106B Delta Dart, Grumman F-14 Tomcat, McDonnell Douglas F-4 Phantom, NASA Langley Free-Flying Aircraft for Sub-scale Experimental Research (FASER), NASA HL-20 Lifting Body, NASA / DARPA X-31 Enhanced Fighter Maneuverability Demonstrator, and the Vought A-7 Corsair II. All nonlinear simulations and 3-D displays run in real time in response to pilot inputs, using contemporary desktop personal computer hardware. The simulations can also be run in batch mode. Each nonlinear simulation includes the full nonlinear dynamics of the bare airframe, with a scaled direct connection from pilot inputs to control surface deflections to provide adequate pilot control. Since all the nonlinear simulations are implemented entirely in MATLAB, user-defined control laws can be added in a straightforward fashion, and the simulations are portable across various computing platforms. Routines for trim, linearization, and numerical integration are included. The general nonlinear simulation framework and the specifics for each particular aircraft are documented.

A simple dynamic subgrid-scale model for LES of particle-laden turbulence

NASA Astrophysics Data System (ADS)

Park, George Ilhwan; Bassenne, Maxime; Urzay, Javier; Moin, Parviz

2017-04-01

In this study, a dynamic model for large-eddy simulations is proposed in order to describe the motion of small inertial particles in turbulent flows. The model is simple, involves no significant computational overhead, contains no adjustable parameters, and is flexible enough to be deployed in any type of flow solvers and grids, including unstructured setups. The approach is based on the use of elliptic differential filters to model the subgrid-scale velocity. The only model parameter, which is related to the nominal filter width, is determined dynamically by imposing consistency constraints on the estimated subgrid energetics. The performance of the model is tested in large-eddy simulations of homogeneous-isotropic turbulence laden with particles, where improved agreement with direct numerical simulation results is observed in the dispersed-phase statistics, including particle acceleration, local carrier-phase velocity, and preferential-concentration metrics.

Molecular Dynamics Simulations to Determine the Structure and Dynamics of Hepatitis B Virus Capsid Bound to a Novel Anti-viral Drug.

PubMed

Watanabe, Go; Sato, Shunsuke; Iwadate, Mitsuo; Umeyama, Hideaki; Hayakawa, Michiyo; Murakami, Yoshiki; Yoneda, Shigetaka

2016-01-01

Hepatitis B virus (HBV) chronically infects millions of people worldwide and is a major cause of serious liver diseases, including liver cirrhosis and liver cancer. In our previous study, in silico screening was used to isolate new anti-viral compounds predicted to bind to the HBV capsid. Four of the isolated compounds have been reported to suppress the cellular multiplication of HBV experimentally. In the present study, molecular dynamics simulations of the HBV capsid were performed under rotational symmetry boundary conditions, to clarify how the structure and dynamics of the capsid are affected at the atomic level by the binding of one of the isolated compounds, C13. Two simulations of the free HBV capsid, two further simulations of the capsid-C13 complex, and one simulation of the capsid-AT-130 complex were performed. For statistical confidence, each set of simulations was repeated by five times, changing the simulation conditions. C13 continued to bind at the predicted binding site during the simulations, supporting the hypothesis that C13 is a capsid-binding compound. The structure and dynamics of the HBV capsid were greatly influenced by the binding and release of C13, and these effects were essentially identical to those seen for AT-130, indicating that C13 likely inhibits the function of the HBV capsid.

A model for including thermal conduction in molecular dynamics simulations

NASA Technical Reports Server (NTRS)

Wu, Yue; Friauf, Robert J.

1989-01-01

A technique is introduced for including thermal conduction in molecular dynamics simulations for solids. A model is developed to allow energy flow between the computational cell and the bulk of the solid when periodic boundary conditions cannot be used. Thermal conduction is achieved by scaling the velocities of atoms in a transitional boundary layer. The scaling factor is obtained from the thermal diffusivity, and the results show good agreement with the solution for a continuous medium at long times. The effects of different temperature and size of the system, and of variations in strength parameter, atomic mass, and thermal diffusivity were investigated. In all cases, no significant change in simulation results has been found.

Evaporation kinetics of Mg2SiO4 crystals and melts from molecular dynamics simulations

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Using molecular simulation to explore the nanoscale dynamics of the plant kinome.

PubMed

Moffett, Alexander S; Shukla, Diwakar

2018-03-09

Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants. In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved understanding of how PKs become catalytically active and why mutations cause pathological PK behavior, at spatial and temporal resolutions inaccessible to current experimental methods alone. In this review, we argue for the value of applying MD simulation to plant PKs. We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. We conclude with a discussion of the future of MD simulations and plant PKs, arguing for the importance of molecular simulation in the future of plant PK research. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

PubMed

Richings, Gareth W; Habershon, Scott

2017-09-12

We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

Mechanical impact of dynamic phenomena in Francis turbines at off design conditions

NASA Astrophysics Data System (ADS)

Duparchy, F.; Brammer, J.; Thibaud, M.; Favrel, A.; Lowys, P. Y.; Avellan, F.

2017-04-01

At partial load and overload conditions, Francis turbines are subjected to hydraulic instabilities that can potentially result in high dynamic solicitations of the turbine components and significantly reduce their lifetime. This study presents both experimental data and numerical simulations that were used as complementary approaches to study these dynamic solicitations. Measurements performed on a reduced scale physical model, including a special runner instrumented with on-board strain gauges and pressure sensors, were used to investigate the dynamic phenomena experienced by the runner. They were also taken as reference to validate the numerical simulation results. After validation, advantage was taken from the numerical simulations to highlight the mechanical response of the structure to the unsteady hydraulic phenomena, as well as their impact on the fatigue damage of the runner.

Massively parallel simulations of relativistic fluid dynamics on graphics processing units with CUDA

NASA Astrophysics Data System (ADS)

Bazow, Dennis; Heinz, Ulrich; Strickland, Michael

2018-04-01

Relativistic fluid dynamics is a major component in dynamical simulations of the quark-gluon plasma created in relativistic heavy-ion collisions. Simulations of the full three-dimensional dissipative dynamics of the quark-gluon plasma with fluctuating initial conditions are computationally expensive and typically require some degree of parallelization. In this paper, we present a GPU implementation of the Kurganov-Tadmor algorithm which solves the 3 + 1d relativistic viscous hydrodynamics equations including the effects of both bulk and shear viscosities. We demonstrate that the resulting CUDA-based GPU code is approximately two orders of magnitude faster than the corresponding serial implementation of the Kurganov-Tadmor algorithm. We validate the code using (semi-)analytic tests such as the relativistic shock-tube and Gubser flow.

Moving Contact Lines: Linking Molecular Dynamics and Continuum-Scale Modeling.

PubMed

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-17

Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide a link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which governs the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modeling and highlight the opportunities for future developments in this area.

Dynamic model of the force driving kinesin to move along microtubule-Simulation with a model system

NASA Astrophysics Data System (ADS)

Chou, Y. C.; Hsiao, Yi-Feng; To, Kiwing

2015-09-01

A dynamic model for the motility of kinesin, including stochastic-force generation and step formation is proposed. The force driving the motion of kinesin motor is generated by the impulse from the collision between the randomly moving long-chain stalk and the ratchet-shaped outer surface of microtubule. Most of the dynamical and statistical features of the motility of kinesin are reproduced in a simulation system, with (a) ratchet structures similar to the outer surface of microtubule, (b) a bead chain connected to two heads, similarly to the stalk of the real kinesin motor, and (c) the interaction between the heads of the simulated kinesin and microtubule. We also propose an experiment to discriminate between the conventional hand-over-hand model and the dynamic model.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

PubMed

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

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.

Entangled trajectories Hamiltonian dynamics for treating quantum nuclear effects

NASA Astrophysics Data System (ADS)

Smith, Brendan; Akimov, Alexey V.

2018-04-01

A simple and robust methodology, dubbed Entangled Trajectories Hamiltonian Dynamics (ETHD), is developed to capture quantum nuclear effects such as tunneling and zero-point energy through the coupling of multiple classical trajectories. The approach reformulates the classically mapped second-order Quantized Hamiltonian Dynamics (QHD-2) in terms of coupled classical trajectories. The method partially enforces the uncertainty principle and facilitates tunneling. The applicability of the method is demonstrated by studying the dynamics in symmetric double well and cubic metastable state potentials. The methodology is validated using exact quantum simulations and is compared to QHD-2. We illustrate its relationship to the rigorous Bohmian quantum potential approach, from which ETHD can be derived. Our simulations show a remarkable agreement of the ETHD calculation with the quantum results, suggesting that ETHD may be a simple and inexpensive way of including quantum nuclear effects in molecular dynamics simulations.

Solving Equations of Multibody Dynamics

NASA Technical Reports Server (NTRS)

Jain, Abhinandan; Lim, Christopher

2007-01-01

Darts++ is a computer program for solving the equations of motion of a multibody system or of a multibody model of a dynamic system. It is intended especially for use in dynamical simulations performed in designing and analyzing, and developing software for the control of, complex mechanical systems. Darts++ is based on the Spatial-Operator- Algebra formulation for multibody dynamics. This software reads a description of a multibody system from a model data file, then constructs and implements an efficient algorithm that solves the dynamical equations of the system. The efficiency and, hence, the computational speed is sufficient to make Darts++ suitable for use in realtime closed-loop simulations. Darts++ features an object-oriented software architecture that enables reconfiguration of system topology at run time; in contrast, in related prior software, system topology is fixed during initialization. Darts++ provides an interface to scripting languages, including Tcl and Python, that enable the user to configure and interact with simulation objects at run time.

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

Bush, Brian W; Brunhart-Lupo, Nicholas J; Gruchalla, Kenny M

This brochure describes a system dynamics simulation (SD) framework that supports an end-to-end analysis workflow that is optimized for deployment on ESIF facilities(Peregrine and the Insight Center). It includes (I) parallel and distributed simulation of SD models, (ii) real-time 3D visualization of running simulations, and (iii) comprehensive database-oriented persistence of simulation metadata, inputs, and outputs.

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

Bush, Brian W; Brunhart-Lupo, Nicholas J; Gruchalla, Kenny M

This presentation describes a system dynamics simulation (SD) framework that supports an end-to-end analysis workflow that is optimized for deployment on ESIF facilities(Peregrine and the Insight Center). It includes (I) parallel and distributed simulation of SD models, (ii) real-time 3D visualization of running simulations, and (iii) comprehensive database-oriented persistence of simulation metadata, inputs, and outputs.

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Dynamic Inversion based Control of a Docking Mechanism

NASA Technical Reports Server (NTRS)

Kulkarni, Nilesh V.; Ippolito, Corey; Krishnakumar, Kalmanje

2006-01-01

The problem of position and attitude control of the Stewart platform based docking mechanism is considered motivated by its future application in space missions requiring the autonomous docking capability. The control design is initiated based on the framework of the intelligent flight control architecture being developed at NASA Ames Research Center. In this paper, the baseline position and attitude control system is designed using dynamic inversion with proportional-integral augmentation. The inverse dynamics uses a Newton-Euler formulation that includes the platform dynamics, the dynamics of the individual legs along with viscous friction in the joints. Simulation results are presented using forward dynamics simulated by a commercial physics engine that builds the system as individual elements with appropriate joints and uses constrained numerical integration,

A Novel Interfacing Technique for Distributed Hybrid Simulations Combining EMT and Transient Stability Models

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

Shu, Dewu; Xie, Xiaorong; Jiang, Qirong

With steady increase of power electronic devices and nonlinear dynamic loads in large scale AC/DC systems, the traditional hybrid simulation method, which incorporates these components into a single EMT subsystem and hence causes great difficulty for network partitioning and significant deterioration in simulation efficiency. To resolve these issues, a novel distributed hybrid simulation method is proposed in this paper. The key to realize this method is a distinct interfacing technique, which includes: i) a new approach based on the two-level Schur complement to update the interfaces by taking full consideration of the couplings between different EMT subsystems; and ii) amore » combined interaction protocol to further improve the efficiency while guaranteeing the simulation accuracy. The advantages of the proposed method in terms of both efficiency and accuracy have been verified by using it for the simulation study of an AC/DC hybrid system including a two-terminal VSC-HVDC and nonlinear dynamic loads.« less

Scaling laws in granular flow and pedestrian flow

NASA Astrophysics Data System (ADS)

Chen, Shumiao; Alonso-Marroquin, Fernando; Busch, Jonathan; Hidalgo, Raúl Cruz; Sathianandan, Charmila; Ramírez-Gómez, Álvaro; Mora, Peter

2013-06-01

We use particle-based simulations to examine the flow of particles through an exit. Simulations involve both gravity-driven particles (representing granular material) and velocity-driven particles (mimicking pedestrian dynamics). Contact forces between particles include elastic, viscous, and frictional forces; and simulations use bunker geometry. Power laws are observed in the relation between flow rate and exit width. Simulations of granular flow showed that the power law has little dependence on the coefficient of friction. Polydisperse granular systems produced higher flow rates than those produced by monodisperse ones. We extend the particle model to include the main features of pedestrian dynamics: thoracic shape, shoulder rotation, and desired velocity oriented towards the exit. Higher desired velocity resulted in higher flow rate. Granular simulations always give higher flow rate than pedestrian simulations, despite the values of aspect ratio of the particles. In terms of force distribution, pedestrians and granulates share similar properties with the non-democratic distribution of forces that poses high risks of injuries in a bottleneck situation.

Dynamics Modeling and Simulation of Large Transport Airplanes in Upset Conditions

NASA Technical Reports Server (NTRS)

Foster, John V.; Cunningham, Kevin; Fremaux, Charles M.; Shah, Gautam H.; Stewart, Eric C.; Rivers, Robert A.; Wilborn, James E.; Gato, William

2005-01-01

As part of NASA's Aviation Safety and Security Program, research has been in progress to develop aerodynamic modeling methods for simulations that accurately predict the flight dynamics characteristics of large transport airplanes in upset conditions. The motivation for this research stems from the recognition that simulation is a vital tool for addressing loss-of-control accidents, including applications to pilot training, accident reconstruction, and advanced control system analysis. The ultimate goal of this effort is to contribute to the reduction of the fatal accident rate due to loss-of-control. Research activities have involved accident analyses, wind tunnel testing, and piloted simulation. Results have shown that significant improvements in simulation fidelity for upset conditions, compared to current training simulations, can be achieved using state-of-the-art wind tunnel testing and aerodynamic modeling methods. This paper provides a summary of research completed to date and includes discussion on key technical results, lessons learned, and future research needs.

Short-Range Order and Collective Dynamics of DMPC Bilayers: A Comparison between Molecular Dynamics Simulations, X-Ray, and Neutron Scattering Experiments

PubMed Central

Hub, Jochen S.; Salditt, Tim; Rheinstädter, Maikel C.; de Groot, Bert L.

2007-01-01

We present an extensive comparison of short-range order and short wavelength dynamics of a hydrated phospholipid bilayer derived by molecular dynamics simulations, elastic x-ray, and inelastic neutron scattering experiments. The quantities that are compared between simulation and experiment include static and dynamic structure factors, reciprocal space mappings, and electron density profiles. We show that the simultaneous use of molecular dynamics and diffraction data can help to extract real space properties like the area per lipid and the lipid chain ordering from experimental data. In addition, we assert that the interchain distance can be computed to high accuracy from the interchain correlation peak of the structure factor. Moreover, it is found that the position of the interchain correlation peak is not affected by the area per lipid, while its correlation length decreases linearly with the area per lipid. This finding allows us to relate a property of the structure factor quantitatively to the area per lipid. Finally, the short wavelength dynamics obtained from the simulations and from inelastic neutron scattering are analyzed and compared. The conventional interpretation in terms of the three-effective-eigenmode model is found to be only partly suitable to describe the complex fluid dynamics of lipid chains. PMID:17631531

Fixed gain and adaptive techniques for rotorcraft vibration control

NASA Technical Reports Server (NTRS)

Roy, R. H.; Saberi, H. A.; Walker, R. A.

1985-01-01

The results of an analysis effort performed to demonstrate the feasibility of employing approximate dynamical models and frequency shaped cost functional control law desgin techniques for helicopter vibration suppression are presented. Both fixed gain and adaptive control designs based on linear second order dynamical models were implemented in a detailed Rotor Systems Research Aircraft (RSRA) simulation to validate these active vibration suppression control laws. Approximate models of fuselage flexibility were included in the RSRA simulation in order to more accurately characterize the structural dynamics. The results for both the fixed gain and adaptive approaches are promising and provide a foundation for pursuing further validation in more extensive simulation studies and in wind tunnel and/or flight tests.

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

PubMed Central

2017-01-01

The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments. PMID:28666087

i3Drive, a 3D interactive driving simulator.

PubMed

Ambroz, Miha; Prebil, Ivan

2010-01-01

i3Drive, a wheeled-vehicle simulator, can accurately simulate vehicles of various configurations with up to eight wheels in real time on a desktop PC. It presents the vehicle dynamics as an interactive animation in a virtual 3D environment. The application is fully GUI-controlled, giving users an easy overview of the simulation parameters and letting them adjust those parameters interactively. It models all relevant vehicle systems, including the mechanical models of the suspension, power train, and braking and steering systems. The simulation results generally correspond well with actual measurements, making the system useful for studying vehicle performance in various driving scenarios. i3Drive is thus a worthy complement to other, more complex tools for vehicle-dynamics simulation and analysis.

Higher-order harmonics coupling in different free-electron laser codes

NASA Astrophysics Data System (ADS)

Giannessi, L.; Freund, H. P.; Musumeci, P.; Reiche, S.

2008-08-01

The capability for simulation of the dynamics of a free-electron laser including the higher-order harmonics in linear undulators exists in several existing codes as MEDUSA [H.P. Freund, S.G. Biedron, and S.V. Milton, IEEE J. Quantum Electron. 27 (2000) 243; H.P. Freund, Phys. Rev. ST-AB 8 (2005) 110701] and PERSEO [L. Giannessi, Overview of Perseo, a system for simulating FEL dynamics in Mathcad, < http://www.jacow.org>, in: Proceedings of FEL 2006 Conference, BESSY, Berlin, Germany, 2006, p. 91], and has been recently implemented in GENESIS 1.3 [See < http://www.perseo.enea.it>]. MEDUSA and GENESIS also include the dynamics of even harmonics induced by the coupling through the betatron motion. In addition MEDUSA, which is based on a non-wiggler averaged model, is capable of simulating the generation of even harmonics in the transversally cold beam regime, i.e. when the even harmonic coupling arises from non-linear effects associated with longitudinal particle dynamics and not to a finite beam emittance. In this paper a comparison between the predictions of the codes in different conditions is given.

Background and Pickup Ion Velocity Distribution Dynamics in Titan's Plasma Environment: 3D Hybrid Simulation and Comparison with CAPS T9 Observations

NASA Technical Reports Server (NTRS)

Lipatov, A. S.; Sittler, E. C., Jr.; Hartle, R. E.; Cooper, J. F.; Simpson, D. G.

2011-01-01

In this report we discuss the ion velocity distribution dynamics from the 3D hybrid simulation. In our model the background, pickup, and ionospheric ions are considered as a particles, whereas the electrons are described as a fluid. Inhomogeneous photoionization, electron-impact ionization and charge exchange are included in our model. We also take into account the collisions between the ions and neutrals. The current simulation shows that mass loading by pickup ions H(+); H2(+), CH4(+) and N2(+) is stronger than in the previous simulations when O+ ions are introduced into the background plasma. In our hybrid simulations we use Chamberlain profiles for the atmospheric components. We also include a simple ionosphere model with average mass M = 28 amu ions that were generated inside the ionosphere. The moon is considered as a weakly conducting body. Special attention will be paid to comparing the simulated pickup ion velocity distribution with CAPS T9 observations. Our simulation shows an asymmetry of the ion density distribution and the magnetic field, including the formation of the Alfve n wing-like structures. The simulation also shows that the ring-like velocity distribution for pickup ions relaxes to a Maxwellian core and a shell-like halo.

A simulation study of the flight dynamics of elastic aircraft. Volume 2: Data

NASA Technical Reports Server (NTRS)

Waszak, Martin R.; Davidson, John B.; Schmidt, David K.

1987-01-01

The simulation experiment described addresses the effects of structural flexibility on the dynamic characteristics of a generic family of aircraft. The simulation was performed using the NASA Langley VMS simulation facility. The vehicle models were obtained as part of this research project. The simulation results include complete response data and subjective pilot ratings and comments and so allow a variety of analyses. The subjective ratings and analysis of the time histories indicate that increased flexibility can lead to increased tracking errors, degraded handling qualities, and changes in the frequency content of the pilot inputs. These results, furthermore, are significantly affected by the visual cues available to the pilot.

Dynamics of the GB3 loop regions from MD simulation: how much of it is real?

PubMed

Li, Tong; Jing, Qingqing; Yao, Lishan

2011-04-07

A total of 1.1 μs of molecular dynamics (MD) simulations were performed to study the structure and dynamics of protein GB3. The simulation motional amplitude of the loop regions is generally overestimated in comparison with the experimental backbone N-H order parameters S(2). Two-state behavior is observed for several residues in these regions, with the minor state population in the range of 3-13%. Further inspection suggests that the (φ, ψ) dihedral angles of the minor states deviate from the GB3 experimental values, implying the existence of nonnative states. After fitting the MD trajectories of these residues to the NMR RDCs, the minor state populations are significantly reduced by at least 80%, suggesting that MD simulations are strongly biased toward the minor states, thus overestimating the dynamics of the loop regions. The optimized trajectories produce intra, sequential H(N)-H(α) RDCs and intra (3)J(HNHα) that are not included in the trajectories fitting for these residues that are closer to the experimental data. Unlike GB3, 0.55 μs MD simulations of protein ubiquitin do not show distinctive minor states, and the derived NMR order parameters are better converged. Our findings indicate that the artifacts of the simulations depend on the specific system studied and that one should be cautious interpreting the enhanced dihedral dynamics from long MD simulations.

Charge and energy dynamics in photo-excited poly(para-phenylenevinylene) systems

NASA Astrophysics Data System (ADS)

Gisslén, L.; Johansson, A.˚.; Stafström, S.

2004-07-01

We report results from simulations of charge and energy dynamics in poly(para-phenylenevinylene) (PPV) and PPV interacting with C60. The simulations were performed by solving the time-dependent Schrödinger equation and the lattice equation of motion simultaneously and nonadiabatically. The electronic system and the coupling of the electrons to the lattice were described by an extended three-dimensional version of the Su-Schrieffer-Heeger model, which also included an external electric field. Electron and lattice dynamics following electronic excitations at different energies have been simulated. The effect of additional lattice energy was also included in the simulations. Our results show that both exciton diffusion and transitions from high to lower lying excitations are stimulated by increasing the lattice energy. Also field induced charge separation occurs faster if the lattice energy is increased. This separation process is highly nonadiabatic and involves a significant rearrangement of the electron distribution. In the case of PPV coupled to C60, we observe a spontaneous charge separation. The separation time is in this case limited by the local concentration of C60 molecules close to the PPV chain.

Collaborative Research Program on Advanced Metals and Ceramics for Armor and Anti-Armor Applications Dynamic Behavior of Non-Crystalline and Crystalline Metallic Systems

DTIC Science & Technology

2006-09-01

compression, including real-time cinematography of failure under dynamic compression, was evaluated. The results (figure 10) clearly show that the failure... art of simulations of dynamic failure and damage mechanisms. An explicit dynamic parallel code has been developed to track damage mechanisms in the

Simulations of SSLV Ascent and Debris Transport

NASA Technical Reports Server (NTRS)

Rogers, Stuart; Aftosmis, Michael; Murman, Scott; Chan, William; Gomez, Ray; Gomez, Ray; Vicker, Darby; Stuart, Phil

2006-01-01

A viewgraph presentation on Computational Fluid Dynamic (CFD) Simulation of Space Shuttle Launch Vehicle (SSLV) ascent and debris transport analysis is shown. The topics include: 1) CFD simulations of the Space Shuttle Launch Vehicle ascent; 2) Debris transport analysis; 3) Debris aerodynamic modeling; and 4) Other applications.

Dynamic Simulation of a Helium Liquefier

NASA Astrophysics Data System (ADS)

Maekawa, R.; Ooba, K.; Nobutoki, M.; Mito, T.

2004-06-01

Dynamic behavior of a helium liquefier has been studied in detail with a Cryogenic Process REal-time SimulaTor (C-PREST) at the National Institute for Fusion Science (NIFS). The C-PREST is being developed to integrate large-scale helium cryogenic plant design, operation and maintenance for optimum process establishment. As a first step of simulations of cooldown to 4.5 K with the helium liquefier model is conducted, which provides a plant-process validation platform. The helium liquefier consists of seven heat exchangers, a liquid-nitrogen (LN2) precooler, two expansion turbines and a liquid-helium (LHe) reservoir. Process simulations are fulfilled with sequence programs, which were implemented with C-PREST based on an existing liquefier operation. The interactions of a JT valve, a JT-bypass valve and a reservoir-return valve have been dynamically simulated. The paper discusses various aspects of refrigeration process simulation, including its difficulties such as a balance between complexity of the adopted models and CPU time.

First-Principle Simulations of Water

NASA Astrophysics Data System (ADS)

Schwegler, Eric

2004-03-01

The structural and dynamical properties of water are investigated with a series of first-principle and classical molecular dynamics simulations. A number of effects that can influence the simulated properties of water will be discussed including temperature, intramolecular flexibility [1], and the quantum nature of protons. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48. [1] M. Allesch, E. Schwegler, G. Galli, F. Gygi, J. Chem. Phys. in press 2004.

Study on the After Cavity Interaction in a 140 GHz Gyrotron Using 3D CFDTD PIC Simulations

NASA Astrophysics Data System (ADS)

Lin, M. C.; Illy, S.; Avramidis, K.; Thumm, M.; Jelonnek, J.

2016-10-01

A computational study on after cavity interaction (ACI) in a 140 GHz gryotron for fusion research has been performed using a 3-D conformal finite-difference time-domain (CFDTD) particle-in-cell (PIC) method. The ACI, i.e. beam wave interaction in the non-linear uptaper after the cavity has attracted a lot of attention and been widely investigated in recent years. In a dynamic ACI, a TE mode is excited by the electron beam at the same frequency as in the cavity, and the same mode is also interacting with the spent electron beam at a different frequency in the non-linear uptaper after the cavity while in a static ACI, a mode interacts with the beam both at the cavity and at the uptaper, but at the same frequency. A previous study on the dynamic ACI on a 140 GHz gyrotron has concluded that more advanced numerical simulations such as particle-in-cell (PIC) modeling should be employed to study or confirm the dynamic ACI in addition to using trajectory codes. In this work, we use a 3-D full wave time domain simulation based on the CFDTD PIC method to include the rippled-wall launcher of the quasi-optical output coupler into the simulations which breaks the axial symmetry of the original model employing a symmetric one. A preliminary simulation result has confirmed the dynamic ACI effect in this 140 GHz gyrotron in good agreement with the former study. A realistic launcher will be included in the model for studying the dynamic ACI and compared with the homogenous one.

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

PubMed Central

Swails, Jason; Zhao, Yutong; Beauchamp, Kyle A.; Wang, Lee-Ping; Stern, Chaya D.; Brooks, Bernard R.; Pande, Vijay S.

2017-01-01

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community. PMID:28746339

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Fluid Dynamics Lagrangian Simulation Model

NASA Astrophysics Data System (ADS)

Hyman, Ellis

1994-02-01

The work performed by Science Applications International Corporation (SAIC) on this contract, Fluid Dynamics Lagrangian Simulation Model, Contract Number N00014-89-C-2106, SAIC Project Number 01-0157-03-0768, focused on a number of research topics in fluid dynamics. The work was in support of the programs of NRL's Laboratory for Computational Physics and Fluid Dynamics and covered the period from 10 September 1989 to 9 December 1993. In the following sections, we describe each of the efforts and the results obtained. Much of the research work has resulted in journal publications. These are included in Appendices of this report for which the reader is referred for complete details.

INCLUDING AORTIC VALVE MORPHOLOGY IN COMPUTATIONAL FLUID DYNAMICS SIMULATIONS: INITIAL FINDINGS AND APPLICATION TO AORTIC COARCTATION

PubMed Central

Wendell, David C.; Samyn, Margaret M.; Cava, Joseph R.; Ellwein, Laura M.; Krolikowski, Mary M.; Gandy, Kimberly L.; Pelech, Andrew N.; Shadden, Shawn C.; LaDisa, John F.

2012-01-01

Computational fluid dynamics (CFD) simulations quantifying thoracic aortic flow patterns have not included disturbances from the aortic valve (AoV). 80% of patients with aortic coarctation (CoA) have a bicuspid aortic valve (BAV) which may cause adverse flow patterns contributing to morbidity. Our objectives were to develop a method to account for the AoV in CFD simulations, and quantify its impact on local hemodynamics. The method developed facilitates segmentation of the AoV, spatiotemporal interpolation of segments, and anatomic positioning of segments at the CFD model inlet. The AoV was included in CFD model examples of a normal (tricuspid AoV) and a post-surgical CoA patient (BAV). Velocity, turbulent kinetic energy (TKE), time-averaged wall shear stress (TAWSS), and oscillatory shear index (OSI) results were compared to equivalent simulations using a plug inlet profile. The plug inlet greatly underestimated TKE for both examples. TAWSS differences extended throughout the thoracic aorta for the CoA BAV, but were limited to the arch for the normal example. OSI differences existed mainly in the ascending aorta for both cases. The impact of AoV can now be included with CFD simulations to identify regions of deleterious hemodynamics thereby advancing simulations of the thoracic aorta one step closer to reality. PMID:22917990

The Virtual Habitat - A tool for dynamic life support system simulations

NASA Astrophysics Data System (ADS)

Czupalla, M.; Zhukov, A.; Schnaitmann, J.; Olthoff, C.; Deiml, M.; Plötner, P.; Walter, U.

2015-06-01

In this paper we present the Virtual Habitat (V-HAB) model, which simulates on a system level the dynamics of entire mission scenarios for any given life support system (LSS) including a dynamic representation of the crew. We first present the V-HAB architecture. Thereafter we validate in selected case studies the V-HAB submodules. Finally, we demonstrate the overall abilities of V-HAB by first simulating the LSS of the International Space Station (ISS) and showing how close this comes to real data. In a second case study we simulate the LSS dynamics of a Mars mission scenario. We thus show that V-HAB is able to support LSS design processes, giving LSS designers a set of dynamic decision parameters (e.g. stability, robustness, effective crew time) at hand that supplement or even substitute the common Equivalent System Mass (ESM) quantities as a proxy for LSS hardware costs. The work presented here builds on a LSS heritage by the exploration group at the Technical University at Munich (TUM) dating from even before 2006.

Engine management during NTRE start up

NASA Technical Reports Server (NTRS)

Bulman, Mel; Saltzman, Dave

1993-01-01

The topics are presented in viewgraph form and include the following: total engine system management critical to successful nuclear thermal rocket engine (NTRE) start up; NERVA type engine start windows; reactor power control; heterogeneous reactor cooling; propellant feed system dynamics; integrated NTRE start sequence; moderator cooling loop and efficient NTRE starting; analytical simulation and low risk engine development; accurate simulation through dynamic coupling of physical processes; and integrated NTRE and mission performance.

Molecular dynamics: deciphering the data.

PubMed

Dauber-Osguthorpe, P; Maunder, C M; Osguthorpe, D J

1996-06-01

The dynamic behaviour of molecules is important in determining their activity. Molecular dynamics (MD) simulations give a detailed description of motion, from small fluctuations to conformational transitions, and can include solvent effects. However, extracting useful information about conformational motion from a trajectory is not trivial. We have used digital signal-processing techniques to characterise the motion in MD simulations, including: calculating the frequency distribution, applying filtering functions, and extraction of vectors defining the characteristic motion for each frequency in an MD simulation. We describe here some typical results obtained for peptides and proteins. The nature of the low-frequency modes of motion, as obtained from MD and normal mode (NM) analysis, of Ace-(Ala)31-Nma and of a proline mutant is discussed. Low-frequency modes extracted from the MD trajectories of Rop protein and phospholipase A2 reveal characteristic motions of secondary structure elements, as well as concerned motions that are of significance to the protein's biological activity. MD simulations are also used frequently as a tool for conformational searches and for investigating protein folding/unfolding. We have developed a novel method that uses time-domain filtering to channel energy into conformational motion and thus enhance conformational transitions. The selectively enhanced molecular dynamics method is tested on the small molecule hexane.

MAGI: many-component galaxy initializer

NASA Astrophysics Data System (ADS)

Miki, Yohei; Umemura, Masayuki

2018-04-01

Providing initial conditions is an essential procedure for numerical simulations of galaxies. The initial conditions for idealized individual galaxies in N-body simulations should resemble observed galaxies and be dynamically stable for time-scales much longer than their characteristic dynamical times. However, generating a galaxy model ab initio as a system in dynamical equilibrium is a difficult task, since a galaxy contains several components, including a bulge, disc, and halo. Moreover, it is desirable that the initial-condition generator be fast and easy to use. We have now developed an initial-condition generator for galactic N-body simulations that satisfies these requirements. The developed generator adopts a distribution-function-based method, and it supports various kinds of density models, including custom-tabulated inputs and the presence of more than one disc. We tested the dynamical stability of systems generated by our code, representing early- and late-type galaxies, with N = 2097 152 and 8388 608 particles, respectively, and we found that the model galaxies maintain their initial distributions for at least 1 Gyr. The execution times required to generate the two models were 8.5 and 221.7 seconds, respectively, which is negligible compared to typical execution times for N-body simulations. The code is provided as open-source software and is publicly and freely available at https://bitbucket.org/ymiki/magi.

Molecular dynamics: Deciphering the data

NASA Astrophysics Data System (ADS)

Dauber-Osguthorpe, Pnina; Maunder, Colette M.; Osguthorpe, David J.

1996-06-01

The dynamic behaviour of molecules is important in determining their activity. Molecular dynamics (MD) simulations give a detailed description of motion, from small fluctuations to conformational transitions, and can include solvent effects. However, extracting useful information about conformational motion from a trajectory is not trivial. We have used digital signal-processing techniques to characterise the motion in MD simulations, including: calculating the frequency distribution, applying filtering functions, and extraction of vectors defining the characteristic motion for each frequency in an MD simulation. We describe here some typical results obtained for peptides and proteins. The nature of the low-frequency modes of motion, as obtained from MD and normal mode (NM) analysis, of Ace-(Ala)31-Nma and of a proline mutant is discussed. Low-frequency modes extracted from the MD trajectories of Rop protein and phospholipase A2 reveal characteristic motions of secondary structure elements, as well as concerted motions that are of significance to the protein's biological activity. MD simulations are also used frequently as a tool for conformational searches and for investigating protein folding/unfolding. We have developed a novel method that uses time-domain filtering to channel energy into conformational motion and thus enhance conformational transitions. The selectively enhanced molecular dynamics method is tested on the small molecule hexane.

Gaining insight into the physics of dynamic atomic force microscopy in complex environments using the VEDA simulator

NASA Astrophysics Data System (ADS)

Kiracofe, Daniel; Melcher, John; Raman, Arvind

2012-01-01

Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In this article we describe recent developments in the VEDA (virtual environment for dynamic AFM) simulator, which is a suite of freely available, open-source simulation tools that are delivered through the cloud computing cyber-infrastructure of nanoHUB (www.nanohub.org). Here we describe three major developments. First, simulations in liquid environments are improved by enhancements in the modeling of cantilever dynamics, excitation methods, and solvation shell forces. Second, VEDA is now able to simulate many new advanced modes of operation (bimodal, phase-modulation, frequency-modulation, etc.). Finally, nineteen different tip-sample models are available to simulate the surface physics of a wide variety different material systems including capillary, specific adhesion, van der Waals, electrostatic, viscoelasticity, and hydration forces. These features are demonstrated through example simulations and validated against experimental data, in order to provide insight into practical problems in dynamic AFM.

Gaining insight into the physics of dynamic atomic force microscopy in complex environments using the VEDA simulator.

PubMed

Kiracofe, Daniel; Melcher, John; Raman, Arvind

2012-01-01

Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In this article we describe recent developments in the VEDA (virtual environment for dynamic AFM) simulator, which is a suite of freely available, open-source simulation tools that are delivered through the cloud computing cyber-infrastructure of nanoHUB (www.nanohub.org). Here we describe three major developments. First, simulations in liquid environments are improved by enhancements in the modeling of cantilever dynamics, excitation methods, and solvation shell forces. Second, VEDA is now able to simulate many new advanced modes of operation (bimodal, phase-modulation, frequency-modulation, etc.). Finally, nineteen different tip-sample models are available to simulate the surface physics of a wide variety different material systems including capillary, specific adhesion, van der Waals, electrostatic, viscoelasticity, and hydration forces. These features are demonstrated through example simulations and validated against experimental data, in order to provide insight into practical problems in dynamic AFM.

Molecular dynamics simulation of highly charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

PubMed Central

Gargallo, Raimundo; Hünenberger, Philippe H.; Avilés, Francesc X.; Oliva, Baldomero

2003-01-01

Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3M method leads to slightly higher atomic positional fluctuations and deviations from the crystallographic structure, along with somewhat lower values of the total energy and solvation free energy. However, the ED analysis of the system leads to nearly identical results for both simulations. Because of the strong similarity between the results, both methods appear well suited for the simulation of highly charged globular proteins in explicit solvent. However, the lower computational demand of the RF method in the present implementation represents a clear advantage over the P3M method. PMID:14500874

Particle-based solid for nonsmooth multidomain dynamics

NASA Astrophysics Data System (ADS)

Nordberg, John; Servin, Martin

2018-04-01

A method for simulation of elastoplastic solids in multibody systems with nonsmooth and multidomain dynamics is developed. The solid is discretised into pseudo-particles using the meshfree moving least squares method for computing the strain tensor. The particle's strain and stress tensor variables are mapped to a compliant deformation constraint. The discretised solid model thus fit a unified framework for nonsmooth multidomain dynamics simulations including rigid multibodies with complex kinematic constraints such as articulation joints, unilateral contacts with dry friction, drivelines, and hydraulics. The nonsmooth formulation allows for impact impulses to propagate instantly between the rigid multibody and the solid. Plasticity is introduced through an associative perfectly plastic modified Drucker-Prager model. The elastic and plastic dynamics are verified for simple test systems, and the capability of simulating tracked terrain vehicles driving on a deformable terrain is demonstrated.

Thermal Hydraulic Computational Fluid Dynamics Simulations and Experimental Investigation of Deformed Fuel Assemblies

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

Mays, Brian; Jackson, R. Brian

2017-03-08

The project, Toward a Longer Life Core: Thermal Hydraulic CFD Simulations and Experimental Investigation of Deformed Fuel Assemblies, DOE Project code DE-NE0008321, was a verification and validation project for flow and heat transfer through wire wrapped simulated liquid metal fuel assemblies that included both experiments and computational fluid dynamics simulations of those experiments. This project was a two year collaboration between AREVA, TerraPower, Argonne National Laboratory and Texas A&M University. Experiments were performed by AREVA and Texas A&M University. Numerical simulations of these experiments were performed by TerraPower and Argonne National Lab. Project management was performed by AREVA Federal Services.more » The first of a kind project resulted in the production of both local point temperature measurements and local flow mixing experiment data paired with numerical simulation benchmarking of the experiments. The project experiments included the largest wire-wrapped pin assembly Mass Index of Refraction (MIR) experiment in the world, the first known wire-wrapped assembly experiment with deformed duct geometries and the largest numerical simulations ever produced for wire-wrapped bundles.« less

Perspective: chemical dynamics simulations of non-statistical reaction dynamics

PubMed Central

Ma, Xinyou; Hase, William L.

2017-01-01

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320906

Computer simulation of aircraft motions and propulsion system dynamics for the YF-12 aircraft at supersonic cruise conditions

NASA Technical Reports Server (NTRS)

Brown, S. C.

1973-01-01

A computer simulation of the YF-12 aircraft motions and propulsion system dynamics is presented. The propulsion system was represented in sufficient detail so that interactions between aircraft motions and the propulsion system dynamics could be investigated. Six degree-of-freedom aircraft motions together with the three-axis stability augmentation system were represented. The mixed compression inlets and their controls were represented in the started mode for a range of flow conditions up to the inlet unstart boundary. Effects of inlet moving geometry on aircraft forces and movements as well as effects of aircraft motions on the inlet behavior were simulated. The engines, which are straight subjects, were represented in the afterburning mode, with effects of changes in aircraft flight conditions included. The simulation was capable of operating in real time.

Contact Line Dynamics

NASA Astrophysics Data System (ADS)

Kreiss, Gunilla; Holmgren, Hanna; Kronbichler, Martin; Ge, Anthony; Brant, Luca

2017-11-01

The conventional no-slip boundary condition leads to a non-integrable stress singularity at a moving contact line. This makes numerical simulations of two-phase flow challenging, especially when capillarity of the contact point is essential for the dynamics of the flow. We will describe a modeling methodology, which is suitable for numerical simulations, and present results from numerical computations. The methodology is based on combining a relation between the apparent contact angle and the contact line velocity, with the similarity solution for Stokes flow at a planar interface. The relation between angle and velocity can be determined by theoretical arguments, or from simulations using a more detailed model. In our approach we have used results from phase field simulations in a small domain, but using a molecular dynamics model should also be possible. In both cases more physics is included and the stress singularity is removed.

A dual-waveband dynamic IR scene projector based on DMD

NASA Astrophysics Data System (ADS)

Hu, Yu; Zheng, Ya-wei; Gao, Jiao-bo; Sun, Ke-feng; Li, Jun-na; Zhang, Lei; Zhang, Fang

2016-10-01

Infrared scene simulation system can simulate multifold objects and backgrounds to perform dynamic test and evaluate EO detecting system in the hardware in-the-loop test. The basic structure of a dual-waveband dynamic IR scene projector was introduced in the paper. The system's core device is an IR Digital Micro-mirror Device (DMD) and the radiant source is a mini-type high temperature IR plane black-body. An IR collimation optical system which transmission range includes 3-5μm and 8-12μm is designed as the projection optical system. Scene simulation software was developed with Visual C++ and Vega soft tools and a software flow chart was presented. The parameters and testing results of the system were given, and this system was applied with satisfying performance in an IR imaging simulation testing.

Ion Move Brownian Dynamics (IMBD)--simulations of ion transport.

PubMed

Kurczynska, Monika; Kotulska, Malgorzata

2014-01-01

Comparison of the computed characteristics and physiological measurement of ion transport through transmembrane proteins could be a useful method to assess the quality of protein structures. Simulations of ion transport should be detailed but also timeefficient. The most accurate method could be Molecular Dynamics (MD), which is very time-consuming, hence is not used for this purpose. The model which includes ion-ion interactions and reduces the simulation time by excluding water, protein and lipid molecules is Brownian Dynamics (BD). In this paper a new computer program for BD simulation of the ion transport is presented. We evaluate two methods for calculating the pore accessibility (round and irregular shape) and two representations of ion sizes (van der Waals diameter and one voxel). Ion Move Brownian Dynamics (IMBD) was tested with two nanopores: alpha-hemolysin and potassium channel KcsA. In both cases during the simulation an ion passed through the pore in less than 32 ns. Although two types of ions were in solution (potassium and chloride), only ions which agreed with the selectivity properties of the channels passed through the pores. IMBD is a new tool for the ion transport modelling, which can be used in the simulations of wide and narrow pores.

Mathematical multi-scale model of the cardiovascular system including mitral valve dynamics. Application to ischemic mitral insufficiency

PubMed Central

2011-01-01

Background Valve dysfunction is a common cardiovascular pathology. Despite significant clinical research, there is little formal study of how valve dysfunction affects overall circulatory dynamics. Validated models would offer the ability to better understand these dynamics and thus optimize diagnosis, as well as surgical and other interventions. Methods A cardiovascular and circulatory system (CVS) model has already been validated in silico, and in several animal model studies. It accounts for valve dynamics using Heaviside functions to simulate a physiologically accurate "open on pressure, close on flow" law. However, it does not consider real-time valve opening dynamics and therefore does not fully capture valve dysfunction, particularly where the dysfunction involves partial closure. This research describes an updated version of this previous closed-loop CVS model that includes the progressive opening of the mitral valve, and is defined over the full cardiac cycle. Results Simulations of the cardiovascular system with healthy mitral valve are performed, and, the global hemodynamic behaviour is studied compared with previously validated results. The error between resulting pressure-volume (PV) loops of already validated CVS model and the new CVS model that includes the progressive opening of the mitral valve is assessed and remains within typical measurement error and variability. Simulations of ischemic mitral insufficiency are also performed. Pressure-Volume loops, transmitral flow evolution and mitral valve aperture area evolution follow reported measurements in shape, amplitude and trends. Conclusions The resulting cardiovascular system model including mitral valve dynamics provides a foundation for clinical validation and the study of valvular dysfunction in vivo. The overall models and results could readily be generalised to other cardiac valves. PMID:21942971

Investigation of North American Vegetation Variability under Recent Climate: A Study Using the SSiB4/TRIFFID Biophysical/Dynamic Vegetation Model

NASA Technical Reports Server (NTRS)

Zhang, Zhengqiu; Xue, Yongkang; MacDonald, Glen; Cox, Peter M.; Collatz, George J.

2015-01-01

Recent studies have shown that current dynamic vegetation models have serious weaknesses in reproducing the observed vegetation dynamics and contribute to bias in climate simulations. This study intends to identify the major factors that underlie the connections between vegetation dynamics and climate variability and investigates vegetation spatial distribution and temporal variability at seasonal to decadal scales over North America (NA) to assess a 2-D biophysical model/dynamic vegetation model's (Simplified Simple Biosphere Model version 4, coupled with the Top-down Representation of Interactive Foliage and Flora Including Dynamics Model (SSiB4/TRIFFID)) ability to simulate these characteristics for the past 60 years (1948 through 2008). Satellite data are employed as constraints for the study and to compare the relationships between vegetation and climate from the observational and the simulation data sets. Trends in NA vegetation over this period are examined. The optimum temperature for photosynthesis, leaf drop threshold temperatures, and competition coefficients in the Lotka-Volterra equation, which describes the population dynamics of species competing for some common resource, have been identified as having major impacts on vegetation spatial distribution and obtaining proper initial vegetation conditions in SSiB4/TRIFFID. The finding that vegetation competition coefficients significantly affect vegetation distribution suggests the importance of including biotic effects in dynamical vegetation modeling. The improved SSiB4/TRIFFID can reproduce the main features of the NA distributions of dominant vegetation types, the vegetation fraction, and leaf area index (LAI), including its seasonal, interannual, and decadal variabilities. The simulated NA LAI also shows a general increasing trend after the 1970s in responding to warming. Both simulation and satellite observations reveal that LAI increased substantially in the southeastern U.S. starting from the 1980s. The effects of the severe drought during 1987-1992 and the last decade in the southwestern U.S. on vegetation are also evident from decreases in the simulated and satellite-derived LAIs. Both simulated and satellite-derived LAIs have the strongest correlations with air temperature at northern middle to high latitudes in spring reflecting the effect of these climatic variables on photosynthesis and phenological processes. Meanwhile, in southwestern dry lands, negative correlations appear due to the heat and moisture stress there during the summer. Furthermore, there are also positive correlations between soil wetness and LAI, which increases from spring to summer. The present study shows both the current improvements and remaining weaknesses in dynamical vegetation models. It also highlights large continental-scale variations that have occurred in NA vegetation over the past six decades and their potential relations to climate. With more observational data availability, more studies with differentmodels and focusing on different regions will be possible and are necessary to achieve comprehensive understanding of the vegetation dynamics and climate interactions.

A concentrated parameter model for the human cardiovascular system including heart valve dynamics and atrioventricular interaction.

PubMed

Korakianitis, Theodosios; Shi, Yubing

2006-09-01

Numerical modeling of the human cardiovascular system has always been an active research direction since the 19th century. In the past, various simulation models of different complexities were proposed for different research purposes. In this paper, an improved numerical model to study the dynamic function of the human circulation system is proposed. In the development of the mathematical model, the heart chambers are described with a variable elastance model. The systemic and pulmonary loops are described based on the resistance-compliance-inertia concept by considering local effects of flow friction, elasticity of blood vessels and inertia of blood in different segments of the blood vessels. As an advancement from previous models, heart valve dynamics and atrioventricular interaction, including atrial contraction and motion of the annulus fibrosus, are specifically modeled. With these improvements the developed model can predict several important features that were missing in previous numerical models, including regurgitant flow on heart valve closure, the value of E/A velocity ratio in mitral flow, the motion of the annulus fibrosus (called the KG diaphragm pumping action), etc. These features have important clinical meaning and their changes are often related to cardiovascular diseases. Successful simulation of these features enhances the accuracy of simulations of cardiovascular dynamics, and helps in clinical studies of cardiac function.

Modeling and simulation of consumer response to dynamic pricing.

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

Valenzuela, J.; Thimmapuram, P.; Kim, J

2012-08-01

Assessing the impacts of dynamic-pricing under the smart grid concept is becoming extremely important for deciding its full deployment. In this paper, we develop a model that represents the response of consumers to dynamic pricing. In the model, consumers use forecasted day-ahead prices to shift daily energy consumption from hours when the price is expected to be high to hours when the price is expected to be low while maintaining the total energy consumption as unchanged. We integrate the consumer response model into the Electricity Market Complex Adaptive System (EMCAS). EMCAS is an agent-based model that simulates restructured electricity markets.more » We explore the impacts of dynamic-pricing on price spikes, peak demand, consumer energy bills, power supplier profits, and congestion costs. A simulation of an 11-node test network that includes eight generation companies and five aggregated consumers is performed for a period of 1 month. In addition, we simulate the Korean power system.« less

Research in Distance Education: A System Modeling Approach.

ERIC Educational Resources Information Center

Saba, Farhad; Twitchell, David

1988-01-01

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

Three dimensional, non-linear, finite element analysis of compactable soil interaction with a hyperelastic wheel

NASA Astrophysics Data System (ADS)

Chiroux, Robert Charles

The objective of this research was to produce a three dimensional, non-linear, dynamic simulation of the interaction between a hyperelastic wheel rolling over compactable soil. The finite element models developed to produce the simulation utilized the ABAQUS/Explicit computer code. Within the simulation two separate bodies were modeled, the hyperelastic wheel and a compactable soil-bed. Interaction between the bodies was achieved by allowing them to come in contact but not to penetrate the contact surface. The simulation included dynamic loading of a hyperelastic, rubber tire in contact with compactable soil with an applied constant angular velocity or torque, including a tow load, applied to the wheel hub. The constraints on the wheel model produced a straight and curved path. In addition the simulation included a shear limit between the tire and soil allowing for the introduction of slip. Soil properties were simulated using the Drucker-Prager, Cap Plasticity model available within the ABAQUS/Explicit program. Numerical results obtained from the three dimensional model were compared with related experimental data and showed good correlation for similar conditions. Numerical and experimental data compared well for both stress and wheel rut formation depth under a weight of 5.8 kN and a constant angular velocity applied to the wheel hub. The simulation results provided a demonstration of the benefit of three-dimensional simulation in comparison to previous two-dimensional, plane strain simulations.

Calibration and validation of a spar-type floating offshore wind turbine model using the FAST dynamic simulation tool

DOE PAGES

Browning, J. R.; Jonkman, J.; Robertson, A.; ...

2014-12-16

In this study, high-quality computer simulations are required when designing floating wind turbines because of the complex dynamic responses that are inherent with a high number of degrees of freedom and variable metocean conditions. In 2007, the FAST wind turbine simulation tool, developed and maintained by the U.S. Department of Energy's (DOE's) National Renewable Energy Laboratory (NREL), was expanded to include capabilities that are suitable for modeling floating offshore wind turbines. In an effort to validate FAST and other offshore wind energy modeling tools, DOE funded the DeepCwind project that tested three prototype floating wind turbines at 1/50 th scalemore » in a wave basin, including a semisubmersible, a tension-leg platform, and a spar buoy. This paper describes the use of the results of the spar wave basin tests to calibrate and validate the FAST offshore floating simulation tool, and presents some initial results of simulated dynamic responses of the spar to several combinations of wind and sea states. Wave basin tests with the spar attached to a scale model of the NREL 5-megawatt reference wind turbine were performed at the Maritime Research Institute Netherlands under the DeepCwind project. This project included free-decay tests, tests with steady or turbulent wind and still water (both periodic and irregular waves with no wind), and combined wind/wave tests. The resulting data from the 1/50th model was scaled using Froude scaling to full size and used to calibrate and validate a full-size simulated model in FAST. Results of the model calibration and validation include successes, subtleties, and limitations of both wave basin testing and FAST modeling capabilities.« less

Solvation and Dynamics of Sodium and Potassium in Ethylene Carbonate from ab Initio Molecular Dynamics Simulations

DOE PAGES

Pham, Tuan Anh; Kweon, Kyoung E.; Samanta, Amit; ...

2017-09-18

The development of sodium and potassium batteries offers a promising way to meet the scaling and cost challenges of energy storage. However, compared to Li +, several intrinsic properties of Na + and K +, including their solvation and dynamics in typical organic electrolytes utilized in battery applications, are less well-understood. Here in this paper, we report a systematic investigation of Na + and K + in ethylene carbonate (EC) using first-principles molecular dynamics simulations. Our simulations reveal significant differences in the solvation structure and dynamical properties of Na + and K + compared to Li +. We find that,more » in contrast to Li + which exhibits a well-defined first solvation shell, the larger Na+ and K+ ions show more disordered and flexible solvation structures. These differences in solvation were found to significantly influence the ion dynamics, leading to larger diffusion coefficients of Na + and K + compared to Li +. Our simulations also reveal a clear and interesting analog in the behavior of the ions in EC and aqueous environments, particularly in the specific ion effects on the solvent dynamics. Lastly, this work provides fundamental understanding of the intrinsic properties of Na + and K + in organic electrolytes, which may ultimately influence the intercalation mechanism at the electrode–electrolyte interface and therefore battery performance, lifetime, and safety.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

Dynamically downscaling predictions for deciduous tree leaf emergence in California under current and future climate.

PubMed

Medvigy, David; Kim, Seung Hee; Kim, Jinwon; Kafatos, Menas C

2016-07-01

Models that predict the timing of deciduous tree leaf emergence are typically very sensitive to temperature. However, many temperature data products, including those from climate models, have been developed at a very coarse spatial resolution. Such coarse-resolution temperature products can lead to highly biased predictions of leaf emergence. This study investigates how dynamical downscaling of climate models impacts simulations of deciduous tree leaf emergence in California. Models for leaf emergence are forced with temperatures simulated by a general circulation model (GCM) at ~200-km resolution for 1981-2000 and 2031-2050 conditions. GCM simulations are then dynamically downscaled to 32- and 8-km resolution, and leaf emergence is again simulated. For 1981-2000, the regional average leaf emergence date is 30.8 days earlier in 32-km simulations than in ~200-km simulations. Differences between the 32 and 8 km simulations are small and mostly local. The impact of downscaling from 200 to 8 km is ~15 % smaller in 2031-2050 than in 1981-2000, indicating that the impacts of downscaling are unlikely to be stationary.

Simulation of Attitude and Trajectory Dynamics and Control of Multiple Spacecraft

NASA Technical Reports Server (NTRS)

Stoneking, Eric T.

2009-01-01

Agora software is a simulation of spacecraft attitude and orbit dynamics. It supports spacecraft models composed of multiple rigid bodies or flexible structural models. Agora simulates multiple spacecraft simultaneously, supporting rendezvous, proximity operations, and precision formation flying studies. The Agora environment includes ephemerides for all planets and major moons in the solar system, supporting design studies for deep space as well as geocentric missions. The environment also contains standard models for gravity, atmospheric density, and magnetic fields. Disturbance force and torque models include aerodynamic, gravity-gradient, solar radiation pressure, and third-body gravitation. In addition to the dynamic and environmental models, Agora supports geometrical visualization through an OpenGL interface. Prototype models are provided for common sensors, actuators, and control laws. A clean interface accommodates linking in actual flight code in place of the prototype control laws. The same simulation may be used for rapid feasibility studies, and then used for flight software validation as the design matures. Agora is open-source and portable across computing platforms, making it customizable and extensible. It is written to support the entire GNC (guidance, navigation, and control) design cycle, from rapid prototyping and design analysis, to high-fidelity flight code verification. As a top-down design, Agora is intended to accommodate a large range of missions, anywhere in the solar system. Both two-body and three-body flight regimes are supported, as well as seamless transition between them. Multiple spacecraft may be simultaneously simulated, enabling simulation of rendezvous scenarios, as well as formation flying. Built-in reference frames and orbit perturbation dynamics provide accurate modeling of precision formation control.

Climate-based models for West Nile Culex mosquito vectors in the Northeastern US

NASA Astrophysics Data System (ADS)

Gong, Hongfei; Degaetano, Arthur T.; Harrington, Laura C.

2011-05-01

Climate-based models simulating Culex mosquito population abundance in the Northeastern US were developed. Two West Nile vector species, Culex pipiens and Culex restuans, were included in model simulations. The model was optimized by a parameter-space search within biological bounds. Mosquito population dynamics were driven by major environmental factors including temperature, rainfall, evaporation rate and photoperiod. The results show a strong correlation between the timing of early population increases (as early warning of West Nile virus risk) and decreases in late summer. Simulated abundance was highly correlated with actual mosquito capture in New Jersey light traps and validated with field data. This climate-based model simulates the population dynamics of both the adult and immature mosquito life stage of Culex arbovirus vectors in the Northeastern US. It is expected to have direct and practical application for mosquito control and West Nile prevention programs.

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein-Protein Interactions.

PubMed

Tan, Yaw Sing; Spring, David R; Abell, Chris; Verma, Chandra S

2015-07-14

A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

DOE PAGES

Abhyankar, Shrirang; Constantinescu, Emil M.; Smith, Barry F.; ...

2016-11-07

Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including amore » real utility network, show good scalability on different computing architectures.« less

BRENDA: a dynamic simulator for a sodium-cooled fast reactor power plant

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

Hetrick, D.L.; Sowers, G.W.

1978-06-01

This report is a users' manual for one version of BRENDA (Breeder Reactor Nuclear Dynamic Analysis), which is a digital program for simulating the dynamic behavior of a sodium-cooled fast reactor power plant. This version, which contains 57 differential equations, represents a simplified model of the Clinch River Breeder Reactor Project (CRBRP). BRENDA is an input deck for DARE P (Differential Analyzer Replacement, Portable), which is a continuous-system simulation language developed at the University of Arizona. This report contains brief descriptions of DARE P and BRENDA, instructions for using BRENDA in conjunction with DARE P, and some sample output. Amore » list of variable names and a listing for BRENDA are included as appendices.« less

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

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

Abhyankar, Shrirang; Constantinescu, Emil M.; Smith, Barry F.

Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including amore » real utility network, show good scalability on different computing architectures.« less

Real-time maritime scene simulation for ladar sensors

NASA Astrophysics Data System (ADS)

Christie, Chad L.; Gouthas, Efthimios; Swierkowski, Leszek; Williams, Owen M.

2011-06-01

Continuing interest exists in the development of cost-effective synthetic environments for testing Laser Detection and Ranging (ladar) sensors. In this paper we describe a PC-based system for real-time ladar scene simulation of ships and small boats in a dynamic maritime environment. In particular, we describe the techniques employed to generate range imagery accompanied by passive radiance imagery. Our ladar scene generation system is an evolutionary extension of the VIRSuite infrared scene simulation program and includes all previous features such as ocean wave simulation, the physically-realistic representation of boat and ship dynamics, wake generation and simulation of whitecaps, spray, wake trails and foam. A terrain simulation extension is also under development. In this paper we outline the development, capabilities and limitations of the VIRSuite extensions.

Implementing ADM1 for plant-wide benchmark simulations in Matlab/Simulink.

PubMed

Rosen, C; Vrecko, D; Gernaey, K V; Pons, M N; Jeppsson, U

2006-01-01

The IWA Anaerobic Digestion Model No.1 (ADM1) was presented in 2002 and is expected to represent the state-of-the-art model within this field in the future. Due to its complexity the implementation of the model is not a simple task and several computational aspects need to be considered, in particular if the ADM1 is to be included in dynamic simulations of plant-wide or even integrated systems. In this paper, the experiences gained from a Matlab/Simulink implementation of ADM1 into the extended COST/IWA Benchmark Simulation Model (BSM2) are presented. Aspects related to system stiffness, model interfacing with the ASM family, mass balances, acid-base equilibrium and algebraic solvers for pH and other troublesome state variables, numerical solvers and simulation time are discussed. The main conclusion is that if implemented properly, the ADM1 will also produce high-quality results in dynamic plant-wide simulations including noise, discrete sub-systems, etc. without imposing any major restrictions due to extensive computational efforts.

Ocean Thermal Energy Conversion power system development. Phase I: preliminary design. Final report. [ODSP-3 code; OTEC Steady-State Analysis Program

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

Not Available

1978-12-04

The following appendices are included; Dynamic Simulation Program (ODSP-3); sample results of dynamic simulation; trip report - NH/sub 3/ safety precautions/accident records; trip report - US Coast Guard Headquarters; OTEC power system development, preliminary design test program report; medium turbine generator inspection point program; net energy analysis; bus bar cost of electricity; OTEC technical specifications; and engineer drawings. (WHK)

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

Nonlinear absorption dynamics using field-induced surface hopping: zinc porphyrin in water.

PubMed

Röhr, Merle I S; Petersen, Jens; Wohlgemuth, Matthias; Bonačić-Koutecký, Vlasta; Mitrić, Roland

2013-05-10

We wish to present the application of our field-induced surface-hopping (FISH) method to simulate nonlinear absorption dynamics induced by strong nonresonant laser fields. We provide a systematic comparison of the FISH approach with exact quantum dynamics simulations on a multistate model system and demonstrate that FISH allows for accurate simulations of nonlinear excitation processes including multiphoton electronic transitions. In particular, two different approaches for simulating two-photon transitions are compared. The first approach is essentially exact and involves the solution of the time-dependent Schrödinger equation in an extended manifold of excited states, while in the second one only transiently populated nonessential states are replaced by an effective quadratic coupling term, and dynamics is performed in a considerably smaller manifold of states. We illustrate the applicability of our method to complex molecular systems by simulating the linear and nonlinear laser-driven dynamics in zinc (Zn) porphyrin in the gas phase and in water. For this purpose, the FISH approach is connected with the quantum mechanical-molecular mechanical approach (QM/MM) which is generally applicable to large classes of complex systems. Our findings that multiphoton absorption and dynamics increase the population of higher excited states of Zn porphyrin in the nonlinear regime, in particular in solution, provides a means for manipulating excited-state properties, such as transient absorption dynamics and electronic relaxation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Operational modeling system with dynamic-wave routing

USGS Publications Warehouse

Ishii, A.L.; Charlton, T.J.; Ortel, T.W.; Vonnahme, C.C.; ,

1998-01-01

A near real-time streamflow-simulation system utilizing continuous-simulation rainfall-runoff generation with dynamic-wave routing is being developed by the U.S. Geological Survey in cooperation with the Du Page County Department of Environmental Concerns for a 24-kilometer reach of Salt Creek in Du Page County, Illinois. This system is needed in order to more effectively manage the Elmhurst Quarry Flood Control Facility, an off-line stormwater diversion reservoir located along Salt Creek. Near real time simulation capabilities will enable the testing and evaluation of potential rainfall, diversion, and return-flow scenarios on water-surface elevations along Salt Creek before implementing diversions or return-flows. The climatological inputs for the continuous-simulation rainfall-runoff model, Hydrologic Simulation Program - FORTRAN (HSPF) are obtained by Internet access and from a network of radio-telemetered precipitation gages reporting to a base-station computer. The unit area runoff time series generated from HSPF are the input for the dynamic-wave routing model. Full Equations (FEQ). The Generation and Analysis of Model Simulation Scenarios (GENSCN) interface is used as a pre- and post-processor for managing input data and displaying and managing simulation results. The GENSCN interface includes a variety of graphical and analytical tools for evaluation and quick visualization of the results of operational scenario simulations and thereby makes it possible to obtain the full benefit of the fully distributed dynamic routing results.

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Influence of feedbacks from simulated crop growth on integrated regional hydrologic simulations under climate scenarios

NASA Astrophysics Data System (ADS)

van Walsum, P. E. V.

2011-11-01

Climate change impact modelling of hydrologic responses is hampered by climate-dependent model parameterizations. Reducing this dependency was one of the goals of extending the regional hydrologic modelling system SIMGRO with a two-way coupling to the crop growth simulation model WOFOST. The coupling includes feedbacks to the hydrologic model in terms of the root zone depth, soil cover, leaf area index, interception storage capacity, crop height and crop factor. For investigating whether such feedbacks lead to significantly different simulation results, two versions of the model coupling were set up for a test region: one with exogenous vegetation parameters, the "static" model, and one with endogenous simulation of the crop growth, the "dynamic" model WOFOST. The used parameterization methods of the static/dynamic vegetation models ensure that for the current climate the simulated long-term average of the actual evapotranspiration is the same for both models. Simulations were made for two climate scenarios. Owing to the higher temperatures in combination with a higher CO2-concentration of the atmosphere, a forward time shift of the crop development is simulated in the dynamic model; the used arable land crop, potatoes, also shows a shortening of the growing season. For this crop, a significant reduction of the potential transpiration is simulated compared to the static model, in the example by 15% in a warm, dry year. In consequence, the simulated crop water stress (the unit minus the relative transpiration) is lower when the dynamic model is used; also the simulated increase of crop water stress due to climate change is lower; in the example, the simulated increase is 15 percentage points less (of 55) than when a static model is used. The static/dynamic models also simulate different absolute values of the transpiration. The difference is most pronounced for potatoes at locations with ample moisture supply; this supply can either come from storage release of a good soil or from capillary rise. With good supply of moisture, the dynamic model simulates up to 10% less actual evapotranspiration than the static one in the example. This can lead to cases where the dynamic model predicts a slight increase of the recharge in a climate scenario, where the static model predicts a decrease. The use of a dynamic model also affects the simulated demand for surface water from external sources; especially the timing is affected. The proposed modelling approach uses postulated relationships that require validation with controlled field trials. In the Netherlands there is a lack of experimental facilities for performing such validations.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

PubMed

Wall, Michael E; Van Benschoten, Andrew H; Sauter, Nicholas K; Adams, Paul D; Fraser, James S; Terwilliger, Thomas C

2014-12-16

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

Regularity Aspects in Inverse Musculoskeletal Biomechanics

NASA Astrophysics Data System (ADS)

Lund, Marie; Stâhl, Fredrik; Gulliksson, Mârten

2008-09-01

Inverse simulations of musculoskeletal models computes the internal forces such as muscle and joint reaction forces, which are hard to measure, using the more easily measured motion and external forces as input data. Because of the difficulties of measuring muscle forces and joint reactions, simulations are hard to validate. One way of reducing errors for the simulations is to ensure that the mathematical problem is well-posed. This paper presents a study of regularity aspects for an inverse simulation method, often called forward dynamics or dynamical optimization, that takes into account both measurement errors and muscle dynamics. Regularity is examined for a test problem around the optimum using the approximated quadratic problem. The results shows improved rank by including a regularization term in the objective that handles the mechanical over-determinancy. Using the 3-element Hill muscle model the chosen regularization term is the norm of the activation. To make the problem full-rank only the excitation bounds should be included in the constraints. However, this results in small negative values of the activation which indicates that muscles are pushing and not pulling, which is unrealistic but the error maybe small enough to be accepted for specific applications. These results are a start to ensure better results of inverse musculoskeletal simulations from a numerical point of view.

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.

From force-fields to photons: MD simulations of dye-labeled nucleic acids and Monte Carlo modeling of FRET

NASA Astrophysics Data System (ADS)

Milas, Peker; Gamari, Ben; Parrot, Louis; Buckman, Richard; Goldner, Lori

2011-11-01

Fluorescence resonance energy transfer (FRET) is a powerful experimental technique for understanding the structural fluctuations and transformations of RNA, DNA and proteins. Molecular dynamics (MD) simulations provide a window into the nature of these fluctuations on a faster time scale inaccessible to experiment. We use Monte Carlo methods to model and compare FRET data from dye-labeled RNA with what might be predicted from the MD simulation. With a few notable exceptions, the contribution of fluorophore and linker dynamics to these FRET measurements has not been investigated. We include the dynamics of the ground state dyes and linkers along with an explicit water solvent in our study of a 16mer double-stranded RNA. Cyanine dyes are attached at either the 3' or 5' ends with a three carbon linker, providing a basis for contrasting the dynamics of similar but not identical molecular structures.

Communication: Polymer entanglement dynamics: Role of attractive interactions

DOE PAGES

Grest, Gary S.

2016-10-10

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes to the late time diffusive regime, highly coarse grained models with purely repulsive interactions between monomers are widely used since they are computationally the most efficient. In this paper, using large scale molecular dynamics simulations, the effect of including the attractive interaction between monomers on the dynamics of entangled polymer melts is explored for the first time over a wide temperature range. Attractive interactions have little effect onmore » the local packing for all temperatures T and on the chain mobility for T higher than about twice the glass transition T g. Finally, these results, across a broad range of molecular weight, show that to study the dynamics of entangled polymer melts, the interactions can be treated as pure repulsive, confirming a posteriori the validity of previous studies and opening the way to new large scale numerical simulations.« less

Guidelines for Computing Longitudinal Dynamic Stability Characteristics of a Subsonic Transport

NASA Technical Reports Server (NTRS)

Thompson, Joseph R.; Frank, Neal T.; Murphy, Patrick C.

2010-01-01

A systematic study is presented to guide the selection of a numerical solution strategy for URANS computation of a subsonic transport configuration undergoing simulated forced oscillation about its pitch axis. Forced oscillation is central to the prevalent wind tunnel methodology for quantifying aircraft dynamic stability derivatives from force and moment coefficients, which is the ultimate goal for the computational simulations. Extensive computations are performed that lead in key insights of the critical numerical parameters affecting solution convergence. A preliminary linear harmonic analysis is included to demonstrate the potential of extracting dynamic stability derivatives from computational solutions.

2-kW Solar Dynamic Space Power System Tested in Lewis' Thermal Vacuum Facility

NASA Technical Reports Server (NTRS)

1995-01-01

Working together, a NASA/industry team successfully operated and tested a complete solar dynamic space power system in a large thermal vacuum facility with a simulated sun. This NASA Lewis Research Center facility, known as Tank 6 in building 301, accurately simulates the temperatures, high vacuum, and solar flux encountered in low-Earth orbit. The solar dynamic space power system shown in the photo in the Lewis facility, includes the solar concentrator and the solar receiver with thermal energy storage integrated with the power conversion unit. Initial testing in December 1994 resulted in the world's first operation of an integrated solar dynamic system in a relevant environment.

A Prediction of the Damping Properties of Hindered Phenol AO-60/polyacrylate Rubber (AO-60/ACM) Composites through Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Yang, Da-Wei; Zhao, Xiu-Ying; Zhang, Geng; Li, Qiang-Guo; Wu, Si-Zhu

2016-05-01

Molecule dynamics (MD) simulation, a molecular-level method, was applied to predict the damping properties of AO-60/polyacrylate rubber (AO-60/ACM) composites before experimental measures were performed. MD simulation results revealed that two types of hydrogen bond, namely, type A (AO-60) -OH•••O=C- (ACM), type B (AO-60) - OH•••O=C- (AO-60) were formed. Then, the AO-60/ACM composites were fabricated and tested to verify the accuracy of the MD simulation through dynamic mechanical thermal analysis (DMTA). DMTA results showed that the introduction of AO-60 could remarkably improve the damping properties of the composites, including the increase of glass transition temperature (Tg) alongside with the loss factor (tan δ), also indicating the AO-60/ACM(98/100) had the best damping performance amongst the composites which verified by the experimental.

Stochastic Simulation of Actin Dynamics Reveals the Role of Annealing and Fragmentation

PubMed Central

Fass, Joseph; Pak, Chi; Bamburg, James; Mogilner, Alex

2008-01-01

Recent observations of F-actin dynamics call for theoretical models to interpret and understand the quantitative data. A number of existing models rely on simplifications and do not take into account F-actin fragmentation and annealing. We use Gillespie’s algorithm for stochastic simulations of the F-actin dynamics including fragmentation and annealing. The simulations vividly illustrate that fragmentation and annealing have little influence on the shape of the polymerization curve and on nucleotide profiles within filaments but drastically affect the F-actin length distribution, making it exponential. We find that recent surprising measurements of high length diffusivity at the critical concentration cannot be explained by fragmentation and annealing events unless both fragmentation rates and frequency of undetected fragmentation and annealing events are greater than previously thought. The simulations compare well with experimentally measured actin polymerization data and lend additional support to a number of existing theoretical models. PMID:18279896

Convective - TTU

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

Kosovic, Branko

This dataset includes large-eddy simulation (LES) output from a convective atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on July 4, 2012. The dataset was used to assess the LES models for simulation of canonical convective ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

LANL - Convective - TTU

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

Kosovic, Branko

This dataset includes large-eddy simulation (LES) output from a convective atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on July 4, 2012. The dataset was used to assess the LES models for simulation of canonical convective ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

LANL - Neutral - TTU

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

Kosovic, Branko

This dataset includes large-eddy simulation (LES) output from a neutrally stratified atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on Aug. 17, 2012. The dataset was used to assess LES models for simulation of canonical neutral ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

Web-Based Simulation Games for the Integration of Engineering and Business Fundamentals

ERIC Educational Resources Information Center

Calfa, Bruno; Banholzer, William; Alger, Monty; Doherty, Michael

2017-01-01

This paper describes a web-based suite of simulation games that have the purpose to enhance the chemical engineering curriculum with business-oriented decisions. Two simulation cases are discussed whose teaching topics include closing material and energy balances, importance of recycle streams, price-volume relationship in a dynamic market, impact…

Nucleic acids: theory and computer simulation, Y2K.

PubMed

Beveridge, D L; McConnell, K J

2000-04-01

Molecular dynamics simulations on DNA and RNA that include solvent are now being performed under realistic environmental conditions of water activity and salt. Improvements to force-fields and treatments of long-range interactions have significantly increased the reliability of simulations. New studies of sequence effects, axis bending, solvation and conformational transitions have appeared.

Simulating Descent and Landing of a Spacecraft

NASA Technical Reports Server (NTRS)

Balaram, J.; Jain, Abhinandan; Martin, Bryan; Lim, Christopher; Henriquez, David; McMahon, Elihu; Sohl, Garrett; Banerjee, Pranab; Steele, Robert; Bentley, Timothy

2005-01-01

The Dynamics Simulator for Entry, Descent, and Surface landing (DSENDS) software performs high-fidelity simulation of the Entry, Descent, and Landing (EDL) of a spacecraft into the atmosphere and onto the surface of a planet or a smaller body. DSENDS is an extension of the DShell and DARTS programs, which afford capabilities for mathematical modeling of the dynamics of a spacecraft as a whole and of its instruments, actuators, and other subsystems. DSENDS enables the modeling (including real-time simulation) of flight-train elements and all spacecraft responses during various phases of EDL. DSENDS provides high-fidelity models of the aerodynamics of entry bodies and parachutes plus supporting models of atmospheres. Terrain and real-time responses of terrain-imaging radar and lidar instruments can also be modeled. The program includes modules for simulation of guidance, navigation, hypersonic steering, and powered descent. Automated state-machine-driven model switching is used to represent spacecraft separations and reconfigurations. Models for computing landing contact and impact forces are expected to be added. DSENDS can be used as a stand-alone program or incorporated into a larger program that simulates operations in real time.

Modelling and simulation of biased agonism dynamics at a G protein-coupled receptor.

PubMed

Bridge, L J; Mead, J; Frattini, E; Winfield, I; Ladds, G

2018-04-07

Theoretical models of G protein-coupled receptor (GPCR) concentration-response relationships often assume an agonist producing a single functional response via a single active state of the receptor. These models have largely been analysed assuming steady-state conditions. There is now much experimental evidence to suggest that many GPCRs can exist in multiple receptor conformations and elicit numerous functional responses, with ligands having the potential to activate different signalling pathways to varying extents-a concept referred to as biased agonism, functional selectivity or pluri-dimensional efficacy. Moreover, recent experimental results indicate a clear possibility for time-dependent bias, whereby an agonist's bias with respect to different pathways may vary dynamically. Efforts towards understanding the implications of temporal bias by characterising and quantifying ligand effects on multiple pathways will clearly be aided by extending current equilibrium binding and biased activation models to include G protein activation dynamics. Here, we present a new model of time-dependent biased agonism, based on ordinary differential equations for multiple cubic ternary complex activation models with G protein cycle dynamics. This model allows simulation and analysis of multi-pathway activation bias dynamics at a single receptor for the first time, at the level of active G protein (α GTP ), towards the analysis of dynamic functional responses. The model is generally applicable to systems with N G G proteins and N* active receptor states. Numerical simulations for N G =N * =2 reveal new insights into the effects of system parameters (including cooperativities, and ligand and receptor concentrations) on bias dynamics, highlighting new phenomena including the dynamic inter-conversion of bias direction. Further, we fit this model to 'wet' experimental data for two competing G proteins (G i and G s ) that become activated upon stimulation of the adenosine A 1 receptor with adenosine derivative compounds. Finally, we show that our model can qualitatively describe the temporal dynamics of this competing G protein activation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

DOE PAGES

Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

2014-10-29

We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

Using collective variables to drive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

2013-12-01

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

Two-temperature model in molecular dynamics simulations of cascades in Ni-based alloys

DOE PAGES

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

2017-01-03

In high-energy irradiation events, energy from the fast moving ion is transferred to the system via nuclear and electronic energy loss mechanisms. The nuclear energy loss results in the creation of point defects and clusters, while the energy transferred to the electrons results in the creation of high electronic temperatures, which can affect the damage evolution. In this paper, we perform molecular dynamics simulations of 30 keV and 50 keV Ni ion cascades in nickel-based alloys without and with the electronic effects taken into account. We compare the results of classical molecular dynamics (MD) simulations, where the electronic effects aremore » ignored, with results from simulations that include the electronic stopping only, as well as simulations where both the electronic stopping and the electron-phonon coupling are incorporated, as described by the two temperature model (2T-MD). Finally, our results indicate that the 2T-MD leads to a smaller amount of damage, more isolated defects and smaller defect clusters.« less

Simulating the frontal instability of lock-exchange density currents with dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Li, Yanggui; Geng, Xingguo; Wang, Heping; Zhuang, Xin; Ouyang, Jie

2016-06-01

The frontal instability of lock-exchange density currents is numerically investigated using dissipative particle dynamics (DPD) at the mesoscopic particle level. For modeling two-phase flow, the “color” repulsion model is adopted to describe binary fluids according to Rothman-Keller method. The present DPD simulation can reproduce the flow phenomena of lock-exchange density currents, including the lobe-and-cleft instability that appears at the head, as well as the formation of coherent billow structures at the interface behind the head due to the growth of Kelvin-Helmholtz instability. Furthermore, through the DPD simulation, some small-scale characteristics can be observed, which are difficult to be captured in macroscopic simulation and experiment.

AVESTAR Center for Operational Excellence of Electricity Generation Plants

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

Zitney, Stephen

2012-08-29

To address industry challenges in attaining operational excellence for electricity generation plants, the U.S. Department of Energy’s (DOE) National Energy Technology Laboratory (NETL) has launched a world-class facility for Advanced Virtual Energy Simulation Training and Research (AVESTARTM). This presentation will highlight the AVESTARTM Center simulators, facilities, and comprehensive training, education, and research programs focused on the operation and control of high-efficiency, near-zero-emission electricity generation plants. The AVESTAR Center brings together state-of-the-art, real-time, high-fidelity dynamic simulators with full-scope operator training systems (OTSs) and 3D virtual immersive training systems (ITSs) into an integrated energy plant and control room environment. AVESTAR’s initial offeringmore » combines--for the first time--a “gasification with CO2 capture” process simulator with a “combined-cycle” power simulator together in a single OTS/ITS solution for an integrated gasification combined cycle (IGCC) power plant with carbon dioxide (CO2) capture. IGCC systems are an attractive technology option for power generation, especially when capturing and storing CO2 is necessary to satisfy emission targets. The AVESTAR training program offers a variety of courses that merge classroom learning, simulator-based OTS learning in a control-room operations environment, and immersive learning in the interactive 3D virtual plant environment or ITS. All of the courses introduce trainees to base-load plant operation, control, startups, and shutdowns. Advanced courses require participants to become familiar with coordinated control, fuel switching, power-demand load shedding, and load following, as well as to problem solve equipment and process malfunctions. Designed to ensure work force development, training is offered for control room and plant field operators, as well as engineers and managers. Such comprehensive simulator-based instruction allows for realistic training without compromising worker, equipment, and environmental safety. It also better prepares operators and engineers to manage the plant closer to economic constraints while minimizing or avoiding the impact of any potentially harmful, wasteful, or inefficient events. The AVESTAR Center is also used to augment graduate and undergraduate engineering education in the areas of process simulation, dynamics, control, and safety. Students and researchers gain hands-on simulator-based training experience and learn how the commercial-scale power plants respond dynamically to changes in manipulated inputs, such as coal feed flow rate and power demand. Students also analyze how the regulatory control system impacts power plant performance and stability. In addition, students practice start-up, shutdown, and malfunction scenarios. The 3D virtual ITSs are used for plant familiarization, walk-through, equipment animations, and safety scenarios. To further leverage the AVESTAR facilities and simulators, NETL and its university partners are pursuing an innovative and collaborative R&D program. In the area of process control, AVESTAR researchers are developing enhanced strategies for regulatory control and coordinated plant-wide control, including gasifier and gas turbine lead, as well as advanced process control using model predictive control (MPC) techniques. Other AVESTAR R&D focus areas include high-fidelity equipment modeling using partial differential equations, dynamic reduced order modeling, optimal sensor placement, 3D virtual plant simulation, and modern grid. NETL and its partners plan to continue building the AVESTAR portfolio of dynamic simulators, immersive training systems, and advanced research capabilities to satisfy industry’s growing need for training and experience with the operation and control of clean energy plants. Future dynamic simulators under development include natural gas combined cycle (NGCC) and supercritical pulverized coal (SCPC) plants with post-combustion CO2 capture. These dynamic simulators are targeted for use in establishing a Virtual Carbon Capture Center (VCCC), similar in concept to the DOE’s National Carbon Capture Center for slipstream testing. The VCCC will enable developers of CO2 capture technologies to integrate, test, and optimize the operation of their dynamic capture models within the context of baseline power plant dynamic models. The objective is to provide hands-on, simulator-based “learn-by-operating” test platforms to accelerate the scale-up and deployment of CO2 capture technologies. Future AVESTAR plans also include pursuing R&D on the dynamics, operation, and control of integrated electricity generation and storage systems for the modern grid era. Special emphasis will be given to combining load-following energy plants with renewable and distributed generating supplies and fast-ramping energy storage systems to provide near constant baseload power.« less

Wind Energy System Time-domain (WEST) analyzers using hybrid simulation techniques

NASA Technical Reports Server (NTRS)

Hoffman, J. A.

1979-01-01

Two stand-alone analyzers constructed for real time simulation of the complex dynamic characteristics of horizontal-axis wind energy systems are described. Mathematical models for an aeroelastic rotor, including nonlinear aerodynamic and elastic loads, are implemented with high speed digital and analog circuitry. Models for elastic supports, a power train, a control system, and a rotor gimbal system are also included. Limited correlation efforts show good comparisons between results produced by the analyzers and results produced by a large digital simulation. The digital simulation results correlate well with test data.

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

PubMed

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

2006-02-24

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

Update: Advancement of Contact Dynamics Modeling for Human Spaceflight Simulation Applications

NASA Technical Reports Server (NTRS)

Brain, Thomas A.; Kovel, Erik B.; MacLean, John R.; Quiocho, Leslie J.

2017-01-01

Pong is a new software tool developed at the NASA Johnson Space Center that advances interference-based geometric contact dynamics based on 3D graphics models. The Pong software consists of three parts: a set of scripts to extract geometric data from 3D graphics models, a contact dynamics engine that provides collision detection and force calculations based on the extracted geometric data, and a set of scripts for visualizing the dynamics response with the 3D graphics models. The contact dynamics engine can be linked with an external multibody dynamics engine to provide an integrated multibody contact dynamics simulation. This paper provides a detailed overview of Pong including the overall approach and modeling capabilities, which encompasses force generation from contact primitives and friction to computational performance. Two specific Pong-based examples of International Space Station applications are discussed, and the related verification and validation using this new tool are also addressed.

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

NASA Astrophysics Data System (ADS)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

CALM: Complex Adaptive System (CAS)-Based Decision Support for Enabling Organizational Change

NASA Astrophysics Data System (ADS)

Adler, Richard M.; Koehn, David J.

Guiding organizations through transformational changes such as restructuring or adopting new technologies is a daunting task. Such changes generate workforce uncertainty, fear, and resistance, reducing morale, focus and performance. Conventional project management techniques fail to mitigate these disruptive effects, because social and individual changes are non-mechanistic, organic phenomena. CALM (for Change, Adaptation, Learning Model) is an innovative decision support system for enabling change based on CAS principles. CALM provides a low risk method for validating and refining change strategies that combines scenario planning techniques with "what-if" behavioral simulation. In essence, CALM "test drives" change strategies before rolling them out, allowing organizations to practice and learn from virtual rather than actual mistakes. This paper describes the CALM modeling methodology, including our metrics for measuring organizational readiness to respond to change and other major CALM scenario elements: prospective change strategies; alternate futures; and key situational dynamics. We then describe CALM's simulation engine for projecting scenario outcomes and its associated analytics. CALM's simulator unifies diverse behavioral simulation paradigms including: adaptive agents; system dynamics; Monte Carlo; event- and process-based techniques. CALM's embodiment of CAS dynamics helps organizations reduce risk and improve confidence and consistency in critical strategies for enabling transformations.

Open source Matrix Product States: Opening ways to simulate entangled many-body quantum systems in one dimension

NASA Astrophysics Data System (ADS)

Jaschke, Daniel; Wall, Michael L.; Carr, Lincoln D.

2018-04-01

Numerical simulations are a powerful tool to study quantum systems beyond exactly solvable systems lacking an analytic expression. For one-dimensional entangled quantum systems, tensor network methods, amongst them Matrix Product States (MPSs), have attracted interest from different fields of quantum physics ranging from solid state systems to quantum simulators and quantum computing. Our open source MPS code provides the community with a toolset to analyze the statics and dynamics of one-dimensional quantum systems. Here, we present our open source library, Open Source Matrix Product States (OSMPS), of MPS methods implemented in Python and Fortran2003. The library includes tools for ground state calculation and excited states via the variational ansatz. We also support ground states for infinite systems with translational invariance. Dynamics are simulated with different algorithms, including three algorithms with support for long-range interactions. Convenient features include built-in support for fermionic systems and number conservation with rotational U(1) and discrete Z2 symmetries for finite systems, as well as data parallelism with MPI. We explain the principles and techniques used in this library along with examples of how to efficiently use the general interfaces to analyze the Ising and Bose-Hubbard models. This description includes the preparation of simulations as well as dispatching and post-processing of them.

Numerical simulation of hydrogen fluorine overtone chemical lasers

NASA Astrophysics Data System (ADS)

Chen, Jinbao; Jiang, Zhongfu; Hua, Weihong; Liu, Zejin; Shu, Baihong

1998-08-01

A two-dimensional program was applied to simulate the chemical dynamic process, gas dynamic process and lasing process of a combustion-driven CW HF overtone chemical lasers. Some important parameters in the cavity were obtained. The calculated results included HF molecule concentration on each vibration energy level while lasing, averaged pressure and temperature, zero power gain coefficient of each spectral line, laser spectrum, the averaged laser intensity, output power, chemical efficiency and the length of lasing zone.

Multiscale modeling and simulation of microtubule-motor-protein assemblies

NASA Astrophysics Data System (ADS)

Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; Betterton, M. D.; Shelley, Michael J.

2015-12-01

Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.

Multiscale modeling and simulation of microtubule-motor-protein assemblies.

PubMed

Gao, Tong; Blackwell, Robert; Glaser, Matthew A; Betterton, M D; Shelley, Michael J

2015-01-01

Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.

Dynamics of crystalline acetanilide: Analysis using neutron scattering and computer simulation

NASA Astrophysics Data System (ADS)

Hayward, R. L.; Middendorf, H. D.; Wanderlingh, U.; Smith, J. C.

1995-04-01

The unusual temperature dependence of several optical spectroscopic vibrational bands in crystalline acetanilide has been interpreted as providing evidence for dynamic localization. Here we examine the vibrational dynamics of crystalline acetanilide over a spectral range of ˜20-4000 cm-1 using incoherent neutron scattering experiments, phonon normal mode calculations and molecular dynamics simulations. A molecular mechanics energy function is parametrized and used to perform the normal mode analyses in the full configurational space of the crystal i.e., including the intramolecular and intermolecular degrees of freedom. One- and multiphonon incoherent inelastic neutron scattering intensities are calculated from harmonic analyses in the first Brillouin zone and compared with the experimental data presented here. Phonon dispersion relations and mean-square atomic displacements are derived from the harmonic model and compared with data derived from coherent inelastic neutron scattering and neutron and x-ray diffraction. To examine the temperature effects on the vibrations the full, anharmonic potential function is used in molecular dynamics simulations of the crystal at 80, 140, and 300 K. Several, but not all, of the spectral features calculated from the molecular dynamics simulations exhibit temperature-dependent behavior in agreement with experiment. The significance of the results for the interpretation of the optical spectroscopic results and possible improvements to the model are discussed.

Multiscale modeling and simulation of microtubule–motor-protein assemblies

PubMed Central

Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; Betterton, M. D.; Shelley, Michael J.

2016-01-01

Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate–consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation. PMID:26764729

Molecular dynamics simulations and novel drug discovery.

PubMed

Liu, Xuewei; Shi, Danfeng; Zhou, Shuangyan; Liu, Hongli; Liu, Huanxiang; Yao, Xiaojun

2018-01-01

Molecular dynamics (MD) simulations can provide not only plentiful dynamical structural information on biomacromolecules but also a wealth of energetic information about protein and ligand interactions. Such information is very important to understanding the structure-function relationship of the target and the essence of protein-ligand interactions and to guiding the drug discovery and design process. Thus, MD simulations have been applied widely and successfully in each step of modern drug discovery. Areas covered: In this review, the authors review the applications of MD simulations in novel drug discovery, including the pathogenic mechanisms of amyloidosis diseases, virtual screening and the interaction mechanisms between drugs and targets. Expert opinion: MD simulations have been used widely in investigating the pathogenic mechanisms of diseases caused by protein misfolding, in virtual screening, and in investigating drug resistance mechanisms caused by mutations of the target. These issues are very difficult to solve by experimental methods alone. Thus, in the future, MD simulations will have wider application with the further improvement of computational capacity and the development of better sampling methods and more accurate force fields together with more efficient analysis methods.

Simulation of adaptive semi-active magnetorheological seat damper for vehicle occupant blast protection

NASA Astrophysics Data System (ADS)

Yoo, Jin-Hyeong; Murugan, Muthuvel; Wereley, Norman M.

2013-04-01

This study investigates a lumped-parameter human body model which includes lower leg in seated posture within a quarter-car model for blast injury assessment simulation. To simulate the shock acceleration of the vehicle, mine blast analysis was conducted on a generic land vehicle crew compartment (sand box) structure. For the purpose of simulating human body dynamics with non-linear parameters, a physical model of a lumped-parameter human body within a quarter car model was implemented using multi-body dynamic simulation software. For implementing the control scheme, a skyhook algorithm was made to work with the multi-body dynamic model by running a co-simulation with the control scheme software plug-in. The injury criteria and tolerance levels for the biomechanical effects are discussed for each of the identified vulnerable body regions, such as the relative head displacement and the neck bending moment. The desired objective of this analytical model development is to study the performance of adaptive semi-active magnetorheological damper that can be used for vehicle-occupant protection technology enhancements to the seat design in a mine-resistant military vehicle.

Construction of dynamic stochastic simulation models using knowledge-based techniques

NASA Technical Reports Server (NTRS)

Williams, M. Douglas; Shiva, Sajjan G.

1990-01-01

Over the past three decades, computer-based simulation models have proven themselves to be cost-effective alternatives to the more structured deterministic methods of systems analysis. During this time, many techniques, tools and languages for constructing computer-based simulation models have been developed. More recently, advances in knowledge-based system technology have led many researchers to note the similarities between knowledge-based programming and simulation technologies and to investigate the potential application of knowledge-based programming techniques to simulation modeling. The integration of conventional simulation techniques with knowledge-based programming techniques is discussed to provide a development environment for constructing knowledge-based simulation models. A comparison of the techniques used in the construction of dynamic stochastic simulation models and those used in the construction of knowledge-based systems provides the requirements for the environment. This leads to the design and implementation of a knowledge-based simulation development environment. These techniques were used in the construction of several knowledge-based simulation models including the Advanced Launch System Model (ALSYM).

Development of automation and robotics for space via computer graphic simulation methods

NASA Technical Reports Server (NTRS)

Fernandez, Ken

1988-01-01

A robot simulation system, has been developed to perform automation and robotics system design studies. The system uses a procedure-oriented solid modeling language to produce a model of the robotic mechanism. The simulator generates the kinematics, inverse kinematics, dynamics, control, and real-time graphic simulations needed to evaluate the performance of the model. Simulation examples are presented, including simulation of the Space Station and the design of telerobotics for the Orbital Maneuvering Vehicle.

Biomechanics and muscle coordination of human walking. Part I: introduction to concepts, power transfer, dynamics and simulations.

PubMed

Zajac, Felix E; Neptune, Richard R; Kautz, Steven A

2002-12-01

Current understanding of how muscles coordinate walking in humans is derived from analyses of body motion, ground reaction force and EMG measurements. This is Part I of a two-part review that emphasizes how muscle-driven dynamics-based simulations assist in the understanding of individual muscle function in walking, especially the causal relationships between muscle force generation and walking kinematics and kinetics. Part I reviews the strengths and limitations of Newton-Euler inverse dynamics and dynamical simulations, including the ability of each to find the contributions of individual muscles to the acceleration/deceleration of the body segments. We caution against using the concept of biarticular muscles transferring power from one joint to another to infer muscle coordination principles because energy flow among segments, even the adjacent segments associated with the joints, cannot be inferred from computation of joint powers and segmental angular velocities alone. Rather, we encourage the use of dynamical simulations to perform muscle-induced segmental acceleration and power analyses. Such analyses have shown that the exchange of segmental energy caused by the forces or accelerations induced by a muscle can be fundamentally invariant to whether the muscle is shortening, lengthening, or neither. How simulation analyses lead to understanding the coordination of seated pedaling, rather than walking, is discussed in this first part because the dynamics of pedaling are much simpler, allowing important concepts to be revealed. We elucidate how energy produced by muscles is delivered to the crank through the synergistic action of other non-energy producing muscles; specifically, that a major function performed by a muscle arises from the instantaneous segmental accelerations and redistribution of segmental energy throughout the body caused by its force generation. Part II reviews how dynamical simulations provide insight into muscle coordination of walking.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Stratosphere-resolving CMIP5 models simulate different changes in the Southern Hemisphere

NASA Astrophysics Data System (ADS)

Rea, Gloria; Riccio, Angelo; Fierli, Federico; Cairo, Francesco; Cagnazzo, Chiara

2018-03-01

This work documents long-term changes in the Southern Hemisphere circulation in the austral spring-summer season in the Coupled Intercomparison Project Phase 5 models, showing that those changes are larger in magnitude and closer to ERA-Interim and other reanalyses if models include a dynamical representation of the stratosphere. Specifically, models with a high-top and included dynamical and—in some cases—chemical feedbacks within the stratosphere better simulate the lower stratospheric cooling observed over 1979-2001 and strongly driven by ozone depletion, when compared to the other models. This occurs because high-top models can fully capture the stratospheric large scale circulation response to the ozone-induced cooling. Interestingly, this difference is also found at the surface for the Southern Annular Mode (SAM) changes, even though all model categories tend to underestimate SAM trends over those decades. In this analysis, models including a proper dynamical stratosphere are more sensitive to lower stratospheric cooling in their tropospheric circulation response. After a brief discussion of two RCP scenarios, our study confirms that at least for large changes in the extratropical regions, stratospheric changes induced by external forcing have to be properly simulated, as they are important drivers of tropospheric climate variations.

Photodissociation Dynamics of Phenol: Multistate Trajectory Simulations including Tunneling

DOE PAGES

Xu, Xuefei; Zheng, Jingjing; Yang, Ke R.; ...

2014-10-27

We report multistate trajectory simulations, including coherence, decoherence, and multidimensional tunneling, of phenol photodissociation dynamics. The calculations are based on full-dimensional anchor-points reactive potential surfaces and state couplings fit to electronic structure calculations including dynamical correlation with an augmented correlation-consistent polarized valence double-ζ basis set. The calculations successfully reproduce the experimentally observed bimodal character of the total kinetic energy release spectra and confirm the interpretation of the most recent experiments that the photodissociation process is dominated by tunneling. Analysis of the trajectories uncovers an unexpected dissociation pathway for one quantum excitation of the O–H stretching mode of the S 1more » state, namely, tunneling in a coherent mixture of states starting in a smaller R OH (~0.9–1.0 Å) region than has previously been invoked. The simulations also show that most trajectories do not pass close to the S 1–S 2 conical intersection (they have a minimum gap greater than 0.6 eV), they provide statistics on the out-of-plane angles at the locations of the minimum energy adiabatic gap, and they reveal information about which vibrational modes are most highly activated in the products.« less

Generic solar photovoltaic system dynamic simulation model specification

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

Ellis, Abraham; Behnke, Michael Robert; Elliott, Ryan Thomas

This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intendedmore » to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.« less

Molecular dynamics simulation of a piston driven shock wave in a hard sphere gas. Final Contractor ReportPh.D. Thesis

NASA Technical Reports Server (NTRS)

Woo, Myeung-Jouh; Greber, Isaac

1995-01-01

Molecular dynamics simulation is used to study the piston driven shock wave at Mach 1.5, 3, and 10. A shock tube, whose shape is a circular cylinder, is filled with hard sphere molecules having a Maxwellian thermal velocity distribution and zero mean velocity. The piston moves and a shock wave is generated. All collisions are specular, including those between the molecules and the computational boundaries, so that the shock development is entirely causal, with no imposed statistics. The structure of the generated shock is examined in detail, and the wave speed; profiles of density, velocity, and temperature; and shock thickness are determined. The results are compared with published results of other methods, especially the direct simulation Monte-Carlo method. Property profiles are similar to those generated by direct simulation Monte-Carlo method. The shock wave thicknesses are smaller than the direct simulation Monte-Carlo results, but larger than those of the other methods. Simulation of a shock wave, which is one-dimensional, is a severe test of the molecular dynamics method, which is always three-dimensional. A major challenge of the thesis is to examine the capability of the molecular dynamics methods by choosing a difficult task.

The Effects of Longitudinal Control-System Dynamics on Pilot Opinion and Response Characteristics as Determined from Flight Tests and from Ground Simulator Studies

NASA Technical Reports Server (NTRS)

Sadoff, Melvin

1958-01-01

The results of a fixed-base simulator study of the effects of variable longitudinal control-system dynamics on pilot opinion are presented and compared with flight-test data. The control-system variables considered in this investigation included stick force per g, time constant, and dead-band, or stabilizer breakout force. In general, the fairly good correlation between flight and simulator results for two pilots demonstrates the validity of fixed-base simulator studies which are designed to complement and supplement flight studies and serve as a guide in control-system preliminary design. However, in the investigation of certain problem areas (e.g., sensitive control-system configurations associated with pilot- induced oscillations in flight), fixed-base simulator results did not predict the occurrence of an instability, although the pilots noted the system was extremely sensitive and unsatisfactory. If it is desired to predict pilot-induced-oscillation tendencies, tests in moving-base simulators may be required. It was found possible to represent the human pilot by a linear pilot analog for the tracking task assumed in the present study. The criterion used to adjust the pilot analog was the root-mean-square tracking error of one of the human pilots on the fixed-base simulator. Matching the tracking error of the pilot analog to that of the human pilot gave an approximation to the variation of human-pilot behavior over a range of control-system dynamics. Results of the pilot-analog study indicated that both for optimized control-system dynamics (for poor airplane dynamics) and for a region of good airplane dynamics, the pilot response characteristics are approximately the same.

Validating clustering of molecular dynamics simulations using polymer models.

PubMed

Phillips, Joshua L; Colvin, Michael E; Newsam, Shawn

2011-11-14

Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers.

Validating clustering of molecular dynamics simulations using polymer models

PubMed Central

2011-01-01

Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers. PMID:22082218

Simulation and analysis of a model dinoflagellate predator-prey system

NASA Astrophysics Data System (ADS)

Mazzoleni, M. J.; Antonelli, T.; Coyne, K. J.; Rossi, L. F.

2015-12-01

This paper analyzes the dynamics of a model dinoflagellate predator-prey system and uses simulations to validate theoretical and experimental studies. A simple model for predator-prey interactions is derived by drawing upon analogies from chemical kinetics. This model is then modified to account for inefficiencies in predation. Simulation results are shown to closely match the model predictions. Additional simulations are then run which are based on experimental observations of predatory dinoflagellate behavior, and this study specifically investigates how the predatory dinoflagellate Karlodinium veneficum uses toxins to immobilize its prey and increase its feeding rate. These simulations account for complex dynamics that were not included in the basic models, and the results from these computational simulations closely match the experimentally observed predatory behavior of K. veneficum and reinforce the notion that predatory dinoflagellates utilize toxins to increase their feeding rate.

Communication: Multiple atomistic force fields in a single enhanced sampling simulation

NASA Astrophysics Data System (ADS)

Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

2015-07-01

The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

Dynamic Simulation of 1D Cellular Automata in the Active aTAM.

PubMed

Jonoska, Nataša; Karpenko, Daria; Seki, Shinnosuke

2015-07-01

The Active aTAM is a tile based model for self-assembly where tiles are able to transfer signals and change identities according to the signals received. We extend Active aTAM to include deactivation signals and thereby allow detachment of tiles. We show that the model allows a dynamic simulation of cellular automata with assemblies that do not record the entire computational history but only the current updates of the states, and thus provide a way for (a) algorithmic dynamical structural changes in the assembly and (b) reusable space in self-assembly. The simulation is such that at a given location the sequence of tiles that attach and detach corresponds precisely to the sequence of states the synchronous cellular automaton generates at that location.

A dynamic model of the marriage market-Part 2: simulation of marital states and application to empirical data.

PubMed

Matthews, A P; Garenne, M L

2013-09-01

A dynamic, two-sex, age-structured marriage model is presented. Part 1 focused on first marriage only and described a marriage market matching algorithm. In Part 2 the model is extended to include divorce, widowing, and remarriage. The model produces a self-consistent set of marital states distributed by age and sex in a stable population by means of a gender-symmetric numerical method. The model is compared with empirical data for the case of Zambia. Furthermore, a dynamic marriage function for a changing population is demonstrated in simulations of three hypothetical scenarios of elevated mortality in young to middle adulthood. The marriage model has its primary application to simulation of HIV-AIDS epidemics in African countries. Copyright © 2013 Elsevier Inc. All rights reserved.

Dynamic Simulation of 1D Cellular Automata in the Active aTAM

PubMed Central

Jonoska, Nataša; Karpenko, Daria; Seki, Shinnosuke

2016-01-01

The Active aTAM is a tile based model for self-assembly where tiles are able to transfer signals and change identities according to the signals received. We extend Active aTAM to include deactivation signals and thereby allow detachment of tiles. We show that the model allows a dynamic simulation of cellular automata with assemblies that do not record the entire computational history but only the current updates of the states, and thus provide a way for (a) algorithmic dynamical structural changes in the assembly and (b) reusable space in self-assembly. The simulation is such that at a given location the sequence of tiles that attach and detach corresponds precisely to the sequence of states the synchronous cellular automaton generates at that location. PMID:27789918

System Dynamics in Medical Education: A Tool for Life

ERIC Educational Resources Information Center

Rubin, David M.; Richards, Christopher L.; Keene, Penelope A. C.; Paiker, Janice E.; Gray, A. Rosemary T.; Herron, Robyn F. R.; Russell, Megan J.; Wigdorowitz, Brian

2012-01-01

A course in system dynamics has been included in the first year of our university's six-year medical curriculum. System Dynamics is a discipline that facilitates the modelling, simulation and analysis of a wide range of problems in terms of two fundamental concepts viz. rates and levels. Many topics encountered in the medical school curriculum,…

Simulation model of a twin-tail, high performance airplane

NASA Technical Reports Server (NTRS)

Buttrill, Carey S.; Arbuckle, P. Douglas; Hoffler, Keith D.

1992-01-01

The mathematical model and associated computer program to simulate a twin-tailed high performance fighter airplane (McDonnell Douglas F/A-18) are described. The simulation program is written in the Advanced Continuous Simulation Language. The simulation math model includes the nonlinear six degree-of-freedom rigid-body equations, an engine model, sensors, and first order actuators with rate and position limiting. A simplified form of the F/A-18 digital control laws (version 8.3.3) are implemented. The simulated control law includes only inner loop augmentation in the up and away flight mode. The aerodynamic forces and moments are calculated from a wind-tunnel-derived database using table look-ups with linear interpolation. The aerodynamic database has an angle-of-attack range of -10 to +90 and a sideslip range of -20 to +20 degrees. The effects of elastic deformation are incorporated in a quasi-static-elastic manner. Elastic degrees of freedom are not actively simulated. In the engine model, the throttle-commanded steady-state thrust level and the dynamic response characteristics of the engine are based on airflow rate as determined from a table look-up. Afterburner dynamics are switched in at a threshold based on the engine airflow and commanded thrust.

Towards a comprehensive framework for cosimulation of dynamic models with an emphasis on time stepping

NASA Astrophysics Data System (ADS)

Hoepfer, Matthias

Over the last two decades, computer modeling and simulation have evolved as the tools of choice for the design and engineering of dynamic systems. With increased system complexities, modeling and simulation become essential enablers for the design of new systems. Some of the advantages that modeling and simulation-based system design allows for are the replacement of physical tests to ensure product performance, reliability and quality, the shortening of design cycles due to the reduced need for physical prototyping, the design for mission scenarios, the invoking of currently nonexisting technologies, and the reduction of technological and financial risks. Traditionally, dynamic systems are modeled in a monolithic way. Such monolithic models include all the data, relations and equations necessary to represent the underlying system. With increased complexity of these models, the monolithic model approach reaches certain limits regarding for example, model handling and maintenance. Furthermore, while the available computer power has been steadily increasing according to Moore's Law (a doubling in computational power every 10 years), the ever-increasing complexities of new models have negated the increased resources available. Lastly, modern systems and design processes are interdisciplinary, enforcing the necessity to make models more flexible to be able to incorporate different modeling and design approaches. The solution to bypassing the shortcomings of monolithic models is cosimulation. In a very general sense, co-simulation addresses the issue of linking together different dynamic sub-models to a model which represents the overall, integrated dynamic system. It is therefore an important enabler for the design of interdisciplinary, interconnected, highly complex dynamic systems. While a basic co-simulation setup can be very easy, complications can arise when sub-models display behaviors such as algebraic loops, singularities, or constraints. This work frames the co-simulation approach to modeling and simulation. It lays out the general approach to dynamic system co-simulation, and gives a comprehensive overview of what co-simulation is and what it is not. It creates a taxonomy of the requirements and limits of co-simulation, and the issues arising with co-simulating sub-models. Possible solutions towards resolving the stated problems are investigated to a certain depth. A particular focus is given to the issue of time stepping. It will be shown that for dynamic models, the selection of the simulation time step is a crucial issue with respect to computational expense, simulation accuracy, and error control. The reasons for this are discussed in depth, and a time stepping algorithm for co-simulation with unknown dynamic sub-models is proposed. Motivations and suggestions for the further treatment of selected issues are presented.

Understanding the influence of topography on the dynamics of the North American monsoon in climate model simulations

NASA Astrophysics Data System (ADS)

Varuolo-Clarke, A. M.; Medeiros, B.; Reed, K. A.

2017-12-01

This project examines the influence of topography on the dynamics of the North American monsoon (NAM), including the genesis, peak, and demise of the monsoon. The monsoon season occurs from July to September in the southwestern United States and northwestern Mexico and is characterized by an increase in rainfall that accounts for 40-80% of the total annual rainfall. We use a simple "monsoon index" and show that simulations with the Community Atmosphere model capture the essential nature of the NAM. Comparing standard low-resolution (1o latitude x 1o longitude) simulations where the topography over North America is either retained or removed we evaluate the models' representations of the NAM. To understand the origin of differences between the simulations we analyze the moist static energy budget in the monsoon region. Our preliminary results from simulations with realistic topography indicate that the simulated NAM is driven by locally-generated convection, with advection processes being secondary; this is consistent with the NAM being a result of the thermal contrast between the hot, summertime continent and relatively cool ocean. When topography is removed the simulated NAM will be relatively weak and be driven primarily by locally-generated convection. A better understanding of the monsoon dynamics and the impact topography has on these dynamics will allow for a more accurate representation of the monsoon in projections of future climate.

Examining Projected Changes in Weather & Air Quality Extremes Between 2000 & 2030 using Dynamical Downscaling

EPA Science Inventory

Climate change may alter regional weather extremes resulting in a range of environmental impacts including changes in air quality, water quality and availability, energy demands, agriculture, and ecology. Dynamical downscaling simulations were conducted with the Weather Research...

Effects of Solid Fraction on Droplet Wetting and Vapor Condensation: A Molecular Dynamic Simulation Study.

PubMed

Gao, Shan; Liao, Quanwen; Liu, Wei; Liu, Zhichun

2017-10-31

Recently, numerous studies focused on the wetting process of droplets on various surfaces at a microscale level. However, there are a limited number of studies about the mechanism of condensation on patterned surfaces. The present study performed the dynamic wetting behavior of water droplets and condensation process of water molecules on substrates with different pillar structure parameters, through molecular dynamic simulation. The dynamic wetting results indicated that droplets exhibit Cassie state, PW state, and Wenzel state successively on textured surfaces with decreasing solid fraction. The droplets possess a higher static contact angle and a smaller spreading exponent on textured surfaces than those on smooth surfaces. The condensation processes, including the formation, growth, and coalescence of a nanodroplet, are simulated and quantitatively recorded, which are difficult to be observed by experiments. In addition, a wetting transition and a dewetting transition were observed and analyzed in condensation on textured surfaces. Combining these simulation results with previous theoretical and experimental studies will guide us to understand the hypostasis and mechanism of the condensation more clearly.

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

PubMed Central

Chen, Alan A.; García, Angel E.

2013-01-01

We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations. PMID:24043821

Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation.

PubMed

Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

2017-02-21

Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation

PubMed Central

Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

2017-01-01

Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance. PMID:28772570

Development of a hardware-in-loop attitude control simulator for a CubeSat satellite

NASA Astrophysics Data System (ADS)

Tapsawat, Wittawat; Sangpet, Teerawat; Kuntanapreeda, Suwat

2018-01-01

Attitude control is an important part in satellite on-orbit operation. It greatly affects the performance of satellites. Testing of an attitude determination and control subsystem (ADCS) is very challenging since it might require attitude dynamics and space environment in the orbit. This paper develops a low-cost hardware-in-loop (HIL) simulator for testing an ADCS of a CubeSat satellite. The simulator consists of a numerical simulation part, a hardware part, and a HIL interface hardware unit. The numerical simulation part includes orbital dynamics, attitude dynamics and Earth’s magnetic field. The hardware part is the real ADCS board of the satellite. The simulation part outputs satellite’s angular velocity and geomagnetic field information to the HIL interface hardware. Then, based on this information, the HIL interface hardware generates I2C signals mimicking the signals of the on-board rate-gyros and magnetometers and consequently outputs the signals to the ADCS board. The ADCS board reads the rate-gyro and magnetometer signals, calculates control signals, and drives the attitude actuators which are three magnetic torquers (MTQs). The responses of the MTQs sensed by a separated magnetometer are feedback to the numerical simulation part completing the HIL simulation loop. Experimental studies are conducted to demonstrate the feasibility and effectiveness of the simulator.

NREL - SOWFA - Neutral - TTU

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

Kosovic, Branko

This dataset includes large-eddy simulation (LES) output from a neutrally stratified atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on Aug. 17, 2012. The dataset was used to assess LES models for simulation of canonical neutral ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

Standalone engine simulator (SAES), Engine Dynamics simulator (EDS) Xerox Sigma 5 interface hardware manual

NASA Technical Reports Server (NTRS)

Kirshten, P. M.; Black, S.; Pearson, R.

1979-01-01

The ESS-EDS and EDS-Sigma interfaces within the standalone engine simulator are described. The operation of these interfaces, including the definition and use of special function signals and data flow paths within them during data transfers, is presented along with detailed schematics and circuit layouts of the described equipment.

PNNL - WRF-LES - Convective - TTU

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

Kosovic, Branko

This dataset includes large-eddy simulation (LES) output from a convective atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on July 4, 2012. The dataset was used to assess the LES models for simulation of canonical convective ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

ANL - WRF-LES - Convective - TTU

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

Kosovic, Branko

This dataset includes large-eddy simulation (LES) output from a convective atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on July 4, 2012. The dataset was used to assess the LES models for simulation of canonical convective ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

LLNL - WRF-LES - Neutral - TTU

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

Kosovic, Branko

This dataset includes large-eddy simulation (LES) output from a neutrally stratified atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on Aug. 17, 2012. The dataset was used to assess LES models for simulation of canonical neutral ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

ANL - WRF-LES - Neutral - TTU

DOE Data Explorer

Kosovic, Branko

2018-06-20

This dataset includes large-eddy simulation (LES) output from a neutrally stratified atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on Aug. 17, 2012. The dataset was used to assess LES models for simulation of canonical neutral ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

LANL - WRF-LES - Neutral - TTU

DOE Data Explorer

Kosovic, Branko

2018-06-20

This dataset includes large-eddy simulation (LES) output from a neutrally stratified atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on Aug. 17, 2012. The dataset was used to assess LES models for simulation of canonical neutral ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

LANL - WRF-LES - Convective - TTU

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

Kosovic, Branko

This dataset includes large-eddy simulation (LES) output from a convective atmospheric boundary layer (ABL) simulation of observations at the SWIFT tower near Lubbock, Texas on July 4, 2012. The dataset was used to assess the LES models for simulation of canonical convective ABL. The dataset can be used for comparison with other LES and computational fluid dynamics model outputs.

Integration of visual and motion cues for flight simulator requirements and ride quality investigation

NASA Technical Reports Server (NTRS)

Young, L. R.

1976-01-01

Investigations for the improvement of flight simulators are reported. Topics include: visual cues in landing, comparison of linear and nonlinear washout filters using a model of the vestibular system, and visual vestibular interactions (yaw axis). An abstract is given for a thesis on the applications of human dynamic orientation models to motion simulation.

Artistic understanding as embodied simulation.

PubMed

Gibbs, Raymond W

2013-04-01

Bullot & Reber (B&R) correctly include historical perspectives into the scientific study of art appreciation. But artistic understanding always emerges from embodied simulation processes that incorporate the ongoing dynamics of brains, bodies, and world interactions. There may not be separate modes of artistic understanding, but a continuum of processes that provide imaginative simulations of the artworks we see or hear.

A Flight Dynamics Model for a Small Glider in Ambient Winds

NASA Technical Reports Server (NTRS)

Beeler, Scott C.; Moerder, Daniel D.; Cox, David E.

2003-01-01

In this paper we describe the equations of motion developed for a point-mass zero-thrust (gliding) aircraft model operating in an environment of spatially varying atmospheric winds. The wind effects are included as an integral part of the flight dynamics equations, and the model is controlled through the three aerodynamic control angles. Formulas for the aerodynamic coefficients for this model are constructed to include the effects of several different aspects contributing to the aerodynamic performance of the vehicle. Characteristic parameter values of the model are compared with those found in a different set of small glider simulations. We execute a set of example problems which solve the glider dynamics equations to find the aircraft trajectory given specified control inputs. The ambient wind conditions and glider characteristics are varied to compare the simulation results under these different circumstances.

A Flight Dynamics Model for a Small Glider in Ambient Winds

NASA Technical Reports Server (NTRS)

Beeler, Scott C.; Moerder, Daniel D.; Cox, David E.

2003-01-01

In this paper we describe the equations of motion developed for a point-mass zero-thrust (gliding) aircraft model operating in an environment of spatially varying atmospheric winds. The wind effects are included as an integral part of the flight dynamics equations, and the model is controlled through the three aerodynamic control angles. Formulas for the aerodynamic coefficients for this model are constructed to include the effects of several different aspects contributing to the aerodynamic performance of the vehicle. Characteristic parameter values of the model are compared with those found in a different set of small glider simulations. We execute a set of example problems which solve the glider dynamics equations to find aircraft trajectory given specified control inputs. The ambient wind conditions and glider characteristics are varied to compare the simulation results under these different circumstances.

New Editions for the Apple II of the Chelsea Science Simulations.

ERIC Educational Resources Information Center

Pipeline, 1983

1983-01-01

Ten computer simulations for the Apple II are described. Subject areas of programs include: population dynamics, plant competition, enzyme kinetics, evolution and natural selection, genetic mapping, ammonia synthesis, reaction kinetics, wave interference/diffraction, satellite orbits, and particle scattering. (JN)

Accelerated molecular dynamics simulations of protein folding.

PubMed

Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

2015-07-30

Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.

End-To-End Simulation of Launch Vehicle Trajectories Including Stage Separation Dynamics

NASA Technical Reports Server (NTRS)

Albertson, Cindy W.; Tartabini, Paul V.; Pamadi, Bandu N.

2012-01-01

The development of methodologies, techniques, and tools for analysis and simulation of stage separation dynamics is critically needed for successful design and operation of multistage reusable launch vehicles. As a part of this activity, the Constraint Force Equation (CFE) methodology was developed and implemented in the Program to Optimize Simulated Trajectories II (POST2). The objective of this paper is to demonstrate the capability of POST2/CFE to simulate a complete end-to-end mission. The vehicle configuration selected was the Two-Stage-To-Orbit (TSTO) Langley Glide Back Booster (LGBB) bimese configuration, an in-house concept consisting of a reusable booster and an orbiter having identical outer mold lines. The proximity and isolated aerodynamic databases used for the simulation were assembled using wind-tunnel test data for this vehicle. POST2/CFE simulation results are presented for the entire mission, from lift-off, through stage separation, orbiter ascent to orbit, and booster glide back to the launch site. Additionally, POST2/CFE stage separation simulation results are compared with results from industry standard commercial software used for solving dynamics problems involving multiple bodies connected by joints.

Hyper-X Stage Separation Trajectory Validation Studies

NASA Technical Reports Server (NTRS)

Tartabini, Paul V.; Bose, David M.; McMinn, John D.; Martin, John G.; Strovers, Brian K.

2003-01-01

An independent twelve degree-of-freedom simulation of the X-43A separation trajectory was created with the Program to Optimize Simulated trajectories (POST II). This simulation modeled the multi-body dynamics of the X-43A and its booster and included the effect of two pyrotechnically actuated pistons used to push the vehicles apart as well as aerodynamic interaction forces and moments between the two vehicles. The simulation was developed to validate trajectory studies conducted with a 14 degree-of-freedom simulation created early in the program using the Automatic Dynamic Analysis of Mechanics Systems (ADAMS) simulation software. The POST simulation was less detailed than the official ADAMS-based simulation used by the Project, but was simpler, more concise and ran faster, while providing similar results. The increase in speed provided by the POST simulation provided the Project with an alternate analysis tool. This tool was ideal for performing separation control logic trade studies that required the running of numerous Monte Carlo trajectories.

SRG110 Stirling Generator Dynamic Simulator Vibration Test Results and Analysis Correlation

NASA Technical Reports Server (NTRS)

Suarez, Vicente J.; Lewandowski, Edward J.; Callahan, John

2006-01-01

The U.S. Department of Energy (DOE), Lockheed Martin (LM), and NASA Glenn Research Center (GRC) have been developing the Stirling Radioisotope Generator (SRG110) for use as a power system for space science missions. The launch environment enveloping potential missions results in a random input spectrum that is significantly higher than historical RPS launch levels and is a challenge for designers. Analysis presented in prior work predicted that tailoring the compliance at the generator-spacecraft interface reduced the dynamic response of the system thereby allowing higher launch load input levels and expanding the range of potential generator missions. To confirm analytical predictions, a dynamic simulator representing the generator structure, Stirling convertors and heat sources was designed and built for testing with and without a compliant interface. Finite element analysis was performed to guide the generator simulator and compliant interface design so that test modes and frequencies were representative of the SRG110 generator. This paper presents the dynamic simulator design, the test setup and methodology, test article modes and frequencies and dynamic responses, and post-test analysis results. With the compliant interface, component responses to an input environment exceeding the SRG110 qualification level spectrum were all within design allowables. Post-test analysis included finite element model tuning to match test frequencies and random response analysis using the test input spectrum. Analytical results were in good overall agreement with the test results and confirmed previous predictions that the SRG110 power system may be considered for a broad range of potential missions, including those with demanding launch environments.

SRG110 Stirling Generator Dynamic Simulator Vibration Test Results and Analysis Correlation

NASA Technical Reports Server (NTRS)

Lewandowski, Edward J.; Suarez, Vicente J.; Goodnight, Thomas W.; Callahan, John

2007-01-01

The U.S. Department of Energy (DOE), Lockheed Martin (LM), and NASA Glenn Research Center (GRC) have been developing the Stirling Radioisotope Generator (SRG110) for use as a power system for space science missions. The launch environment enveloping potential missions results in a random input spectrum that is significantly higher than historical radioisotope power system (RPS) launch levels and is a challenge for designers. Analysis presented in prior work predicted that tailoring the compliance at the generator-spacecraft interface reduced the dynamic response of the system thereby allowing higher launch load input levels and expanding the range of potential generator missions. To confirm analytical predictions, a dynamic simulator representing the generator structure, Stirling convertors and heat sources were designed and built for testing with and without a compliant interface. Finite element analysis was performed to guide the generator simulator and compliant interface design so that test modes and frequencies were representative of the SRG110 generator. This paper presents the dynamic simulator design, the test setup and methodology, test article modes and frequencies and dynamic responses, and post-test analysis results. With the compliant interface, component responses to an input environment exceeding the SRG110 qualification level spectrum were all within design allowables. Post-test analysis included finite element model tuning to match test frequencies and random response analysis using the test input spectrum. Analytical results were in good overall agreement with the test results and confirmed previous predictions that the SRG110 power system may be considered for a broad range of potential missions, including those with demanding launch environments.

Effect of water phase transition on dynamic ruptures with thermal pressurization: Numerical simulations with changes in physical properties of water

NASA Astrophysics Data System (ADS)

Urata, Yumi; Kuge, Keiko; Kase, Yuko

2015-02-01

Phase transitions of pore water have never been considered in dynamic rupture simulations with thermal pressurization (TP), although they may control TP. From numerical simulations of dynamic rupture propagation including TP, in the absence of any water phase transition process, we predict that frictional heating and TP are likely to change liquid pore water into supercritical water for a strike-slip fault under depth-dependent stress. This phase transition causes changes of a few orders of magnitude in viscosity, compressibility, and thermal expansion among physical properties of water, thus affecting the diffusion of pore pressure. Accordingly, we perform numerical simulations of dynamic ruptures with TP, considering physical properties that vary with the pressure and temperature of pore water on a fault. To observe the effects of the phase transition, we assume uniform initial stress and no fault-normal variations in fluid density and viscosity. The results suggest that the varying physical properties decrease the total slip in cases with high stress at depth and small shear zone thickness. When fault-normal variations in fluid density and viscosity are included in the diffusion equation, they activate TP much earlier than the phase transition. As a consequence, the total slip becomes greater than that in the case with constant physical properties, eradicating the phase transition effect. Varying physical properties do not affect the rupture velocity, irrespective of the fault-normal variations. Thus, the phase transition of pore water has little effect on dynamic ruptures. Fault-normal variations in fluid density and viscosity may play a more significant role.

NETL to establish Dynamic Simulation Research and Training Center to promote IGCC technology with CO2 cpture

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

Provost, G.; Zitney, S.; Turton, R.

2009-01-01

To meet increasing demand for education and experience with commercial-scale, coal-fired, integrated gasification combined cycle (IGCC) plants with CO2 capture, the Department of Energy’s (DOE) National Energy Technology Laboratory (NETL) is leading a project to deploy a generic, full-scope, real-time IGCC dynamic plant simulator for use in establishing a world-class research and training center, and to promote and demonstrate IGCC technology to power industry personnel. The simulator, being built by Invensys Process Systems (IPS), will be installed at two separate sites, at NETL and West Virginia University (WVU), and will combine a process/gasification simulator with a power/combined-cycle simulator together inmore » a single dynamic simulation framework for use in engineering research studies and training applications. The simulator, scheduled to be launched in mid-year 2010, will have the following capabilities: High-fidelity, dynamic model of process-side (gasification and gas cleaning with CO2 capture) and power-block-side (combined cycle) for a generic IGCC plant fueled by coal and/or petroleum coke. Highly flexible configuration that allows concurrent training on separate gasification and combined cycle simulators, or up to two IGCC simulators. Ability to enhance and modify the plant model to facilitate studies of changes in plant configuration, equipment, and control strategies to support future R&D efforts. Training capabilities including startup, shutdown, load following and shedding, response to fuel and ambient condition variations, control strategy analysis (turbine vs. gasifier lead, etc.), representative malfunctions/trips, alarms, scenarios, trending, snapshots, data historian, etc. To support this effort, process descriptions and control strategies were developed for key sections of the plant as part of the detailed functional specification, which is serving as the basis of the simulator development. In this paper, we highlight the contents of the detailed functional specification for the simulator. We also describe the engineering, design, and expert testing process that the simulator will undergo in order to ensure that maximum fidelity is built into the generic simulator. Future applications and training programs associated with gasification, combined cycle, and IGCC simulations are discussed, including plant operation and control demonstrations, as well as education and training services.« less

A flexible object-oriented software framework for developing complex multimedia simulations.

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

Sydelko, P. J.; Dolph, J. E.; Christiansen, J. H.

Decision makers involved in brownfields redevelopment and long-term stewardship must consider environmental conditions, future-use potential, site ownership, area infrastructure, funding resources, cost recovery, regulations, risk and liability management, community relations, and expected return on investment in a comprehensive and integrated fashion to achieve desired results. Successful brownfields redevelopment requires the ability to assess the impacts of redevelopment options on multiple interrelated aspects of the ecosystem, both natural and societal. Computer-based tools, such as simulation models, databases, and geographical information systems (GISs) can be used to address brownfields planning and project execution. The transparent integration of these tools into a comprehensivemore » and dynamic decision support system would greatly enhance the brownfields assessment process. Such a system needs to be able to adapt to shifting and expanding analytical requirements and contexts. The Dynamic Information Architecture System (DIAS) is a flexible, extensible, object-oriented framework for developing and maintaining complex multidisciplinary simulations of a wide variety of application domains. The modeling domain of a specific DIAS-based simulation is determined by (1) software objects that represent the real-world entities that comprise the problem space (atmosphere, watershed, human), and (2) simulation models and other data processing applications that express the dynamic behaviors of the domain entities. Models and applications used to express dynamic behaviors can be either internal or external to DIAS, including existing legacy models written in various languages (FORTRAN, C, etc.). The flexible design framework of DIAS makes the objects adjustable to the context of the problem without a great deal of recoding. The DIAS Spatial Data Set facility allows parameters to vary spatially depending on the simulation context according to any of a number of 1-D, 2-D, or 3-D topologies. DIAS is also capable of interacting with other GIS packages and can import many standard spatial data formats. DIAS simulation capabilities can also be extended by including societal process models. Models that implement societal behaviors of individuals and organizations within larger DIAS-based natural systems simulations allow for interaction and feedback among natural and societal processes. The ability to simulate the complex interplay of multimedia processes makes DIAS a promising tool for constructing applications for comprehensive community planning, including the assessment of multiple development and redevelopment scenarios.« less

The dynamical core, physical parameterizations, and basic simulation characteristics of the atmospheric component AM3 of the GFDL global coupled model CM3

USGS Publications Warehouse

Donner, L.J.; Wyman, B.L.; Hemler, R.S.; Horowitz, L.W.; Ming, Y.; Zhao, M.; Golaz, J.-C.; Ginoux, P.; Lin, S.-J.; Schwarzkopf, M.D.; Austin, J.; Alaka, G.; Cooke, W.F.; Delworth, T.L.; Freidenreich, S.M.; Gordon, C.T.; Griffies, S.M.; Held, I.M.; Hurlin, W.J.; Klein, S.A.; Knutson, T.R.; Langenhorst, A.R.; Lee, H.-C.; Lin, Y.; Magi, B.I.; Malyshev, S.L.; Milly, P.C.D.; Naik, V.; Nath, M.J.; Pincus, R.; Ploshay, J.J.; Ramaswamy, V.; Seman, C.J.; Shevliakova, E.; Sirutis, J.J.; Stern, W.F.; Stouffer, R.J.; Wilson, R.J.; Winton, M.; Wittenberg, A.T.; Zeng, F.

2011-01-01

The Geophysical Fluid Dynamics Laboratory (GFDL) has developed a coupled general circulation model (CM3) for the atmosphere, oceans, land, and sea ice. The goal of CM3 is to address emerging issues in climate change, including aerosol-cloud interactions, chemistry-climate interactions, and coupling between the troposphere and stratosphere. The model is also designed to serve as the physical system component of earth system models and models for decadal prediction in the near-term future-for example, through improved simulations in tropical land precipitation relative to earlier-generation GFDL models. This paper describes the dynamical core, physical parameterizations, and basic simulation characteristics of the atmospheric component (AM3) of this model. Relative to GFDL AM2, AM3 includes new treatments of deep and shallow cumulus convection, cloud droplet activation by aerosols, subgrid variability of stratiform vertical velocities for droplet activation, and atmospheric chemistry driven by emissions with advective, convective, and turbulent transport. AM3 employs a cubed-sphere implementation of a finite-volume dynamical core and is coupled to LM3, a new land model with ecosystem dynamics and hydrology. Its horizontal resolution is approximately 200 km, and its vertical resolution ranges approximately from 70 m near the earth's surface to 1 to 1.5 km near the tropopause and 3 to 4 km in much of the stratosphere. Most basic circulation features in AM3 are simulated as realistically, or more so, as in AM2. In particular, dry biases have been reduced over South America. In coupled mode, the simulation of Arctic sea ice concentration has improved. AM3 aerosol optical depths, scattering properties, and surface clear-sky downward shortwave radiation are more realistic than in AM2. The simulation of marine stratocumulus decks remains problematic, as in AM2. The most intense 0.2% of precipitation rates occur less frequently in AM3 than observed. The last two decades of the twentieth century warm in CM3 by 0.328C relative to 1881-1920. The Climate Research Unit (CRU) and Goddard Institute for Space Studies analyses of observations show warming of 0.568 and 0.528C, respectively, over this period. CM3 includes anthropogenic cooling by aerosol-cloud interactions, and its warming by the late twentieth century is somewhat less realistic than in CM2.1, which warmed 0.668C but did not include aerosol-cloud interactions. The improved simulation of the direct aerosol effect (apparent in surface clear-sky downward radiation) in CM3 evidently acts in concert with its simulation of cloud-aerosol interactions to limit greenhouse gas warming. ?? 2011 American Meteorological Society.

Liquid Water from First Principles: Validation of Different Sampling Approaches

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

Mundy, C J; Kuo, W; Siepmann, J

2004-05-20

A series of first principles molecular dynamics and Monte Carlo simulations were carried out for liquid water to assess the validity and reproducibility of different sampling approaches. These simulations include Car-Parrinello molecular dynamics simulations using the program CPMD with different values of the fictitious electron mass in the microcanonical and canonical ensembles, Born-Oppenheimer molecular dynamics using the programs CPMD and CP2K in the microcanonical ensemble, and Metropolis Monte Carlo using CP2K in the canonical ensemble. With the exception of one simulation for 128 water molecules, all other simulations were carried out for systems consisting of 64 molecules. It is foundmore » that the structural and thermodynamic properties of these simulations are in excellent agreement with each other as long as adiabatic sampling is maintained in the Car-Parrinello molecular dynamics simulations either by choosing a sufficiently small fictitious mass in the microcanonical ensemble or by Nos{acute e}-Hoover thermostats in the canonical ensemble. Using the Becke-Lee-Yang-Parr exchange and correlation energy functionals and norm-conserving Troullier-Martins or Goedecker-Teter-Hutter pseudopotentials, simulations at a fixed density of 1.0 g/cm{sup 3} and a temperature close to 315 K yield a height of the first peak in the oxygen-oxygen radial distribution function of about 3.0, a classical constant-volume heat capacity of about 70 J K{sup -1} mol{sup -1}, and a self-diffusion constant of about 0.1 Angstroms{sup 2}/ps.« less

Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation.

PubMed

Villa, Elizabeth; Balaeff, Alexander; Schulten, Klaus

2005-05-10

A multiscale simulation of a complex between the lac repressor protein (LacI) and a 107-bp-long DNA segment is reported. The complex between the repressor and two operator DNA segments is described by all-atom molecular dynamics; the size of the simulated system comprises either 226,000 or 314,000 atoms. The DNA loop connecting the operators is modeled as a continuous elastic ribbon, described mathematically by the nonlinear Kirchhoff differential equations with boundary conditions obtained from the coordinates of the terminal base pairs of each operator. The forces stemming from the looped DNA are included in the molecular dynamics simulations; the loop structure and the forces are continuously recomputed because the protein motions during the simulations shift the operators and the presumed termini of the loop. The simulations reveal the structural dynamics of the LacI-DNA complex in unprecedented detail. The multiple domains of LacI exhibit remarkable structural stability during the simulation, moving much like rigid bodies. LacI is shown to absorb the strain from the looped DNA mainly through its mobile DNA-binding head groups. Even with large fluctuating forces applied, the head groups tilt strongly and keep their grip on the operator DNA, while the remainder of the protein retains its V-shaped structure. A simulated opening of the cleft of LacI by 500-pN forces revealed the interactions responsible for locking LacI in the V-conformation.

Numerical approach on dynamic self-assembly of colloidal particles

NASA Astrophysics Data System (ADS)

Ibrahimi, Muhamet; Ilday, Serim; Makey, Ghaith; Pavlov, Ihor; Yavuz, Özgàn; Gulseren, Oguz; Ilday, Fatih Omer

Far from equilibrium systems of artificial ensembles are crucial for understanding many intelligent features in self-organized natural systems. However, the lack of established theory underlies a need for numerical implementations. Inspired by a novel work, we simulate a solution-suspended colloidal system that dynamically self assembles due to convective forces generated in the solvent when heated by a laser. In order to incorporate with random fluctuations of particles and continuously changing flow, we exploit a random-walk based Brownian motion model and a fluid dynamics solver prepared for games, respectively. Simulation results manage to fit to experiments and show many quantitative features of a non equilibrium dynamic self assembly, including phase space compression and an ensemble-energy input feedback loop.

Coherent dynamic structure factors of strongly coupled plasmas: A generalized hydrodynamic approach

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

Luo, Di; Hu, GuangYue; Gong, Tao

2016-05-15

A generalized hydrodynamic fluctuation model is proposed to simplify the calculation of the dynamic structure factor S(ω, k) of non-ideal plasmas using the fluctuation-dissipation theorem. In this model, the kinetic and correlation effects are both included in hydrodynamic coefficients, which are considered as functions of the coupling strength (Γ) and collision parameter (kλ{sub ei}), where λ{sub ei} is the electron-ion mean free path. A particle-particle particle-mesh molecular dynamics simulation code is also developed to simulate the dynamic structure factors, which are used to benchmark the calculation of our model. A good agreement between the two different approaches confirms the reliabilitymore » of our model.« less

Simulation of hydrodynamically interacting particles near a no-slip boundary

NASA Astrophysics Data System (ADS)

Swan, James W.; Brady, John F.

2007-11-01

The dynamics of spherical particles near a single plane wall are computed using an extension of the Stokesian dynamics method that includes long-range many-body and pairwise lubrication interactions between the spheres and the wall in Stokes flow. Extra care is taken to ensure that the mobility and resistance tensors are symmetric, positive, and definite—something which is ineluctable for particles in low-Reynolds-number flows. We discuss why two previous simulation methods for particles near a plane wall, one using multipole expansions and the other using the Rotne-Prager tensor, fail to produce symmetric resistance and mobility tensors. Additionally, we offer some insight on how the Stokesian dynamics paradigm might be extended to study the dynamics of particles in any confining geometry.

Dynamics Analysis of Anti-predator Model on Intermediate Predator With Ratio Dependent Functional Responses

NASA Astrophysics Data System (ADS)

Savitri, D.

2018-01-01

This articel discusses a predator prey model with anti-predator on intermediate predator using ratio dependent functional responses. Dynamical analysis performed on the model includes determination of equilibrium point, stability and simulation. Three kinds of equilibrium points have been discussed, namely the extinction of prey point, the extinction of intermediate predator point and the extinction of predator point are exists under certain conditions. It can be shown that the result of numerical simulations are in accordance with analitical results

NASA Computational Fluid Dynamics Conference. Volume 1: Sessions 1-6

NASA Technical Reports Server (NTRS)

1989-01-01

Presentations given at the NASA Computational Fluid Dynamics (CFD) Conference held at the NASA Ames Research Center, Moffett Field, California, March 7-9, 1989 are given. Topics covered include research facility overviews of CFD research and applications, validation programs, direct simulation of compressible turbulence, turbulence modeling, advances in Runge-Kutta schemes for solving 3-D Navier-Stokes equations, grid generation and invicid flow computation around aircraft geometries, numerical simulation of rotorcraft, and viscous drag prediction for rotor blades.

Effects of electronic excitation on cascade dynamics in nickel–iron and nickel–palladium systems

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

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

Using molecular dynamics simulations and the two-temperature model, we provide in this paper a comparison of the surviving damage from single ion irradiation events in nickel-based alloys, for cascades with and without taking into account the effects of the electronic excitations. We find that including the electronic effects impacts the amount of the resulting damage and the production of isolated defects. Finally, irradiation of nickel–palladium systems results in larger numbers of defects compared to nickel–iron systems, with similar numbers of isolated defects. We additionally investigate the mass effect on the two-temperature model in molecular dynamics simulations of cascades.

Development of an Integrated Nonlinear Aeroservoelastic Flight Dynamic Model of the NASA Generic Transport Model

NASA Technical Reports Server (NTRS)

Nguyen, Nhan; Ting, Eric

2018-01-01

This paper describes a recent development of an integrated fully coupled aeroservoelastic flight dynamic model of the NASA Generic Transport Model (GTM). The integrated model couples nonlinear flight dynamics to a nonlinear aeroelastic model of the GTM. The nonlinearity includes the coupling of the rigid-body aircraft states in the partial derivatives of the aeroelastic angle of attack. Aeroservoelastic modeling of the control surfaces which are modeled by the Variable Camber Continuous Trailing Edge Flap is also conducted. The R.T. Jones' method is implemented to approximate unsteady aerodynamics. Simulations of the GTM are conducted with simulated continuous and discrete gust loads..

Initial results from the Solar Dynamic (SD) Ground Test Demonstration (GTD) project at NASA Lewis

NASA Technical Reports Server (NTRS)

Shaltens, Richard K.; Boyle, Robert V.

1995-01-01

A government/industry team designed, built, and tested a 2 kWe solar dynamic space power system in a large thermal/vacuum facility with a simulated sun at the NASA Lewis Research Center. The Lewis facility provides an accurate simulation of temperatures, high vacuum, and solar flux as encountered in low earth orbit. This paper reviews the goals and status of the Solar Dynamic (SD) Ground Test Demonstration (GTD) program and describes the initial testing, including both operational and performance data. This SD technology has the potential as a future power source for the International Space Station Alpha.

Effects of electronic excitation on cascade dynamics in nickel–iron and nickel–palladium systems

DOE PAGES

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

2017-06-10

Using molecular dynamics simulations and the two-temperature model, we provide in this paper a comparison of the surviving damage from single ion irradiation events in nickel-based alloys, for cascades with and without taking into account the effects of the electronic excitations. We find that including the electronic effects impacts the amount of the resulting damage and the production of isolated defects. Finally, irradiation of nickel–palladium systems results in larger numbers of defects compared to nickel–iron systems, with similar numbers of isolated defects. We additionally investigate the mass effect on the two-temperature model in molecular dynamics simulations of cascades.

MagIC: Fluid dynamics in a spherical shell simulator

NASA Astrophysics Data System (ADS)

Wicht, J.; Gastine, T.; Barik, A.; Putigny, B.; Yadav, R.; Duarte, L.; Dintrans, B.

2017-09-01

MagIC simulates fluid dynamics in a spherical shell. It solves for the Navier-Stokes equation including Coriolis force, optionally coupled with an induction equation for Magneto-Hydro Dynamics (MHD), a temperature (or entropy) equation and an equation for chemical composition under both the anelastic and the Boussinesq approximations. MagIC uses either Chebyshev polynomials or finite differences in the radial direction and spherical harmonic decomposition in the azimuthal and latitudinal directions. The time-stepping scheme relies on a semi-implicit Crank-Nicolson for the linear terms of the MHD equations and a Adams-Bashforth scheme for the non-linear terms and the Coriolis force.

Mathematical Model Of Nerve/Muscle Interaction

NASA Technical Reports Server (NTRS)

Hannaford, Blake

1990-01-01

Phasic Excitation/Activation (PEA) mathematical model simulates short-term nonlinear dynamics of activation and control of muscle by nerve. Includes electronic and mechanical elements. Is homeomorphic at level of its three major building blocks, which represent motoneuron, dynamics of activation of muscle, and mechanics of muscle.

Generic process design and control strategies used to develop a dynamic model and training software for an IGCC plant with CO2 sequestration

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

Provost, G.; Stone, H.; McClintock, M.

2008-01-01

To meet the growing demand for education and experience with the analysis, operation, and control of commercial-scale Integrated Gasification Combined Cycle (IGCC) plants, the Department of Energy’s (DOE) National Energy Technology Laboratory (NETL) is leading a collaborative R&D project with participants from government, academia, and industry. One of the goals of this project is to develop a generic, full-scope, real-time generic IGCC dynamic plant simulator for use in establishing a world-class research and training center, as well as to promote and demonstrate the technology to power industry personnel. The NETL IGCC dynamic plant simulator will combine for the first timemore » a process/gasification simulator and a power/combined-cycle simulator together in a single dynamic simulation framework for use in training applications as well as engineering studies. As envisioned, the simulator will have the following features and capabilities: A high-fidelity, real-time, dynamic model of process-side (gasification and gas cleaning with CO2 capture) and power-block-side (combined cycle) for a generic IGCC plant fueled by coal and/or petroleum coke Full-scope training simulator capabilities including startup, shutdown, load following and shedding, response to fuel and ambient condition variations, control strategy analysis (turbine vs. gasifier lead, etc.), representative malfunctions/trips, alarms, scenarios, trending, snapshots, data historian, and trainee performance monitoring The ability to enhance and modify the plant model to facilitate studies of changes in plant configuration and equipment and to support future R&D efforts To support this effort, process descriptions and control strategies were developed for key sections of the plant as part of the detailed functional specification, which will form the basis of the simulator development. These plant sections include: Slurry Preparation Air Separation Unit Gasifiers Syngas Scrubbers Shift Reactors Gas Cooling, Medium Pressure (MP) and Low Pressure (LP) Steam Generation, and Knockout Sour Water Stripper Mercury Removal Selexol™ Acid Gas Removal System CO2 Compression Syngas Reheat and Expansion Claus Plant Hydrogenation Reactor and Gas Cooler Combustion Turbine (CT)-Generator Assemblies Heat Recovery Steam Generators (HRSGs) and Steam Turbine (ST)-Generator In this paper, process descriptions, control strategies, and Process & Instrumentation Diagram (P&ID) drawings for key sections of the generic IGCC plant are presented, along with discussions of some of the operating procedures and representative faults that the simulator will cover. Some of the intended future applications for the simulator are discussed, including plant operation and control demonstrations as well as education and training services such as IGCC familiarization courses.« less

Implications of Stellar Feedback for Dynamical Modeling of the Milky Way and Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Wetzel, Andrew

2018-04-01

I will present recent results on dynamical modeling of stellar populations from the FIRE cosmological zoom-in baryonic simulations of Milky Way-like and dwarf galaxies. First, I will discuss the dynamical formation of the Milky Way, including the origin of thin+thick stellar disk morphology. I also will discuss the curious origin of metal-rich stars on halo-like orbits near the Sun, as recently measured by Gaia, with new insights from FIRE simulations on stellar radial migration/heating. Next, I will discuss role of stellar feedback in generating non-equilibrium fluctuations of the gravitational potential in low-mass 'dwarf' galaxies, which can explain the origin of cores in their dark-matter density profiles. In particular, we predict significant observable effects on stellar dynamics, including radial migration, size fluctuations, and population gradients, which can provide observational tests of feedback-driven core formation. Finally, this scenario can explain the formation of newly discovered 'ultra-diffuse' galaxies.

Application of Probabilistic Analysis to Aircraft Impact Dynamics

NASA Technical Reports Server (NTRS)

Lyle, Karen H.; Padula, Sharon L.; Stockwell, Alan E.

2003-01-01

Full-scale aircraft crash simulations performed with nonlinear, transient dynamic, finite element codes can incorporate structural complexities such as: geometrically accurate models; human occupant models; and advanced material models to include nonlinear stressstrain behaviors, laminated composites, and material failure. Validation of these crash simulations is difficult due to a lack of sufficient information to adequately determine the uncertainty in the experimental data and the appropriateness of modeling assumptions. This paper evaluates probabilistic approaches to quantify the uncertainty in the simulated responses. Several criteria are used to determine that a response surface method is the most appropriate probabilistic approach. The work is extended to compare optimization results with and without probabilistic constraints.

Research of TREETOPS Structural Dynamics Controls Simulation Upgrade

NASA Technical Reports Server (NTRS)

Yates, Rose M.

1996-01-01

Under the provisions of contract number NAS8-40194, which was entitled 'TREETOPS Structural Dynamics and Controls Simulation System Upgrade', Oakwood College contracted to produce an upgrade to the existing TREETOPS suite of analysis tools. This suite includes the main simulation program, TREETOPS, two interactive preprocessors, TREESET and TREEFLX, an interactive post processor, TREEPLOT, and an adjunct program, TREESEL. A 'Software Design Document', which provides descriptions of the argument lists and internal variables for each subroutine in the TREETOPS suite, was established. Additionally, installation guides for both DOS and UNIX platforms were developed. Finally, updated User's Manuals, as well as a Theory Manual, were generated.

A Wsbnd Ne interatomic potential for simulation of neon implantation in tungsten

NASA Astrophysics Data System (ADS)

Backman, Marie; Juslin, Niklas; Huang, Guiyang; Wirth, Brian D.

2016-08-01

An interatomic pair potential for Wsbnd Ne is developed for atomistic molecular dynamics simulations of neon implantation in tungsten. The new potential predicts point defect energies and binding energies of small clusters that are in good agreement with electronic structure calculations. Molecular dynamics simulations of small neon clusters in tungsten show that trap mutation, in which an interstitial neon cluster displaces a tungsten atom from its lattice site, occurs for clusters of three or more neon atoms. However, near a free surface, trap mutation can occur at smaller sizes, including even a single neon interstitial in close proximity to a (100) or (110) surface.

COLLABORATIVE RESEARCH AND DEVELOPMENT (CR&D) Delivery Order 0059: Molecular Dynamics Modeling Support

DTIC Science & Technology

2008-03-01

Molecular Dynamics Simulations 5 Theory: Equilibrium Molecular Dynamics Simulations 6 Theory: Non...Equilibrium Molecular Dynamics Simulations 8 Carbon Nanotube Simulations : Approach and results from equilibrium and non-equilibrium molecular dynamics ...touched from the perspective of molecular dynamics simulations . However, ordered systems such as “Carbon Nanotubes” have been investigated in terms

Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

NASA Astrophysics Data System (ADS)

Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín

2010-12-01

Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; ...

2014-12-01

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

PubMed Central

Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

2014-01-01

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions. PMID:25453071

Bivalves: From individual to population modelling

NASA Astrophysics Data System (ADS)

Saraiva, S.; van der Meer, J.; Kooijman, S. A. L. M.; Ruardij, P.

2014-11-01

An individual based population model for bivalves was designed, built and tested in a 0D approach, to simulate the population dynamics of a mussel bed located in an intertidal area. The processes at the individual level were simulated following the dynamic energy budget theory, whereas initial egg mortality, background mortality, food competition, and predation (including cannibalism) were additional population processes. Model properties were studied through the analysis of theoretical scenarios and by simulation of different mortality parameter combinations in a realistic setup, imposing environmental measurements. Realistic criteria were applied to narrow down the possible combination of parameter values. Field observations obtained in the long-term and multi-station monitoring program were compared with the model scenarios. The realistically selected modeling scenarios were able to reproduce reasonably the timing of some peaks in the individual abundances in the mussel bed and its size distribution but the number of individuals was not well predicted. The results suggest that the mortality in the early life stages (egg and larvae) plays an important role in population dynamics, either by initial egg mortality, larvae dispersion, settlement failure or shrimp predation. Future steps include the coupling of the population model with a hydrodynamic and biogeochemical model to improve the simulation of egg/larvae dispersion, settlement probability, food transport and also to simulate the feedback of the organisms' activity on the water column properties, which will result in an improvement of the food quantity and quality characterization.

Validating empirical force fields for molecular-level simulation of cellulose dissolution

USDA-ARS?s Scientific Manuscript database

The calculations presented here, which include dynamics simulations using analytical force fields and first principles studies, indicate that the COMPASS force field is preferred over the Dreiding and Universal force fields for studying dissolution of large cellulose structures. The validity of thes...

Update on ORNL TRANSFORM Tool: Simulating Multi-Module Advanced Reactor with End-to-End I&C

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

Hale, Richard Edward; Fugate, David L.; Cetiner, Sacit M.

2015-05-01

The Small Modular Reactor (SMR) Dynamic System Modeling Tool project is in the fourth year of development. The project is designed to support collaborative modeling and study of various advanced SMR (non-light water cooled reactor) concepts, including the use of multiple coupled reactors at a single site. The focus of this report is the development of a steam generator and drum system model that includes the complex dynamics of typical steam drum systems, the development of instrumentation and controls for the steam generator with drum system model, and the development of multi-reactor module models that reflect the full power reactormore » innovative small module design concept. The objective of the project is to provide a common simulation environment and baseline modeling resources to facilitate rapid development of dynamic advanced reactor models; ensure consistency among research products within the Instrumentation, Controls, and Human-Machine Interface technical area; and leverage cross-cutting capabilities while minimizing duplication of effort. The combined simulation environment and suite of models are identified as the TRANSFORM tool. The critical elements of this effort include (1) defining a standardized, common simulation environment that can be applied throughout the Advanced Reactors Technology program; (2) developing a library of baseline component modules that can be assembled into full plant models using available geometry, design, and thermal-hydraulic data; (3) defining modeling conventions for interconnecting component models; and (4) establishing user interfaces and support tools to facilitate simulation development (i.e., configuration and parameterization), execution, and results display and capture.« less

Modeling to predict pilot performance during CDTI-based in-trail following experiments

NASA Technical Reports Server (NTRS)

Sorensen, J. A.; Goka, T.

1984-01-01

A mathematical model was developed of the flight system with the pilot using a cockpit display of traffic information (CDTI) to establish and maintain in-trail spacing behind a lead aircraft during approach. Both in-trail and vertical dynamics were included. The nominal spacing was based on one of three criteria (Constant Time Predictor; Constant Time Delay; or Acceleration Cue). This model was used to simulate digitally the dynamics of a string of multiple following aircraft, including response to initial position errors. The simulation was used to predict the outcome of a series of in-trail following experiments, including pilot performance in maintaining correct longitudinal spacing and vertical position. The experiments were run in the NASA Ames Research Center multi-cab cockpit simulator facility. The experimental results were then used to evaluate the model and its prediction accuracy. Model parameters were adjusted, so that modeled performance matched experimental results. Lessons learned in this modeling and prediction study are summarized.

Including Memory Friction in Single- and Two-State Quantum Dynamics Simulations.

PubMed

Brown, Paul A; Messina, Michael

2016-03-03

We present a simple computational algorithm that allows for the inclusion of memory friction in a quantum dynamics simulation of a small, quantum, primary system coupled to many atoms in the surroundings. We show how including a memory friction operator, F̂, in the primary quantum system's Hamiltonian operator builds memory friction into the dynamics of the primary quantum system. We show that, in the harmonic, semi-classical limit, this friction operator causes the classical phase-space centers of a wavepacket to evolve exactly as if it were a classical particle experiencing memory friction. We also show that this friction operator can be used to include memory friction in the quantum dynamics of an anharmonic primary system. We then generalize the algorithm so that it can be used to treat a primary quantum system that is evolving, non-adiabatically on two coupled potential energy surfaces, i.e., a model that can be used to model H atom transfer, for example. We demonstrate this approach's computational ease and flexibility by showing numerical results for both harmonic and anharmonic primary quantum systems in the single surface case. Finally, we present numerical results for a model of non-adiabatic H atom transfer between a reactant and product state that includes memory friction on one or both of the non-adiabatic potential energy surfaces and uncover some interesting dynamical effects of non-memory friction on the H atom transfer process.

A real time Pegasus propulsion system model for VSTOL piloted simulation evaluation

NASA Technical Reports Server (NTRS)

Mihaloew, J. R.; Roth, S. P.; Creekmore, R.

1981-01-01

A real time propulsion system modeling technique suitable for use in man-in-the-loop simulator studies was developd. This technique provides the system accuracy, stability, and transient response required for integrated aircraft and propulsion control system studies. A Pegasus-Harrier propulsion system was selected as a baseline for developing mathematical modeling and simulation techniques for VSTOL. Initially, static and dynamic propulsion system characteristics were modeled in detail to form a nonlinear aerothermodynamic digital computer simulation of a Pegasus engine. From this high fidelity simulation, a real time propulsion model was formulated by applying a piece-wise linear state variable methodology. A hydromechanical and water injection control system was also simulated. The real time dynamic model includes the detail and flexibility required for the evaluation of critical control parameters and propulsion component limits over a limited flight envelope. The model was programmed for interfacing with a Harrier aircraft simulation. Typical propulsion system simulation results are presented.

DYNSYL: a general-purpose dynamic simulator for chemical processes

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

Patterson, G.K.; Rozsa, R.B.

1978-09-05

Lawrence Livermore Laboratory is conducting a safeguards program for the Nuclear Regulatory Commission. The goal of the Material Control Project of this program is to evaluate material control and accounting (MCA) methods in plants that handle special nuclear material (SNM). To this end we designed and implemented the dynamic chemical plant simulation program DYNSYL. This program can be used to generate process data or to provide estimates of process performance; it simulates both steady-state and dynamic behavior. The MCA methods that may have to be evaluated range from sophisticated on-line material trackers such as Kalman filter estimators, to relatively simplemore » material balance procedures. This report describes the overall structure of DYNSYL and includes some example problems. The code is still in the experimental stage and revision is continuing.« less

Software for Engineering Simulations of a Spacecraft

NASA Technical Reports Server (NTRS)

Shireman, Kirk; McSwain, Gene; McCormick, Bernell; Fardelos, Panayiotis

2005-01-01

Spacecraft Engineering Simulation II (SES II) is a C-language computer program for simulating diverse aspects of operation of a spacecraft characterized by either three or six degrees of freedom. A functional model in SES can include a trajectory flight plan; a submodel of a flight computer running navigational and flight-control software; and submodels of the environment, the dynamics of the spacecraft, and sensor inputs and outputs. SES II features a modular, object-oriented programming style. SES II supports event-based simulations, which, in turn, create an easily adaptable simulation environment in which many different types of trajectories can be simulated by use of the same software. The simulation output consists largely of flight data. SES II can be used to perform optimization and Monte Carlo dispersion simulations. It can also be used to perform simulations for multiple spacecraft. In addition to its generic simulation capabilities, SES offers special capabilities for space-shuttle simulations: for this purpose, it incorporates submodels of the space-shuttle dynamics and a C-language version of the guidance, navigation, and control components of the space-shuttle flight software.

Development of a Stirling System Dynamic Model With Enhanced Thermodynamics

NASA Technical Reports Server (NTRS)

Regan, Timothy F.; Lewandowski, Edward J.

2005-01-01

The Stirling Convertor System Dynamic Model developed at NASA Glenn Research Center is a software model developed from first principles that includes the mechanical and mounting dynamics, the thermodynamics, the linear alternator, and the controller of a free-piston Stirling power convertor, along with the end user load. As such it represents the first detailed modeling tool for fully integrated Stirling convertor-based power systems. The thermodynamics of the model were originally a form of the isothermal Stirling cycle. In some situations it may be desirable to improve the accuracy of the Stirling cycle portion of the model. An option under consideration is to enhance the SDM thermodynamics by coupling the model with Gedeon Associates Sage simulation code. The result will be a model that gives a more accurate prediction of the performance and dynamics of the free-piston Stirling convertor. A method of integrating the Sage simulation code with the System Dynamic Model is described. Results of SDM and Sage simulation are compared to test data. Model parameter estimation and model validation are discussed.

Development of a Stirling System Dynamic Model with Enhanced Thermodynamics

NASA Astrophysics Data System (ADS)

Regan, Timothy F.; Lewandowski, Edward J.

2005-02-01

The Stirling Convertor System Dynamic Model developed at NASA Glenn Research Center is a software model developed from first principles that includes the mechanical and mounting dynamics, the thermodynamics, the linear alternator, and the controller of a free-piston Stirling power convertor, along with the end user load. As such it represents the first detailed modeling tool for fully integrated Stirling convertor-based power systems. The thermodynamics of the model were originally a form of the isothermal Stirling cycle. In some situations it may be desirable to improve the accuracy of the Stirling cycle portion of the model. An option under consideration is to enhance the SDM thermodynamics by coupling the model with Gedeon Associates' Sage simulation code. The result will be a model that gives a more accurate prediction of the performance and dynamics of the free-piston Stirling convertor. A method of integrating the Sage simulation code with the System Dynamic Model is described. Results of SDM and Sage simulation are compared to test data. Model parameter estimation and model validation are discussed.

Simulation modeling of forest landscape disturbances: Where do we go from here?

Treesearch

Ajith H. Perera; Brian R. Sturtevant; Lisa J. Buse

2015-01-01

It was nearly a quarter-century ago when Turner and Gardner (1991) drew attention to methods of quantifying landscape patterns and processes, including simulation modeling. The many authors who contributed to that seminal text collectively signaled the emergence of a new field—spatially explicit simulation modeling of broad-scale ecosystem dynamics. Of particular note...

Troponin structure: its modulation by Ca(2+) and phosphorylation studied by molecular dynamics simulations.

PubMed

Zamora, Juan Eiros; Papadaki, Maria; Messer, Andrew E; Marston, Steven B; Gould, Ian R

2016-07-27

The only available crystal structure of the human cardiac troponin molecule (cTn) in the Ca(2+) activated state does not include crucial segments, including the N-terminus of the cTn inhibitory subunit (cTnI). We have applied all-atom molecular dynamics (MD) simulations to study the structure and dynamics of cTn, both in the unphosphorylated and bis-phosphorylated states at Ser23/Ser24 of cTnI. We performed multiple microsecond MD simulations of wild type (WT) cTn (6, 5 μs) and bisphosphorylated (SP23/SP24) cTn (9 μs) on a 419 amino acid cTn model containing human sequence cTnC (1-161), cTnI (1-171) and cTnT (212-298), including residues not present in the crystal structure. We have compared our results to previous computational studies, and proven that longer simulations and a water box of at least 25 Å are needed to sample the interesting conformational shifts both in the native and bis-phosphorylated states. As a consequence of the introduction into the model of the C-terminus of cTnT that was missing in previous studies, cTnC-cTnI interactions that are responsible for the cTn dynamics are altered. We have also shown that phosphorylation does not increase cTn fluctuations, and its effects on the protein-protein interaction profiles cannot be assessed in a significant way. Finally, we propose that phosphorylation could provoke a loss of Ca(2+) by stabilizing out-of-coordination distances of the cTnC's EF hand II residues, and in particular Ser 69.

Simulation analysis of an integrated model for dynamic cellular manufacturing system

NASA Astrophysics Data System (ADS)

Hao, Chunfeng; Luan, Shichao; Kong, Jili

2017-05-01

Application of dynamic cellular manufacturing system (DCMS) is a well-known strategy to improve manufacturing efficiency in the production environment with high variety and low volume of production. Often, neither the trade-off of inter and intra-cell material movements nor the trade-off of hiring and firing of operators are examined in details. This paper presents simulation results of an integrated mixed-integer model including sensitivity analysis for several numerical examples. The comprehensive model includes cell formation, inter and intracellular materials handling, inventory and backorder holding, operator assignment (including resource adjustment) and flexible production routing. The model considers multi-production planning with flexible resources (machines and operators) where each period has different demands. The results verify the validity and sensitivity of the proposed model using a genetic algorithm.

The SCEC/USGS dynamic earthquake rupture code verification exercise

USGS Publications Warehouse

Harris, R.A.; Barall, M.; Archuleta, R.; Dunham, E.; Aagaard, Brad T.; Ampuero, J.-P.; Bhat, H.; Cruz-Atienza, Victor M.; Dalguer, L.; Dawson, P.; Day, S.; Duan, B.; Ely, G.; Kaneko, Y.; Kase, Y.; Lapusta, N.; Liu, Yajing; Ma, S.; Oglesby, D.; Olsen, K.; Pitarka, A.; Song, S.; Templeton, E.

2009-01-01

Numerical simulations of earthquake rupture dynamics are now common, yet it has been difficult to test the validity of these simulations because there have been few field observations and no analytic solutions with which to compare the results. This paper describes the Southern California Earthquake Center/U.S. Geological Survey (SCEC/USGS) Dynamic Earthquake Rupture Code Verification Exercise, where codes that simulate spontaneous rupture dynamics in three dimensions are evaluated and the results produced by these codes are compared using Web-based tools. This is the first time that a broad and rigorous examination of numerous spontaneous rupture codes has been performed—a significant advance in this science. The automated process developed to attain this achievement provides for a future where testing of codes is easily accomplished.Scientists who use computer simulations to understand earthquakes utilize a range of techniques. Most of these assume that earthquakes are caused by slip at depth on faults in the Earth, but hereafter the strategies vary. Among the methods used in earthquake mechanics studies are kinematic approaches and dynamic approaches.The kinematic approach uses a computer code that prescribes the spatial and temporal evolution of slip on the causative fault (or faults). These types of simulations are very helpful, especially since they can be used in seismic data inversions to relate the ground motions recorded in the field to slip on the fault(s) at depth. However, these kinematic solutions generally provide no insight into the physics driving the fault slip or information about why the involved fault(s) slipped that much (or that little). In other words, these kinematic solutions may lack information about the physical dynamics of earthquake rupture that will be most helpful in forecasting future events.To help address this issue, some researchers use computer codes to numerically simulate earthquakes and construct dynamic, spontaneous rupture (hereafter called “spontaneous rupture”) solutions. For these types of numerical simulations, rather than prescribing the slip function at each location on the fault(s), just the friction constitutive properties and initial stress conditions are prescribed. The subsequent stresses and fault slip spontaneously evolve over time as part of the elasto-dynamic solution. Therefore, spontaneous rupture computer simulations of earthquakes allow us to include everything that we know, or think that we know, about earthquake dynamics and to test these ideas against earthquake observations.

NetFlow Dynamics

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

Corbet Jr., Thomas F; Beyeler, Walter E; Vanwestrienen, Dirk

NetFlow Dynamics is a web-accessible analysis environment for simulating dynamic flows of materials on model networks. Performing a simulation requires both the NetFlow Dynamics application and a network model which is a description of the structure of the nodes and edges of a network including the flow capacity of each edge and the storage capacity of each node, and the sources and sinks of the material flowing on the network. NetFlow Dynamics consists of databases for storing network models, algorithms to calculate flows on networks, and a GIS-based graphical interface for performing simulations and viewing simulation results. Simulated flows aremore » dynamic in the sense that flows on each edge of the network and inventories at each node change with time and can be out of equilibrium with boundary conditions. Any number of network models could be simulated using Net Flow Dynamics. To date, the models simulated have been models of petroleum infrastructure. The main model has been the National Transportation Fuels Model (NTFM), a network of U.S. oil fields, transmission pipelines, rail lines, refineries, tank farms, and distribution terminals. NetFlow Dynamics supports two different flow algorithms, the Gradient Flow algorithm and the Inventory Control algorithm, that were developed specifically for the NetFlow Dynamics application. The intent is to add additional algorithms in the future as needed. The ability to select from multiple algorithms is desirable because a single algorithm never covers all analysis needs. The current algorithms use a demand-driven capacity-constrained formulation which means that the algorithms strive to use all available capacity and stored inventory to meet desired flows to sinks, subject to the capacity constraints of each network component. The current flow algorithms are best suited for problems in which a material flows on a capacity-constrained network representing a supply chain in which the material supplied can be stored at each node of the network. In the petroleum models, the flowing materials are crude oil and refined products that can be stored at tank farms, refineries, or terminals (i.e. the nodes of the network). Examples of other network models that could be simulated are currency flowing in a financial network, agricultural products moving to market, or natural gas flowing on a pipeline network.« less

Simulation model of a variable-speed pumped-storage power plant in unstable operating conditions in pumping mode

NASA Astrophysics Data System (ADS)

Martínez-Lucas, G.; Pérez-Díaz, J. I.; Sarasúa, J. I.; Cavazzini, G.; Pavesi, G.; Ardizzon, G.

2017-04-01

This paper presents a dynamic simulation model of a laboratory-scale pumped-storage power plant (PSPP) operating in pumping mode with variable speed. The model considers the dynamic behavior of the conduits by means of an elastic water column approach, and synthetically generates both pressure and torque pulsations that reproduce the operation of the hydraulic machine in its instability region. The pressure and torque pulsations are generated each from a different set of sinusoidal functions. These functions were calibrated from the results of a CFD model, which was in turn validated from experimental data. Simulation model results match the numerical results of the CFD model with reasonable accuracy. The pump-turbine model (the functions used to generate pressure and torque pulsations inclusive) was up-scaled by hydraulic similarity according to the design parameters of a real PSPP and included in a dynamic simulation model of the said PSPP. Preliminary conclusions on the impact of unstable operation conditions on the penstock fatigue were obtained by means of a Monte Carlo simulation-based fatigue analysis.

Volcano Modelling and Simulation gateway (VMSg): A new web-based framework for collaborative research in physical modelling and simulation of volcanic phenomena

NASA Astrophysics Data System (ADS)

Esposti Ongaro, T.; Barsotti, S.; de'Michieli Vitturi, M.; Favalli, M.; Longo, A.; Nannipieri, L.; Neri, A.; Papale, P.; Saccorotti, G.

2009-12-01

Physical and numerical modelling is becoming of increasing importance in volcanology and volcanic hazard assessment. However, new interdisciplinary problems arise when dealing with complex mathematical formulations, numerical algorithms and their implementations on modern computer architectures. Therefore new frameworks are needed for sharing knowledge, software codes, and datasets among scientists. Here we present the Volcano Modelling and Simulation gateway (VMSg, accessible at http://vmsg.pi.ingv.it), a new electronic infrastructure for promoting knowledge growth and transfer in the field of volcanological modelling and numerical simulation. The new web portal, developed in the framework of former and ongoing national and European projects, is based on a dynamic Content Manager System (CMS) and was developed to host and present numerical models of the main volcanic processes and relationships including magma properties, magma chamber dynamics, conduit flow, plume dynamics, pyroclastic flows, lava flows, etc. Model applications, numerical code documentation, simulation datasets as well as model validation and calibration test-cases are also part of the gateway material.

Simulating Flying Insects Using Dynamics and Data-Driven Noise Modeling to Generate Diverse Collective Behaviors

PubMed Central

Ren, Jiaping; Wang, Xinjie; Manocha, Dinesh

2016-01-01

We present a biologically plausible dynamics model to simulate swarms of flying insects. Our formulation, which is based on biological conclusions and experimental observations, is designed to simulate large insect swarms of varying densities. We use a force-based model that captures different interactions between the insects and the environment and computes collision-free trajectories for each individual insect. Furthermore, we model the noise as a constructive force at the collective level and present a technique to generate noise-induced insect movements in a large swarm that are similar to those observed in real-world trajectories. We use a data-driven formulation that is based on pre-recorded insect trajectories. We also present a novel evaluation metric and a statistical validation approach that takes into account various characteristics of insect motions. In practice, the combination of Curl noise function with our dynamics model is used to generate realistic swarm simulations and emergent behaviors. We highlight its performance for simulating large flying swarms of midges, fruit fly, locusts and moths and demonstrate many collective behaviors, including aggregation, migration, phase transition, and escape responses. PMID:27187068

A method for landing gear modeling and simulation with experimental validation

NASA Technical Reports Server (NTRS)

Daniels, James N.

1996-01-01

This document presents an approach for modeling and simulating landing gear systems. Specifically, a nonlinear model of an A-6 Intruder Main Gear is developed, simulated, and validated against static and dynamic test data. This model includes nonlinear effects such as a polytropic gas model, velocity squared damping, a geometry governed model for the discharge coefficients, stick-slip friction effects and a nonlinear tire spring and damping model. An Adams-Moulton predictor corrector was used to integrate the equations of motion until a discontinuity caused by a stick-slip friction model was reached, at which point, a Runga-Kutta routine integrated past the discontinuity and returned the problem solution back to the predictor corrector. Run times of this software are around 2 mins. per 1 sec. of simulation under dynamic circumstances. To validate the model, engineers at the Aircraft Landing Dynamics facilities at NASA Langley Research Center installed one A-6 main gear on a drop carriage and used a hydraulic shaker table to provide simulated runway inputs to the gear. Model parameters were tuned to produce excellent agreement for many cases.

All-atom molecular dynamics of virus capsids as drug targets

DOE PAGES

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...

2016-04-29

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

All-atom molecular dynamics of virus capsids as drug targets

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

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

The influence of track modelling options on the simulation of rail vehicle dynamics

NASA Astrophysics Data System (ADS)

Di Gialleonardo, Egidio; Braghin, Francesco; Bruni, Stefano

2012-09-01

This paper investigates the effect of different models for track flexibility on the simulation of railway vehicle running dynamics on tangent and curved track. To this end, a multi-body model of the rail vehicle is defined including track flexibility effects on three levels of detail: a perfectly rigid pair of rails, a sectional track model and a three-dimensional finite element track model. The influence of the track model on the calculation of the nonlinear critical speed is pointed out and it is shown that neglecting the effect of track flexibility results in an overestimation of the critical speed by more than 10%. Vehicle response to stochastic excitation from track irregularity is also investigated, analysing the effect of track flexibility models on the vertical and lateral wheel-rail contact forces. Finally, the effect of the track model on the calculation of dynamic forces produced by wheel out-of-roundness is analysed, showing that peak dynamic loads are very sensitive to the track model used in the simulation.

Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles.

PubMed

Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F; Perez, Danny

2017-10-21

Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which have to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex accelerated molecular dynamics trajectories exhibiting shape fluctuations in Pt nanoclusters. This analysis provides an easily interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

NASA Astrophysics Data System (ADS)

Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F.; Perez, Danny

2017-10-01

Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which have to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex accelerated molecular dynamics trajectories exhibiting shape fluctuations in Pt nanoclusters. This analysis provides an easily interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

Functional mechanism of C-terminal tail in the enzymatic role of porcine testicular carbonyl reductase: a combined experiment and molecular dynamics simulation study of the C-terminal tail in the enzymatic role of PTCR.

PubMed

Son, Minky; Bang, Woo Young; Park, Chanin; Lee, Yuno; Kwon, Seul Gi; Kim, Sam Woong; Kim, Chul Wook; Lee, Keun Woo

2014-01-01

Porcine testicular carbonyl reductase, PTCR which is one of the short chain dehydrogenases/reductases (SDR) superfamily catalyzes the NADPH-dependent reduction of carbonyl compounds including steroids and prostaglandins. Previously we reported C-terminal tail of PTCR was deleted due to a nonsynonymous single nucleotide variation (nsSNV). Here we identified from kinetic studies that the enzymatic properties for 5α-dihydrotestosterone (5α-DHT) were different between wild-type and C-terminal-deleted PTCRs. Compared to wild-type PTCR, C-terminal-deleted PTCR has much higher reduction rate. To investigate structural difference between wild-type and C-terminal-deleted PTCRs upon 5α-DHT binding, we performed molecular dynamics simulations for two complexes. Using trajectories, molecular interactions including hydrogen bonding patterns, distance between 5α-DHT and catalytic Tyr193, and interaction energies are analyzed and compared. During the MD simulation time, the dynamic behavior of C-terminal tail in wild-type PTCR is also examined using essential dynamics analysis. The results of our simulations reveal that the binding conformation of 5α-DHT in C-terminal-deleted PTCR is more favorable for reduction reaction in PTCR, which shows strong agreement with kinetic data. These structural findings provide valuable information to understand substrate specificity of PTCR and further kinetic properties of enzymes belonging to the SDR superfamily.

Functional Mechanism of C-Terminal Tail in the Enzymatic Role of Porcine Testicular Carbonyl Reductase: A Combined Experiment and Molecular Dynamics Simulation Study of the C-Terminal Tail in the Enzymatic Role of PTCR

PubMed Central

Park, Chanin; Lee, Yuno; Kwon, Seul Gi; Kim, Sam Woong; Kim, Chul Wook; Lee, Keun Woo

2014-01-01

Porcine testicular carbonyl reductase, PTCR which is one of the short chain dehydrogenases/reductases (SDR) superfamily catalyzes the NADPH-dependent reduction of carbonyl compounds including steroids and prostaglandins. Previously we reported C- terminal tail of PTCR was deleted due to a nonsynonymous single nucleotide variation (nsSNV). Here we identified from kinetic studies that the enzymatic properties for 5α-dihydrotestosterone (5α-DHT) were different between wild-type and C-terminal-deleted PTCRs. Compared to wild-type PTCR, C-terminal-deleted PTCR has much higher reduction rate. To investigate structural difference between wild-type and C-terminal-deleted PTCRs upon 5α-DHT binding, we performed molecular dynamics simulations for two complexes. Using trajectories, molecular interactions including hydrogen bonding patterns, distance between 5α-DHT and catalytic Tyr193, and interaction energies are analyzed and compared. During the MD simulation time, the dynamic behavior of C-terminal tail in wild-type PTCR is also examined using essential dynamics analysis. The results of our simulations reveal that the binding conformation of 5α-DHT in C-terminal-deleted PTCR is more favorable for reduction reaction in PTCR, which shows strong agreement with kinetic data. These structural findings provide valuable information to understand substrate specificity of PTCR and further kinetic properties of enzymes belonging to the SDR superfamily. PMID:24646606

Spatially Distributed Assimilation of Remotely Sensed Leaf Area Index and Potential Evapotranspiration for Hydrologic Modeling in Wetland Landscapes

EPA Science Inventory

Evapotranspiration (ET), a highly dynamic flux in wetland landscapes, regulates the accuracy of surface/sub-surface runoff simulation in a hydrologic model. However, considerable uncertainty in simulating ET-related processes remains, including our limited ability to incorporate ...

A time domain simulation of a beam control system

NASA Astrophysics Data System (ADS)

Mitchell, J. R.

1981-02-01

The Airborne Laser Laboratory (ALL) is being developed by the Air Force to investigate the integration and operation of high energy laser components in a dynamic airborne environment and to study the propagation of laser light from an airborne vehicle to an airborne target. The ALL is composed of several systems; among these are the Airborne Pointing and Tracking System (APT) and the Automatic Alignment System (AAS). This report presents the results of performing a time domain dynamic simulation for an integrated beam control system composed of the APT and AAS. The simulation is performed on a digital computer using the MIMIC language. It includes models of the dynamics of the system and of disturbances. Also presented in the report are the rationales and developments of these models. The data from the simulation code is summarized by several plots. In addition results from massaging the data with waveform analysis packages are presented. The results are discussed and conclusions are drawn.

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications.

PubMed

Du, Likai; Lan, Zhenggang

2015-04-14

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

Accounting for Fault Roughness in Pseudo-Dynamic Ground-Motion Simulations

NASA Astrophysics Data System (ADS)

Mai, P. Martin; Galis, Martin; Thingbaijam, Kiran K. S.; Vyas, Jagdish C.; Dunham, Eric M.

2017-09-01

Geological faults comprise large-scale segmentation and small-scale roughness. These multi-scale geometrical complexities determine the dynamics of the earthquake rupture process, and therefore affect the radiated seismic wavefield. In this study, we examine how different parameterizations of fault roughness lead to variability in the rupture evolution and the resulting near-fault ground motions. Rupture incoherence naturally induced by fault roughness generates high-frequency radiation that follows an ω-2 decay in displacement amplitude spectra. Because dynamic rupture simulations are computationally expensive, we test several kinematic source approximations designed to emulate the observed dynamic behavior. When simplifying the rough-fault geometry, we find that perturbations in local moment tensor orientation are important, while perturbations in local source location are not. Thus, a planar fault can be assumed if the local strike, dip, and rake are maintained. We observe that dynamic rake angle variations are anti-correlated with the local dip angles. Testing two parameterizations of dynamically consistent Yoffe-type source-time function, we show that the seismic wavefield of the approximated kinematic ruptures well reproduces the radiated seismic waves of the complete dynamic source process. This finding opens a new avenue for an improved pseudo-dynamic source characterization that captures the effects of fault roughness on earthquake rupture evolution. By including also the correlations between kinematic source parameters, we outline a new pseudo-dynamic rupture modeling approach for broadband ground-motion simulation.

WWTP dynamic disturbance modelling--an essential module for long-term benchmarking development.

PubMed

Gernaey, K V; Rosen, C; Jeppsson, U

2006-01-01

Intensive use of the benchmark simulation model No. 1 (BSM1), a protocol for objective comparison of the effectiveness of control strategies in biological nitrogen removal activated sludge plants, has also revealed a number of limitations. Preliminary definitions of the long-term benchmark simulation model No. 1 (BSM1_LT) and the benchmark simulation model No. 2 (BSM2) have been made to extend BSM1 for evaluation of process monitoring methods and plant-wide control strategies, respectively. Influent-related disturbances for BSM1_LT/BSM2 are to be generated with a model, and this paper provides a general overview of the modelling methods used. Typical influent dynamic phenomena generated with the BSM1_LT/BSM2 influent disturbance model, including diurnal, weekend, seasonal and holiday effects, as well as rainfall, are illustrated with simulation results. As a result of the work described in this paper, a proposed influent model/file has been released to the benchmark developers for evaluation purposes. Pending this evaluation, a final BSM1_LT/BSM2 influent disturbance model definition is foreseen. Preliminary simulations with dynamic influent data generated by the influent disturbance model indicate that default BSM1 activated sludge plant control strategies will need extensions for BSM1_LT/BSM2 to efficiently handle 1 year of influent dynamics.

Influence of backup bearings and support structure dynamics on the behavior of rotors with active supports

NASA Technical Reports Server (NTRS)

Flowers, George T.

1994-01-01

Substantial progress has been made toward the goals of this research effort in the past six months. A simplified rotor model with a flexible shaft and backup bearings has been developed. The model is based upon the work of Ishii and Kirk. Parameter studies of the behavior of this model are currently being conducted. A simple rotor model which includes a flexible disk and bearings with clearance has been developed and the dynamics of the model investigated. The study consists of simulation work coupled with experimental verification. The work is documented in the attached paper. A rotor model based upon the T-501 engine has been developed which includes backup bearing effects. The dynamics of this model are currently being studied with the objective of verifying the conclusions obtained from the simpler models. Parallel simulation runs are being conducted using an ANSYS based finite element model of the T-501.

A Flying Qualities Study of Longitudinal Long-Term Dynamics of Hypersonic Planes

NASA Technical Reports Server (NTRS)

Cox, Timothy H.; Sachs, G.; Knoll, A.; Stich, R.

1995-01-01

The NASA Dryden Flight Research Center and the Technical University of Munich are cooperating in a research program to assess the impact of unstable long-term dynamics on the flying qualities of planes in hypersonic flight. These flying qualities issues are being investigated with a dedicated flight simulator for hypersonic vehicles located at NASA Dryden. Several NASA research pilots have flown the simulator through well defined steady-level turns with varying phugoid and height mode instabilities. The data collected include Pilot ratings and comments, performance measurements, and Pilot workload measurements. The results presented in this paper include design guidelines for height and Phugoid mode instabilities, an evaluation of the tapping method used to measure pilot workload, a discussion of techniques developed by the pilots to control large instabilities, and a discussion of how flying qualities of unstable long-term dynamics influence control Power design requirements.

A flying qualities study of longitudinal long-term dynamics of hypersonic planes

NASA Technical Reports Server (NTRS)

Cox, T.; Sachs, G.; Knoll, A.; Stich, R.

1995-01-01

The NASA Dryden Flight Research Center and the Technical University of Munich are cooperating in a research program to assess the impact of unstable long-term dynamics on the flying qualities of planes in hypersonic flight. These flying qualities issues are being investigated with a dedicated flight simulator for hypersonic vehicles located at NASA Dryden. Several NASA research pilots have flown the simulator through well-defined steady-level turns with varying phugoid and height mode instabilities. Th data collected include pilot ratings and comments, performance measurements, and pilot workload measurements. The results presented in this paper include design guidelines for height and phugoid mode instabilities, an evaluation of the tapping method used to measure pilot workload, a discussion of techniques developed by the pilots to control large instabilities, and a discussion of how flying qualities of unstable long-term dynamics influence control power design requirements.

Material Model Evaluation of a Composite Honeycomb Energy Absorber

NASA Technical Reports Server (NTRS)

Jackson, Karen E.; Annett, Martin S.; Fasanella, Edwin L.; Polanco, Michael A.

2012-01-01

A study was conducted to evaluate four different material models in predicting the dynamic crushing response of solid-element-based models of a composite honeycomb energy absorber, designated the Deployable Energy Absorber (DEA). Dynamic crush tests of three DEA components were simulated using the nonlinear, explicit transient dynamic code, LS-DYNA . In addition, a full-scale crash test of an MD-500 helicopter, retrofitted with DEA blocks, was simulated. The four material models used to represent the DEA included: *MAT_CRUSHABLE_FOAM (Mat 63), *MAT_HONEYCOMB (Mat 26), *MAT_SIMPLIFIED_RUBBER/FOAM (Mat 181), and *MAT_TRANSVERSELY_ANISOTROPIC_CRUSHABLE_FOAM (Mat 142). Test-analysis calibration metrics included simple percentage error comparisons of initial peak acceleration, sustained crush stress, and peak compaction acceleration of the DEA components. In addition, the Roadside Safety Verification and Validation Program (RSVVP) was used to assess similarities and differences between the experimental and analytical curves for the full-scale crash test.

A Systematic Evaluation of Noah-MP in Simulating Land-Atmosphere Energy, Water, and Carbon Exchanges Over the Continental United States

NASA Astrophysics Data System (ADS)

Ma, Ning; Niu, Guo-Yue; Xia, Youlong; Cai, Xitian; Zhang, Yinsheng; Ma, Yaoming; Fang, Yuanhao

2017-11-01

Accurate simulation of energy, water, and carbon fluxes exchanging between the land surface and the atmosphere is beneficial for improving terrestrial ecohydrological and climate predictions. We systematically assessed the Noah land surface model (LSM) with mutiparameterization options (Noah-MP) in simulating these fluxes and associated variations in terrestrial water storage (TWS) and snow cover fraction (SCF) against various reference products over 18 United States Geological Survey two-digital hydrological unit code regions of the continental United States (CONUS). In general, Noah-MP captures better the observed seasonal and interregional variability of net radiation, SCF, and runoff than other variables. With a dynamic vegetation model, it overestimates gross primary productivity by 40% and evapotranspiration (ET) by 22% over the whole CONUS domain; however, with a prescribed climatology of leaf area index, it greatly improves ET simulation with relative bias dropping to 4%. It accurately simulates regional TWS dynamics in most regions except those with large lakes or severely affected by irrigation and/or impoundments. Incorporating the lake water storage variations into the modeled TWS variations largely reduces the TWS simulation bias more obviously over the Great Lakes with model efficiency increasing from 0.18 to 0.76. Noah-MP simulates runoff well in most regions except an obvious overestimation (underestimation) in the Rio Grande and Lower Colorado (New England). Compared with North American Land Data Assimilation System Phase 2 (NLDAS-2) LSMs, Noah-MP shows a better ability to simulate runoff and a comparable skill in simulating Rn but a worse skill in simulating ET over most regions. This study suggests that future model developments should focus on improving the representations of vegetation dynamics, lake water storage dynamics, and human activities including irrigation and impoundments.

Supercomputing in Aerospace

NASA Technical Reports Server (NTRS)

Kutler, Paul; Yee, Helen

1987-01-01

Topics addressed include: numerical aerodynamic simulation; computational mechanics; supercomputers; aerospace propulsion systems; computational modeling in ballistics; turbulence modeling; computational chemistry; computational fluid dynamics; and computational astrophysics.

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.

Modeling and 2-D discrete simulation of dislocation dynamics for plastic deformation of metal

NASA Astrophysics Data System (ADS)

Liu, Juan; Cui, Zhenshan; Ou, Hengan; Ruan, Liqun

2013-05-01

Two methods are employed in this paper to investigate the dislocation evolution during plastic deformation of metal. One method is dislocation dynamic simulation of two-dimensional discrete dislocation dynamics (2D-DDD), and the other is dislocation dynamics modeling by means of nonlinear analysis. As screw dislocation is prone to disappear by cross-slip, only edge dislocation is taken into account in simulation. First, an approach of 2D-DDD is used to graphically simulate and exhibit the collective motion of a large number of discrete dislocations. In the beginning, initial grains are generated in the simulation cells according to the mechanism of grain growth and the initial dislocation is randomly distributed in grains and relaxed under the internal stress. During the simulation process, the externally imposed stress, the long range stress contribution of all dislocations and the short range stress caused by the grain boundaries are calculated. Under the action of these forces, dislocations begin to glide, climb, multiply, annihilate and react with each other. Besides, thermal activation process is included. Through the simulation, the distribution of dislocation and the stress-strain curves can be obtained. On the other hand, based on the classic dislocation theory, the variation of the dislocation density with time is described by nonlinear differential equations. Finite difference method (FDM) is used to solve the built differential equations. The dislocation evolution at a constant strain rate is taken as an example to verify the rationality of the model.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

State-and-transition simulation models: a framework for forecasting landscape change

USGS Publications Warehouse

Daniel, Colin; Frid, Leonardo; Sleeter, Benjamin M.; Fortin, Marie-Josée

2016-01-01

SummaryA wide range of spatially explicit simulation models have been developed to forecast landscape dynamics, including models for projecting changes in both vegetation and land use. While these models have generally been developed as separate applications, each with a separate purpose and audience, they share many common features.We present a general framework, called a state-and-transition simulation model (STSM), which captures a number of these common features, accompanied by a software product, called ST-Sim, to build and run such models. The STSM method divides a landscape into a set of discrete spatial units and simulates the discrete state of each cell forward as a discrete-time-inhomogeneous stochastic process. The method differs from a spatially interacting Markov chain in several important ways, including the ability to add discrete counters such as age and time-since-transition as state variables, to specify one-step transition rates as either probabilities or target areas, and to represent multiple types of transitions between pairs of states.We demonstrate the STSM method using a model of land-use/land-cover (LULC) change for the state of Hawai'i, USA. Processes represented in this example include expansion/contraction of agricultural lands, urbanization, wildfire, shrub encroachment into grassland and harvest of tree plantations; the model also projects shifts in moisture zones due to climate change. Key model output includes projections of the future spatial and temporal distribution of LULC classes and moisture zones across the landscape over the next 50 years.State-and-transition simulation models can be applied to a wide range of landscapes, including questions of both land-use change and vegetation dynamics. Because the method is inherently stochastic, it is well suited for characterizing uncertainty in model projections. When combined with the ST-Sim software, STSMs offer a simple yet powerful means for developing a wide range of models of landscape dynamics.

Langevin Equation for DNA Dynamics

NASA Astrophysics Data System (ADS)

Grych, David; Copperman, Jeremy; Guenza, Marina

Under physiological conditions, DNA oligomers can contain well-ordered helical regions and also flexible single-stranded regions. We describe the site-specific motion of DNA with a modified Rouse-Zimm Langevin equation formalism that describes DNA as a coarse-grained polymeric chain with global structure and local flexibility. The approach has successfully described the protein dynamics in solution and has been extended to nucleic acids. Our approach provides diffusive mode analytical solutions for the dynamics of global rotational diffusion and internal motion. The internal DNA dynamics present a rich energy landscape that accounts for an interior where hydrogen bonds and base-stacking determine structure and experience limited solvent exposure. We have implemented several models incorporating different coarse-grained sites with anisotropic rotation, energy barrier crossing, and local friction coefficients that include a unique internal viscosity and our models reproduce dynamics predicted by atomistic simulations. The models reproduce bond autocorrelation along the sequence as compared to that directly calculated from atomistic molecular dynamics simulations. The Langevin equation approach captures the essence of DNA dynamics without a cumbersome atomistic representation.

Active Curved Polymers Form Vortex Patterns on Membranes.

PubMed

Denk, Jonas; Huber, Lorenz; Reithmann, Emanuel; Frey, Erwin

2016-04-29

Recent in vitro experiments with FtsZ polymers show self-organization into different dynamic patterns, including structures reminiscent of the bacterial Z ring. We model FtsZ polymers as active particles moving along chiral, circular paths by Brownian dynamics simulations and a Boltzmann approach. Our two conceptually different methods point to a generic phase behavior. At intermediate particle densities, we find self-organization into vortex structures including closed rings. Moreover, we show that the dynamics at the onset of pattern formation is described by a generalized complex Ginzburg-Landau equation.

Dynamic analysis of space structures including elastic, multibody, and control behavior

NASA Technical Reports Server (NTRS)

Pinson, Larry; Soosaar, Keto

1989-01-01

The problem is to develop analysis methods, modeling stategies, and simulation tools to predict with assurance the on-orbit performance and integrity of large complex space structures that cannot be verified on the ground. The problem must incorporate large reliable structural models, multi-body flexible dynamics, multi-tier controller interaction, environmental models including 1g and atmosphere, various on-board disturbances, and linkage to mission-level performance codes. All areas are in serious need of work, but the weakest link is multi-body flexible dynamics.

How much rainfall sustained a Green Sahara during the mid-Holocene?

NASA Astrophysics Data System (ADS)

Hopcroft, Peter; Valdes, Paul; Harper, Anna

2016-04-01

The present-day Sahara desert has periodically transformed to an area of lakes and vegetation during the Quaternary in response to orbitally-induced changes in the monsoon circulation. Coupled atmosphere-ocean general circulation model simulations of the mid-Holocene generally underestimate the required monsoon shift, casting doubt on the fidelity of these models. However, the climatic regime that characterised this period remains unclear. To address this, we applied an ensemble of dynamic vegetation model simulations using two different models: JULES (Joint UK Land Environment Simulator) a comprehensive land surface model, and LPJ (Lund-Potsdam-Jena model) a widely used dynamic vegetation model. The simulations are forced with a number of idealized climate scenarios, in which an observational climatology is progressively altered with imposed anomalies of precipitation and other related variables, including cloud cover and humidity. The applied anomalies are based on an ensemble of general circulation model simulations, and include seasonal variations but are spatially uniform across the region. When perturbing precipitation alone, a significant increase of at least 700mm/year is required to produce model simulations with non-negligible vegetation coverage in the Sahara region. Changes in related variables including cloud cover, surface radiation fluxes and humidity are found to be important in the models, as they modify the water balance and so affect plant growth. Including anomalies in all of these variables together reduces the precipitation change required for a Green Sahara compared to the case of increasing precipitation alone. We assess whether the precipitation changes implied by these vegetation model simulations are consistent with reconstructions for the mid-Holocene from pollen samples. Further, Earth System models predict precipitation increases that are significantly smaller than that inferred from these vegetation model simulations. Understanding this difference presents an ongoing challenge.

Modelling and Analysis on Biomechanical Dynamic Characteristics of Knee Flexion Movement under Squatting

PubMed Central

Wang, Jianping; Tao, Kun; Li, Huanyi; Wang, Chengtao

2014-01-01

The model of three-dimensional (3D) geometric knee was built, which included femoral-tibial, patellofemoral articulations and the bone and soft tissues. Dynamic finite element (FE) model of knee was developed to simulate both the kinematics and the internal stresses during knee flexion. The biomechanical experimental system of knee was built to simulate knee squatting using cadaver knees. The flexion motion and dynamic contact characteristics of knee were analyzed, and verified by comparing with the data from in vitro experiment. The results showed that the established dynamic FE models of knee are capable of predicting kinematics and the contact stresses during flexion, and could be an efficient tool for the analysis of total knee replacement (TKR) and knee prosthesis design. PMID:25013852

Communication: Methane dissociation on Ni(111) surface: Importance of azimuth and surface impact site

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

Shen, Xiangjian; State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023; Zhang, Zhaojun, E-mail: zhangzhj@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn

2016-03-14

Understanding the role of reactant ro-vibrational degrees of freedom (DOFs) in reaction dynamics of polyatomic molecular dissociation on metal surfaces is of great importance to explore the complex chemical reaction mechanism. Here, we present an expensive quantum dynamics study of the dissociative chemisorption of CH{sub 4} on a rigid Ni(111) surface by developing an accurate nine-dimensional quantum dynamical model including the DOF of azimuth. Based on a highly accurate fifteen-dimensional potential energy surface built from first principles, our simulations elucidate that the dissociation probability of CH{sub 4} has the strong dependence on azimuth and surface impact site. Some improvements aremore » suggested to obtain the accurate dissociation probability from quantum dynamics simulations.« less

Integration of Continuous-Time Dynamics in a Spiking Neural Network Simulator.

PubMed

Hahne, Jan; Dahmen, David; Schuecker, Jannis; Frommer, Andreas; Bolten, Matthias; Helias, Moritz; Diesmann, Markus

2017-01-01

Contemporary modeling approaches to the dynamics of neural networks include two important classes of models: biologically grounded spiking neuron models and functionally inspired rate-based units. We present a unified simulation framework that supports the combination of the two for multi-scale modeling, enables the quantitative validation of mean-field approaches by spiking network simulations, and provides an increase in reliability by usage of the same simulation code and the same network model specifications for both model classes. While most spiking simulations rely on the communication of discrete events, rate models require time-continuous interactions between neurons. Exploiting the conceptual similarity to the inclusion of gap junctions in spiking network simulations, we arrive at a reference implementation of instantaneous and delayed interactions between rate-based models in a spiking network simulator. The separation of rate dynamics from the general connection and communication infrastructure ensures flexibility of the framework. In addition to the standard implementation we present an iterative approach based on waveform-relaxation techniques to reduce communication and increase performance for large-scale simulations of rate-based models with instantaneous interactions. Finally we demonstrate the broad applicability of the framework by considering various examples from the literature, ranging from random networks to neural-field models. The study provides the prerequisite for interactions between rate-based and spiking models in a joint simulation.

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.

PubMed

Curuksu, Jeremy; Zacharias, Martin

2009-03-14

Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simulations performed at different temperatures (T-RexMD) can achieve improved conformational sampling. However, in the case of T-RexMD the computational demand grows rapidly with system size. A Hamiltonian RexMD method that specifically enhances coupled dihedral angle transitions has been developed. The method employs added biasing potentials as replica parameters that destabilize available dihedral substates and was applied to study coupled dihedral transitions in nucleic acid molecules. The biasing potentials can be either fixed at the beginning of the simulation or optimized during an equilibration phase. The method was extensively tested and compared to conventional MD simulations and T-RexMD simulations on an adenine dinucleotide system and on a DNA abasic site. The biasing potential RexMD method showed improved sampling of conformational substates compared to conventional MD simulations similar to T-RexMD simulations but at a fraction of the computational demand. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules.

Integration of Continuous-Time Dynamics in a Spiking Neural Network Simulator

PubMed Central

Hahne, Jan; Dahmen, David; Schuecker, Jannis; Frommer, Andreas; Bolten, Matthias; Helias, Moritz; Diesmann, Markus

2017-01-01

Contemporary modeling approaches to the dynamics of neural networks include two important classes of models: biologically grounded spiking neuron models and functionally inspired rate-based units. We present a unified simulation framework that supports the combination of the two for multi-scale modeling, enables the quantitative validation of mean-field approaches by spiking network simulations, and provides an increase in reliability by usage of the same simulation code and the same network model specifications for both model classes. While most spiking simulations rely on the communication of discrete events, rate models require time-continuous interactions between neurons. Exploiting the conceptual similarity to the inclusion of gap junctions in spiking network simulations, we arrive at a reference implementation of instantaneous and delayed interactions between rate-based models in a spiking network simulator. The separation of rate dynamics from the general connection and communication infrastructure ensures flexibility of the framework. In addition to the standard implementation we present an iterative approach based on waveform-relaxation techniques to reduce communication and increase performance for large-scale simulations of rate-based models with instantaneous interactions. Finally we demonstrate the broad applicability of the framework by considering various examples from the literature, ranging from random networks to neural-field models. The study provides the prerequisite for interactions between rate-based and spiking models in a joint simulation. PMID:28596730

Prediction of time-integrated activity coefficients in PRRT using simulated dynamic PET and a pharmacokinetic model.

PubMed

Hardiansyah, Deni; Attarwala, Ali Asgar; Kletting, Peter; Mottaghy, Felix M; Glatting, Gerhard

2017-10-01

To investigate the accuracy of predicted time-integrated activity coefficients (TIACs) in peptide-receptor radionuclide therapy (PRRT) using simulated dynamic PET data and a physiologically based pharmacokinetic (PBPK) model. PBPK parameters were estimated using biokinetic data of 15 patients after injection of (152±15)MBq of 111 In-DTPAOC (total peptide amount (5.78±0.25)nmol). True mathematical phantoms of patients (MPPs) were the PBPK model with the estimated parameters. Dynamic PET measurements were simulated as being done after bolus injection of 150MBq 68 Ga-DOTATATE using the true MPPs. Dynamic PET scans around 35min p.i. (P 1 ), 4h p.i. (P 2 ) and the combination of P 1 and P 2 (P 3 ) were simulated. Each measurement was simulated with four frames of 5min each and 2 bed positions. PBPK parameters were fitted to the PET data to derive the PET-predicted MPPs. Therapy was simulated assuming an infusion of 5.1GBq of 90 Y-DOTATATE over 30min in both true and PET-predicted MPPs. TIACs of simulated therapy were calculated, true MPPs (true TIACs) and predicted MPPs (predicted TIACs) followed by the calculation of variabilities v. For P 1 and P 2 the population variabilities of kidneys, liver and spleen were acceptable (v<10%). For the tumours and the remainders, the values were large (up to 25%). For P 3 , population variabilities for all organs including the remainder further improved, except that of the tumour (v>10%). Treatment planning of PRRT based on dynamic PET data seems possible for the kidneys, liver and spleen using a PBPK model and patient specific information. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Evaluation of subgrid-scale models in large-eddy simulations of turbulent flow in a centrifugal pump impeller

NASA Astrophysics Data System (ADS)

Yang, Zhengjun; Wang, Fujun; Zhou, Peijian

2012-09-01

The current research of large eddy simulation (LES) of turbulent flow in pumps mainly concentrates in applying conventional subgrid-scale (SGS) model to simulate turbulent flow, which aims at obtaining the flow field in pump. The selection of SGS model is usually not considered seriously, so the accuracy and efficiency of the simulation cannot be ensured. Three SGS models including Smagorinsky-Lilly model, dynamic Smagorinsky model and dynamic mixed model are comparably studied by using the commercial CFD code Fluent combined with its user define function. The simulations are performed for the turbulent flow in a centrifugal pump impeller. The simulation results indicate that the mean flows predicted by the three SGS models agree well with the experimental data obtained from the test that detailed measurements of the flow inside the rotating passages of a six-bladed shrouded centrifugal pump impeller performed using particle image velocimetry (PIV) and laser Doppler velocimetry (LDV). The comparable results show that dynamic mixed model gives the most accurate results for mean flow in the centrifugal pump impeller. The SGS stress of dynamic mixed model is decompose into the scale similar part and the eddy viscous part. The scale similar part of SGS stress plays a significant role in high curvature regions, such as the leading edge and training edge of pump blade. It is also found that the dynamic mixed model is more adaptive to compute turbulence in the pump impeller. The research results presented is useful to improve the computational accuracy and efficiency of LES for centrifugal pumps, and provide important reference for carrying out simulation in similar fluid machineries.

Hybrid Cascading Outage Analysis of Extreme Events with Optimized Corrective Actions

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

Vallem, Mallikarjuna R.; Vyakaranam, Bharat GNVSR; Holzer, Jesse T.

2017-10-19

Power system are vulnerable to extreme contingencies (like an outage of a major generating substation) that can cause significant generation and load loss and can lead to further cascading outages of other transmission facilities and generators in the system. Some cascading outages are seen within minutes following a major contingency, which may not be captured exclusively using the dynamic simulation of the power system. The utilities plan for contingencies either based on dynamic or steady state analysis separately which may not accurately capture the impact of one process on the other. We address this gap in cascading outage analysis bymore » developing Dynamic Contingency Analysis Tool (DCAT) that can analyze hybrid dynamic and steady state behavior of the power system, including protection system models in dynamic simulations, and simulating corrective actions in post-transient steady state conditions. One of the important implemented steady state processes is to mimic operator corrective actions to mitigate aggravated states caused by dynamic cascading. This paper presents an Optimal Power Flow (OPF) based formulation for selecting corrective actions that utility operators can take during major contingency and thus automate the hybrid dynamic-steady state cascading outage process. The improved DCAT framework with OPF based corrective actions is demonstrated on IEEE 300 bus test system.« less

Using sea surface temperatures to improve performance of single dynamical downscaling model in flood simulation under climate change

NASA Astrophysics Data System (ADS)

Chao, Y.; Cheng, C. T.; Hsiao, Y. H.; Hsu, C. T.; Yeh, K. C.; Liu, P. L.

2017-12-01

There are 5.3 typhoons hit Taiwan per year on average in last decade. Typhoon Morakot in 2009, the most severe typhoon, causes huge damage in Taiwan, including 677 casualties and roughly NT 110 billion (3.3 billion USD) in economic loss. Some researches documented that typhoon frequency will decrease but increase in intensity in western North Pacific region. It is usually preferred to use high resolution dynamical model to get better projection of extreme events; because coarse resolution models cannot simulate intense extreme events. Under that consideration, dynamical downscaling climate data was chosen to describe typhoon satisfactorily, this research used the simulation data from AGCM of Meteorological Research Institute (MRI-AGCM). Considering dynamical downscaling methods consume massive computing power, and typhoon number is very limited in a single model simulation, using dynamical downscaling data could cause uncertainty in disaster risk assessment. In order to improve the problem, this research used four sea surfaces temperatures (SSTs) to increase the climate change scenarios under RCP 8.5. In this way, MRI-AGCMs project 191 extreme typhoons in Taiwan (when typhoon center touches 300 km sea area of Taiwan) in late 21th century. SOBEK, a two dimensions flood simulation model, was used to assess the flood risk under four SSTs climate change scenarios in Tainan, Taiwan. The results show the uncertainty of future flood risk assessment is significantly decreased in Tainan, Taiwan in late 21th century. Four SSTs could efficiently improve the problems of limited typhoon numbers in single model simulation.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

A 45-ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the earth simulator: dynamics of tertiary and quaternary structures.

PubMed

Saito, Minoru; Okazaki, Isao

2007-04-30

Molecular dynamics (MD) simulations of human adult hemoglobin (HbA) were carried out for 45 ns in water with all degrees of freedom including bond stretching and without any artificial constraints. To perform such large-scale simulations, one of the authors (M.S.) accelerated his own software COSMOS90 on the Earth Simulator by vectorization and parallelization. The dynamical features of HbA were investigated by evaluating root-mean-square deviations from the initial X-ray structure (an oxy T-state hemoglobin with PDB code: 1GZX) and root-mean-square fluctuations around the average structure from the simulation trajectories. The four subunits (alpha(1), alpha(2), beta(1), and beta(2)) of HbA maintained structures close to their respective X-ray structures during the simulations even though no constraints were applied to HbA in the simulations. Dimers alpha(1)beta(1) and alpha(2)beta(2) also maintained structures close to their respective X-ray structures while they moved relative to each other like two stacks of dumbbells. The distance between the two dimers (alpha(1)beta(1) and alpha(2)beta(2)) increased by 2 A (7.4%) in the initial 15 ns and stably fluctuated at the distance with the standard deviation 0.2 A. The relative orientation of the two dimers fluctuated between the initial X-ray angle -100 degrees and about -105 degrees with intervals of a few tens of nanoseconds.

Studying Turbulence Using Numerical Simulation Databases. Part 6; Proceedings of the 1996 Summer Program

NASA Technical Reports Server (NTRS)

1996-01-01

Topics considered include: New approach to turbulence modeling; Second moment closure analysis of the backstep flow database; Prediction of the backflow and recovery regions in the backward facing step at various Reynolds numbers; Turbulent flame propagation in partially premixed flames; Ensemble averaged dynamic modeling. Also included a study of the turbulence structures of wall-bounded shear flows; Simulation and modeling of the elliptic streamline flow.

Simulations of Dynamical Friction Including Spatially-Varying Magnetic Fields

NASA Astrophysics Data System (ADS)

Bell, G. I.; Bruhwiler, D. L.; Litvinenko, V. N.; Busby, R.; Abell, D. T.; Messmer, P.; Veitzer, S.; Cary, J. R.

2006-03-01

A proposed luminosity upgrade to the Relativistic Heavy Ion Collider (RHIC) includes a novel electron cooling section, which would use ˜55 MeV electrons to cool fully-ionized 100 GeV/nucleon gold ions. We consider the dynamical friction force exerted on individual ions due to a relevant electron distribution. The electrons may be focussed by a strong solenoid field, with sensitive dependence on errors, or by a wiggler field. In the rest frame of the relativistic co-propagating electron and ion beams, where the friction force can be simulated for nonrelativistic motion and electrostatic fields, the Lorentz transform of these spatially-varying magnetic fields includes strong, rapidly-varying electric fields. Previous friction force simulations for unmagnetized electrons or error-free solenoids used a 4th-order Hermite algorithm, which is not well-suited for the inclusion of strong, rapidly-varying external fields. We present here a new algorithm for friction force simulations, using an exact two-body collision model to accurately resolve close interactions between electron/ion pairs. This field-free binary-collision model is combined with a modified Boris push, using an operator-splitting approach, to include the effects of external fields. The algorithm has been implemented in the VORPAL code and successfully benchmarked.

Chemical equilibria model of strontium-90 adsorption and transport in soil in response to dynamic alkaline conditions.

PubMed

Spalding, B P; Spalding, I R

2001-01-15

Strontium-90 is a major hazardous contaminant of radioactive wastewater and its processing sludges at many Department of Energy (DOE) facilities. In the past, such contaminated wastewater and sludge have been disposed in soil seepage pits, lagoons, or cribs often under highly perturbed alkaline conditions (pH > 12) where 90Sr solubility is low and its adsorption to surrounding soil is high. As natural weathering returns these soils to near-neutral or slightly acidic conditions, the adsorbed and precipitated calcium and magnesium phases, in which 90Sr is carried, change significantly in both nature and amounts. No comprehensive computational method has been formulated previously to quantitatively simulate the dynamics of 90Sr in the soil-groundwater environment under such dynamic and wide-ranging conditions. A computational code, the Hydrologic Utility Model for Demonstrating Integrated Nuclear Geochemical Environmental Responses (HUMDINGER), was composed to describe the changing equilibria of 90Sr in soil based on its causative chemical reactions including soil buffering, pH-dependent cation-exchange capacity, cation selectivity, and the precipitation/dissolution of calcium carbonate, calcium hydroxide, and magnesium hydroxide in response to leaching groundwater characteristics including pH, acid-neutralizing capacity, dissolved cations, and inorganic carbonate species. The code includes a simulation of one-dimensional transport of 90Sr through a soil column as a series of soil mixing cells where the equilibrium soluble output from one cell is applied to the next cell. Unamended soil leaching and highly alkaline soil treatments, including potassium hydroxide, sodium silicate, and sodium aluminate, were simulated and compared with experimental findings using large (10 kg) soil columns that were leached with 90Sr-contaminated groundwater after treatment. HUMDINGER's simulations were in good agreement with dynamic experimental observations of soil exchange capacity, exchangeable cations, total 90Sr, and pH values of layers within the soil columns and of column effluents.

DayCent model simulations for estimating soil carbon dynamics and greenhouse gas fluxes from agricultural production systems

USDA-ARS?s Scientific Manuscript database

DayCent is a biogeochemical model of intermediate complexity used to simulate carbon, nutrient, and greenhouse gas fluxes for crop, grassland, forest, and savanna ecosystems. Model inputs include: soil texture and hydraulic properties, current and historical land use, vegetation cover, daily maximum...

Lectures and Simulation Laboratories to Improve Learners' Conceptual Understanding

ERIC Educational Resources Information Center

Brophy, Sean P.; Magana, Alejandra J.; Strachan, Alejandro

2013-01-01

We studied the use of online molecular dynamics simulations (MD) to enhance student abilities to understand the atomic processes governing plastic deformation in materials. The target population included a second-year undergraduate engineering course in the School of Materials Engineering at Purdue University. The objectives of the study were to…

GRODY - GAMMA RAY OBSERVATORY DYNAMICS SIMULATOR IN ADA

NASA Technical Reports Server (NTRS)

Stark, M.

1994-01-01

Analysts use a dynamics simulator to test the attitude control system algorithms used by a satellite. The simulator must simulate the hardware, dynamics, and environment of the particular spacecraft and provide user services which enable the analyst to conduct experiments. Researchers at Goddard's Flight Dynamics Division developed GRODY alongside GROSS (GSC-13147), a FORTRAN simulator which performs the same functions, in a case study to assess the feasibility and effectiveness of the Ada programming language for flight dynamics software development. They used popular object-oriented design techniques to link the simulator's design with its function. GRODY is designed for analysts familiar with spacecraft attitude analysis. The program supports maneuver planning as well as analytical testing and evaluation of the attitude determination and control system used on board the Gamma Ray Observatory (GRO) satellite. GRODY simulates the GRO on-board computer and Control Processor Electronics. The analyst/user sets up and controls the simulation. GRODY allows the analyst to check and update parameter values and ground commands, obtain simulation status displays, interrupt the simulation, analyze previous runs, and obtain printed output of simulation runs. The video terminal screen display allows visibility of command sequences, full-screen display and modification of parameters using input fields, and verification of all input data. Data input available for modification includes alignment and performance parameters for all attitude hardware, simulation control parameters which determine simulation scheduling and simulator output, initial conditions, and on-board computer commands. GRODY generates eight types of output: simulation results data set, analysis report, parameter report, simulation report, status display, plots, diagnostic output (which helps the user trace any problems that have occurred during a simulation), and a permanent log of all runs and errors. The analyst can send results output in graphical or tabular form to a terminal, disk, or hardcopy device, and can choose to have any or all items plotted against time or against each other. Goddard researchers developed GRODY on a VAX 8600 running VMS version 4.0. For near real time performance, GRODY requires a VAX at least as powerful as a model 8600 running VMS 4.0 or a later version. To use GRODY, the VAX needs an Ada Compilation System (ACS), Code Management System (CMS), and 1200K memory. GRODY is written in Ada and FORTRAN.

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator: Preprint

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

The effects of mixed layer dynamics on ice growth in the central Arctic

NASA Astrophysics Data System (ADS)

Kitchen, Bruce R.

1992-09-01

The thermodynamic model of Thorndike (1992) is coupled to a one dimensional, two layer ocean entrainment model to study the effect of mixed layer dynamics on ice growth and the variation in the ocean heat flux into the ice due to mixed layer entrainment. Model simulations show the existence of a negative feedback between the ice growth and the mixed layer entrainment, and that the underlying ocean salinity has a greater effect on the ocean beat flux than does variations in the underlying ocean temperature. Model simulations for a variety of surface forcings and initial conditions demonstrate the need to include mixed layer dynamics for realistic ice prediction in the arctic.

Influence of changes in initial conditions for the simulation of dynamic systems

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

Kotyrba, Martin

2015-03-10

Chaos theory is a field of study in mathematics, with applications in several disciplines including meteorology, sociology, physics, engineering, economics, biology, and philosophy. Chaos theory studies the behavior of dynamical systems that are highly sensitive to initial conditions—a paradigm popularly referred to as the butterfly effect. Small differences in initial conditions field widely diverging outcomes for such dynamical systems, rendering long-term prediction impossible in general. This happens even though these systems are deterministic, meaning that their future behavior is fully determined by their initial conditions, with no random elements involved. In this paperinfluence of changes in initial conditions will bemore » presented for the simulation of Lorenz system.« less

Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

PubMed

Emperador, Agustí; Orozco, Modesto

2017-03-14

We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

Modeling Quantum Dynamics in Multidimensional Systems

NASA Astrophysics Data System (ADS)

Liss, Kyle; Weinacht, Thomas; Pearson, Brett

2017-04-01

Coupling between different degrees-of-freedom is an inherent aspect of dynamics in multidimensional quantum systems. As experiments and theory begin to tackle larger molecular structures and environments, models that account for vibrational and/or electronic couplings are essential for interpretation. Relevant processes include intramolecular vibrational relaxation, conical intersections, and system-bath coupling. We describe a set of simulations designed to model coupling processes in multidimensional molecular systems, focusing on models that provide insight and allow visualization of the dynamics. Undergraduates carried out much of the work as part of a senior research project. In addition to the pedagogical value, the simulations allow for comparison between both explicit and implicit treatments of a system's many degrees-of-freedom.

ReaxFF based molecular dynamics simulations of ignition front propagation in hydrocarbon/oxygen mixtures under high temperature and pressure conditions.

PubMed

Ashraf, Chowdhury; Jain, Abhishek; Xuan, Yuan; van Duin, Adri C T

2017-02-15

In this paper, we present the first atomistic-scale based method for calculating ignition front propagation speed and hypothesize that this quantity is related to laminar flame speed. This method is based on atomistic-level molecular dynamics (MD) simulations with the ReaxFF reactive force field. Results reported in this study are for supercritical (P = 55 MPa and T u = 1800 K) combustion of hydrocarbons as elevated pressure and temperature are required to accelerate the dynamics for reactive MD simulations. These simulations are performed for different types of hydrocarbons, including alkyne, alkane, and aromatic, and are able to successfully reproduce the experimental trend of reactivity of these hydrocarbons. Moreover, our results indicate that the ignition front propagation speed under supercritical conditions has a strong dependence on equivalence ratio, similar to experimentally measured flame speeds at lower temperatures and pressures which supports our hypothesis that ignition front speed is a related quantity to laminar flame speed. In addition, comparisons between results obtained from ReaxFF simulation and continuum simulations performed under similar conditions show good qualitative, and reasonable quantitative agreement. This demonstrates that ReaxFF based MD-simulations are a promising tool to study flame speed/ignition front speed in supercritical hydrocarbon combustion.

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

PubMed Central

Somogyi, Endre; Glazier, James A.

2017-01-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment. PMID:29303160

Chaos in plasma simulation and experiment

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

Watts, C.; Newman, D.E.; Sprott, J.C.

1993-09-01

We investigate the possibility that chaos and simple determinism are governing the dynamics of reversed field pinch (RFP) plasmas using data from both numerical simulations and experiment. A large repertoire of nonlinear analysis techniques is used to identify low dimensional chaos. These tools include phase portraits and Poincard sections, correlation dimension, the spectrum of Lyapunov exponents and short term predictability. In addition, nonlinear noise reduction techniques are applied to the experimental data in an attempt to extract any underlying deterministic dynamics. Two model systems are used to simulate the plasma dynamics. These are -the DEBS code, which models global RFPmore » dynamics, and the dissipative trapped electron mode (DTEM) model, which models drift wave turbulence. Data from both simulations show strong indications of low,dimensional chaos and simple determinism. Experimental data were obtained from the Madison Symmetric Torus RFP and consist of a wide array of both global and local diagnostic signals. None of the signals shows any indication of low dimensional chaos or other simple determinism. Moreover, most of the analysis tools indicate the experimental system is very high dimensional with properties similar to noise. Nonlinear noise reduction is unsuccessful at extracting an underlying deterministic system.« less

Reconfigurable Control with Neural Network Augmentation for a Modified F-15 Aircraft

NASA Technical Reports Server (NTRS)

Burken, John J.; Williams-Hayes, Peggy; Kaneshige, John T.; Stachowiak, Susan J.

2006-01-01

Description of the performance of a simplified dynamic inversion controller with neural network augmentation follows. Simulation studies focus on the results with and without neural network adaptation through the use of an F-15 aircraft simulator that has been modified to include canards. Simulated control law performance with a surface failure, in addition to an aerodynamic failure, is presented. The aircraft, with adaptation, attempts to minimize the inertial cross-coupling effect of the failure (a control derivative anomaly associated with a jammed control surface). The dynamic inversion controller calculates necessary surface commands to achieve desired rates. The dynamic inversion controller uses approximate short period and roll axis dynamics. The yaw axis controller is a sideslip rate command system. Methods are described to reduce the cross-coupling effect and maintain adequate tracking errors for control surface failures. The aerodynamic failure destabilizes the pitching moment due to angle of attack. The results show that control of the aircraft with the neural networks is easier (more damped) than without the neural networks. Simulation results show neural network augmentation of the controller improves performance with aerodynamic and control surface failures in terms of tracking error and cross-coupling reduction.

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

PubMed

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

Adaptive Control Using Neural Network Augmentation for a Modified F-15 Aircraft

NASA Technical Reports Server (NTRS)

Burken, John J.; Williams-Hayes, Peggy; Karneshige, J. T.; Stachowiak, Susan J.

2006-01-01

Description of the performance of a simplified dynamic inversion controller with neural network augmentation follows. Simulation studies focus on the results with and without neural network adaptation through the use of an F-15 aircraft simulator that has been modified to include canards. Simulated control law performance with a surface failure, in addition to an aerodynamic failure, is presented. The aircraft, with adaptation, attempts to minimize the inertial cross-coupling effect of the failure (a control derivative anomaly associated with a jammed control surface). The dynamic inversion controller calculates necessary surface commands to achieve desired rates. The dynamic inversion controller uses approximate short period and roll axis dynamics. The yaw axis controller is a sideslip rate command system. Methods are described to reduce the cross-coupling effect and maintain adequate tracking errors for control surface failures. The aerodynamic failure destabilizes the pitching moment due to angle of attack. The results show that control of the aircraft with the neural networks is easier (more damped) than without the neural networks. Simulation results show neural network augmentation of the controller improves performance with aerodynamic and control surface failures in terms of tracking error and cross-coupling reduction.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Wind Energy Modeling and Simulation | Wind | NREL

Science.gov Websites

Wind Energy Modeling and Simulation Wind Turbine Modeling and Simulation Wind turbines are unique wind turbines. It enables the analysis of a range of wind turbine configurations, including: Two- or (SOWFA) employs computational fluid dynamics to allow users to investigate wind turbine and wind power

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

NASA Technical Reports Server (NTRS)

1977-01-01

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

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control

PubMed Central

Zhang, Xingwu; Chen, Xuefeng; You, Shangqin; He, Zhengjia; Li, Bing

2012-01-01

In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC) is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results. PMID:22666072

Simulation and experimental investigation of structural dynamic frequency characteristics control.

PubMed

Zhang, Xingwu; Chen, Xuefeng; You, Shangqin; He, Zhengjia; Li, Bing

2012-01-01

In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC) is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results.

An Assessment of Molecular Dynamic Force Fields for Silica for Use in Simulating Laser Damage Mitigation

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

Soules, T F; Gilmer, G H; Matthews, M J

2010-10-21

We compare force fields (FF's) that have been used in molecular dynamic (MD) simulations of silica in order to assess their applicability for use in simulating IR-laser damage mitigation. Although pairwise FF?s obtained by fitting quantum mechanical calculations such as the BKS and CHIK potentials have been shown to reproduce many of the properties of silica including the stability of silica polymorphs and the densification of the liquid, we show that melting temperatures and fictive temperatures are much too high. Softer empirical force fields give liquid and glass properties at experimental temperatures but may not predict all properties important tomore » laser mitigation experiments.« less

Effects of two-temperature model on cascade evolution in Ni and NiFe

DOE PAGES

Samolyuk, German D.; Xue, Haizhou; Bei, Hongbin; ...

2016-07-05

We perform molecular dynamics simulations of Ni ion cascades in Ni and equiatomic NiFe under the following conditions: (a) classical molecular dynamics (MD) simulations without consideration of electronic energy loss, (b) classical MD simulations with the electronic stopping included, and (c) using the coupled two-temperature MD (2T-MD) model that incorporates both the electronic stopping and the electron-phonon interactions. Our results indicate that the electronic effects are more profound in the higher-energy cascades, and that the 2T-MD model results in a smaller amount of surviving damage and smaller defect clusters, while less damage is produced in NiFe than in Ni.

Dissipative-particle-dynamics model of biofilm growth

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

Xu, Zhijie; Meakin, Paul; Tartakovsky, Alexandre M.

2011-06-13

A dissipative particle dynamics (DPD) model for the quantitative simulation of biofilm growth controlled by substrate (nutrient) consumption, advective and diffusive substrate transport, and hydrodynamic interactions with fluid flow (including fragmentation and reattachment) is described. The model was used to simulate biomass growth, decay, and spreading. It predicts how the biofilm morphology depends on flow conditions, biofilm growth kinetics, the rheomechanical properties of the biofilm and adhesion to solid surfaces. The morphology of the model biofilm depends strongly on its rigidity and the magnitude of the body force that drives the fluid over the biofilm.

Dynamic modeling of wheeled planetary rovers: A model based on the pseudo-coordiates approach

NASA Astrophysics Data System (ADS)

Chen, Feng; Genta, Giancarlo

2012-12-01

The paper deals with the dynamic modeling of wheeled planetary rovers operating on rough terrain. The dedicated model here presented, although kept as simple as possible, includes the effect of nonlinearities and models the suspensions in a realistic, albeit simplified, way. It can be interfaced with a model of the control system so that different control strategies can be studied in detail and, in case of teleoperated rovers, it can be used as a simulator for training the operators. Different implementations, with different degrees of complexity, are presented and compared with each other so that the user can simulate the dynamics of the rover making a tradeoff between simulation accuracy and computer time. The model allows to study the effects of the terrain characteristics, of the ground irregularities and the operating speed on the behavior of the rover. Some examples dealing with rovers with different configurations conclude the paper.

Modeling structural change in spatial system dynamics: A Daisyworld example.

PubMed

Neuwirth, C; Peck, A; Simonović, S P

2015-03-01

System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed.

A Review of Enhanced Sampling Approaches for Accelerated Molecular Dynamics

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush; van de Walle, Axel

Molecular dynamics (MD) simulations have become a tool of immense use and popularity for simulating a variety of systems. With the advent of massively parallel computer resources, one now routinely sees applications of MD to systems as large as hundreds of thousands to even several million atoms, which is almost the size of most nanomaterials. However, it is not yet possible to reach laboratory timescales of milliseconds and beyond with MD simulations. Due to the essentially sequential nature of time, parallel computers have been of limited use in solving this so-called timescale problem. Instead, over the years a large range of statistical mechanics based enhanced sampling approaches have been proposed for accelerating molecular dynamics, and accessing timescales that are well beyond the reach of the fastest computers. In this review we provide an overview of these approaches, including the underlying theory, typical applications, and publicly available software resources to implement them.

A simple electric circuit model for proton exchange membrane fuel cells

NASA Astrophysics Data System (ADS)

Lazarou, Stavros; Pyrgioti, Eleftheria; Alexandridis, Antonio T.

A simple and novel dynamic circuit model for a proton exchange membrane (PEM) fuel cell suitable for the analysis and design of power systems is presented. The model takes into account phenomena like activation polarization, ohmic polarization, and mass transport effect present in a PEM fuel cell. The proposed circuit model includes three resistors to approach adequately these phenomena; however, since for the PEM dynamic performance connection or disconnection of an additional load is of crucial importance, the proposed model uses two saturable inductors accompanied by an ideal transformer to simulate the double layer charging effect during load step changes. To evaluate the effectiveness of the proposed model its dynamic performance under load step changes is simulated. Experimental results coming from a commercial PEM fuel cell module that uses hydrogen from a pressurized cylinder at the anode and atmospheric oxygen at the cathode, clearly verify the simulation results.

High frequency dynamic engine simulation. [TF-30 engine

NASA Technical Reports Server (NTRS)

Schuerman, J. A.; Fischer, K. E.; Mclaughlin, P. W.

1977-01-01

A digital computer simulation of a mixed flow, twin spool turbofan engine was assembled to evaluate and improve the dynamic characteristics of the engine simulation to disturbance frequencies of at least 100 Hz. One dimensional forms of the dynamic mass, momentum and energy equations were used to model the engine. A TF30 engine was simulated so that dynamic characteristics could be evaluated against results obtained from testing of the TF30 engine at the NASA Lewis Research Center. Dynamic characteristics of the engine simulation were improved by modifying the compression system model. Modifications to the compression system model were established by investigating the influence of size and number of finite dynamic elements. Based on the results of this program, high frequency engine simulations using finite dynamic elements can be assembled so that the engine dynamic configuration is optimum with respect to dynamic characteristics and computer execution time. Resizing of the compression systems finite elements improved the dynamic characteristics of the engine simulation but showed that additional refinements are required to obtain close agreement simulation and actual engine dynamic characteristics.

Numerical simulations of earthquakes and the dynamics of fault systems using the Finite Element method.

NASA Astrophysics Data System (ADS)

Kettle, L. M.; Mora, P.; Weatherley, D.; Gross, L.; Xing, H.

2006-12-01

Simulations using the Finite Element method are widely used in many engineering applications and for the solution of partial differential equations (PDEs). Computational models based on the solution of PDEs play a key role in earth systems simulations. We present numerical modelling of crustal fault systems where the dynamic elastic wave equation is solved using the Finite Element method. This is achieved using a high level computational modelling language, escript, available as open source software from ACcESS (Australian Computational Earth Systems Simulator), the University of Queensland. Escript is an advanced geophysical simulation software package developed at ACcESS which includes parallel equation solvers, data visualisation and data analysis software. The escript library was implemented to develop a flexible Finite Element model which reliably simulates the mechanism of faulting and the physics of earthquakes. Both 2D and 3D elastodynamic models are being developed to study the dynamics of crustal fault systems. Our final goal is to build a flexible model which can be applied to any fault system with user-defined geometry and input parameters. To study the physics of earthquake processes, two different time scales must be modelled, firstly the quasi-static loading phase which gradually increases stress in the system (~100years), and secondly the dynamic rupture process which rapidly redistributes stress in the system (~100secs). We will discuss the solution of the time-dependent elastic wave equation for an arbitrary fault system using escript. This involves prescribing the correct initial stress distribution in the system to simulate the quasi-static loading of faults to failure; determining a suitable frictional constitutive law which accurately reproduces the dynamics of the stick/slip instability at the faults; and using a robust time integration scheme. These dynamic models generate data and information that can be used for earthquake forecasting.

Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.

PubMed

Xiao, Li; Luo, Ray

2017-12-07

We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.

Six-degree-of-freedom aircraft simulation with mixed-data structure using the applied dynamics simulation language, ADSIM

NASA Technical Reports Server (NTRS)

Savaglio, Clare

1989-01-01

A realistic simulation of an aircraft in the flight using the AD 100 digital computer is presented. The implementation of three model features is specifically discussed: (1) a large aerodynamic data base (130,00 function values) which is evaluated using function interpolation to obtain the aerodynamic coefficients; (2) an option to trim the aircraft in longitudinal flight; and (3) a flight control system which includes a digital controller. Since the model includes a digital controller the simulation implements not only continuous time equations but also discrete time equations, thus the model has a mixed-data structure.

Atomic quantum simulation of the lattice gauge-Higgs model: Higgs couplings and emergence of exact local gauge symmetry.

PubMed

Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

2013-09-13

Recently, the possibility of quantum simulation of dynamical gauge fields was pointed out by using a system of cold atoms trapped on each link in an optical lattice. However, to implement exact local gauge invariance, fine-tuning the interaction parameters among atoms is necessary. In the present Letter, we study the effect of violation of the U(1) local gauge invariance by relaxing the fine-tuning of the parameters and showing that a wide variety of cold atoms is still a faithful quantum simulator for a U(1) gauge-Higgs model containing a Higgs field sitting on sites. The clarification of the dynamics of this gauge-Higgs model sheds some light upon various unsolved problems, including the inflation process of the early Universe. We study the phase structure of this model by Monte Carlo simulation and also discuss the atomic characteristics of the Higgs phase in each simulator.

Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.

PubMed

Rajendiran, Nivedita; Durrant, Jacob D

2018-05-05

Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting-edge rendering techniques. We expect Pyrite-generated images to appeal to students and non-specialists alike. A copy of the plugin is available at http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Turbulence simulation mechanization for Space Shuttle Orbiter dynamics and control studies

NASA Technical Reports Server (NTRS)

Tatom, F. B.; King, R. L.

1977-01-01

The current version of the NASA turbulent simulation model in the form of a digital computer program, TBMOD, is described. The logic of the program is discussed and all inputs and outputs are defined. An alternate method of shear simulation suitable for incorporation into the model is presented. The simulation is based on a von Karman spectrum and the assumption of isotropy. The resulting spectral density functions for the shear model are included.

Solar Sail Spaceflight Simulation

NASA Technical Reports Server (NTRS)

Lisano, Michael; Evans, James; Ellis, Jordan; Schimmels, John; Roberts, Timothy; Rios-Reyes, Leonel; Scheeres, Daniel; Bladt, Jeff; Lawrence, Dale; Piggott, Scott

2007-01-01

The Solar Sail Spaceflight Simulation Software (S5) toolkit provides solar-sail designers with an integrated environment for designing optimal solar-sail trajectories, and then studying the attitude dynamics/control, navigation, and trajectory control/correction of sails during realistic mission simulations. Unique features include a high-fidelity solar radiation pressure model suitable for arbitrarily-shaped solar sails, a solar-sail trajectory optimizer, capability to develop solar-sail navigation filter simulations, solar-sail attitude control models, and solar-sail high-fidelity force models.

Passive-dynamic ankle-foot orthosis replicates soleus but not gastrocnemius muscle function during stance in gait: Insights for orthosis prescription.

PubMed

Arch, Elisa S; Stanhope, Steven J; Higginson, Jill S

2016-10-01

Passive-dynamic ankle-foot orthosis characteristics, including bending stiffness, should be customized for individuals. However, while conventions for customizing passive-dynamic ankle-foot orthosis characteristics are often described and implemented in clinical practice, there is little evidence to explain their biomechanical rationale. To develop and combine a model of a customized passive-dynamic ankle-foot orthosis with a healthy musculoskeletal model and use simulation tools to explore the influence of passive-dynamic ankle-foot orthosis bending stiffness on plantar flexor function during gait. Dual case study. The customized passive-dynamic ankle-foot orthosis characteristics were integrated into a healthy musculoskeletal model available in OpenSim. Quasi-static forward dynamic simulations tracked experimental gait data under several passive-dynamic ankle-foot orthosis conditions. Predicted muscle activations were calculated through a computed muscle control optimization scheme. Simulations predicted that the passive-dynamic ankle-foot orthoses substituted for soleus but not gastrocnemius function. Induced acceleration analyses revealed the passive-dynamic ankle-foot orthosis acts like a uniarticular plantar flexor by inducing knee extension accelerations, which are counterproductive to natural knee kinematics in early midstance. These passive-dynamic ankle-foot orthoses can provide plantar flexion moments during mid and late stance to supplement insufficient plantar flexor strength. However, the passive-dynamic ankle-foot orthoses negatively influenced knee kinematics in early midstance. Identifying the role of passive-dynamic ankle-foot orthosis stiffness during gait provides biomechanical rationale for how to customize passive-dynamic ankle-foot orthoses for patients. Furthermore, these findings can be used in the future as the basis for developing objective prescription models to help drive the customization of passive-dynamic ankle-foot orthosis characteristics. © The International Society for Prosthetics and Orthotics 2015.

Variable-Speed Simulation of a Dual-Clutch Gearbox Tiltrotor Driveline

NASA Technical Reports Server (NTRS)

DeSmidt, Hans; Wang, Kon-Well; Smith, Edward C.; Lewicki, David G.

2012-01-01

This investigation explores the variable-speed operation and shift response of a prototypical two-speed dual-clutch transmission tiltrotor driveline in forward flight. Here, a Comprehensive Variable-Speed Rotorcraft Propulsion System Modeling (CVSRPM) tool developed under a NASA funded NRA program is utilized to simulate the drive system dynamics. In this study, a sequential shifting control strategy is analyzed under a steady forward cruise condition. This investigation attempts to build upon previous variable-speed rotorcraft propulsion studies by 1) including a fully nonlinear transient gas-turbine engine model, 2) including clutch stick-slip friction effects, 3) including shaft flexibility, 4) incorporating a basic flight dynamics model to account for interactions with the flight control system. Through exploring the interactions between the various subsystems, this analysis provides important insights into the continuing development of variable-speed rotorcraft propulsion systems.

Simulated GOLD Observations of Atmospheric Waves

NASA Astrophysics Data System (ADS)

Correira, J.; Evans, J. S.; Lumpe, J. D.; Rusch, D. W.; Chandran, A.; Eastes, R.; Codrescu, M.

2016-12-01

The Global-scale Observations of the Limb and Disk (GOLD) mission will measure structures in the Earth's airglow layer due to dynamical forcing by vertically and horizontally propagating waves. These measurements focus on global-scale structures, including compositional and temperature responses resulting from dynamical forcing. Daytime observations of far-UV emissions by GOLD will be used to generate two-dimensional maps of the ratio of atomic oxygen and molecular nitrogen column densities (ΣO/N2 ) as well as neutral temperature that provide signatures of large-scale spatial structure. In this presentation, we use simulations to demonstrate GOLD's capability to deduce periodicities and spatial dimensions of large-scale waves from the spatial and temporal evolution observed in composition and temperature maps. Our simulations include sophisticated forward modeling of the upper atmospheric airglow that properly accounts for anisotropy in neutral and ion composition, temperature, and solar illumination. Neutral densities and temperatures used in the simulations are obtained from global circulation and climatology models that have been perturbed by propagating waves with a range of amplitudes, periods, and sources of excitation. Modeling of airglow emission and predictions of ΣO/N2 and neutral temperatures are performed with the Atmospheric Ultraviolet Radiance Integrated Code (AURIC) and associated derived product algorithms. Predicted structure in ΣO/N2 and neutral temperature due to dynamical forcing by propagating waves is compared to existing observations. Realistic GOLD Level 2 data products are generated from simulated airglow emission using algorithm code that will be implemented operationally at the GOLD Science Data Center.

Concurrent musculoskeletal dynamics and finite element analysis predicts altered gait patterns to reduce foot tissue loading.

PubMed

Halloran, Jason P; Ackermann, Marko; Erdemir, Ahmet; van den Bogert, Antonie J

2010-10-19

Current computational methods for simulating locomotion have primarily used muscle-driven multibody dynamics, in which neuromuscular control is optimized. Such simulations generally represent joints and soft tissue as simple kinematic or elastic elements for computational efficiency. These assumptions limit application in studies such as ligament injury or osteoarthritis, where local tissue loading must be predicted. Conversely, tissue can be simulated using the finite element method with assumed or measured boundary conditions, but this does not represent the effects of whole body dynamics and neuromuscular control. Coupling the two domains would overcome these limitations and allow prediction of movement strategies guided by tissue stresses. Here we demonstrate this concept in a gait simulation where a musculoskeletal model is coupled to a finite element representation of the foot. Predictive simulations incorporated peak plantar tissue deformation into the objective of the movement optimization, as well as terms to track normative gait data and minimize fatigue. Two optimizations were performed, first without the strain minimization term and second with the term. Convergence to realistic gait patterns was achieved with the second optimization realizing a 44% reduction in peak tissue strain energy density. The study demonstrated that it is possible to alter computationally predicted neuromuscular control to minimize tissue strain while including desired kinematic and muscular behavior. Future work should include experimental validation before application of the methodology to patient care. Copyright © 2010 Elsevier Ltd. All rights reserved.

Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations.

PubMed

Simms, Andrew M; Toofanny, Rudesh D; Kehl, Catherine; Benson, Noah C; Daggett, Valerie

2008-06-01

Dynameomics is a project to investigate and catalog the native-state dynamics and thermal unfolding pathways of representatives of all protein folds using solvated molecular dynamics simulations, as described in the preceding paper. Here we introduce the design of the molecular dynamics data warehouse, a scalable, reliable repository that houses simulation data that vastly simplifies management and access. In the succeeding paper, we describe the development of a complementary multidimensional database. A single protein unfolding or native-state simulation can take weeks to months to complete, and produces gigabytes of coordinate and analysis data. Mining information from over 3000 completed simulations is complicated and time-consuming. Even the simplest queries involve writing intricate programs that must be built from low-level file system access primitives and include significant logic to correctly locate and parse data of interest. As a result, programs to answer questions that require data from hundreds of simulations are very difficult to write. Thus, organization and access to simulation data have been major obstacles to the discovery of new knowledge in the Dynameomics project. This repository is used internally and is the foundation of the Dynameomics portal site http://www.dynameomics.org. By organizing simulation data into a scalable, manageable and accessible form, we can begin to address substantial questions that move us closer to solving biomedical and bioengineering problems.

Simulation verification techniques study. Subsystem simulation validation techniques

NASA Technical Reports Server (NTRS)

Duncan, L. M.; Reddell, J. P.; Schoonmaker, P. B.

1974-01-01

Techniques for validation of software modules which simulate spacecraft onboard systems are discussed. An overview of the simulation software hierarchy for a shuttle mission simulator is provided. A set of guidelines for the identification of subsystem/module performance parameters and critical performance parameters are presented. Various sources of reference data to serve as standards of performance for simulation validation are identified. Environment, crew station, vehicle configuration, and vehicle dynamics simulation software are briefly discussed from the point of view of their interfaces with subsystem simulation modules. A detailed presentation of results in the area of vehicle subsystems simulation modules is included. A list of references, conclusions and recommendations are also given.

Exploration of the Energy Landscape of Acetylcholinesterase by Molecular Dynamics Simulation.

NASA Astrophysics Data System (ADS)

McCammon, J. Andrew

2002-03-01

Proteins have rough energy landscapes. Often more states than just the ground state are occupied and have biological functions. It is essential to study these conformational substates and the dynamical transitions among them. Acetylcholinesterase (AChE) is an important enzyme that has biological functions including the termination of synaptic transmission signals. X-ray structures show that it has an active site that is accessible only via a long and narrow channel from its surface. Therefore the fact that acetylcholine and larger ligands can reach the active site is believed to reflect the protein's structural fluctuation. We carried out long molecular dynamics simulations to investigate the dynamics of AChE and its relation to biological function, and compared our results with experiments. The results reveal several "doors" that open intermittantly between the active site and the surface. Instead of having simple exponential decay correlation functions, the time series of these channels reveal complex, fractal gating between conformations. We also compared the AChE dynamics data with those from an AchE-fasciculin complex. (Fasciculin is a small protein that is a natural inhibitor of AChE.) The results show remarkable effects of the protein-protein interaction, including allosteric and dynamical inhibition by fasciculin besides direct steric blocking. More information and images can be found at http://mccammon.ucsd.edu

Impact of climate variability on tropospheric ozone.

PubMed

Grewe, Volker

2007-03-01

A simulation with the climate-chemistry model (CCM) E39/C is presented, which covers both the troposphere and stratosphere dynamics and chemistry during the period 1960 to 1999. Although the CCM, by its nature, is not exactly representing observed day-by-day meteorology, there is an overall model's tendency to correctly reproduce the variability pattern due to an inclusion of realistic external forcings, like observed sea surface temperatures (e.g. El Niño), major volcanic eruption, solar cycle, concentrations of greenhouse gases, and Quasi-Biennial Oscillation. Additionally, climate-chemistry interactions are included, like the impact of ozone, methane, and other species on radiation and dynamics, and the impact of dynamics on emissions (lightning). However, a number of important feedbacks are not yet included (e.g. feedbacks related to biogenic emissions and emissions due to biomass burning). The results show a good representation of the evolution of the stratospheric ozone layer, including the ozone hole, which plays an important role for the simulation of natural variability of tropospheric ozone. Anthropogenic NO(x) emissions are included with a step-wise linear trend for each sector, but no interannual variability is included. The application of a number of diagnostics (e.g. marked ozone tracers) allows the separation of the impact of various processes/emissions on tropospheric ozone and shows that the simulated Northern Hemisphere tropospheric ozone budget is not only dominated by nitrogen oxide emissions and other ozone pre-cursors, but also by changes of the stratospheric ozone budget and its flux into the troposphere, which tends to reduce the simulated positive trend in tropospheric ozone due to emissions from industry and traffic during the late 80s and early 90s. For tropical regions the variability in ozone is dominated by variability in lightning (related to ENSO) and stratosphere-troposphere exchange (related to Northern Hemisphere Stratospheric dynamics and solar activity). Since tropospheric background chemistry is regarded only, the results are quantitatively limited with respect to derived trends. However, the main results are regarded to be robust. Although the horizontal resolution is rather coarse in comparison to regional models, such kind of simulations provide useful and necessary information on the impact of large-scale processes and inter-annual/decadal variations on regional air quality.

Coupling of Large Eddy Simulations with Meteorological Models to simulate Methane Leaks from Natural Gas Storage Facilities

NASA Astrophysics Data System (ADS)

Prasad, K.

2017-12-01

Atmospheric transport is usually performed with weather models, e.g., the Weather Research and Forecasting (WRF) model that employs a parameterized turbulence model and does not resolve the fine scale dynamics generated by the flow around buildings and features comprising a large city. The NIST Fire Dynamics Simulator (FDS) is a computational fluid dynamics model that utilizes large eddy simulation methods to model flow around buildings at length scales much smaller than is practical with models like WRF. FDS has the potential to evaluate the impact of complex topography on near-field dispersion and mixing that is difficult to simulate with a mesoscale atmospheric model. A methodology has been developed to couple the FDS model with WRF mesoscale transport models. The coupling is based on nudging the FDS flow field towards that computed by WRF, and is currently limited to one way coupling performed in an off-line mode. This approach allows the FDS model to operate as a sub-grid scale model with in a WRF simulation. To test and validate the coupled FDS - WRF model, the methane leak from the Aliso Canyon underground storage facility was simulated. Large eddy simulations were performed over the complex topography of various natural gas storage facilities including Aliso Canyon, Honor Rancho and MacDonald Island at 10 m horizontal and vertical resolution. The goal of these simulations included improving and validating transport models as well as testing leak hypotheses. Forward simulation results were compared with aircraft and tower based in-situ measurements as well as methane plumes observed using the NASA Airborne Visible InfraRed Imaging Spectrometer (AVIRIS) and the next generation instrument AVIRIS-NG. Comparison of simulation results with measurement data demonstrate the capability of the coupled FDS-WRF models to accurately simulate the transport and dispersion of methane plumes over urban domains. Simulated integrated methane enhancements will be presented and compared with results obtained from spectrometer data to estimate the temporally evolving methane flux during the Aliso Canyon blowout.

Towards Real-Time Pilot-in-the-Loop Simulation of Rotorcraft With Fully-Coupled CFD Solutions of Rotor / Terrain Interactions

NASA Astrophysics Data System (ADS)

Oruc, Ilker

This thesis presents the development of computationally efficient coupling of Navier-Stokes CFD with a helicopter flight dynamics model, with the ultimate goal of real-time simulation of fully coupled aerodynamic interactions between rotor flow and the surrounding terrain. A particular focus of the research is on coupled airwake effects in the helicopter / ship dynamic interface. A computationally efficient coupling interface was developed between the helicopter flight dynamics model, GENHEL-PSU and the Navier-Stokes solvers, CRUNCH/CRAFT-CFD using both FORTRAN and C/C++ programming languages. In order to achieve real-time execution speeds, the main rotor was modeled with a simplified actuator disk using unsteady momentum sources, instead of resolving the full blade geometry in the CFD. All the airframe components, including the fuselage are represented by single aerodynamic control points in the CFD calculations. The rotor downwash influence on the fuselage and empennage are calculated by using the CFD predicted local flow velocities at these aerodynamic control points defined on the helicopter airframe. In the coupled simulations, the flight dynamics model is free to move within a computational domain, where the main rotor forces are translated into source terms in the momentum equations of the Navier-Stokes equations. Simultaneously, the CFD calculates induced velocities those are fed back to the simulation and affect the aerodynamic loads in the flight dynamics. The CFD solver models the inflow, ground effect, and interactional aerodynamics in the flight dynamics simulation, and these calculations can be coupled with solution of the external flow (e.g. ship airwake effects). The developed framework was utilized for various investigations of hovering, forward flight and helicopter/terrain interaction simulations including standard ground effect, partial ground effect, sloped terrain, and acceleration in ground effect; and results compared with different flight and experimental data. In near ground cases, the fully-coupled flight dynamics and CFD simulations predicted roll oscillations due to interactions of the rotor downwash, ground plane, and the feedback controller, which are not predicted by the conventional simulation models. Fully coupled simulations of a helicopter accelerating near ground predicted flow formations similar to the recirculation and ground vortex flow regimes observed in experiments. The predictions of hover power reductions due to ground effect compared well to a recent experimental data and the results showed 22% power reduction for a hover flight z/R=0.55 above ground level. Fully coupled simulations performed for a helicopter hovering over and approaching to a ship flight deck and results compared with the standalone GENHEL-PSU simulations without ship airwake and one-way coupled simulations. The fully-coupled simulations showed higher pilot workload compared to the other two cases. In order to increase the execution speeds of the CFD calculations, several improvements were made on the CFD solver. First, the initial coupling approach File I/O was replaced with a more efficient method called Multiple Program Multiple Data MPI framework, where the two executables communicate with each other by MPI calls. Next, the unstructured solver (CRUNCH CFD), which is 2nd-order accurate in space, was replaced with the faster running structured solver (CRAFT CFD) that is 5th-order accurate in space. Other improvements including a more efficient k-d tree search algorithm and the bounding of the source term search space within a small region of the grid surrounding the rotor were made on the CFD solver. The final improvement was to parallelize the search task with the CFD solver tasks within the solver. To quantify the speed-up of the improvements to the coupling interface described above, a study was performed to demonstrate the speedup achieved from each of the interface improvements. The improvements made on the CFD solver showed more than 40 times speedup from the baseline file I/O and unstructured solver CRUNCH CFD. Using a structured CFD solver with 5th-order spacial accuracy provided the largest reductions in execution times. Disregarding the solver numeric, the total speedup of all of the interface improvements including the MPMD rotor point exchange, k-d tree search algorithm, bounded search space, and paralleled search task, was approximately 231%, more than a factor of 2. All these improvements provided the necessary speedup for approach real-time CFD. (Abstract shortened by ProQuest.).

Enhanced model of gear transmission dynamics for condition monitoring applications: Effects of torque, friction and bearing clearance

NASA Astrophysics Data System (ADS)

Fernandez-del-Rincon, A.; Garcia, P.; Diez-Ibarbia, A.; de-Juan, A.; Iglesias, M.; Viadero, F.

2017-02-01

Gear transmissions remain as one of the most complex mechanical systems from the point of view of noise and vibration behavior. Research on gear modeling leading to the obtaining of models capable of accurately reproduce the dynamic behavior of real gear transmissions has spread out the last decades. Most of these models, although useful for design stages, often include simplifications that impede their application for condition monitoring purposes. Trying to filling this gap, the model presented in this paper allows us to simulate gear transmission dynamics including most of these features usually neglected by the state of the art models. This work presents a model capable of considering simultaneously the internal excitations due to the variable meshing stiffness (including the coupling among successive tooth pairs in contact, the non-linearity linked with the contacts between surfaces and the dissipative effects), and those excitations consequence of the bearing variable compliance (including clearances or pre-loads). The model can also simulate gear dynamics in a realistic torque dependent scenario. The proposed model combines a hybrid formulation for calculation of meshing forces with a non-linear variable compliance approach for bearings. Meshing forces are obtained by means of a double approach which combines numerical and analytical aspects. The methodology used provides a detailed description of the meshing forces, allowing their calculation even when gear center distance is modified due to shaft and bearing flexibilities, which are unavoidable in real transmissions. On the other hand, forces at bearing level were obtained considering a variable number of supporting rolling elements, depending on the applied load and clearances. Both formulations have been developed and applied to the simulation of the vibration of a sample transmission, focusing the attention on the transmitted load, friction meshing forces and bearing preloads.

Modeling SMAP Spacecraft Attitude Control Estimation Error Using Signal Generation Model

NASA Technical Reports Server (NTRS)

Rizvi, Farheen

2016-01-01

Two ground simulation software are used to model the SMAP spacecraft dynamics. The CAST software uses a higher fidelity model than the ADAMS software. The ADAMS software models the spacecraft plant, controller and actuator models, and assumes a perfect sensor and estimator model. In this simulation study, the spacecraft dynamics results from the ADAMS software are used as CAST software is unavailable. The main source of spacecraft dynamics error in the higher fidelity CAST software is due to the estimation error. A signal generation model is developed to capture the effect of this estimation error in the overall spacecraft dynamics. Then, this signal generation model is included in the ADAMS software spacecraft dynamics estimate such that the results are similar to CAST. This signal generation model has similar characteristics mean, variance and power spectral density as the true CAST estimation error. In this way, ADAMS software can still be used while capturing the higher fidelity spacecraft dynamics modeling from CAST software.

Data Intensive Systems (DIS) Benchmark Performance Summary

DTIC Science & Technology

2003-08-01

models assumed by today’s conventional architectures. Such applications include model- based Automatic Target Recognition (ATR), synthetic aperture...radar (SAR) codes, large scale dynamic databases/battlefield integration, dynamic sensor- based processing, high-speed cryptanalysis, high speed...distributed interactive and data intensive simulations, data-oriented problems characterized by pointer- based and other highly irregular data structures

An Open-Access Educational Tool for Teaching Motion Dynamics in Multi-Axis Servomotor Control

ERIC Educational Resources Information Center

Rivera-Guillen, J. R.; de Jesus Rangel-Magdaleno, J.; de Jesus Romero-Troncoso, R.; Osornio-Rios, R. A.; Guevara-Gonzalez, R. G.

2012-01-01

Servomotors are widely used in computerized numerically controlled (CNC) machines, hence motion control is a major topic covered in undergraduate/graduate engineering courses. Despite the fact that several syllabi include the motion dynamics topic in their courses, there are neither suitable tools available for designing and simulating multi-axis…

76 FR 33981 - Special Conditions: Pratt and Whitney Canada Model PW210S Turboshaft Engine

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-10

... system includes a dual channel full authority digital electronic control. The engine will incorporate a... mode operation. The commenter stated that the 400 cycle dynamic braking test is inappropriate for this engine certification program, that engine dynamics will be difficult to simulate in a test stand, and...

Parallel computational fluid dynamics '91; Conference Proceedings, Stuttgart, Germany, Jun. 10-12, 1991

NASA Technical Reports Server (NTRS)

Reinsch, K. G. (Editor); Schmidt, W. (Editor); Ecer, A. (Editor); Haeuser, Jochem (Editor); Periaux, J. (Editor)

1992-01-01

A conference was held on parallel computational fluid dynamics and produced related papers. Topics discussed in these papers include: parallel implicit and explicit solvers for compressible flow, parallel computational techniques for Euler and Navier-Stokes equations, grid generation techniques for parallel computers, and aerodynamic simulation om massively parallel systems.

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

NASA Astrophysics Data System (ADS)

Fu, Chuan

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

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration

PubMed Central

Miller, Thomas F.

2017-01-01

We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency. PMID:28328943

Improved Density Functional Tight Binding Potentials for Metalloid Aluminum Clusters

DTIC Science & Technology

2016-06-01

simulations of the oxidation of Al4Cp * 4 show reasonable comparison with a DFT-based Car -Parrinello method, including correct prediction of hydride transfers...comparison with a DFT-based Car -Parrinello method, including correct prediction of hydride transfers from Cp* to the metal centers during the...initio molecular dynamics of the oxidation of Al4Cp * 4 using a DFT-based Car -Parrinello method. This simulation, which 43 several months on the

Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein.

PubMed

Zosel, Franziska; Haenni, Dominik; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin

2017-10-21

Intrinsically disordered proteins (IDPs) are increasingly recognized as a class of molecules that can exert essential biological functions even in the absence of a well-defined three-dimensional structure. Understanding the conformational distributions and dynamics of these highly flexible proteins is thus essential for explaining the molecular mechanisms underlying their function. Single-molecule fluorescence spectroscopy in combination with Förster resonance energy transfer (FRET) is a powerful tool for probing intramolecular distances and the rapid long-range distance dynamics in IDPs. To complement the information from FRET, we combine it with photoinduced electron transfer (PET) quenching to monitor local loop-closure kinetics at the same time and in the same molecule. Here we employed this combination to investigate the intrinsically disordered N-terminal domain of HIV-1 integrase. The results show that both long-range dynamics and loop closure kinetics on the sub-microsecond time scale can be obtained reliably from a single set of measurements by the analysis with a comprehensive model of the underlying photon statistics including both FRET and PET. A more detailed molecular interpretation of the results is enabled by direct comparison with a recent extensive atomistic molecular dynamics simulation of integrase. The simulations are in good agreement with experiment and can explain the deviation from simple models of chain dynamics by the formation of persistent local secondary structure. The results illustrate the power of a close combination of single-molecule spectroscopy and simulations for advancing our understanding of the dynamics and detailed mechanisms in unfolded and intrinsically disordered proteins.

Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein

NASA Astrophysics Data System (ADS)

Zosel, Franziska; Haenni, Dominik; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin

2017-10-01

Intrinsically disordered proteins (IDPs) are increasingly recognized as a class of molecules that can exert essential biological functions even in the absence of a well-defined three-dimensional structure. Understanding the conformational distributions and dynamics of these highly flexible proteins is thus essential for explaining the molecular mechanisms underlying their function. Single-molecule fluorescence spectroscopy in combination with Förster resonance energy transfer (FRET) is a powerful tool for probing intramolecular distances and the rapid long-range distance dynamics in IDPs. To complement the information from FRET, we combine it with photoinduced electron transfer (PET) quenching to monitor local loop-closure kinetics at the same time and in the same molecule. Here we employed this combination to investigate the intrinsically disordered N-terminal domain of HIV-1 integrase. The results show that both long-range dynamics and loop closure kinetics on the sub-microsecond time scale can be obtained reliably from a single set of measurements by the analysis with a comprehensive model of the underlying photon statistics including both FRET and PET. A more detailed molecular interpretation of the results is enabled by direct comparison with a recent extensive atomistic molecular dynamics simulation of integrase. The simulations are in good agreement with experiment and can explain the deviation from simple models of chain dynamics by the formation of persistent local secondary structure. The results illustrate the power of a close combination of single-molecule spectroscopy and simulations for advancing our understanding of the dynamics and detailed mechanisms in unfolded and intrinsically disordered proteins.

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

Churchfield, M. J.; Moriarty, P. J.; Hao, Y.

The focus of this work is the comparison of the dynamic wake meandering model and large-eddy simulation with field data from the Egmond aan Zee offshore wind plant composed of 36 3-MW turbines. The field data includes meteorological mast measurements, SCADA information from all turbines, and strain-gauge data from two turbines. The dynamic wake meandering model and large-eddy simulation are means of computing unsteady wind plant aerodynamics, including the important unsteady meandering of wakes as they convect downstream and interact with other turbines and wakes. Both of these models are coupled to a turbine model such that power and mechanicalmore » loads of each turbine in the wind plant are computed. We are interested in how accurately different types of waking (e.g., direct versus partial waking), can be modeled, and how background turbulence level affects these loads. We show that both the dynamic wake meandering model and large-eddy simulation appear to underpredict power and overpredict fatigue loads because of wake effects, but it is unclear that they are really in error. This discrepancy may be caused by wind-direction uncertainty in the field data, which tends to make wake effects appear less pronounced.« less

Mouse Acetylcholinesterase Unliganded and in Complex with Huperzine A: A Comparison of Molecular Dynamics Simulations

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

Tara, Sylvia; Straatsma, TP; Mccammon, Andy

1999-06-01

A 1 ns molecular dynamics simulation of unliganded mouse acetylcholinesterase (AChE) is compared to a previous simulation of mouse AChE complexed with Huperzine A (HupA). Several common features are observed. In both simulations, the active site gorge fluctuates in size during the 1 ns trajectory, and is completely pinched off several times. Many of the residues in the gorge that formed hydrogen bonds with HupA in the simulation of the complex, now form hydrogen bonds with other protein residues and water molecules in the gorge. The opening of a "backdoor" entrance to the active site that was found in themore » simulation of the complex is also observed in the unliganded simulation. Differences between the two simulations include overall lower structural RMS deviations for residues in the gorge in the unliganded simulation, a smaller diameter of the gorge in the absence of HupA, and the disappearance of a side channel that was frequently present in the liganded simulation. The differences between the two simulations can be attributed, in part, to the interaction of AChE with HupA.« less

Kinematic capability in the SVDS

NASA Technical Reports Server (NTRS)

Flanders, H. A.

1977-01-01

The details of the Remote Manipulator System kinematic model implemented into the Space Vehicle Dynamics Simulation are given. Detailed engineering flow diagrams and definitions of terms are included.

Post-Newtonian Dynamical Modeling of Supermassive Black Holes in Galactic-scale Simulations

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

Rantala, Antti; Pihajoki, Pauli; Johansson, Peter H.

We present KETJU, a new extension of the widely used smoothed particle hydrodynamics simulation code GADGET-3. The key feature of the code is the inclusion of algorithmically regularized regions around every supermassive black hole (SMBH). This allows for simultaneously following global galactic-scale dynamical and astrophysical processes, while solving the dynamics of SMBHs, SMBH binaries, and surrounding stellar systems at subparsec scales. The KETJU code includes post-Newtonian terms in the equations of motions of the SMBHs, which enables a new SMBH merger criterion based on the gravitational wave coalescence timescale, pushing the merger separation of SMBHs down to ∼0.005 pc. Wemore » test the performance of our code by comparison to NBODY7 and rVINE. We set up dynamically stable multicomponent merger progenitor galaxies to study the SMBH binary evolution during galaxy mergers. In our simulation sample the SMBH binaries do not suffer from the final-parsec problem, which we attribute to the nonspherical shape of the merger remnants. For bulge-only models, the hardening rate decreases with increasing resolution, whereas for models that in addition include massive dark matter halos, the SMBH binary hardening rate becomes practically independent of the mass resolution of the stellar bulge. The SMBHs coalesce on average 200 Myr after the formation of the SMBH binary. However, small differences in the initial SMBH binary eccentricities can result in large differences in the SMBH coalescence times. Finally, we discuss the future prospects of KETJU, which allows for a straightforward inclusion of gas physics in the simulations.« less

Momentum-Based Dynamics for Spacecraft with Chained Revolute Appendages

NASA Technical Reports Server (NTRS)

Queen, Steven; London, Ken; Gonzalez, Marcelo

2005-01-01

An efficient formulation is presented for a sub-class of multi-body dynamics problems that involve a six degree-of-freedom base body and a chain of N rigid linkages connected in series by single degree-of-freedom revolute joints. This general method is particularly well suited for simulations of spacecraft dynamics and control that include the modeling of an orbiting platform with or without internal degrees of freedom such as reaction wheels, dampers, and/or booms. In the present work, particular emphasis is placed on dynamic simulation of multi-linkage robotic manipulators. The differential equations of motion are explicitly given in terms of linear and angular momentum states, which can be evaluated recursively along a serial chain of linkages for an efficient real-time solution on par with the best of the O(N3) methods.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

Structural dynamics verification facility study

NASA Technical Reports Server (NTRS)

Kiraly, L. J.; Hirchbein, M. S.; Mcaleese, J. M.; Fleming, D. P.

1981-01-01

The need for a structural dynamics verification facility to support structures programs was studied. Most of the industry operated facilities are used for highly focused research, component development, and problem solving, and are not used for the generic understanding of the coupled dynamic response of major engine subsystems. Capabilities for the proposed facility include: the ability to both excite and measure coupled structural dynamic response of elastic blades on elastic shafting, the mechanical simulation of various dynamical loadings representative of those seen in operating engines, and the measurement of engine dynamic deflections and interface forces caused by alternative engine mounting configurations and compliances.

Testing the skill of numerical hydraulic modeling to simulate spatiotemporal flooding patterns in the Logone floodplain, Cameroon

NASA Astrophysics Data System (ADS)

Fernández, Alfonso; Najafi, Mohammad Reza; Durand, Michael; Mark, Bryan G.; Moritz, Mark; Jung, Hahn Chul; Neal, Jeffrey; Shastry, Apoorva; Laborde, Sarah; Phang, Sui Chian; Hamilton, Ian M.; Xiao, Ningchuan

2016-08-01

Recent innovations in hydraulic modeling have enabled global simulation of rivers, including simulation of their coupled wetlands and floodplains. Accurate simulations of floodplains using these approaches may imply tremendous advances in global hydrologic studies and in biogeochemical cycling. One such innovation is to explicitly treat sub-grid channels within two-dimensional models, given only remotely sensed data in areas with limited data availability. However, predicting inundated area in floodplains using a sub-grid model has not been rigorously validated. In this study, we applied the LISFLOOD-FP hydraulic model using a sub-grid channel parameterization to simulate inundation dynamics on the Logone River floodplain, in northern Cameroon, from 2001 to 2007. Our goal was to determine whether floodplain dynamics could be simulated with sufficient accuracy to understand human and natural contributions to current and future inundation patterns. Model inputs in this data-sparse region include in situ river discharge, satellite-derived rainfall, and the shuttle radar topography mission (SRTM) floodplain elevation. We found that the model accurately simulated total floodplain inundation, with a Pearson correlation coefficient greater than 0.9, and RMSE less than 700 km2, compared to peak inundation greater than 6000 km2. Predicted discharge downstream of the floodplain matched measurements (Nash-Sutcliffe efficiency of 0.81), and indicated that net flow from the channel to the floodplain was modeled accurately. However, the spatial pattern of inundation was not well simulated, apparently due to uncertainties in SRTM elevations. We evaluated model results at 250, 500 and 1000-m spatial resolutions, and found that results are insensitive to spatial resolution. We also compared the model output against results from a run of LISFLOOD-FP in which the sub-grid channel parameterization was disabled, finding that the sub-grid parameterization simulated more realistic dynamics. These results suggest that analysis of global inundation is feasible using a sub-grid model, but that spatial patterns at sub-kilometer resolutions still need to be adequately predicted.

Lunar soil properties and soil mechanics

NASA Technical Reports Server (NTRS)

Mitchell, J. K.; Houston, W. N.; Hovland, H. J.

1972-01-01

The study to identify and define recognizable fabrics in lunar soil in order to determine the history of the lunar regolith in different locations is reported. The fabric of simulated lunar soil, and lunar soil samples are discussed along with the behavior of simulated lunar soil under dynamic and static loading. The planned research is also included.

Xyce

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

Thomquist, Heidi K.; Fixel, Deborah A.; Fett, David Brian

The Xyce Parallel Electronic Simulator simulates electronic circuit behavior in DC, AC, HB, MPDE and transient mode using standard analog (DAE) and/or device (PDE) device models including several age and radiation aware devices. It supports a variety of computing platforms (both serial and parallel) computers. Lastly, it uses a variety of modern solution algorithms dynamic parallel load-balancing and iterative solvers.

6 DOF Nonlinear AUV Simulation Toolbox

DTIC Science & Technology

1997-01-01

is to supply a flexible 3D -simulation platform for motion visualization, in-lab debugging and testing of mission-specific strategies as well as those...Explorer are modular designed [Smith] in order to cut time and cost for vehicle recontlguration. A flexible 3D -simulation platform is desired to... 3D models. Current implemented modules include a nonlinear dynamic model for the OEX, shared memory and semaphore manager tools, shared memory monitor

Evolution of Flow channels and Dipolarization Using THEMIS Observations and Global MHD Simulations

NASA Astrophysics Data System (ADS)

El-Alaoui, M.; McPherron, R. L.; Nishimura, Y.

2017-12-01

We have extensively analyzed a substorm on March 14, 2008 for which we have observations from THEMIS spacecraft located beyond 9 RE near 2100 local time. The available data include an extensive network of all sky cameras and ground magnetometers that establish the times of various auroral and magnetic events. This arrangement provided an excellent data set with which to investigate meso-scale structures in the plasma sheet. We have used a global magnetohydrodynamic simulation to investigate the structure and dynamics of the magnetotail current sheet during this substorm. Both earthward and tailward flows were found in the observations as well as the simulations. The simulation shows that the flow channels follow tortuous paths that are often reflected or deflected before arriving at the inner magnetosphere. The simulation shows a sequence of fast flows and dipolarization events similar to what is seen in the data, though not at precisely the same times or locations. We will use our simulation results combined with the observations to investigate the global convection systems and current sheet structure during this event, showing how meso-scale structures fit into the context of the overall tail dynamics during this event. Our study includes determining the location, timing and strength of several current wedges and expansion onsets during an 8-hour interval.

Dynamic Modeling of Process Technologies for Closed-Loop Water Recovery Systems

NASA Technical Reports Server (NTRS)

Allada, Rama Kumar; Lange, Kevin E.; Anderson, Molly S.

2012-01-01

Detailed chemical process simulations are a useful tool in designing and optimizing complex systems and architectures for human life support. Dynamic and steady-state models of these systems help contrast the interactions of various operating parameters and hardware designs, which become extremely useful in trade-study analyses. NASA s Exploration Life Support technology development project recently made use of such models to compliment a series of tests on different waste water distillation systems. This paper presents dynamic simulations of chemical process for primary processor technologies including: the Cascade Distillation System (CDS), the Vapor Compression Distillation (VCD) system, the Wiped-Film Rotating Disk (WFRD), and post-distillation water polishing processes such as the Volatiles Removal Assembly (VRA). These dynamic models were developed using the Aspen Custom Modeler (Registered TradeMark) and Aspen Plus(Registered TradeMark) process simulation tools. The results expand upon previous work for water recovery technology models and emphasize dynamic process modeling and results. The paper discusses system design, modeling details, and model results for each technology and presents some comparisons between the model results and available test data. Following these initial comparisons, some general conclusions and forward work are discussed.

High accuracy switched-current circuits using an improved dynamic mirror

NASA Technical Reports Server (NTRS)

Zweigle, G.; Fiez, T.

1991-01-01

The switched-current technique, a recently developed circuit approach to analog signal processing, has emerged as an alternative/compliment to the well established switched-capacitor circuit technique. High speed switched-current circuits offer potential cost and power savings over slower switched-capacitor circuits. Accuracy improvements are a primary concern at this stage in the development of the switched-current technique. Use of the dynamic current mirror has produced circuits that are insensitive to transistor matching errors. The dynamic current mirror has been limited by other sources of error including clock-feedthrough and voltage transient errors. In this paper we present an improved switched-current building block using the dynamic current mirror. Utilizing current feedback the errors due to current imbalance in the dynamic current mirror are reduced. Simulations indicate that this feedback can reduce total harmonic distortion by as much as 9 dB. Additionally, we have developed a clock-feedthrough reduction scheme for which simulations reveal a potential 10 dB total harmonic distortion improvement. The clock-feedthrough reduction scheme also significantly reduces offset errors and allows for cancellation with a constant current source. Experimental results confirm the simulated improvements.

Realization of planning design of mechanical manufacturing system by Petri net simulation model

NASA Astrophysics Data System (ADS)

Wu, Yanfang; Wan, Xin; Shi, Weixiang

1991-09-01

Planning design is to work out a more overall long-term plan. In order to guarantee a mechanical manufacturing system (MMS) designed to obtain maximum economical benefit, it is necessary to carry out a reasonable planning design for the system. First, some principles on planning design for MMS are introduced. Problems of production scheduling and their decision rules for computer simulation are presented. Realizable method of each production scheduling decision rule in Petri net model is discussed. Second, the solution of conflict rules for conflict problems during running Petri net is given. Third, based on the Petri net model of MMS which includes part flow and tool flow, according to the principle of minimum event time advance, a computer dynamic simulation of the Petri net model, that is, a computer dynamic simulation of MMS, is realized. Finally, the simulation program is applied to a simulation exmple, so the scheme of a planning design for MMS can be evaluated effectively.

Deployment Simulation Methods for Ultra-Lightweight Inflatable Structures

NASA Technical Reports Server (NTRS)

Wang, John T.; Johnson, Arthur R.

2003-01-01

Two dynamic inflation simulation methods are employed for modeling the deployment of folded thin-membrane tubes. The simulations are necessary because ground tests include gravity effects and may poorly represent deployment in space. The two simulation methods are referred to as the Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method. They are available in the LS-DYNA nonlinear dynamic finite element code. Both methods are suitable for modeling the interactions between the inflation gas and the thin-membrane tube structures. The CV method only considers the pressure induced by the inflation gas in the simulation, while the ALE method models the actual flow of the inflation gas. Thus, the transient fluid properties at any location within the tube can be predicted by the ALE method. Deployment simulations of three packaged tube models; namely coiled, Z-folded, and telescopically-folded configurations, are performed. Results predicted by both methods for the telescopically-folded configuration are correlated and computational efficiency issues are discussed.

Role of Dynamics in the Autoinhibition and Activation of the Exchange Protein Directly Activated by Cyclic AMP (EPAC)*

PubMed Central

VanSchouwen, Bryan; Selvaratnam, Rajeevan; Fogolari, Federico; Melacini, Giuseppe

2011-01-01

The exchange protein directly activated by cAMP (EPAC) is a key receptor of cAMP in eukaryotes and controls critical signaling pathways. Currently, no residue resolution information is available on the full-length EPAC dynamics, which are known to be pivotal determinants of allostery. In addition, no information is presently available on the intermediates for the classical induced fit and conformational selection activation pathways. Here these questions are addressed through molecular dynamics simulations on five key states along the thermodynamic cycle for the cAMP-dependent activation of a fully functional construct of EPAC2, which includes the cAMP-binding domain and the integral catalytic region. The simulations are not only validated by the agreement with the experimental trends in cAMP-binding domain dynamics determined by NMR, but they also reveal unanticipated dynamic attributes, rationalizing previously unexplained aspects of EPAC activation and autoinhibition. Specifically, the simulations show that cAMP binding causes an extensive perturbation of dynamics in the distal catalytic region, assisting the recognition of the Rap1b substrate. In addition, analysis of the activation intermediates points to a possible hybrid mechanism of EPAC allostery incorporating elements of both the induced fit and conformational selection models. In this mechanism an entropy compensation strategy results in a low free-energy pathway of activation. Furthermore, the simulations indicate that the autoinhibitory interactions of EPAC are more dynamic than previously anticipated, leading to a revised model of autoinhibition in which dynamics fine tune the stability of the autoinhibited state, optimally sensitizing it to cAMP while avoiding constitutive activation. PMID:21873431

A Three-Wave Model of the Stratosphere with Coupled Dynamics, Radiation and Photochemistry. Appendix M

NASA Technical Reports Server (NTRS)

Shia, Run-Lie; Zhou, Shuntai; Ko, Malcolm K. W.; Sze, Nien-Dak; Salstein, David; Cady-Pereira, Karen

1997-01-01

A zonal mean chemistry transport model (2-D CTM) coupled with a semi-spectral dynamical model is used to simulate the distributions of trace gases in the present day atmosphere. The zonal-mean and eddy equations for the velocity and the geopotential height are solved in the semi-spectral dynamical model. The residual mean circulation is derived from these dynamical variables and used to advect the chemical species in the 2- D CTM. Based on a linearized wave transport equation, the eddy diffusion coefficients for chemical tracers are expressed in terms of the amplitude, frequency and growth rate of dynamical waves; local chemical loss rates; and a time constant parameterizing small scale mixing. The contributions to eddy flux are from the time varying wave amplitude (transient eddy), chemical reactions (chemical eddy) and small scale mixing. In spite of the high truncation in the dynamical module (only three longest waves are resolved), the model has simulated many observed characteristics of stratospheric dynamics and distribution of chemical species including ozone. Compared with the values commonly used in 2-D CTMs, the eddy diffusion coefficients for chemical species calculated in this model are smaller, especially in the subtropics. It is also found that the chemical eddy diffusion has only a small effects in determining the distribution of most slow species, including ozone in the stratosphere.

Molecular Dynamics Simulations of Creatine Kinase and Adenine Nucleotide Translocase in Mitochondrial Membrane Patch*

PubMed Central

Karo, Jaanus; Peterson, Pearu; Vendelin, Marko

2012-01-01

Interaction between mitochondrial creatine kinase (MtCK) and adenine nucleotide translocase (ANT) can play an important role in determining energy transfer pathways in the cell. Although the functional coupling between MtCK and ANT has been demonstrated, the precise mechanism of the coupling is not clear. To study the details of the coupling, we turned to molecular dynamics simulations. We introduce a new coarse-grained molecular dynamics model of a patch of the mitochondrial inner membrane containing a transmembrane ANT and an MtCK above the membrane. The membrane model consists of three major types of lipids (phosphatidylcholine, phosphatidylethanolamine, and cardiolipin) in a roughly 2:1:1 molar ratio. A thermodynamics-based coarse-grained force field, termed MARTINI, has been used together with the GROMACS molecular dynamics package for all simulated systems in this work. Several physical properties of the system are reproduced by the model and are in agreement with known data. This includes membrane thickness, dimension of the proteins, and diffusion constants. We have studied the binding of MtCK to the membrane and demonstrated the effect of cardiolipin on the stabilization of the binding. In addition, our simulations predict which part of the MtCK protein sequence interacts with the membrane. Taken together, the model has been verified by dynamical and structural data and can be used as the basis for further studies. PMID:22241474

NETIMIS: Dynamic Simulation of Health Economics Outcomes Using Big Data.

PubMed

Johnson, Owen A; Hall, Peter S; Hulme, Claire

2016-02-01

Many healthcare organizations are now making good use of electronic health record (EHR) systems to record clinical information about their patients and the details of their healthcare. Electronic data in EHRs is generated by people engaged in complex processes within complex environments, and their human input, albeit shaped by computer systems, is compromised by many human factors. These data are potentially valuable to health economists and outcomes researchers but are sufficiently large and complex enough to be considered part of the new frontier of 'big data'. This paper describes emerging methods that draw together data mining, process modelling, activity-based costing and dynamic simulation models. Our research infrastructure includes safe links to Leeds hospital's EHRs with 3 million secondary and tertiary care patients. We created a multidisciplinary team of health economists, clinical specialists, and data and computer scientists, and developed a dynamic simulation tool called NETIMIS (Network Tools for Intervention Modelling with Intelligent Simulation; http://www.netimis.com ) suitable for visualization of both human-designed and data-mined processes which can then be used for 'what-if' analysis by stakeholders interested in costing, designing and evaluating healthcare interventions. We present two examples of model development to illustrate how dynamic simulation can be informed by big data from an EHR. We found the tool provided a focal point for multidisciplinary team work to help them iteratively and collaboratively 'deep dive' into big data.

Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

PubMed

Shao, Qiang; Shi, Jiye; Zhu, Weiliang

2012-09-28

The ability of molecular dynamics simulation to capturing the transient states within the folding pathway of protein is important to the understanding of protein folding mechanism. In the present study, the integrated-tempering-sampling molecular dynamics (ITS-MD) simulation was performed to investigate the transient states including intermediate and unfolded ones in the folding pathway of a miniprotein, Trp-cage. Three force fields (FF03, FF99SB, and FF96) were tested, and both intermediate and unfolded states with their characteristics in good agreement with experiments were observed during the simulations, which supports the hypothesis that observable intermediates might present in the folding pathway of small polypeptides. In addition, it was demonstrated that FF03 force field as combined with ITS-MD is in overall a more proper force field than the others in reproducing experimentally recorded properties in UVRS, ECD, and NMR, Photo-CIDNP NMR, and IR T-jump experiments, and the folding∕unfolding thermodynamics parameters, such as ΔG(U), ΔC(p), and ΔH(U) (T(m)). In summary, the present study showed that using suitable force field and energy sampling method, molecular dynamics simulation could capture the transient states within the folding pathway of protein which are consistent with the experimental measurements, and thus provide information of protein folding mechanism and thermodynamics.

Effects of Aircraft Wake Dynamics on Measured and Simulated NO(x) and HO(x) Wake Chemistry. Appendix B

NASA Technical Reports Server (NTRS)

Lewellen, D. C.; Lewellen, W. S.

2001-01-01

High-resolution numerical large-eddy simulations of the near wake of a B757 including simplified NOx and HOx chemistry were performed to explore the effects of dynamics on chemistry in wakes of ages from a few seconds to several minutes. Dilution plays an important basic role in the NOx-O3 chemistry in the wake, while a more interesting interaction between the chemistry and dynamics occurs for the HOx species. These simulation results are compared with published measurements of OH and HO2 within a B757 wake under cruise conditions in the upper troposphere taken during the Subsonic Aircraft Contrail and Cloud Effects Special Study (SUCCESS) mission in May 1996. The simulation provides a much finer grained representation of the chemistry and dynamics of the early wake than is possible from the 1 s data samples taken in situ. The comparison suggests that the previously reported discrepancy of up to a factor of 20 - 50 between the SUCCESS measurements of the [HO2]/[OH] ratio and that predicted by simplified theoretical computations is due to the combined effects of large mixing rates around the wake plume edges and averaging over volumes containing large species fluctuations. The results demonstrate the feasibility of using three-dimensional unsteady large-eddy simulations with coupled chemistry to study such phenomena.

SU-F-T-242: A Method for Collision Avoidance in External Beam Radiation Therapy

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

Buzurovic, I; Cormack, R

2016-06-15

Purpose: We proposed a method for collision avoidance (CA) in external beam radiation therapy (EBRT). The method encompasses the analysis of all positions of the moving components of the beam delivery system such as the treatment table and gantry, including patient specific information obtained from the CT images. This method eliminates the need for time-consuming dry-runs prior to the actual treatments. Methods: The QA procedure for EBRT requires that the collision should be checked prior to treatment. We developed a system capable of a rigorous computer simulation of all moving components including positions of the couch and gantry during themore » delivery, position of the patients, and imaging equipment. By running this treatment simulation it is possible to quantify and graphically represent all positions and corresponding trajectories of all points of the moving parts during the treatment delivery. The development of the workflow for implementation of the CA includes several steps: a) derivation of combined dynamic equation of motion of the EBRT delivery systems, b) developing the simulation model capable of drawing the motion trajectories of the specific points, c) developing the interface between the model and the treatment plan parameters such as couch and gantry parameters for each field. Results: The patient CT images were registered to the treatment couch so the patient dimensions were included into the simulation. The treatment field parameters were structured in the xml-file which was used as the input into the dynamic equations. The trajectories of the moving components were plotted on the same graph using the dynamic equations. If the trajectories intersect that was the signal that collision exists. Conclusion: This CA method was proved to be effective in the simulation of treatment delivery. The proper implementation of this system can potentially improve the QA program and increase the efficacy in the clinical setup.« less

Molecular Dynamics Study of Thermally Augmented Nanodroplet Motion on Chemical Energy Induced Wettability Gradient Surfaces.

PubMed

Chakraborty, Monojit; Chowdhury, Anamika; Bhusan, Richa; DasGupta, Sunando

2015-10-20

Droplet motion on a surface with chemical energy induced wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics of molecular movement near the solid-liquid interface including the contact line friction. The simulations mimic experiments in a comprehensive manner wherein microsized droplets are propelled by the surface wettability gradient against forces opposed to motion. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature are varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction is observed to be a strong function of temperature at atomistic scales, confirming their experimentally observed inverse functionality. Additionally, the MD simulation results are successfully compared with those from an analytical model for self-propelled droplet motion on gradient surfaces.

Lightweight computational steering of very large scale molecular dynamics simulations

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

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less

Simulations of 4D edge transport and dynamics using the TEMPEST gyro-kinetic code

NASA Astrophysics Data System (ADS)

Rognlien, T. D.; Cohen, B. I.; Cohen, R. H.; Dorr, M. R.; Hittinger, J. A. F.; Kerbel, G. D.; Nevins, W. M.; Xiong, Z.; Xu, X. Q.

2006-10-01

Simulation results are presented for tokamak edge plasmas with a focus on the 4D (2r,2v) option of the TEMPEST continuum gyro-kinetic code. A detailed description of a variety of kinetic simulations is reported, including neoclassical radial transport from Coulomb collisions, electric field generation, dynamic response to perturbations by geodesic acoustic modes, and parallel transport on open magnetic-field lines. Comparison is made between the characteristics of the plasma solutions on closed and open magnetic-field line regions separated by a magnetic separatrix, and simple physical models are used to qualitatively explain the differences observed in mean flow and electric-field generation. The status of extending the simulations to 5D turbulence will be summarized. The code structure used in this ongoing project is also briefly described, together with future plans.

Using Multi-scale Dynamic Rupture Models to Improve Ground Motion Estimates: ALCF-2 Early Science Program Technical Report

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

Ely, Geoffrey P.

2013-10-31

This project uses dynamic rupture simulations to investigate high-frequency seismic energy generation. The relevant phenomena (frictional breakdown, shear heating, effective normal-stress fluctuations, material damage, etc.) controlling rupture are strongly interacting and span many orders of magnitude in spatial scale, requiring highresolution simulations that couple disparate physical processes (e.g., elastodynamics, thermal weakening, pore-fluid transport, and heat conduction). Compounding the computational challenge, we know that natural faults are not planar, but instead have roughness that can be approximated by power laws potentially leading to large, multiscale fluctuations in normal stress. The capacity to perform 3D rupture simulations that couple these processes willmore » provide guidance for constructing appropriate source models for high-frequency ground motion simulations. The improved rupture models from our multi-scale dynamic rupture simulations will be used to conduct physicsbased (3D waveform modeling-based) probabilistic seismic hazard analysis (PSHA) for California. These calculation will provide numerous important seismic hazard results, including a state-wide extended earthquake rupture forecast with rupture variations for all significant events, a synthetic seismogram catalog for thousands of scenario events and more than 5000 physics-based seismic hazard curves for California.« less

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

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

NASA Astrophysics Data System (ADS)

Jaisankar, S.; Sheshadri, T. S.

2018-05-01

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

TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.

PubMed

Li, Min; Liu, Fengjiao; Zhang, John Z H

2016-12-13

Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.

Self-consistency tests of large-scale dynamics parameterizations for single-column modeling

DOE PAGES

Edman, Jacob P.; Romps, David M.

2015-03-18

Large-scale dynamics parameterizations are tested numerically in cloud-resolving simulations, including a new version of the weak-pressure-gradient approximation (WPG) introduced by Edman and Romps (2014), the weak-temperature-gradient approximation (WTG), and a prior implementation of WPG. We perform a series of self-consistency tests with each large-scale dynamics parameterization, in which we compare the result of a cloud-resolving simulation coupled to WTG or WPG with an otherwise identical simulation with prescribed large-scale convergence. In self-consistency tests based on radiative-convective equilibrium (RCE; i.e., no large-scale convergence), we find that simulations either weakly coupled or strongly coupled to either WPG or WTG are self-consistent, butmore » WPG-coupled simulations exhibit a nonmonotonic behavior as the strength of the coupling to WPG is varied. We also perform self-consistency tests based on observed forcings from two observational campaigns: the Tropical Warm Pool International Cloud Experiment (TWP-ICE) and the ARM Southern Great Plains (SGP) Summer 1995 IOP. In these tests, we show that the new version of WPG improves upon prior versions of WPG by eliminating a potentially troublesome gravity-wave resonance.« less

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

PubMed Central

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-01-01

We studied the microsecond folding dynamics of three β hairpins (Trp zippers 1–3, TZ1–TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1–TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations. PMID:15020773

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-03-01

We studied the microsecond folding dynamics of three hairpins (Trp zippers 1-3, TZ1-TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1-TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations.

Modeling and Simulation of U-tube Steam Generator

NASA Astrophysics Data System (ADS)

Zhang, Mingming; Fu, Zhongguang; Li, Jinyao; Wang, Mingfei

2018-03-01

The U-tube natural circulation steam generator was mainly researched with modeling and simulation in this article. The research is based on simuworks system simulation software platform. By analyzing the structural characteristics and the operating principle of U-tube steam generator, there are 14 control volumes in the model, including primary side, secondary side, down channel and steam plenum, etc. The model depends completely on conservation laws, and it is applied to make some simulation tests. The results show that the model is capable of simulating properly the dynamic response of U-tube steam generator.

Large eddy simulation of a boundary layer with concave streamwise curvature

NASA Technical Reports Server (NTRS)

Lund, Thomas S.

1993-01-01

One of the most exciting recent developments in the field of large eddy simulation (LES) is the dynamic subgrid-scale model. The dynamic model concept is a general procedure for evaluating model constants by sampling a band of the smallest scales actually resolved in the simulation. To date, the procedure has been used primarily in conjunction with the Smagorinsky model. The dynamic procedure has the advantage that the value of the model constant need not be specified a priori, but rather is calculated as a function of space and time as the simulation progresses. This feature makes the dynamic model especially attractive for flows in complex geometries where it is difficult or impossible to calibrate model constants. The dynamic model was highly successful in benchmark tests involving homogeneous and channel flows. Having demonstrated the potential of the dynamic model in these simple flows, the overall direction of the LES effort at CTR shifted toward an evaluation of the model in more complex situations. The current test cases are basic engineering-type flows for which Reynolds averaged approaches were unable to model the turbulence to within engineering accuracy. Flows currently under investigation include a backward-facing step, wake behind a circular cylinder, airfoil at high angles of attack, separated flow in a diffuser, and boundary layer over a concave surface. Preliminary results from the backward-facing step and cylinder wake simulations are encouraging. Progress on the LES of a boundary layer on a concave surface is discussed. Although the geometry of a concave wall is not very complex, the boundary layer that develops on its surface is difficult to model due to the presence of streamwise Taylor-Gortler vortices. These vortices arise as a result of a centrifugal instability associated with the convex curvature.

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

Ortoleva, Peter J.

Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

Real-Time and High-Fidelity Simulation Environment for Autonomous Ground Vehicle Dynamics

NASA Technical Reports Server (NTRS)

Cameron, Jonathan; Myint, Steven; Kuo, Calvin; Jain, Abhi; Grip, Havard; Jayakumar, Paramsothy; Overholt, Jim

2013-01-01

This paper reports on a collaborative project between U.S. Army TARDEC and Jet Propulsion Laboratory (JPL) to develop a unmanned ground vehicle (UGV) simulation model using the ROAMS vehicle modeling framework. Besides modeling the physical suspension of the vehicle, the sensing and navigation of the HMMWV vehicle are simulated. Using models of urban and off-road environments, the HMMWV simulation was tested in several ways, including navigation in an urban environment with obstacle avoidance and the performance of a lane change maneuver.

Dynamic Modeling and Control of Nuclear Reactors Coupled to Closed-Loop Brayton Cycle Systems using SIMULINK{sup TM}

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

Wright, Steven A.; Sanchez, Travis

2005-02-06

The operation of space reactors for both in-space and planetary operations will require unprecedented levels of autonomy and control. Development of these autonomous control systems will require dynamic system models, effective control methodologies, and autonomous control logic. This paper briefly describes the results of reactor, power-conversion, and control models that are implemented in SIMULINK{sup TM} (Simulink, 2004). SIMULINK{sup TM} is a development environment packaged with MatLab{sup TM} (MatLab, 2004) that allows the creation of dynamic state flow models. Simulation modules for liquid metal, gas cooled reactors, and electrically heated systems have been developed, as have modules for dynamic power-conversion componentsmore » such as, ducting, heat exchangers, turbines, compressors, permanent magnet alternators, and load resistors. Various control modules for the reactor and the power-conversion shaft speed have also been developed and simulated. The modules are compiled into libraries and can be easily connected in different ways to explore the operational space of a number of potential reactor, power-conversion system configurations, and control approaches. The modularity and variability of these SIMULINK{sup TM} models provides a way to simulate a variety of complete power generation systems. To date, both Liquid Metal Reactors (LMR), Gas Cooled Reactors (GCR), and electric heaters that are coupled to gas-dynamics systems and thermoelectric systems have been simulated and are used to understand the behavior of these systems. Current efforts are focused on improving the fidelity of the existing SIMULINK{sup TM} modules, extending them to include isotopic heaters, heat pipes, Stirling engines, and on developing state flow logic to provide intelligent autonomy. The simulation code is called RPC-SIM (Reactor Power and Control-Simulator)« less

Modeling soil thermal and carbon dynamics of a fire chronosequence in interior Alaska

USGS Publications Warehouse

Zhuang, Q.; McGuire, A.D.; O'Neill, K. P.; Harden, J.W.; Romanovsky, V.E.; Yarie, J.

2003-01-01

In this study, the dynamics of soil thermal, hydrologic, and ecosystem processes were coupled to project how the carbon budgets of boreal forests will respond to changes in atmospheric CO2, climate, and fire disturbance. The ability of the model to simulate gross primary production and ecosystem respiration was verified for a mature black spruce ecosystem in Canada, the age-dependent pattern of the simulated vegetation carbon was verified with inventory data on aboveground growth of Alaskan black spruce forests, and the model was applied to a postfire chronosequence in interior Alaska. The comparison between the simulated soil temperature and field-based estimates during the growing season (May to September) of 1997 revealed that the model was able to accurately simulate monthly temperatures at 10 cm (R > 0.93) for control and burned stands of the fire chronosequence. Similarly, the simulated and field-based estimates of soil respiration for control and burned stands were correlated (R = 0.84 and 0.74 for control and burned stands, respectively). The simulated and observed decadal to century-scale dynamics of soil temperature and carbon dynamics, which are represented by mean monthly values of these variables during the growing season, were correlated among stands (R = 0.93 and 0.71 for soil temperature at 20- and 10-cm depths, R = 0.95 and 0.91 for soil respiration and soil carbon, respectively). Sensitivity analyses indicate that along with differences in fire and climate history a number of other factors influence the response of carbon dynamics to fire disturbance. These factors include nitrogen fixation, the growth of moss, changes in the depth of the organic layer, soil drainage, and fire severity.

Adaptive hybrid simulations for multiscale stochastic reaction networks

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

Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa

2015-01-21

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

Adaptive hybrid simulations for multiscale stochastic reaction networks.

PubMed

Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa

2015-01-21

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

Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations.

PubMed

Stock, Philipp; Monroe, Jacob I; Utzig, Thomas; Smith, David J; Shell, M Scott; Valtiner, Markus

2017-03-28

Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS) 5 peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 k B T per leucine. In good agreement, simulations indicate a similar trend with 2.1 k B T per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.

Simulating galactic dust grain evolution on a moving mesh

NASA Astrophysics Data System (ADS)

McKinnon, Ryan; Vogelsberger, Mark; Torrey, Paul; Marinacci, Federico; Kannan, Rahul

2018-05-01

Interstellar dust is an important component of the galactic ecosystem, playing a key role in multiple galaxy formation processes. We present a novel numerical framework for the dynamics and size evolution of dust grains implemented in the moving-mesh hydrodynamics code AREPO suited for cosmological galaxy formation simulations. We employ a particle-based method for dust subject to dynamical forces including drag and gravity. The drag force is implemented using a second-order semi-implicit integrator and validated using several dust-hydrodynamical test problems. Each dust particle has a grain size distribution, describing the local abundance of grains of different sizes. The grain size distribution is discretised with a second-order piecewise linear method and evolves in time according to various dust physical processes, including accretion, sputtering, shattering, and coagulation. We present a novel scheme for stochastically forming dust during stellar evolution and new methods for sub-cycling of dust physics time-steps. Using this model, we simulate an isolated disc galaxy to study the impact of dust physical processes that shape the interstellar grain size distribution. We demonstrate, for example, how dust shattering shifts the grain size distribution to smaller sizes resulting in a significant rise of radiation extinction from optical to near-ultraviolet wavelengths. Our framework for simulating dust and gas mixtures can readily be extended to account for other dynamical processes relevant in galaxy formation, like magnetohydrodynamics, radiation pressure, and thermo-chemical processes.

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

DTIC Science & Technology

2010-01-01

formulations of molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage...ad hoc force term in the SGLD model. Introduction Molecular dynamics (MD) simulations of small proteins provide insight into the mechanisms and... molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage mini-protein. All

A gene network simulator to assess reverse engineering algorithms.

PubMed

Di Camillo, Barbara; Toffolo, Gianna; Cobelli, Claudio

2009-03-01

In the context of reverse engineering of biological networks, simulators are helpful to test and compare the accuracy of different reverse-engineering approaches in a variety of experimental conditions. A novel gene-network simulator is presented that resembles some of the main features of transcriptional regulatory networks related to topology, interaction among regulators of transcription, and expression dynamics. The simulator generates network topology according to the current knowledge of biological network organization, including scale-free distribution of the connectivity and clustering coefficient independent of the number of nodes in the network. It uses fuzzy logic to represent interactions among the regulators of each gene, integrated with differential equations to generate continuous data, comparable to real data for variety and dynamic complexity. Finally, the simulator accounts for saturation in the response to regulation and transcription activation thresholds and shows robustness to perturbations. It therefore provides a reliable and versatile test bed for reverse engineering algorithms applied to microarray data. Since the simulator describes regulatory interactions and expression dynamics as two distinct, although interconnected aspects of regulation, it can also be used to test reverse engineering approaches that use both microarray and protein-protein interaction data in the process of learning. A first software release is available at http://www.dei.unipd.it/~dicamill/software/netsim as an R programming language package.

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

PubMed

Serçinoglu, Onur; Ozbek, Pemra

2018-05-25

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Effect of Turbulence Modeling on an Excited Jet

NASA Technical Reports Server (NTRS)

Brown, Clifford A.; Hixon, Ray

2010-01-01

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

Simulation of crash tests for high impact levels of a new bridge safety barrier

NASA Astrophysics Data System (ADS)

Drozda, Jiří; Rotter, Tomáš

2017-09-01

The purpose is to show the opportunity of a non-linear dynamic impact simulation and to explain the possibility of using finite element method (FEM) for developing new designs of safety barriers. The main challenge is to determine the means to create and validate the finite element (FE) model. The results of accurate impact simulations can help to reduce necessary costs for developing of a new safety barrier. The introductory part deals with the creation of the FE model, which includes the newly-designed safety barrier and focuses on the application of an experimental modal analysis (EMA). The FE model has been created in ANSYS Workbench and is formed from shell and solid elements. The experimental modal analysis, which was performed on a real pattern, was employed for measuring the modal frequencies and shapes. After performing the EMA, the FE mesh was calibrated after comparing the measured modal frequencies with the calculated ones. The last part describes the process of the numerical non-linear dynamic impact simulation in LS-DYNA. This simulation was validated after comparing the measured ASI index with the calculated ones. The aim of the study is to improve professional public knowledge about dynamic non-linear impact simulations. This should ideally lead to safer, more accurate and profitable designs.

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.

Complex dynamics of a new 3D Lorenz-type autonomous chaotic system

NASA Astrophysics Data System (ADS)

Zhang, Fuchen; Liao, Xiaofeng; Zhang, Guangyun; Mu, Chunlai

2017-12-01

This paper investigates a new three-dimensional continuous quadratic autonomous chaotic system which is not topologically equivalent to the Lorenz system. The dynamical behaviours of this system are further investigated in detail, including the ultimate boundedness, the invariant sets and the global attraction domain according to Lyapunov stability theory of dynamical systems. The innovation of the paper lies in the fact that this paper not only proves this chaotic system is globally bounded for the parameters of this system but also gives a family of mathematical expressions of global exponential attractive sets with respect to the parameters of this system. To validate the ultimate bound estimation, numerical simulations are also investigated. Numerical simulations verify the effectiveness and feasibility of the theoretical scheme.

Beam dynamics simulation of a double pass proton linear accelerator

DOE PAGES

Hwang, Kilean; Qiang, Ji

2017-04-03

A recirculating superconducting linear accelerator with the advantage of both straight and circular accelerator has been demonstrated with relativistic electron beams. The acceleration concept of a recirculating proton beam was recently proposed and is currently under study. In order to further support the concept, the beam dynamics study on a recirculating proton linear accelerator has to be carried out. In this paper, we study the feasibility of a two-pass recirculating proton linear accelerator through the direct numerical beam dynamics design optimization and the start-to-end simulation. This study shows that the two-pass simultaneous focusing without particle losses is attainable including fullymore » 3D space-charge effects through the entire accelerator system.« less

Integrating Flight Dynamics & Control Analysis and Simulation in Rotorcraft Conceptual Design

NASA Technical Reports Server (NTRS)

Lawrence, Ben; Berger, Tom; Tischler, Mark B.; Theodore, Colin R; Elmore, Josh; Gallaher, Andrew; Tobias, Eric L.

2016-01-01

The development of a toolset, SIMPLI-FLYD ('SIMPLIfied FLight dynamics for conceptual Design') is described. SIMPLI-FLYD is a collection of tools that perform flight dynamics and control modeling and analysis of rotorcraft conceptual designs including a capability to evaluate the designs in an X-Plane-based real-time simulation. The establishment of this framework is now facilitating the exploration of this new capability, in terms of modeling fidelity and data requirements, and the investigation of which stability and control and handling qualities requirements are appropriate for conceptual design. Illustrative design variation studies for single main rotor and tiltrotor vehicle configurations show sensitivity of the stability and control characteristics and an approach to highlight potential weight savings by identifying over-design.

Description of the dynamic infrared background/target simulator (DIBS)

NASA Astrophysics Data System (ADS)

Lujan, Ignacio

1988-01-01

The purpose of the Dynamic Infrared Background/Target Simulator (DIBS) is to project dynamic infrared scenes to a test sensor; e.g., a missile seeker that is sensitive to infrared energy. The projected scene will include target(s) and background. This system was designed to present flicker-free infrared scenes in the 8 micron to 12 micron wavelength region. The major subassemblies of the DIBS are the laser write system (LWS), vanadium dioxide modulator assembly, scene data buffer (SDB), and the optical image translator (OIT). This paper describes the overall concept and design of the infrared scene projector followed by some details of the LWS and VO2 modulator. Also presented are brief descriptions of the SDB and OIT.

First-principles quantum-mechanical investigations of biomass conversion at the liquid-solid interfaces

NASA Astrophysics Data System (ADS)

Dang, Hongli; Xue, Wenhua; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2014-03-01

We report first-principles density-functional calculations and ab initio molecular dynamics (MD) simulations for the reactions involving furfural, which is an important intermediate in biomass conversion, at the catalytic liquid-solid interfaces. The different dynamic processes of furfural at the water-Cu(111) and water-Pd(111) interfaces suggest different catalytic reaction mechanisms for the conversion of furfural. Simulations for the dynamic processes with and without hydrogen demonstrate the importance of the liquid-solid interface as well as the presence of hydrogen in possible catalytic reactions including hydrogenation and decarbonylation of furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

Deployment Simulation of Ultra-Lightweight Inflatable Structures

NASA Technical Reports Server (NTRS)

Wang, John T.; Johnson, Arthur R.

2002-01-01

Dynamic deployment analyses of folded inflatable tubes are conducted to investigate modeling issues related to the deployment of solar sail booms. The analyses are necessary because ground tests include gravity effects and may poorly represent deployment in space. A control volume approach, available in the LS-DYNA nonlinear dynamic finite element code, and the ideal gas law are used to simulate the dynamic inflation deployment process. Three deployment issues are investigated for a tube packaged in a Z-fold configuration. The issues are the effect of the rate of inflation, the effect of residual air, and the effect of gravity. The results of the deployment analyses reveal that the time and amount of inflation gas required to achieve a full deployment are related to these issues.

Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions.

PubMed

Materese, Christopher Kroboth; Goldmon, Christa Charisse; Papoian, Garegin A

2008-08-05

The native state dynamics of the small globular serine protease inhibitor eglin c has been studied in a long 336 ns computer simulation in explicit solvent. We have elucidated the energy landscape explored during the course of the simulation by using Principal Component Analysis. We observe several basins in the energy landscape in which the system lingers for extended periods. Through an iterative process we have generated a tree-like hierarchy of states describing the observed dynamics. We observe a range of divergent contact types including salt bridges, hydrogen bonds, hydrophilic interactions, and hydrophobic interactions, pointing to the frustration between competing interactions. Additionally, we find evidence of competing water-mediated interactions. Divergence in water-mediated interactions may be found to supplement existing direct contacts, but they are also found to be independent of such changes. Water-mediated contacts facilitate interactions between residues of like charge as observed in the simulation. Our results provide insight into the complexity of the dynamic native state of a globular protein and directly probe the residual frustration in the native state.

The Potsdam Parallel Ice Sheet Model (PISM-PIK) - Part 2: Dynamic equilibrium simulation of the Antarctic ice sheet

NASA Astrophysics Data System (ADS)

Martin, M. A.; Winkelmann, R.; Haseloff, M.; Albrecht, T.; Bueler, E.; Khroulev, C.; Levermann, A.

2010-08-01

We present a dynamic equilibrium simulation of the ice sheet-shelf system on Antarctica with the Potsdam Parallel Ice Sheet Model (PISM-PIK). The simulation is initialized with present-day conditions for topography and ice thickness and then run to steady state with constant present-day surface mass balance. Surface temperature and basal melt distribution are parameterized. Grounding lines and calving fronts are free to evolve, and their modeled equilibrium state is compared to observational data. A physically-motivated dynamic calving law based on horizontal spreading rates allows for realistic calving fronts for various types of shelves. Steady-state dynamics including surface velocity and ice flux are analyzed for whole Antarctica and the Ronne-Filchner and Ross ice shelf areas in particular. The results show that the different flow regimes in sheet and shelves, and the transition zone between them, are captured reasonably well, supporting the approach of superposition of SIA and SSA for the representation of fast motion of grounded ice. This approach also leads to a natural emergence of streams in this new 3-D marine ice sheet model.

Combustion-Powered Actuation for Dynamic Stall Suppression - Simulations and Low-Mach Experiments

NASA Technical Reports Server (NTRS)

Matalanis, Claude G.; Min, Byung-Young; Bowles, Patrick O.; Jee, Solkeun; Wake, Brian E.; Crittenden, Tom; Woo, George; Glezer, Ari

2014-01-01

An investigation on dynamic-stall suppression capabilities of combustion-powered actuation (COMPACT) applied to a tabbed VR-12 airfoil is presented. In the first section, results from computational fluid dynamics (CFD) simulations carried out at Mach numbers from 0.3 to 0.5 are presented. Several geometric parameters are varied including the slot chordwise location and angle. Actuation pulse amplitude, frequency, and timing are also varied. The simulations suggest that cycle-averaged lift increases of approximately 4% and 8% with respect to the baseline airfoil are possible at Mach numbers of 0.4 and 0.3 for deep and near-deep dynamic-stall conditions. In the second section, static-stall results from low-speed wind-tunnel experiments are presented. Low-speed experiments and high-speed CFD suggest that slots oriented tangential to the airfoil surface produce stronger benefits than slots oriented normal to the chordline. Low-speed experiments confirm that chordwise slot locations suitable for Mach 0.3-0.4 stall suppression (based on CFD) will also be effective at lower Mach numbers.

Dynamic Modeling of Process Technologies for Closed-Loop Water Recovery Systems

NASA Technical Reports Server (NTRS)

Allada, Rama Kumar; Lange, Kevin; Anderson, Molly

2011-01-01

Detailed chemical process simulations are a useful tool in designing and optimizing complex systems and architectures for human life support. Dynamic and steady-state models of these systems help contrast the interactions of various operating parameters and hardware designs, which become extremely useful in trade-study analyses. NASA s Exploration Life Support technology development project recently made use of such models to compliment a series of tests on different waste water distillation systems. This paper presents dynamic simulations of chemical process for primary processor technologies including: the Cascade Distillation System (CDS), the Vapor Compression Distillation (VCD) system, the Wiped-Film Rotating Disk (WFRD), and post-distillation water polishing processes such as the Volatiles Removal Assembly (VRA) that were developed using the Aspen Custom Modeler and Aspen Plus process simulation tools. The results expand upon previous work for water recovery technology models and emphasize dynamic process modeling and results. The paper discusses system design, modeling details, and model results for each technology and presents some comparisons between the model results and available test data. Following these initial comparisons, some general conclusions and forward work are discussed.

A generalized computer code for developing dynamic gas turbine engine models (DIGTEM)

NASA Technical Reports Server (NTRS)

Daniele, C. J.

1984-01-01

This paper describes DIGTEM (digital turbofan engine model), a computer program that simulates two spool, two stream (turbofan) engines. DIGTEM was developed to support the development of a real time multiprocessor based engine simulator being designed at the Lewis Research Center. The turbofan engine model in DIGTEM contains steady state performance maps for all the components and has control volumes where continuity and energy balances are maintained. Rotor dynamics and duct momentum dynamics are also included. DIGTEM features an implicit integration scheme for integrating stiff systems and trims the model equations to match a prescribed design point by calculating correction coefficients that balance out the dynamic equations. It uses the same coefficients at off design points and iterates to a balanced engine condition. Transients are generated by defining the engine inputs as functions of time in a user written subroutine (TMRSP). Closed loop controls can also be simulated. DIGTEM is generalized in the aerothermodynamic treatment of components. This feature, along with DIGTEM's trimming at a design point, make it a very useful tool for developing a model of a specific turbofan engine.

A generalized computer code for developing dynamic gas turbine engine models (DIGTEM)

NASA Technical Reports Server (NTRS)

Daniele, C. J.

1983-01-01

This paper describes DIGTEM (digital turbofan engine model), a computer program that simulates two spool, two stream (turbofan) engines. DIGTEM was developed to support the development of a real time multiprocessor based engine simulator being designed at the Lewis Research Center. The turbofan engine model in DIGTEM contains steady state performance maps for all the components and has control volumes where continuity and energy balances are maintained. Rotor dynamics and duct momentum dynamics are also included. DIGTEM features an implicit integration scheme for integrating stiff systems and trims the model equations to match a prescribed design point by calculating correction coefficients that balance out the dynamic equations. It uses the same coefficients at off design points and iterates to a balanced engine condition. Transients are generated by defining the engine inputs as functions of time in a user written subroutine (TMRSP). Closed loop controls can also be simulated. DIGTEM is generalized in the aerothermodynamic treatment of components. This feature, along with DIGTEM's trimming at a design point, make it a very useful tool for developing a model of a specific turbofan engine.

Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble

NASA Astrophysics Data System (ADS)

Zheng, Lixin; Chen, Mohan; Sun, Zhaoru; Ko, Hsin-Yu; Santra, Biswajit; Dhuvad, Pratikkumar; Wu, Xifan

2018-04-01

We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient approximation (GGA) functional approximation and carry out systematic comparisons with the results obtained from the GGA-level Perdew-Burke-Ernzerhof (PBE) functional and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band gaps, and dipole moments. We find that the SCAN functional is generally more accurate than the other two functionals for liquid water by not only capturing the intermediate-range vdW interactions but also mitigating the overly strong hydrogen bonds prescribed in PBE simulations. We also compare the results of SCAN-based AIMD simulations in the canonical and isothermal-isobaric ensembles. Our results suggest that SCAN provides a reliable description for most structural, electronic, and dynamical properties in liquid water.

Dynamical Modeling of NGC 6397: Simulated HST Imaging

NASA Astrophysics Data System (ADS)

Dull, J. D.; Cohn, H. N.; Lugger, P. M.; Slavin, S. D.; Murphy, B. W.

1994-12-01

The proximity of NGC 6397 (2.2 kpc) provides an ideal opportunity to test current dynamical models for globular clusters with the HST Wide-Field/Planetary Camera (WFPC2)\\@. We have used a Monte Carlo algorithm to generate ensembles of simulated Planetary Camera (PC) U-band images of NGC 6397 from evolving, multi-mass Fokker-Planck models. These images, which are based on the post-repair HST-PC point-spread function, are used to develop and test analysis methods for recovering structural information from actual HST imaging. We have considered a range of exposure times up to 2.4times 10(4) s, based on our proposed HST Cycle 5 observations. Our Fokker-Planck models include energy input from dynamically-formed binaries. We have adopted a 20-group mass spectrum extending from 0.16 to 1.4 M_sun. We use theoretical luminosity functions for red giants and main sequence stars. Horizontal branch stars, blue stragglers, white dwarfs, and cataclysmic variables are also included. Simulated images are generated for cluster models at both maximal core collapse and at a post-collapse bounce. We are carrying out stellar photometry on these images using ``DAOPHOT-assisted aperture photometry'' software that we have developed. We are testing several techniques for analyzing the resulting star counts, to determine the underlying cluster structure, including parametric model fits and the nonparametric density estimation methods. Our simulated images also allow us to investigate the accuracy and completeness of methods for carrying out stellar photometry in HST Planetary Camera images of dense cluster cores.

Relevant interactions of antimicrobial iron chelators and membrane models revealed by nuclear magnetic resonance and molecular dynamics simulations.

PubMed

Coimbra, João T S; Moniz, Tânia; Brás, Natércia F; Ivanova, Galya; Fernandes, Pedro A; Ramos, Maria J; Rangel, Maria

2014-12-18

The dynamics and interaction of 3-hydroxy-4-pyridinone fluorescent iron chelators, exhibiting antimicrobial properties, with biological membranes were evaluated through NMR and molecular dynamics simulations. Both NMR and MD simulation results support a strong interaction of the chelators with the lipid bilayers that seems to be strengthened for the rhodamine containing compounds, in particular for compounds that include ethyl groups and a thiourea link. For the latter type of compounds the interaction reaches the hydrophobic core of the lipid bilayer. The molecular docking and MD simulations performed for the potential interaction of the chelators with DC-SIGN receptors provide valuable information regarding the cellular uptake of these compounds since the results show that the fluorophore fragment of the molecular framework is essential for an efficient binding. Putting together our previous and present results, we put forward the hypothesis that all the studied fluorescent chelators have access to the cell, their uptake occurs through different pathways and their permeation properties correlate with a better access to the cell and its compartments and, consequently, with the chelators antimicrobial properties.

Space robot simulator vehicle

NASA Technical Reports Server (NTRS)

Cannon, R. H., Jr.; Alexander, H.

1985-01-01

A Space Robot Simulator Vehicle (SRSV) was constructed to model a free-flying robot capable of doing construction, manipulation and repair work in space. The SRSV is intended as a test bed for development of dynamic and static control methods for space robots. The vehicle is built around a two-foot-diameter air-cushion vehicle that carries batteries, power supplies, gas tanks, computer, reaction jets and radio equipment. It is fitted with one or two two-link manipulators, which may be of many possible designs, including flexible-link versions. Both the vehicle body and its first arm are nearly complete. Inverse dynamic control of the robot's manipulator has been successfully simulated using equations generated by the dynamic simulation package SDEXACT. In this mode, the position of the manipulator tip is controlled not by fixing the vehicle base through thruster operation, but by controlling the manipulator joint torques to achieve the desired tip motion, while allowing for the free motion of the vehicle base. One of the primary goals is to minimize use of the thrusters in favor of intelligent control of the manipulator. Ways to reduce the computational burden of control are described.

Bicanonical ab Initio Molecular Dynamics for Open Systems.

PubMed

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

Dynamic modeling and verification of an energy-efficient greenhouse with an aquaponic system using TRNSYS

NASA Astrophysics Data System (ADS)

Amin, Majdi Talal

Currently, there is no integrated dynamic simulation program for an energy efficient greenhouse coupled with an aquaponic system. This research is intended to promote the thermal management of greenhouses in order to provide sustainable food production with the lowest possible energy use and material waste. A brief introduction of greenhouses, passive houses, energy efficiency, renewable energy systems, and their applications are included for ready reference. An experimental working scaled-down energy-efficient greenhouse was built to verify and calibrate the results of a dynamic simulation model made using TRNSYS software. However, TRNSYS requires the aid of Google SketchUp to develop 3D building geometry. The simulation model was built following the passive house standard as closely as possible. The new simulation model was then utilized to design an actual greenhouse with Aquaponics. It was demonstrated that the passive house standard can be applied to improve upon conventional greenhouse performance, and that it is adaptable to different climates. The energy-efficient greenhouse provides the required thermal environment for fish and plant growth, while eliminating the need for conventional cooling and heating systems.

Study of a Simulation Tool to Determine Achievable Control Dynamics and Control Power Requirements with Perfect Tracking

NASA Technical Reports Server (NTRS)

Ostroff, Aaron J.

1998-01-01

This paper contains a study of two methods for use in a generic nonlinear simulation tool that could be used to determine achievable control dynamics and control power requirements while performing perfect tracking maneuvers over the entire flight envelope. The two methods are NDI (nonlinear dynamic inversion) and the SOFFT(Stochastic Optimal Feedforward and Feedback Technology) feedforward control structure. Equivalent discrete and continuous SOFFT feedforward controllers have been developed. These equivalent forms clearly show that the closed-loop plant model loop is a plant inversion and is the same as the NDI formulation. The main difference is that the NDI formulation has a closed-loop controller structure whereas SOFFT uses an open-loop command model. Continuous, discrete, and hybrid controller structures have been developed and integrated into the formulation. Linear simulation results show that seven different configurations all give essentially the same response, with the NDI hybrid being slightly different. The SOFFT controller gave better tracking performance compared to the NDI controller when a nonlinear saturation element was added. Future plans include evaluation using a nonlinear simulation.

Modular, high power, variable R dynamic electrical load simulator

NASA Technical Reports Server (NTRS)

Joncas, K. P.

1974-01-01

The design of a previously developed basic variable R load simulator was entended to increase its power dissipation and transient handling capabilities. The delivered units satisfy all design requirements, and provides for a high power, modular simulation capability uniquely suited to the simulation of complex load responses. In addition to presenting conclusions and recommendations and pertinent background information, the report covers program accomplishments; describes the simulator basic circuits, transfer characteristic, protective features, assembly, and specifications; indicates the results of simulator evaluation, including burn-in and acceptance testing; provides acceptance test data; and summarizes the monthly progress reports.

Progress and supercomputing in computational fluid dynamics; Proceedings of U.S.-Israel Workshop, Jerusalem, Israel, December 1984

NASA Technical Reports Server (NTRS)

Murman, E. M. (Editor); Abarbanel, S. S. (Editor)

1985-01-01

Current developments and future trends in the application of supercomputers to computational fluid dynamics are discussed in reviews and reports. Topics examined include algorithm development for personal-size supercomputers, a multiblock three-dimensional Euler code for out-of-core and multiprocessor calculations, simulation of compressible inviscid and viscous flow, high-resolution solutions of the Euler equations for vortex flows, algorithms for the Navier-Stokes equations, and viscous-flow simulation by FEM and related techniques. Consideration is given to marching iterative methods for the parabolized and thin-layer Navier-Stokes equations, multigrid solutions to quasi-elliptic schemes, secondary instability of free shear flows, simulation of turbulent flow, and problems connected with weather prediction.

Use of computational fluid dynamics in respiratory medicine.

PubMed

Fernández Tena, Ana; Casan Clarà, Pere

2015-06-01

Computational Fluid Dynamics (CFD) is a computer-based tool for simulating fluid movement. The main advantages of CFD over other fluid mechanics studies include: substantial savings in time and cost, the analysis of systems or conditions that are very difficult to simulate experimentally (as is the case of the airways), and a practically unlimited level of detail. We used the Ansys-Fluent CFD program to develop a conducting airway model to simulate different inspiratory flow rates and the deposition of inhaled particles of varying diameters, obtaining results consistent with those reported in the literature using other procedures. We hope this approach will enable clinicians to further individualize the treatment of different respiratory diseases. Copyright © 2014 SEPAR. Published by Elsevier Espana. All rights reserved.

Three axis electronic flight motion simulator real time control system design and implementation

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

Gao, Zhiyuan; Miao, Zhonghua, E-mail: zhonghua-miao@163.com; Wang, Xiaohua

2014-12-15

A three axis electronic flight motion simulator is reported in this paper including the modelling, the controller design as well as the hardware implementation. This flight motion simulator could be used for inertial navigation test and high precision inertial navigation system with good dynamic and static performances. A real time control system is designed, several control system implementation problems were solved including time unification with parallel port interrupt, high speed finding-zero method of rotary inductosyn, zero-crossing management with continuous rotary, etc. Tests were carried out to show the effectiveness of the proposed real time control system.

Three axis electronic flight motion simulator real time control system design and implementation.

PubMed

Gao, Zhiyuan; Miao, Zhonghua; Wang, Xuyong; Wang, Xiaohua

2014-12-01

A three axis electronic flight motion simulator is reported in this paper including the modelling, the controller design as well as the hardware implementation. This flight motion simulator could be used for inertial navigation test and high precision inertial navigation system with good dynamic and static performances. A real time control system is designed, several control system implementation problems were solved including time unification with parallel port interrupt, high speed finding-zero method of rotary inductosyn, zero-crossing management with continuous rotary, etc. Tests were carried out to show the effectiveness of the proposed real time control system.

Hand controller commonality evaluation process

NASA Technical Reports Server (NTRS)

Stuart, Mark A.; Bierschwale, John M.; Wilmington, Robert P.; Adam, Susan C.; Diaz, Manuel F.; Jensen, Dean G.

1990-01-01

A hand controller evaluation process has been developed to determine the appropriate hand controller configurations for supporting remotely controlled devices. These devices include remote manipulator systems (RMS), dexterous robots, and remotely-piloted free flyers. Standard interfaces were developed to evaluate six different hand controllers in three test facilities including dynamic computer simulations, kinematic computer simulations, and physical simulations. The hand controllers under consideration were six degree-of-freedom (DOF) position and rate minimaster and joystick controllers, and three-DOF rate controllers. Task performance data, subjective comments, and anthropometric data obtained during tests were used for controller configuration recommendations to the SSF Program.

Impact Damage and Strain Rate Effects for Toughened Epoxy Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Minnetyan, Levon

2006-01-01

Structural integrity of composite systems under dynamic impact loading is investigated herein. The GENOA virtual testing software environment is used to implement the effects of dynamic loading on fracture progression and damage tolerance. Combinations of graphite and glass fibers with a toughened epoxy matrix are investigated. The effect of a ceramic coating for the absorption of impact energy is also included. Impact and post impact simulations include verification and prediction of (1) Load and Impact Energy, (2) Impact Damage Size, (3) Maximum Impact Peak Load, (4) Residual Strength, (5) Maximum Displacement, (6) Contribution of Failure Modes to Failure Mechanisms, (7) Prediction of Impact Load Versus Time, and (8) Damage, and Fracture Pattern. A computer model is utilized for the assessment of structural response, progressive fracture, and defect/damage tolerance characteristics. Results show the damage progression sequence and the changes in the structural response characteristics due to dynamic impact. The fundamental premise of computational simulation is that the complete evaluation of composite fracture requires an assessment of ply and subply level damage/fracture processes as the structure is subjected to loads. Simulation results for the graphite/epoxy composite were compared with the impact and tension failure test data, correlation and verification was obtained that included: (1) impact energy, (2) damage size, (3) maximum impact peak load, (4) residual strength, (5) maximum displacement, and (6) failure mechanisms of the composite structure.

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.

Integrated Simulation Design Challenges to Support TPS Repair Operations

NASA Technical Reports Server (NTRS)

Quiocho, Leslie J.; Crues, Edwin Z.; Huynh, An; Nguyen, Hung T.; MacLean, John

2006-01-01

During the Orbiter Repair Maneuver (OM) operations planned for Return to Flight (RTF), the Shuttle Remote Manipulator System (SRMS) must grapple the International Space Station (ISS), undock the Orbiter, maneuver it through a long duration trajectory, and orient it to an EVA crewman poised at the end of the Space Station Remote Manipulator System (SSRMS) to facilitate the repair of the Thermal Protection System (TPS). Once repair has been completed and confirmed, then the SRMS proceeds back through the trajectory to dock the Orbiter to the Orbiter Docking System. In order to support analysis of the complex dynamic interactions of the integrated system formed by the Orbiter, ISS, SRMS, and SSMS during the ORM, simulation tools used for previous nominal mission support required substantial enhancements. These upgrades were necessary to provide analysts with the capabilities needed to study integrated system performance. Prevalent throughout this ORM operation is a dynamically varying topology. In other words, the ORM starts with the SRMS grappled to the mated Shuttle/ISS stack (closed loop topology), moves to an open loop chain topology consisting of the Shuttle, SRMS, and ISS, and then, at the repair configuration, extends the chain topology to one consisting of the Shuttle, SMS, ISS, and SSRMS/EVA crewman. The resulting long dynamic chain of vehicles and manipulators may exhibit significant motion between the Shuttle worksite and the EVA crewman due to the system flexibility throughout the topology (particularly within the SRMS/SSRMS joints and links). Since the attachment points of both manipulators span the flexible structure of the ISS, simulation analysis may also need to take that into consideration. Moreover, due to the lengthy time duration associated with the maneuver and repair, orbital effects become a factor and require the ISS vehicle control system to maintain active attitude control. Several facets of the ORM operation make the associated analytical efforts different from previous mission support, including: (1) the magnitude of the SRMS handled payload (Le., Orbiter class), (2) the orbital effects induced on the integrated system consisting of the large Shuttle and ISS masses connected by a light flexible SRMS, (3) long duration environmental consequences due to the lengthy operational times associated with the maneuver and repair of the TPS, (4) active attitude control (as opposed to free drift) interacting with the SRMS and SSRMS manipulators (also due to the length of the maneuver and repair), (5) relative dynamics between the EVA crewman and thc worksite influenced by the extended flexible topology. In order to meet these analysis challenges, an O Msi mulation architecture was developed leveraging upon numerous pre-existing simulation elements to analyze the various subsystems individually. For example, core manipulator subsystem simulations for both the SRMS and SSRMS were originally combined to provide the dual-arm dynamics topology simulation (in the absence of orbital dynamics and vehicle control). This capability was later merged with the simulation used to analyze SRMS loading with a heavy payload in the orbital environment with an active payload control system (in this case, the ISS Attitude Control System (ACS)), configured for the ORM. The resulting worksite dynamics simulation, based off of the modified ORM simulation, provided the extended topological chain of vehicles and manipulators, while taking into account the orbital effects of both the Shuttle and ISS (as well as its ACS). Verification and validation (V&V) of these integrated simulations became a challenge in itself. A systematic approach needed to be developed such that integration simulation results could be tested against previous constituent simulations upon which these simulations were built. General V&V categories included: (1) core orbital state propagation, (2), stand-alone SRMS, (3) stand-alone SSRMS, (4) stand-alone ISS ACS, (5)ntegrated Shuttle, SRMS, ISS (with active ACS) in the orbital environment, and (5) dual-arm SRMS/SSRMS dynamics topology. Integrated simulation V&V run suites were created and correlated to verification runs from subsystem simulations, in order to establish the validity of the results. This paper discusses the simulation design challenges encountered while developing simulation capabilities to mirror the ORM operations. The paper also describes the incremental build approach that was utilized, starting with the subsystem simulation elements and integration into increasing more complex simulations until the resulting ORM worksite dynamics simulation had been assembled. Furthermore, the paper presents an overall integrated simulation V&V methodology based upon a subsystem level testing, integrated comparisons, and phased checkout.

A 4-cylinder Stirling engine computer program with dynamic energy equations

NASA Technical Reports Server (NTRS)

Daniele, C. J.; Lorenzo, C. F.

1983-01-01

A computer program for simulating the steady state and transient performance of a four cylinder Stirling engine is presented. The thermodynamic model includes both continuity and energy equations and linear momentum terms (flow resistance). Each working space between the pistons is broken into seven control volumes. Drive dynamics and vehicle load effects are included. The model contains 70 state variables. Also included in the model are piston rod seal leakage effects. The computer program includes a model of a hydrogen supply system, from which hydrogen may be added to the system to accelerate the engine. Flow charts are provided.

Exploring the Dynamics of Exoplanetary Systems in a Young Stellar Cluster

NASA Astrophysics Data System (ADS)

Thornton, Jonathan Daniel; Glaser, Joseph Paul; Wall, Joshua Edward

2018-01-01

I describe a dynamical simulation of planetary systems in a young star cluster. One rather arbitrary aspect of cluster simulations is the choice of initial conditions. These are typically chosen from some standard model, such as Plummer or King, or from a “fractal” distribution to try to model young clumpy systems. Here I adopt the approach of realizing an initial cluster model directly from a detailed magnetohydrodynamical model of cluster formation from a 1000-solar-mass interstellar gas cloud, with magnetic fields and radiative and wind feedback from massive stars included self-consistently. The N-body simulation of the stars and planets starts once star formation is largely over and feedback has cleared much of the gas from the region where the newborn stars reside. It continues until the cluster dissolves in the galactic field. Of particular interest is what would happen to the free-floating planets created in the gas cloud simulation. Are they captured by a star or are they ejected from the cluster? This method of building a dynamical cluster simulation directly from the results of a cluster formation model allows us to better understand the evolution of young star clusters and enriches our understanding of extrasolar planet development in them. These simulations were performed within the AMUSE simulation framework, and combine N-body, multiples and background potential code.

Dynamics of stellar black holes in young star clusters with different metallicities - II. Black hole-black hole binaries

NASA Astrophysics Data System (ADS)

Ziosi, Brunetto Marco; Mapelli, Michela; Branchesi, Marica; Tormen, Giuseppe

2014-07-01

In this paper, we study the formation and dynamical evolution of black hole-black hole (BH-BH) binaries in young star clusters (YSCs), by means of N-body simulations. The simulations include metallicity-dependent recipes for stellar evolution and stellar winds, and have been run for three different metallicities (Z = 0.01, 0.1 and 1 Z⊙). Following recent theoretical models of wind mass-loss and core-collapse supernovae, we assume that the mass of the stellar remnants depends on the metallicity of the progenitor stars. We find that BH-BH binaries form efficiently because of dynamical exchanges: in our simulations, we find about 10 times more BH-BH binaries than double neutron star binaries. The simulated BH-BH binaries form earlier in metal-poor YSCs, which host more massive black holes (BHs) than in metal-rich YSCs. The simulated BH-BH binaries have very large chirp masses (up to 80 M⊙), because the BH mass is assumed to depend on metallicity, and because BHs can grow in mass due to the merger with stars. The simulated BH-BH binaries span a wide range of orbital periods (10-3-107 yr), and only a small fraction of them (0.3 per cent) is expected to merge within a Hubble time. We discuss the estimated merger rate from our simulations and the implications for Advanced VIRGO and LIGO.

Off-fault plasticity in three-dimensional dynamic rupture simulations using a modal Discontinuous Galerkin method on unstructured meshes: Implementation, verification, and application

NASA Astrophysics Data System (ADS)

Wollherr, Stephanie; Gabriel, Alice-Agnes; Uphoff, Carsten

2018-05-01

The dynamics and potential size of earthquakes depend crucially on rupture transfers between adjacent fault segments. To accurately describe earthquake source dynamics, numerical models can account for realistic fault geometries and rheologies such as nonlinear inelastic processes off the slip interface. We present implementation, verification, and application of off-fault Drucker-Prager plasticity in the open source software SeisSol (www.seissol.org). SeisSol is based on an arbitrary high-order derivative modal Discontinuous Galerkin (ADER-DG) method using unstructured, tetrahedral meshes specifically suited for complex geometries. Two implementation approaches are detailed, modelling plastic failure either employing sub-elemental quadrature points or switching to nodal basis coefficients. At fine fault discretizations the nodal basis approach is up to 6 times more efficient in terms of computational costs while yielding comparable accuracy. Both methods are verified in community benchmark problems and by three dimensional numerical h- and p-refinement studies with heterogeneous initial stresses. We observe no spectral convergence for on-fault quantities with respect to a given reference solution, but rather discuss a limitation to low-order convergence for heterogeneous 3D dynamic rupture problems. For simulations including plasticity, a high fault resolution may be less crucial than commonly assumed, due to the regularization of peak slip rate and an increase of the minimum cohesive zone width. In large-scale dynamic rupture simulations based on the 1992 Landers earthquake, we observe high rupture complexity including reverse slip, direct branching, and dynamic triggering. The spatio-temporal distribution of rupture transfers are altered distinctively by plastic energy absorption, correlated with locations of geometrical fault complexity. Computational cost increases by 7% when accounting for off-fault plasticity in the demonstrating application. Our results imply that the combination of fully 3D dynamic modelling, complex fault geometries, and off-fault plastic yielding is important to realistically capture dynamic rupture transfers in natural fault systems.

Parallel replica dynamics with a heterogeneous distribution of barriers: Application to n-hexadecane pyrolysis

NASA Astrophysics Data System (ADS)

Kum, Oyeon; Dickson, Brad M.; Stuart, Steven J.; Uberuaga, Blas P.; Voter, Arthur F.

2004-11-01

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of Ea=79.7 kcal/mol and log A/s-1=14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used.

Development of a rotorcraft. Propulsion dynamics interface analysis, volume 2

NASA Technical Reports Server (NTRS)

Hull, R.

1982-01-01

A study was conducted to establish a coupled rotor/propulsion analysis that would be applicable to a wide range of rotorcraft systems. The effort included the following tasks: (1) development of a model structure suitable for simulating a wide range of rotorcraft configurations; (2) defined a methodology for parameterizing the model structure to represent a particular rotorcraft; (3) constructing a nonlinear coupled rotor/propulsion model as a test case to use in analyzing coupled system dynamics; and (4) an attempt to develop a mostly linear coupled model derived from the complete nonlinear simulations. Documentation of the computer models developed is presented.

First-principles electron dynamics control simulation of diamond under femtosecond laser pulse train irradiation.

PubMed

Wang, Cong; Jiang, Lan; Wang, Feng; Li, Xin; Yuan, Yanping; Xiao, Hai; Tsai, Hai-Lung; Lu, Yongfeng

2012-07-11

A real-time and real-space time-dependent density functional is applied to simulate the nonlinear electron-photon interactions during shaped femtosecond laser pulse train ablation of diamond. Effects of the key pulse train parameters such as the pulse separation, spatial/temporal pulse energy distribution and pulse number per train on the electron excitation and energy absorption are discussed. The calculations show that photon-electron interactions and transient localized electron dynamics can be controlled including photon absorption, electron excitation, electron density, and free electron distribution by the ultrafast laser pulse train.

Wavelet Monte Carlo dynamics: A new algorithm for simulating the hydrodynamics of interacting Brownian particles

NASA Astrophysics Data System (ADS)

Dyer, Oliver T.; Ball, Robin C.

2017-03-01

We develop a new algorithm for the Brownian dynamics of soft matter systems that evolves time by spatially correlated Monte Carlo moves. The algorithm uses vector wavelets as its basic moves and produces hydrodynamics in the low Reynolds number regime propagated according to the Oseen tensor. When small moves are removed, the correlations closely approximate the Rotne-Prager tensor, itself widely used to correct for deficiencies in Oseen. We also include plane wave moves to provide the longest range correlations, which we detail for both infinite and periodic systems. The computational cost of the algorithm scales competitively with the number of particles simulated, N, scaling as N In N in homogeneous systems and as N in dilute systems. In comparisons to established lattice Boltzmann and Brownian dynamics algorithms, the wavelet method was found to be only a factor of order 1 times more expensive than the cheaper lattice Boltzmann algorithm in marginally semi-dilute simulations, while it is significantly faster than both algorithms at large N in dilute simulations. We also validate the algorithm by checking that it reproduces the correct dynamics and equilibrium properties of simple single polymer systems, as well as verifying the effect of periodicity on the mobility tensor.

Structural Properties of Human IAPP Dimer in Membrane Environment Studied by All-Atom Molecular Dynamics Simulations.

PubMed

Liu, Na; Duan, Mojie; Yang, Minghui

2017-08-11

The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP. In this study, all-atom bias-exchange metadynamics (BE-Meta) and unbiased molecular dynamics simulations were employed to study the structural properties of IAPP dimer in the membranes environments. A number of intermediates, including α-helical states, β-sheet states, and fully disordered states, are identified. The formation of N-terminal β-sheet structure is prior to the C-terminal β-sheet structure towards the final fibril-like structures. The α-helical intermediates have lower propensity in the dimeric hIAPP and are off-pathway intermediates. The simulations also demonstrate that the β-sheet intermediates induce more perturbation on the membrane than the α-helical and disordered states and thus pose higher disruption ability.

3D Dynamic Rupture Simulations along Dipping Faults, with a focus on the Wasatch Fault Zone, Utah

NASA Astrophysics Data System (ADS)

Withers, K.; Moschetti, M. P.

2017-12-01

We study dynamic rupture and ground motion from dip-slip faults in regions that have high-seismic hazard, such as the Wasatch fault zone, Utah. Previous numerical simulations have modeled deterministic ground motion along segments of this fault in the heavily populated regions near Salt Lake City but were restricted to low frequencies ( 1 Hz). We seek to better understand the rupture process and assess broadband ground motions and variability from the Wasatch Fault Zone by extending deterministic ground motion prediction to higher frequencies (up to 5 Hz). We perform simulations along a dipping normal fault (40 x 20 km along strike and width, respectively) with characteristics derived from geologic observations to generate a suite of ruptures > Mw 6.5. This approach utilizes dynamic simulations (fully physics-based models, where the initial stress drop and friction law are imposed) using a summation by parts (SBP) method. The simulations include rough-fault topography following a self-similar fractal distribution (over length scales from 100 m to the size of the fault) in addition to off-fault plasticity. Energy losses from heat and other mechanisms, modeled as anelastic attenuation, are also included, as well as free-surface topography, which can significantly affect ground motion patterns. We compare the effect of material structure and both rate and state and slip-weakening friction laws have on rupture propagation. The simulations show reduced slip and moment release in the near surface with the inclusion of plasticity, better agreeing with observations of shallow slip deficit. Long-wavelength fault geometry imparts a non-uniform stress distribution along both dip and strike, influencing the preferred rupture direction and hypocenter location, potentially important for seismic hazard estimation.