AdapChem

NASA Technical Reports Server (NTRS)

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

2012-01-01

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

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

PubMed Central

Schöneberg, Johannes; Noé, Frank

2013-01-01

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics. PMID:24040218

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.

Modeling Tools Predict Flow in Fluid Dynamics

NASA Technical Reports Server (NTRS)

2010-01-01

"Because rocket engines operate under extreme temperature and pressure, they present a unique challenge to designers who must test and simulate the technology. To this end, CRAFT Tech Inc., of Pipersville, Pennsylvania, won Small Business Innovation Research (SBIR) contracts from Marshall Space Flight Center to develop software to simulate cryogenic fluid flows and related phenomena. CRAFT Tech enhanced its CRUNCH CFD (computational fluid dynamics) software to simulate phenomena in various liquid propulsion components and systems. Today, both government and industry clients in the aerospace, utilities, and petrochemical industries use the software for analyzing existing systems as well as designing new ones."

Dynamic Simulation over Long Time Periods with 100% Solar Generation.

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

Concepcion, Ricky James; Elliott, Ryan Thomas

2015-12-01

This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.

A system for automatic evaluation of simulation software

NASA Technical Reports Server (NTRS)

Ryan, J. P.; Hodges, B. C.

1976-01-01

Within the field of computer software, simulation and verification are complementary processes. Simulation methods can be used to verify software by performing variable range analysis. More general verification procedures, such as those described in this paper, can be implicitly, viewed as attempts at modeling the end-product software. From software requirement methodology, each component of the verification system has some element of simulation to it. Conversely, general verification procedures can be used to analyze simulation software. A dynamic analyzer is described which can be used to obtain properly scaled variables for an analog simulation, which is first digitally simulated. In a similar way, it is thought that the other system components and indeed the whole system itself have the potential of being effectively used in a simulation environment.

Virtual acoustic environments for comprehensive evaluation of model-based hearing devices.

PubMed

Grimm, Giso; Luberadzka, Joanna; Hohmann, Volker

2018-06-01

Create virtual acoustic environments (VAEs) with interactive dynamic rendering for applications in audiology. A toolbox for creation and rendering of dynamic virtual acoustic environments (TASCAR) that allows direct user interaction was developed for application in hearing aid research and audiology. The software architecture and the simulation methods used to produce VAEs are outlined. Example environments are described and analysed. With the proposed software, a tool for simulation of VAEs is available. A set of VAEs rendered with the proposed software was described.

Look-ahead Dynamic Simulation

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

2015-10-20

Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.

Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure

NASA Astrophysics Data System (ADS)

Hu, Changjun; Bai, He; He, Xinfu; Zhang, Boyao; Nie, Ningming; Wang, Xianmeng; Ren, Yingwen

2017-02-01

Material irradiation effect is one of the most important keys to use nuclear power. However, the lack of high-throughput irradiation facility and knowledge of evolution process, lead to little understanding of the addressed issues. With the help of high-performance computing, we could make a further understanding of micro-level-material. In this paper, a new data structure is proposed for the massively parallel simulation of the evolution of metal materials under irradiation environment. Based on the proposed data structure, we developed the new molecular dynamics software named Crystal MD. The simulation with Crystal MD achieved over 90% parallel efficiency in test cases, and it takes more than 25% less memory on multi-core clusters than LAMMPS and IMD, which are two popular molecular dynamics simulation software. Using Crystal MD, a two trillion particles simulation has been performed on Tianhe-2 cluster.

FAST Simulation Tool Containing Methods for Predicting the Dynamic Response of Wind Turbines

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

Jonkman, Jason

2015-08-12

FAST is a simulation tool (computer software) for modeling tlie dynamic response of horizontal-axis wind turbines. FAST employs a combined modal and multibody structural-dynamics formulation in the time domain.

Stability analysis using SDSA tool

NASA Astrophysics Data System (ADS)

Goetzendorf-Grabowski, Tomasz; Mieszalski, Dawid; Marcinkiewicz, Ewa

2011-11-01

The SDSA (Simulation and Dynamic Stability Analysis) application is presented as a tool for analysing the dynamic characteristics of the aircraft just in the conceptual design stage. SDSA is part of the CEASIOM (Computerized Environment for Aircraft Synthesis and Integrated Optimization Methods) software environment which was developed within the SimSAC (Simulating Aircraft Stability And Control Characteristics for Use in Conceptual Design) project, funded by the European Commission 6th Framework Program. SDSA can also be used as stand alone software, and integrated with other design and optimisation systems using software wrappers. This paper focuses on the main functionalities of SDSA and presents both computational and free flight experimental results to compare and validate the presented software. Two aircraft are considered, the EADS Ranger 2000 and the Warsaw University designed PW-6 glider. For the two cases considered here the SDSA software is shown to be an excellent tool for predicting dynamic characteristics of an aircraft.

Adaptive Integration of Nonsmooth Dynamical Systems

DTIC Science & Technology

2017-10-11

controlled time stepping method to interactively design running robots. [1] John Shepherd, Samuel Zapolsky, and Evan M. Drumwright, “Fast multi-body...software like this to test software running on my robots. Started working in simulation after attempting to use software like this to test software... running on my robots. The libraries that produce these beautiful results have failed at simulating robotic manipulation. Postulate: It is easier to

Dynamic Modelling with "MLE-Energy Dynamic" for Primary School

NASA Astrophysics Data System (ADS)

Giliberti, Enrico; Corni, Federico

During the recent years simulation and modelling are growing instances in science education. In primary school, however, the main use of software is the simulation, due to the lack of modelling software tools specially designed to fit/accomplish the needs of primary education. In particular primary school teachers need to use simulation in a framework that is both consistent and simple enough to be understandable by children [2]. One of the possible area to approach modelling is about the construction of the concept of energy, in particular for what concerns the relations among substance, potential, power [3]. Following the previous initial research results with this approach [2], and with the static version of the software MLE Energy [1], we suggest the design and the experimentation of a dynamic modelling software—MLE dynamic-capable to represent dynamically the relations occurring when two substance-like quantities exchange energy, modifying their potential. By means of this software the user can graphically choose the dependent and independent variables and leave the other parameters fixed. The software has been initially evaluated, during a course of science education with a group of primary school teachers-to-be, to test the ability of the software to improve teachers' way of thinking in terms of substance-like quantities and their effects (graphical representation of the extensive, intensive variables and their mutual relations); moreover, the software has been tested with a group of primary school teachers, asking their opinion about the software didactical relevance in the class work.

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

USGS Publications Warehouse

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

2004-01-01

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

Using CONFIG for Simulation of Operation of Water Recovery Subsystems for Advanced Control Software Evaluation

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Flores, Luis; Fleming, Land; Throop, Daiv

2002-01-01

A hybrid discrete/continuous simulation tool, CONFIG, has been developed to support evaluation of the operability life support systems. CON FIG simulates operations scenarios in which flows and pressures change continuously while system reconfigurations occur as discrete events. In simulations, intelligent control software can interact dynamically with hardware system models. CONFIG simulations have been used to evaluate control software and intelligent agents for automating life support systems operations. A CON FIG model of an advanced biological water recovery system has been developed to interact with intelligent control software that is being used in a water system test at NASA Johnson Space Center

Dynamic computer simulations of electrophoresis: three decades of active research.

PubMed

Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A

2009-06-01

Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

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

Segre, Daniel

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

A Low Cost Microcomputer System for Process Dynamics and Control Simulations.

ERIC Educational Resources Information Center

Crowl, D. A.; Durisin, M. J.

1983-01-01

Discusses a video simulator microcomputer system used to provide real-time demonstrations to strengthen students' understanding of process dynamics and control. Also discusses hardware/software and simulations developed using the system. The four simulations model various configurations of a process liquid level tank system. (JN)

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.

Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

MD Simulations of P-Type ATPases in a Lipid Bilayer System.

PubMed

Autzen, Henriette Elisabeth; Musgaard, Maria

2016-01-01

Molecular dynamics (MD) simulation is a computational method which provides insight on protein dynamics with high resolution in both space and time, in contrast to many experimental techniques. MD simulations can be used as a stand-alone method to study P-type ATPases as well as a complementary method aiding experimental studies. In particular, MD simulations have proved valuable in generating and confirming hypotheses relating to the structure and function of P-type ATPases. In the following, we describe a detailed practical procedure on how to set up and run a MD simulation of a P-type ATPase embedded in a lipid bilayer using software free of use for academics. We emphasize general considerations and problems typically encountered when setting up simulations. While full coverage of all possible procedures is beyond the scope of this chapter, we have chosen to illustrate the MD procedure with the Nanoscale Molecular Dynamics (NAMD) and the Visual Molecular Dynamics (VMD) software suites.

DynamO: a free O(N) general event-driven molecular dynamics simulator.

PubMed

Bannerman, M N; Sargant, R; Lue, L

2011-11-30

Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo. Copyright © 2011 Wiley Periodicals, Inc.

MOLSIM: A modular molecular simulation software

PubMed Central

Jurij, Reščič

2015-01-01

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25994597

Integrating Multibody Simulation and CFD: toward Complex Multidisciplinary Design Optimization

NASA Astrophysics Data System (ADS)

Pieri, Stefano; Poloni, Carlo; Mühlmeier, Martin

This paper describes the use of integrated multidisciplinary analysis and optimization of a race car model on a predefined circuit. The objective is the definition of the most efficient geometric configuration that can guarantee the lowest lap time. In order to carry out this study it has been necessary to interface the design optimization software modeFRONTIER with the following softwares: CATIA v5, a three dimensional CAD software, used for the definition of the parametric geometry; A.D.A.M.S./Motorsport, a multi-body dynamic simulation software; IcemCFD, a mesh generator, for the automatic generation of the CFD grid; CFX, a Navier-Stokes code, for the fluid-dynamic forces prediction. The process integration gives the possibility to compute, for each geometrical configuration, a set of aerodynamic coefficients that are then used in the multiboby simulation for the computation of the lap time. Finally an automatic optimization procedure is started and the lap-time minimized. The whole process is executed on a Linux cluster running CFD simulations in parallel.

Faster Aerodynamic Simulation With Cart3D

NASA Technical Reports Server (NTRS)

2003-01-01

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

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

NASA Astrophysics Data System (ADS)

Shkurti, Ardita; Goni, Ramon; Andrio, Pau; Breitmoser, Elena; Bethune, Iain; Orozco, Modesto; Laughton, Charles A.

The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.

Software tools for data modelling and processing of human body temperature circadian dynamics.

PubMed

Petrova, Elena S; Afanasova, Anastasia I

2015-01-01

This paper is presenting a software development for simulating and processing thermometry data. The motivation of this research is the miniaturization of actuators attached to human body which allow frequent temperature measurements and improve the medical diagnosis procedures related to circadian dynamics.

The SEL Adapts to Meet Changing Times

NASA Technical Reports Server (NTRS)

Pajerski, Rose S.; Basili, Victor R.

1997-01-01

Since 1976, the Software Engineering Laboratory (SEL) has been dedicated to understanding and improving the way in which one NASA organization, the Flight Dynamics Division (FDD) at Goddard Space Flight Center, develops, maintains, and manages complex flight dynamics systems. It has done this by developing and refining a continual process improvement approach that allows an organization such as the FDD to fine-tune its process for its particular domain. Experimental software engineering and measurement play a significant role in this approach. The SEL is a partnership of NASA Goddard, its major software contractor, Computer Sciences Corporation (CSC), and the University of Maryland's (LTM) Department of Computer Science. The FDD primarily builds software systems that provide ground-based flight dynamics support for scientific satellites. They fall into two sets: ground systems and simulators. Ground systems are midsize systems that average around 250 thousand source lines of code (KSLOC). Ground system development projects typically last 1 - 2 years. Recent systems have been rehosted to workstations from IBM mainframes, and also contain significant new subsystems written in C and C++. The simulators are smaller systems averaging around 60 KSLOC that provide the test data for the ground systems. Simulator development lasts up to 1 year. Most of the simulators have been built in Ada on workstations. The SEL is responsible for the management and continual improvement of the software engineering processes used on these FDD projects.

Finite element for rotor/stator interactive forces in general engine dynamic simulation. Part 1: Development of bearing damper element

NASA Technical Reports Server (NTRS)

Adams, M. L.; Padovan, J.; Fertis, D. G.

1980-01-01

A general purpose squeeze-film damper interactive force element was developed, coded into a software package (module) and debugged. This software package was applied to nonliner dynamic analyses of some simple rotor systems. Results for pressure distributions show that the long bearing (end sealed) is a stronger bearing as compared to the short bearing as expected. Results of the nonlinear dynamic analysis, using a four degree of freedom simulation model, showed that the orbit of the rotating shaft increases nonlinearity to fill the bearing clearance as the unbalanced weight increases.

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.

System Engineering Approach to Assessing Integrated Survivability

DTIC Science & Technology

2009-08-01

based response for the above engagements using LS- Dyna for blast modelling, MADYMO for safety and human response, CFD software (Fluent) is used to...Simulation JFAS Joint Force Analysis Simulation JANUS Joint Army Navy Uniform Simulation LS- DYNA Livermore Software-Dynamics MADYMO...management technologies. The “don’t be killed” layer of survivability protection accounts for many of the mitigation technologies (i.e. blast

Comparisons of Kinematics and Dynamics Simulation Software Tools

NASA Technical Reports Server (NTRS)

Shiue, Yeu-Sheng Paul

2002-01-01

Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.

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

Walker, La Tonya Nicole; Malczynski, Leonard A.

DYNAMO is a computer program for building and running 'continuous' simulation models. It was developed by the Industrial Dynamics Group at the Massachusetts Institute of Technology for simulating dynamic feedback models of business, economic, and social systems. The history of the system dynamics method since 1957 includes many classic models built in DYANMO. It was not until the late 1980s that software was built to take advantage of the rise of personal computers and graphical user interfaces that DYNAMO was supplanted. There is much learning and insight to be gained from examining the DYANMO models and their accompanying research papers.more » We believe that it is a worthwhile exercise to convert DYNAMO models to more recent software packages. We have made an attempt to make it easier to turn these models into a more current system dynamics software language, Powersim © Studio produced by Powersim AS 2 of Bergen, Norway. This guide shows how to convert DYNAMO syntax into Studio syntax.« less

Propulsive Reaction Control System Model

NASA Technical Reports Server (NTRS)

Brugarolas, Paul; Phan, Linh H.; Serricchio, Frederick; San Martin, Alejandro M.

2011-01-01

This software models a propulsive reaction control system (RCS) for guidance, navigation, and control simulation purposes. The model includes the drive electronics, the electromechanical valve dynamics, the combustion dynamics, and thrust. This innovation follows the Mars Science Laboratory entry reaction control system design, and has been created to meet the Mars Science Laboratory (MSL) entry, descent, and landing simulation needs. It has been built to be plug-and-play on multiple MSL testbeds [analysis, Monte Carlo, flight software development, hardware-in-the-loop, and ATLO (assembly, test and launch operations) testbeds]. This RCS model is a C language program. It contains two main functions: the RCS electronics model function that models the RCS FPGA (field-programmable-gate-array) processing and commanding of the RCS valve, and the RCS dynamic model function that models the valve and combustion dynamics. In addition, this software provides support functions to initialize the model states, set parameters, access model telemetry, and access calculated thruster forces.

ATK-ForceField: a new generation molecular dynamics software package

NASA Astrophysics Data System (ADS)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations

NASA Technical Reports Server (NTRS)

Norman, Michael L.

1997-01-01

Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.

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.

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

PubMed Central

Zuckerman, Daniel M.; Chong, Lillian T.

2018-01-01

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling—the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes—protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation. PMID:28301772

ISS Material Science Research Rack HWIL Interface Simulation

NASA Technical Reports Server (NTRS)

Williams, Philip J.; Ballard, Gary H.; Crumbley, Robert T. (Technical Monitor)

2002-01-01

In this paper, the first Material Science Research Rack (MSRR-1) hardware-in-the-loop (HWIL) interface simulation is described. Dynamic Concepts developed this HWIL simulation system with funding and management provided by the Flight Software group (ED14) of NASA-MSFC's Avionics Department. The HWIL system has been used both as a flight software development environment and as a software qualification tool. To fulfill these roles, the HWIL simulator accurately models the system dynamics of many MSRR-1 subsystems and emulates most of the internal interface signals. The modeled subsystems include the Experiment Modules, the Thermal Environment Control System, the Vacuum Access System, the Solid State Power Controller Module, and the Active Rack Isolation Systems. The emulated signals reside on three separate MIL-STD-1553B digital communication buses, the ISS Medium Rate Data Link, and several analog controller and sensor signals. To enhance the range of testing, it was necessary to simulate several off-nominal conditions that may occur in the interfacing subsystems.

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.

PubMed

Zuckerman, Daniel M; Chong, Lillian T

2017-05-22

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.

A Decision Tool that Combines Discrete Event Software Process Models with System Dynamics Pieces for Software Development Cost Estimation and Analysis

NASA Technical Reports Server (NTRS)

Mizell, Carolyn Barrett; Malone, Linda

2007-01-01

The development process for a large software development project is very complex and dependent on many variables that are dynamic and interrelated. Factors such as size, productivity and defect injection rates will have substantial impact on the project in terms of cost and schedule. These factors can be affected by the intricacies of the process itself as well as human behavior because the process is very labor intensive. The complex nature of the development process can be investigated with software development process models that utilize discrete event simulation to analyze the effects of process changes. The organizational environment and its effects on the workforce can be analyzed with system dynamics that utilizes continuous simulation. Each has unique strengths and the benefits of both types can be exploited by combining a system dynamics model and a discrete event process model. This paper will demonstrate how the two types of models can be combined to investigate the impacts of human resource interactions on productivity and ultimately on cost and schedule.

Visual NNet: An Educational ANN's Simulation Environment Reusing Matlab Neural Networks Toolbox

ERIC Educational Resources Information Center

Garcia-Roselló, Emilio; González-Dacosta, Jacinto; Lado, Maria J.; Méndez, Arturo J.; Garcia Pérez-Schofield, Baltasar; Ferrer, Fátima

2011-01-01

Artificial Neural Networks (ANN's) are nowadays a common subject in different curricula of graduate and postgraduate studies. Due to the complex algorithms involved and the dynamic nature of ANN's, simulation software has been commonly used to teach this subject. This software has usually been developed specifically for learning purposes, because…

Training Knowledge Bots for Physics-Based Simulations Using Artificial Neural Networks

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.; Wong, Jay Ming

2014-01-01

Millions of complex physics-based simulations are required for design of an aerospace vehicle. These simulations are usually performed by highly trained and skilled analysts, who execute, monitor, and steer each simulation. Analysts rely heavily on their broad experience that may have taken 20-30 years to accumulate. In addition, the simulation software is complex in nature, requiring significant computational resources. Simulations of system of systems become even more complex and are beyond human capacity to effectively learn their behavior. IBM has developed machines that can learn and compete successfully with a chess grandmaster and most successful jeopardy contestants. These machines are capable of learning some complex problems much faster than humans can learn. In this paper, we propose using artificial neural network to train knowledge bots to identify the idiosyncrasies of simulation software and recognize patterns that can lead to successful simulations. We examine the use of knowledge bots for applications of computational fluid dynamics (CFD), trajectory analysis, commercial finite-element analysis software, and slosh propellant dynamics. We will show that machine learning algorithms can be used to learn the idiosyncrasies of computational simulations and identify regions of instability without including any additional information about their mathematical form or applied discretization approaches.

Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

PubMed

Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

2017-01-01

Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

Dynamic Simulation of AN Helium Refrigerator

NASA Astrophysics Data System (ADS)

Deschildre, C.; Barraud, A.; Bonnay, P.; Briend, P.; Girard, A.; Poncet, J. M.; Roussel, P.; Sequeira, S. E.

2008-03-01

A dynamic simulation of a large scale existing refrigerator has been performed using the software Aspen Hysys®. The model comprises the typical equipments of a cryogenic system: heat exchangers, expanders, helium phase separators and cold compressors. It represents the 400 W @ 1.8 K Test Facility located at CEA—Grenoble. This paper describes the model development and shows the possibilities and limitations of the dynamic module of Aspen Hysys®. Then, comparison between simulation results and experimental data are presented; the simulation of cooldown process was also performed.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

Simulation of a Canard in Fluid Flow Driven by a Piezoelectric Beam with a Software Control Loop

DTIC Science & Technology

2014-04-01

The canard is actuated by a piezoelectric beam that bends as voltage is applied. The voltage is controlled by a software subroutine that measures...Dynamic system Modeling Co-simulation Simulation Abaqus Finite element analysis (FEA) Finite element method (FEM) Computational...is unlimited. i CONTENTS Page Introduction 1 Model Description 1 Fluid Model 2 Structural Model 3 Control Subroutine 4 Results 4

Control Parameters Optimization Based on Co-Simulation of a Mechatronic System for an UA-Based Two-Axis Inertially Stabilized Platform.

PubMed

Zhou, Xiangyang; Zhao, Beilei; Gong, Guohao

2015-08-14

This paper presents a method based on co-simulation of a mechatronic system to optimize the control parameters of a two-axis inertially stabilized platform system (ISP) applied in an unmanned airship (UA), by which high control performance and reliability of the ISP system are achieved. First, a three-dimensional structural model of the ISP is built by using the three-dimensional parametric CAD software SOLIDWORKS(®); then, to analyze the system's kinematic and dynamic characteristics under operating conditions, dynamics modeling is conducted by using the multi-body dynamics software ADAMS™, thus the main dynamic parameters such as displacement, velocity, acceleration and reaction curve are obtained, respectively, through simulation analysis. Then, those dynamic parameters were input into the established MATLAB(®) SIMULINK(®) controller to simulate and test the performance of the control system. By these means, the ISP control parameters are optimized. To verify the methods, experiments were carried out by applying the optimized parameters to the control system of a two-axis ISP. The results show that the co-simulation by using virtual prototyping (VP) is effective to obtain optimized ISP control parameters, eventually leading to high ISP control performance.

Control Parameters Optimization Based on Co-Simulation of a Mechatronic System for an UA-Based Two-Axis Inertially Stabilized Platform

PubMed Central

Zhou, Xiangyang; Zhao, Beilei; Gong, Guohao

2015-01-01

This paper presents a method based on co-simulation of a mechatronic system to optimize the control parameters of a two-axis inertially stabilized platform system (ISP) applied in an unmanned airship (UA), by which high control performance and reliability of the ISP system are achieved. First, a three-dimensional structural model of the ISP is built by using the three-dimensional parametric CAD software SOLIDWORKS®; then, to analyze the system’s kinematic and dynamic characteristics under operating conditions, dynamics modeling is conducted by using the multi-body dynamics software ADAMS™, thus the main dynamic parameters such as displacement, velocity, acceleration and reaction curve are obtained, respectively, through simulation analysis. Then, those dynamic parameters were input into the established MATLAB® SIMULINK® controller to simulate and test the performance of the control system. By these means, the ISP control parameters are optimized. To verify the methods, experiments were carried out by applying the optimized parameters to the control system of a two-axis ISP. The results show that the co-simulation by using virtual prototyping (VP) is effective to obtain optimized ISP control parameters, eventually leading to high ISP control performance. PMID:26287210

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.

MDWiZ: a platform for the automated translation of molecular dynamics simulations.

PubMed

Rusu, Victor H; Horta, Vitor A C; Horta, Bruno A C; Lins, Roberto D; Baron, Riccardo

2014-03-01

A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

NASA Astrophysics Data System (ADS)

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; Ho, Kai-Ming; Travesset, Alex

2018-04-01

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu64.5Zr35.5, and pair correlation function g (r) of liquid Ni3Al. Our code scales well with the size of the simulating system on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. The source code can be accessed through the HOOMD-blue web page for free by any interested user.

Simulation of dental collisions and occlusal dynamics in the virtual environment.

PubMed

Stavness, I K; Hannam, A G; Tobias, D L; Zhang, X

2016-04-01

Semi-adjustable articulators have often been used to simulate occlusal dynamics, but advances in intra-oral scanning and computer software now enable dynamics to be modelled mathematically. Computer simulation of occlusal dynamics requires accurate virtual casts, records to register them and methods to handle mesh collisions during movement. Here, physical casts in a semi-adjustable articulator were scanned with a conventional clinical intra-oral scanner. A coordinate measuring machine was used to index their positions in intercuspation, protrusion, right and left laterotrusion, and to model features of the articulator. Penetrations between the indexed meshes were identified and resolved using restitution forces, and the final registrations were verified by distance measurements between dental landmarks at multiple sites. These sites were confirmed as closely approximating via measurements made from homologous transilluminated vinylpolysiloxane interocclusal impressions in the mounted casts. Movements between the indexed positions were simulated with two models in a custom biomechanical software platform. In model DENTAL, 6 degree-of-freedom movements were made to minimise deviation from a straight line path and also shaped by dynamic mesh collisions detected and resolved mathematically. In model ARTIC, the paths were further constrained by surfaces matching the control settings of the articulator. Despite these differences, the lower mid-incisor point paths were very similar in both models. The study suggests that mathematical simulation utilising interocclusal 'bite' registrations can closely replicate the primary movements of casts mounted in a semi-adjustable articulator. Additional indexing positions and appropriate software could, in some situations, replace the need for mechanical semi-adjustable articulation and/or its virtual representation. © 2015 John Wiley & Sons Ltd.

The design of real time infrared image generation software based on Creator and Vega

NASA Astrophysics Data System (ADS)

Wang, Rui-feng; Wu, Wei-dong; Huo, Jun-xiu

2013-09-01

Considering the requirement of high reality and real-time quality dynamic infrared image of an infrared image simulation, a method to design real-time infrared image simulation application on the platform of VC++ is proposed. This is based on visual simulation software Creator and Vega. The functions of Creator are introduced simply, and the main features of Vega developing environment are analyzed. The methods of infrared modeling and background are offered, the designing flow chart of the developing process of IR image real-time generation software and the functions of TMM Tool and MAT Tool and sensor module are explained, at the same time, the real-time of software is designed.

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.

Simulation verification techniques study. Task report 4: Simulation module performance parameters and performance standards

NASA Technical Reports Server (NTRS)

1974-01-01

Shuttle simulation software modules in the environment, crew station, vehicle configuration and vehicle dynamics categories are discussed. For each software module covered, a description of the module functions and operational modes, its interfaces with other modules, its stored data, inputs, performance parameters and critical performance parameters is given. Reference data sources which provide standards of performance are identified for each module. Performance verification methods are also discussed briefly.

Monte Carlo Methodology Serves Up a Software Success

NASA Technical Reports Server (NTRS)

2003-01-01

Widely used for the modeling of gas flows through the computation of the motion and collisions of representative molecules, the Direct Simulation Monte Carlo method has become the gold standard for producing research and engineering predictions in the field of rarefied gas dynamics. Direct Simulation Monte Carlo was first introduced in the early 1960s by Dr. Graeme Bird, a professor at the University of Sydney, Australia. It has since proved to be a valuable tool to the aerospace and defense industries in providing design and operational support data, as well as flight data analysis. In 2002, NASA brought to the forefront a software product that maintains the same basic physics formulation of Dr. Bird's method, but provides effective modeling of complex, three-dimensional, real vehicle simulations and parallel processing capabilities to handle additional computational requirements, especially in areas where computational fluid dynamics (CFD) is not applicable. NASA's Direct Simulation Monte Carlo Analysis Code (DAC) software package is now considered the Agency s premier high-fidelity simulation tool for predicting vehicle aerodynamics and aerothermodynamic environments in rarified, or low-density, gas flows.

Simulations of Operation Dynamics of Different Type GaN Particle Sensors

PubMed Central

Gaubas, Eugenijus; Ceponis, Tomas; Kalesinskas, Vidas; Pavlov, Jevgenij; Vysniauskas, Juozas

2015-01-01

The operation dynamics of the capacitor-type and PIN diode type detectors based on GaN have been simulated using the dynamic and drift-diffusion models. The drift-diffusion current simulations have been implemented by employing the software package Synopsys TCAD Sentaurus. The monopolar and bipolar drift regimes have been analyzed by using dynamic models based on the Shockley-Ramo theorem. The carrier multiplication processes determined by impact ionization have been considered in order to compensate carrier lifetime reduction due to introduction of radiation defects into GaN detector material. PMID:25751080

Movement Characteristics Analysis and Dynamic Simulation of Collaborative Measuring Robot

NASA Astrophysics Data System (ADS)

guoqing, MA; li, LIU; zhenglin, YU; guohua, CAO; yanbin, ZHENG

2017-03-01

Human-machine collaboration is becoming increasingly more necessary, and so collaborative robot applications are also in high demand. We selected a UR10 robot as our research subject for this study. First, we applied D-H coordinate transformation of the robot to establish a link system, and we then used inverse transformation to solve the robot’s inverse kinematics and find all the joints. Use Lagrange method to analysis UR robot dynamics; use ADAMS multibody dynamics simulation software to dynamic simulation; verifying the correctness of the derived kinetic models.

G-DYN Multibody Dynamics Engine

NASA Technical Reports Server (NTRS)

Acikmese, Behcet; Blackmore, James C.; Broderick, Daniel

2011-01-01

G-DYN is a multi-body dynamic simulation software engine that automatically assembles and integrates equations of motion for arbitrarily connected multibody dynamic systems. The algorithm behind G-DYN is based on a primal-dual formulation of the dynamics that captures the position and velocity vectors (primal variables) of each body and the interaction forces (dual variables) between bodies, which are particularly useful for control and estimation analysis and synthesis. It also takes full advantage of the spare matrix structure resulting from the system dynamics to numerically integrate the equations of motion efficiently. Furthermore, the dynamic model for each body can easily be replaced without re-deriving the overall equations of motion, and the assembly of the equations of motion is done automatically. G-DYN proved an essential software tool in the simulation of spacecraft systems used for small celestial body surface sampling, specifically in simulating touch-and-go (TAG) maneuvers of a robotic sampling system from a comet and asteroid. It is used extensively in validating mission concepts for small body sample return, such as Comet Odyssey and Galahad New Frontiers proposals.

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.

SMI Compatible Simulation Scheduler Design for Reuse of Model Complying with Smp Standard

NASA Astrophysics Data System (ADS)

Koo, Cheol-Hea; Lee, Hoon-Hee; Cheon, Yee-Jin

2010-12-01

Software reusability is one of key factors which impacts cost and schedule on a software development project. It is very crucial also in satellite simulator development since there are many commercial simulator models related to satellite and dynamics. If these models can be used in another simulator platform, great deal of confidence and cost/schedule reduction would be achieved. Simulation model portability (SMP) is maintained by European Space Agency and many models compatible with SMP/simulation model interface (SMI) are available. Korea Aerospace Research Institute (KARI) is developing hardware abstraction layer (HAL) supported satellite simulator to verify on-board software of satellite. From above reasons, KARI wants to port these SMI compatible models to the HAL supported satellite simulator. To port these SMI compatible models to the HAL supported satellite simulator, simulation scheduler is preliminary designed according to the SMI standard.

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

Avoiding Defect Nucleation during Equilibration in Molecular Dynamics Simulations with ReaxFF

DTIC Science & Technology

2015-04-01

respectively. All simulations are performed using the LAMMPS computer code.12 2 Fig. 1 a) Initial and b) final configurations of the molecular centers...Plimpton S. Fast parallel algorithms for short-range molecular dynamics. Comput J Phys. 1995;117:1–19. (Software available at http:// lammps .sandia.gov

PyMUS: Python-Based Simulation Software for Virtual Experiments on Motor Unit System

PubMed Central

Kim, Hojeong; Kim, Minjung

2018-01-01

We constructed a physiologically plausible computationally efficient model of a motor unit and developed simulation software that allows for integrative investigations of the input–output processing in the motor unit system. The model motor unit was first built by coupling the motoneuron model and muscle unit model to a simplified axon model. To build the motoneuron model, we used a recently reported two-compartment modeling approach that accurately captures the key cell-type-related electrical properties under both passive conditions (somatic input resistance, membrane time constant, and signal attenuation properties between the soma and the dendrites) and active conditions (rheobase current and afterhyperpolarization duration at the soma and plateau behavior at the dendrites). To construct the muscle unit, we used a recently developed muscle modeling approach that reflects the experimentally identified dependencies of muscle activation dynamics on isometric, isokinetic and dynamic variation in muscle length over a full range of stimulation frequencies. Then, we designed the simulation software based on the object-oriented programing paradigm and developed the software using open-source Python language to be fully operational using graphical user interfaces. Using the developed software, separate simulations could be performed for a single motoneuron, muscle unit and motor unit under a wide range of experimental input protocols, and a hierarchical analysis could be performed from a single channel to the entire system behavior. Our model motor unit and simulation software may represent efficient tools not only for researchers studying the neural control of force production from a cellular perspective but also for instructors and students in motor physiology classroom settings. PMID:29695959

PyMUS: Python-Based Simulation Software for Virtual Experiments on Motor Unit System.

PubMed

Kim, Hojeong; Kim, Minjung

2018-01-01

We constructed a physiologically plausible computationally efficient model of a motor unit and developed simulation software that allows for integrative investigations of the input-output processing in the motor unit system. The model motor unit was first built by coupling the motoneuron model and muscle unit model to a simplified axon model. To build the motoneuron model, we used a recently reported two-compartment modeling approach that accurately captures the key cell-type-related electrical properties under both passive conditions (somatic input resistance, membrane time constant, and signal attenuation properties between the soma and the dendrites) and active conditions (rheobase current and afterhyperpolarization duration at the soma and plateau behavior at the dendrites). To construct the muscle unit, we used a recently developed muscle modeling approach that reflects the experimentally identified dependencies of muscle activation dynamics on isometric, isokinetic and dynamic variation in muscle length over a full range of stimulation frequencies. Then, we designed the simulation software based on the object-oriented programing paradigm and developed the software using open-source Python language to be fully operational using graphical user interfaces. Using the developed software, separate simulations could be performed for a single motoneuron, muscle unit and motor unit under a wide range of experimental input protocols, and a hierarchical analysis could be performed from a single channel to the entire system behavior. Our model motor unit and simulation software may represent efficient tools not only for researchers studying the neural control of force production from a cellular perspective but also for instructors and students in motor physiology classroom settings.

The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory

NASA Astrophysics Data System (ADS)

Lourderaj, Upakarasamy; Sun, Rui; Kohale, Swapnil C.; Barnes, George L.; de Jong, Wibe A.; Windus, Theresa L.; Hase, William L.

2014-03-01

The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling since the two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface that accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

Two key areas of crucial importance to the computer-based simulation of large space structures are discussed. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area involves massively parallel computers.

Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation.

PubMed

Zhang, Fan; Liu, Runsheng; Zheng, Jie

2016-12-23

Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. In this work, we present Sig2GRN, a Cytoscape plugin that is able to simulate time-course gene expression data given the user-defined external stimuli to the signaling pathways. A generalized logical model is used in modeling the upstream signaling pathways. Then a Boolean model and a thermodynamics-based model are employed to predict the downstream changes in gene expression based on the simulated dynamics of transcription factors in signaling pathways. Our empirical case studies show that the simulation of Sig2GRN can predict changes in gene expression patterns induced by DNA damage signals and drug treatments. As a software tool for modeling cellular dynamics, Sig2GRN can facilitate studies in systems biology by hypotheses generation and wet-lab experimental design. http://histone.scse.ntu.edu.sg/Sig2GRN/.

Flight code validation simulator

NASA Astrophysics Data System (ADS)

Sims, Brent A.

1996-05-01

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

Host computer software specifications for a zero-g payload manhandling simulator

NASA Technical Reports Server (NTRS)

Wilson, S. W.

1986-01-01

The HP PASCAL source code was developed for the Mission Planning and Analysis Division (MPAD) of NASA/JSC, and takes the place of detailed flow charts defining the host computer software specifications for MANHANDLE, a digital/graphical simulator that can be used to analyze the dynamics of onorbit (zero-g) payload manhandling operations. Input and output data for representative test cases are contained.

FAST: A multi-processed environment for visualization of computational fluid dynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

1991-01-01

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

Real-Time and High-Fidelity Simulation Environment for Autonomous Ground Vehicle Dynamics

DTIC Science & Technology

2013-08-01

ENGINEERING AND TECHNOLOGY SYMPOSIUM (GVSETS), SET FOR AUG. 21-22, 2013 14. ABSTRACT briefing charts 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17...EDL & Aero-Flight DSENDS Airships Planetary & Terrain models SimScape Simulation framework Dshell Flex & Multibody dynamics DARTS 3D...7 DARTS Rigid/Flexible Real-Time Multibody Dynamics Engine Recipient of the NASA Software of the Year Award. Abhinandan Jain, "Robot and

Boat, wake, and wave real-time simulation

NASA Astrophysics Data System (ADS)

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

2009-05-01

We describe the extension of our real-time scene generation software VIRSuite to include the dynamic simulation of small boats and their wakes within an ocean environment. Extensive use has been made of the programmabilty available in the current generation of GPUs. We have demonstrated that real-time simulation is feasible, even including such complexities as dynamical calculation of the boat motion, wake generation and calculation of an FFTgenerated sea state.

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.

Application of fire and evacuation models in evaluation of fire safety in railway tunnels

NASA Astrophysics Data System (ADS)

Cábová, Kamila; Apeltauer, Tomáš; Okřinová, Petra; Wald, František

2017-09-01

The paper describes an application of numerical simulation of fire dynamics and evacuation of people in a tunnel. The software tool Fire Dynamics Simulator is used to simulate temperature resolution and development of smoke in a railway tunnel. Comparing to temperature curves which are usually used in the design stage results of the model show that the numerical model gives lower temperature of hot smoke layer. Outputs of the numerical simulation of fire also enable to improve models of evacuation of people during fires in tunnels. In the presented study the calculated high of smoke layer in the tunnel is in 10 min after the fire ignition lower than the level of 2.2 m which is considered as the maximal limit for safe evacuation. Simulation of the evacuation process in bigger scale together with fire dynamics can provide very valuable information about important security conditions like Available Safe Evacuation Time (ASET) vs Required Safe Evacuation Time (RSET). On given example in software EXODUS the paper summarizes selected results of evacuation model which should be in mind of a designer when preparing an evacuation plan.

Unified Approach to Modeling and Simulation of Space Communication Networks and Systems

NASA Technical Reports Server (NTRS)

Barritt, Brian; Bhasin, Kul; Eddy, Wesley; Matthews, Seth

2010-01-01

Network simulator software tools are often used to model the behaviors and interactions of applications, protocols, packets, and data links in terrestrial communication networks. Other software tools that model the physics, orbital dynamics, and RF characteristics of space systems have matured to allow for rapid, detailed analysis of space communication links. However, the absence of a unified toolset that integrates the two modeling approaches has encumbered the systems engineers tasked with the design, architecture, and analysis of complex space communication networks and systems. This paper presents the unified approach and describes the motivation, challenges, and our solution - the customization of the network simulator to integrate with astronautical analysis software tools for high-fidelity end-to-end simulation. Keywords space; communication; systems; networking; simulation; modeling; QualNet; STK; integration; space networks

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

DOE PAGES

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; ...

2018-01-12

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

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

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less

Compression Behavior and Energy Absorption of Aluminum Alloy AA6061 Tubes with Multiple Holes

NASA Astrophysics Data System (ADS)

Simhachalam, Bade; Lakshmana Rao, C.; Srinivas, Krishna

2014-05-01

In this article, compression behavior and energy absorption of aluminum alloy AA6061 tubes are investigated both experimentally and numerically. Static and dynamic simulations are done using LS-Dyna Software for AA6061 tubes. True stress-plastic strain curves from the tensile test are used in the static and dynamic simulations of AA6061 tubes. The energy absorption values between experimental compression results and numeral simulation are found to be in good agreement. Dynamic simulations are done with drop velocity of up to 10 m/s to understand the inertia effects on energy absorption. The deformed modes from the numerical simulation are compared between tubes with and without holes in static and dynamic conditions.

Dynamic Clamp in Cardiac and Neuronal Systems Using RTXI

PubMed Central

Ortega, Francis A.; Butera, Robert J.; Christini, David J.; White, John A.; Dorval, Alan D.

2016-01-01

The injection of computer-simulated conductances through the dynamic clamp technique has allowed researchers to probe the intercellular and intracellular dynamics of cardiac and neuronal systems with great precision. By coupling computational models to biological systems, dynamic clamp has become a proven tool in electrophysiology with many applications, such as generating hybrid networks in neurons or simulating channelopathies in cardiomyocytes. While its applications are broad, the approach is straightforward: synthesizing traditional patch clamp, computational modeling, and closed-loop feedback control to simulate a cellular conductance. Here, we present two example applications: artificial blocking of the inward rectifier potassium current in a cardiomyocyte and coupling of a biological neuron to a virtual neuron through a virtual synapse. The design and implementation of the necessary software to administer these dynamic clamp experiments can be difficult. In this chapter, we provide an overview of designing and implementing a dynamic clamp experiment using the Real-Time eXperiment Interface (RTXI), an open- source software system tailored for real-time biological experiments. We present two ways to achieve this using RTXI’s modular format, through the creation of a custom user-made module and through existing modules found in RTXI’s online library. PMID:25023319

Basic Techniques in Environmental Simulation.

DTIC Science & Technology

1982-07-01

the devel- ’I or oper is liable for all necessary changes in the model or its supporting computer software . After the 90-day warranty expires, the user...processing unit, that part of a computer which accom- plishes arithmetic and logical operations DCFLOS Dynamic cloud -free line-of-sight, a simulation... Software Development ......... 12 1.7.7 Operational Environment, Interfaces, and Constraints. . 12 1.7.8 Effectiveness Evaluation, Value Analysis, and

A verification library for multibody simulation software

NASA Technical Reports Server (NTRS)

Kim, Sung-Soo; Haug, Edward J.; Frisch, Harold P.

1989-01-01

A multibody dynamics verification library, that maintains and manages test and validation data is proposed, based on RRC Robot arm and CASE backhoe validation and a comparitive study of DADS, DISCOS, and CONTOPS that are existing public domain and commercial multibody dynamic simulation programs. Using simple representative problems, simulation results from each program are cross checked, and the validation results are presented. Functionalities of the verification library are defined, in order to automate validation procedure.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

PubMed Central

Martinez, Michael; Romanowska, Julia; Kokh, Daria B.; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan

2015-01-01

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26123630

GneimoSim: A Modular Internal Coordinates Molecular Dynamics Simulation Package

PubMed Central

Larsen, Adrien B.; Wagner, Jeffrey R.; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-01-01

The Generalized Newton Euler Inverse Mass Operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this paper we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. PMID:25263538

GneimoSim: a modular internal coordinates molecular dynamics simulation package.

PubMed

Larsen, Adrien B; Wagner, Jeffrey R; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-12-05

The generalized Newton-Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. © 2014 Wiley Periodicals, Inc.

Ndarts

NASA Technical Reports Server (NTRS)

Jain, Abhinandan

2011-01-01

Ndarts software provides algorithms for computing quantities associated with the dynamics of articulated, rigid-link, multibody systems. It is designed as a general-purpose dynamics library that can be used for the modeling of robotic platforms, space vehicles, molecular dynamics, and other such applications. The architecture and algorithms in Ndarts are based on the Spatial Operator Algebra (SOA) theory for computational multibody and robot dynamics developed at JPL. It uses minimal, internal coordinate models. The algorithms are low-order, recursive scatter/ gather algorithms. In comparison with the earlier Darts++ software, this version has a more general and cleaner design needed to support a larger class of computational dynamics needs. It includes a frames infrastructure, allows algorithms to operate on subgraphs of the system, and implements lazy and deferred computation for better efficiency. Dynamics modeling modules such as Ndarts are core building blocks of control and simulation software for space, robotic, mechanism, bio-molecular, and material systems modeling.

Dynamic simulation of train derailments

DOT National Transportation Integrated Search

2006-11-05

This paper describes a planar rigid-body model to examine the gross motions of rail cars in a train derailment. The model is implemented using a commercial software package called ADAMS (Automatic Dynamic Analysis of Mechanical Systems). The results ...

Tethered satellite system dynamics and control review panel and related activities, phase 3

NASA Technical Reports Server (NTRS)

1991-01-01

Two major tests of the Tethered Satellite System (TSS) engineering and flight units were conducted to demonstrate the functionality of the hardware and software. Deficiencies in the hardware/software integration tests (HSIT) led to a recommendation for more testing to be performed. Selected problem areas of tether dynamics were analyzed, including verification of the severity of skip rope oscillations, verification or comparison runs to explore dynamic phenomena observed in other simulations, and data generation runs to explore the performance of the time domain and frequency domain skip rope observers.

Preliminary Dynamic Feasibility and Analysis of a Spherical, Wind-Driven (Tumbleweed), Martian Rover

NASA Technical Reports Server (NTRS)

Flick, John J.; Toniolo, Matthew D.

2005-01-01

The process and findings are presented from a preliminary feasibility study examining the dynamics characteristics of a spherical wind-driven (or Tumbleweed) rover, which is intended for exploration of the Martian surface. The results of an initial feasibility study involving several worst-case mobility situations that a Tumbleweed rover might encounter on the surface of Mars are discussed. Additional topics include the evaluation of several commercially available analysis software packages that were examined as possible platforms for the development of a Monte Carlo Tumbleweed mission simulation tool. This evaluation lead to the development of the Mars Tumbleweed Monte Carlo Simulator (or Tumbleweed Simulator) using the Vortex physics software package from CM-Labs, Inc. Discussions regarding the development and evaluation of the Tumbleweed Simulator, as well as the results of a preliminary analysis using the tool are also presented. Finally, a brief conclusions section is presented.

Browndye: A Software Package for Brownian Dynamics

PubMed Central

McCammon, J. Andrew

2010-01-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. PMID:21132109

Evolution of Flexible Multibody Dynamics for Simulation Applications Supporting Human Spaceflight

NASA Technical Reports Server (NTRS)

Huynh, An; Brain, Thomas A.; MacLean, John R.; Quiocho, Leslie J.

2016-01-01

During the course of transition from the Space Shuttle and International Space Station programs to the Orion and Journey to Mars exploration programs, a generic flexible multibody dynamics formulation and associated software implementation has evolved to meet an ever changing set of requirements at the NASA Johnson Space Center (JSC). Challenging problems related to large transitional topologies and robotic free-flyer vehicle capture/ release, contact dynamics, and exploration missions concept evaluation through simulation (e.g., asteroid surface operations) have driven this continued development. Coupled with this need is the requirement to oftentimes support human spaceflight operations in real-time. Moreover, it has been desirable to allow even more rapid prototyping of on-orbit manipulator and spacecraft systems, to support less complex infrastructure software for massively integrated simulations, to yield further computational efficiencies, and to take advantage of recent advances and availability of multi-core computing platforms. Since engineering analysis, procedures development, and crew familiarity/training for human spaceflight is fundamental to JSC's charter, there is also a strong desire to share and reuse models in both the non-realtime and real-time domains, with the goal of retaining as much multibody dynamics fidelity as possible. Three specific enhancements are reviewed here: (1) linked list organization to address large transitional topologies, (2) body level model order reduction, and (3) parallel formulation/implementation. This paper provides a detailed overview of these primary updates to JSC's flexible multibody dynamics algorithms as well as a comparison of numerical results to previous formulations and associated software.

Modelling robotic systems with DADS

NASA Technical Reports Server (NTRS)

Churchill, L. W.; Sharf, I.

1993-01-01

With the appearance of general off-the-shelf software packages for the simulation of mechanical systems, modelling and simulation of mechanisms has become an easier task. The authors have recently used one such package, DADS, to model the dynamics of rigid and flexible-link robotic manipulators. In this paper, we present this overview of our learning experiences with DADS, in the hope that it will shorten the learning process for others interested in this software.

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

PubMed

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

1996-01-01

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

Prediction of glass transition temperature of freeze-dried formulations by molecular dynamics simulation.

PubMed

Yoshioka, Sumie; Aso, Yukio; Kojima, Shigeo

2003-06-01

To examine whether the glass transition temperature (Tg) of freeze-dried formulations containing polymer excipients can be accurately predicted by molecular dynamics simulation using software currently available on the market. Molecular dynamics simulations were carried out for isomaltodecaose, a fragment of dextran, and alpha-glucose, the repeated unit of dextran. in the presence or absence of water molecules. Estimated values of Tg were compared with experimental values obtained by differential scanning calorimetry (DSC). Isothermal-isobaric molecular dynamics simulations (NPTMD) and isothermal molecular dynamics simulations at a constant volume (NVTMD) were carried out using the software package DISCOVER (Material Studio) with the Polymer Consortium Force Field. Mean-squared displacement and radial distribution function were calculated. NVTMD using the values of density obtained by NPTMD provided the diffusivity of glucose-ring oxygen and water oxygen in amorphous alpha-glucose and isomaltodecaose, which exhibited a discontinuity in temperature dependence due to glass transition. Tg was estimated to be approximately 400K and 500K for pure amorphous a-glucose and isomaltodecaose, respectively, and in the presence of one water molecule per glucose unit, Tg was 340K and 360K, respectively. Estimated Tg values were higher than experimentally determined values because of the very fast cooling rates in the simulations. However, decreases in Tg on hydration and increases in Tg associated with larger fragment size could be demonstrated. The results indicate that molecular dynamics simulation is a useful method for investigating the effects of hydration and molecular weight on the Tg of lyophilized formulations containing polymer excipients. although the relationship between cooling rates and Tg must first be elucidated to predict Tg vales observed by DSC measurement. January 16.

Microcomputer Simulation of Real Gases--Part 1.

ERIC Educational Resources Information Center

Sperandeo-Mineo, R. M.; Tripi, G.

1987-01-01

Describes some simple computer programs designed to simulate the molecular dynamics of two-dimensional systems with a Lennard-Jones interaction potential. Discusses the use of the software in introductory physics courses at the high school and college level. (TW)

Simulation of the Velocity and Temperature Distribution of Inhalation Thermal Injury in a Human Upper Airway Model by Application of Computational Fluid Dynamics.

PubMed

Chang, Yang; Zhao, Xiao-zhuo; Wang, Cheng; Ning, Fang-gang; Zhang, Guo-an

2015-01-01

Inhalation injury is an important cause of death after thermal burns. This study was designed to simulate the velocity and temperature distribution of inhalation thermal injury in the upper airway in humans using computational fluid dynamics. Cervical computed tomography images of three Chinese adults were imported to Mimics software to produce three-dimensional models. After grids were established and boundary conditions were defined, the simulation time was set at 1 minute and the gas temperature was set to 80 to 320°C using ANSYS software (ANSYS, Canonsburg, PA) to simulate the velocity and temperature distribution of inhalation thermal injury. Cross-sections were cut at 2-mm intervals, and maximum airway temperature and velocity were recorded for each cross-section. The maximum velocity peaked in the lower part of the nasal cavity and then decreased with air flow. The velocities in the epiglottis and glottis were higher than those in the surrounding areas. Further, the maximum airway temperature decreased from the nasal cavity to the trachea. Computational fluid dynamics technology can be used to simulate the velocity and temperature distribution of inhaled heated air.

Dynamic simulation of road vehicle door window regulator mechanism of cross arm type

NASA Astrophysics Data System (ADS)

Miklos, I. Zs; Miklos, C.; Alic, C.

2017-01-01

The paper presents issues related to the dynamic simulation of a motor-drive operating mechanism of cross arm type, for the manipulation of road vehicle door windows, using Autodesk Inventor Professional software. The dynamic simulation of the mechanism involves a 3D modelling, kinematic coupling, drive motion parameters and external loads, as well as the graphically view of the kinematic and kinetostatic results for the various elements and kinematic couplings of the mechanism, under real operating conditions. Also, based on the results, the analysis of the mechanism components has been carried out using the finite element method.

Validation and Verification of LADEE Models and Software

NASA Technical Reports Server (NTRS)

Gundy-Burlet, Karen

2013-01-01

The Lunar Atmosphere Dust Environment Explorer (LADEE) mission will orbit the moon in order to measure the density, composition and time variability of the lunar dust environment. The ground-side and onboard flight software for the mission is being developed using a Model-Based Software methodology. In this technique, models of the spacecraft and flight software are developed in a graphical dynamics modeling package. Flight Software requirements are prototyped and refined using the simulated models. After the model is shown to work as desired in this simulation framework, C-code software is automatically generated from the models. The generated software is then tested in real time Processor-in-the-Loop and Hardware-in-the-Loop test beds. Travelling Road Show test beds were used for early integration tests with payloads and other subsystems. Traditional techniques for verifying computational sciences models are used to characterize the spacecraft simulation. A lightweight set of formal methods analysis, static analysis, formal inspection and code coverage analyses are utilized to further reduce defects in the onboard flight software artifacts. These techniques are applied early and often in the development process, iteratively increasing the capabilities of the software and the fidelity of the vehicle models and test beds.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

This final report on computational methods and software systems for dynamics and control of large space structures covers progress to date, projected developments in the final months of the grant, and conclusions. Pertinent reports and papers that have not appeared in scientific journals (or have not yet appeared in final form) are enclosed. The grant has supported research in two key areas of crucial importance to the computer-based simulation of large space structure. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area, as reported here, involves massively parallel computers.

Cyber Strategic Inquiry: Enabling Change through a Strategic Simulation and Megacommunity Concept

DTIC Science & Technology

2009-02-01

malicious software embedded in thumb drives and CDs that thwarted protections, such as antivirus software , on computers. In the scenario, these...Executives for National Security • The Carlyle Group • Cassat Corporation • Cisco Systems, Inc. • Cyveillance • General Dynamics • General Motors

Parallel-Processing Test Bed For Simulation Software

NASA Technical Reports Server (NTRS)

Blech, Richard; Cole, Gary; Townsend, Scott

1996-01-01

Second-generation Hypercluster computing system is multiprocessor test bed for research on parallel algorithms for simulation in fluid dynamics, electromagnetics, chemistry, and other fields with large computational requirements but relatively low input/output requirements. Built from standard, off-shelf hardware readily upgraded as improved technology becomes available. System used for experiments with such parallel-processing concepts as message-passing algorithms, debugging software tools, and computational steering. First-generation Hypercluster system described in "Hypercluster Parallel Processor" (LEW-15283).

ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies.

PubMed

Barnes, Samuel R; Ng, Thomas S C; Santa-Maria, Naomi; Montagne, Axel; Zlokovic, Berislav V; Jacobs, Russell E

2015-06-16

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a promising technique to characterize pathology and evaluate treatment response. However, analysis of DCE-MRI data is complex and benefits from concurrent analysis of multiple kinetic models and parameters. Few software tools are currently available that specifically focuses on DCE-MRI analysis with multiple kinetic models. Here, we developed ROCKETSHIP, an open-source, flexible and modular software for DCE-MRI analysis. ROCKETSHIP incorporates analyses with multiple kinetic models, including data-driven nested model analysis. ROCKETSHIP was implemented using the MATLAB programming language. Robustness of the software to provide reliable fits using multiple kinetic models is demonstrated using simulated data. Simulations also demonstrate the utility of the data-driven nested model analysis. Applicability of ROCKETSHIP for both preclinical and clinical studies is shown using DCE-MRI studies of the human brain and a murine tumor model. A DCE-MRI software suite was implemented and tested using simulations. Its applicability to both preclinical and clinical datasets is shown. ROCKETSHIP was designed to be easily accessible for the beginner, but flexible enough for changes or additions to be made by the advanced user as well. The availability of a flexible analysis tool will aid future studies using DCE-MRI. A public release of ROCKETSHIP is available at https://github.com/petmri/ROCKETSHIP .

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.

Generation of Simulated Tracking Data for LADEE Operational Readiness Testing

NASA Technical Reports Server (NTRS)

Woodburn, James; Policastri, Lisa; Owens, Brandon

2015-01-01

Operational Readiness Tests were an important part of the pre-launch preparation for the LADEE mission. The generation of simulated tracking data to stress the Flight Dynamics System and the Flight Dynamics Team was important for satisfying the testing goal of demonstrating that the software and the team were ready to fly the operational mission. The simulated tracking was generated in a manner to incorporate the effects of errors in the baseline dynamical model, errors in maneuver execution and phenomenology associated with various tracking system based components. The ability of the mission team to overcome these challenges in a realistic flight dynamics scenario indicated that the team and flight dynamics system were ready to fly the LADEE mission. Lunar Atmosphere and Dust Environment.

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

Malczynski, Leonard A.

This guide addresses software quality in the construction of Powersim{reg_sign} Studio 8 system dynamics simulation models. It is the result of almost ten years of experience with the Powersim suite of system dynamics modeling tools (Constructor and earlier Studio versions). It is a guide that proposes a common look and feel for the construction of Powersim Studio system dynamics models.

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

PubMed

Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A; Head-Gordon, Teresa

2017-06-05

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Comparative Implementation of High Performance Computing for Power System Dynamic Simulations

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

Jin, Shuangshuang; Huang, Zhenyu; Diao, Ruisheng

Dynamic simulation for transient stability assessment is one of the most important, but intensive, computations for power system planning and operation. Present commercial software is mainly designed for sequential computation to run a single simulation, which is very time consuming with a single processer. The application of High Performance Computing (HPC) to dynamic simulations is very promising in accelerating the computing process by parallelizing its kernel algorithms while maintaining the same level of computation accuracy. This paper describes the comparative implementation of four parallel dynamic simulation schemes in two state-of-the-art HPC environments: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP).more » These implementations serve to match the application with dedicated multi-processor computing hardware and maximize the utilization and benefits of HPC during the development process.« less

Software Framework for Advanced Power Plant Simulations

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

John Widmann; Sorin Munteanu; Aseem Jain

2010-08-01

This report summarizes the work accomplished during the Phase II development effort of the Advanced Process Engineering Co-Simulator (APECS). The objective of the project is to develop the tools to efficiently combine high-fidelity computational fluid dynamics (CFD) models with process modeling software. During the course of the project, a robust integration controller was developed that can be used in any CAPE-OPEN compliant process modeling environment. The controller mediates the exchange of information between the process modeling software and the CFD software. Several approaches to reducing the time disparity between CFD simulations and process modeling have been investigated and implemented. Thesemore » include enabling the CFD models to be run on a remote cluster and enabling multiple CFD models to be run simultaneously. Furthermore, computationally fast reduced-order models (ROMs) have been developed that can be 'trained' using the results from CFD simulations and then used directly within flowsheets. Unit operation models (both CFD and ROMs) can be uploaded to a model database and shared between multiple users.« less

The development of an autonomous rendezvous and docking simulation using rapid integration and prototyping technology

NASA Technical Reports Server (NTRS)

Shackelford, John H.; Saugen, John D.; Wurst, Michael J.; Adler, James

1991-01-01

A generic planar 3 degree of freedom simulation was developed that supports hardware in the loop simulations, guidance and control analysis, and can directly generate flight software. This simulation was developed in a small amount of time utilizing rapid prototyping techniques. The approach taken to develop this simulation tool, the benefits seen using this approach to development, and on-going efforts to improve and extend this capability are described. The simulation is composed of 3 major elements: (1) Docker dynamics model, (2) Dockee dynamics model, and (3) Docker Control System. The docker and dockee models are based on simple planar orbital dynamics equations using a spherical earth gravity model. The docker control system is based on a phase plane approach to error correction.

Virtual Satellite

NASA Technical Reports Server (NTRS)

Hammrs, Stephan R.

2008-01-01

Virtual Satellite (VirtualSat) is a computer program that creates an environment that facilitates the development, verification, and validation of flight software for a single spacecraft or for multiple spacecraft flying in formation. In this environment, enhanced functionality and autonomy of navigation, guidance, and control systems of a spacecraft are provided by a virtual satellite that is, a computational model that simulates the dynamic behavior of the spacecraft. Within this environment, it is possible to execute any associated software, the development of which could benefit from knowledge of, and possible interaction (typically, exchange of data) with, the virtual satellite. Examples of associated software include programs for simulating spacecraft power and thermal- management systems. This environment is independent of the flight hardware that will eventually host the flight software, making it possible to develop the software simultaneously with, or even before, the hardware is delivered. Optionally, by use of interfaces included in VirtualSat, hardware can be used instead of simulated. The flight software, coded in the C or C++ programming language, is compilable and loadable into VirtualSat without any special modifications. Thus, VirtualSat can serve as a relatively inexpensive software test-bed for development test, integration, and post-launch maintenance of spacecraft flight software.

Particle-based simulations of self-motile suspensions

NASA Astrophysics Data System (ADS)

Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

2015-11-01

A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

Draper Station Analysis Tool

NASA Technical Reports Server (NTRS)

Bedrossian, Nazareth; Jang, Jiann-Woei; McCants, Edward; Omohundro, Zachary; Ring, Tom; Templeton, Jeremy; Zoss, Jeremy; Wallace, Jonathan; Ziegler, Philip

2011-01-01

Draper Station Analysis Tool (DSAT) is a computer program, built on commercially available software, for simulating and analyzing complex dynamic systems. Heretofore used in designing and verifying guidance, navigation, and control systems of the International Space Station, DSAT has a modular architecture that lends itself to modification for application to spacecraft or terrestrial systems. DSAT consists of user-interface, data-structures, simulation-generation, analysis, plotting, documentation, and help components. DSAT automates the construction of simulations and the process of analysis. DSAT provides a graphical user interface (GUI), plus a Web-enabled interface, similar to the GUI, that enables a remotely located user to gain access to the full capabilities of DSAT via the Internet and Webbrowser software. Data structures are used to define the GUI, the Web-enabled interface, simulations, and analyses. Three data structures define the type of analysis to be performed: closed-loop simulation, frequency response, and/or stability margins. DSAT can be executed on almost any workstation, desktop, or laptop computer. DSAT provides better than an order of magnitude improvement in cost, schedule, and risk assessment for simulation based design and verification of complex dynamic systems.

Simulator predicts transient flow for Malaysian subsea pipeline

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

Inayat-Hussain, A.A.; Ayob, M.S.; Zain, A.B.M.

1996-04-15

In a step towards acquiring in-house capability in multiphase flow technology, Petronas Research and Scientific Services Sdn. Bhd., Kuala Lumpur, has developed two-phase flow simulation software for analyzing slow gas-condensate transient flow. Unlike its general-purpose contemporaries -- TACITE, OLGA, Traflow (OGJ, Jan. 3, 1994, p. 42; OGJ, Jan. 10, 1994, p. 52), and PLAC (AEA Technology, U.K.) -- ABASs is a dedicated software for slow transient flows generated during pigging operations in the Duyong network, offshore Malaysia. This network links the Duyong and Bekok fields to the onshore gas terminal (OGT) on the east coast of peninsular Malaysia. It predictsmore » the steady-state pressure drop vs. flow rates, condensate volume in the network, pigging dynamics including volume of produced slug, and the condensate build-up following pigging. The predictions of ABASs have been verified against field data obtained from the Duyong network. Presented here is an overview of the development, verification, and application of the ABASs software. Field data are presented for verification of the software, and several operational scenarios are simulated using the software. The field data and simulation study documented here will provide software users and developers with a further set of results on which to benchmark their own software and two-phase pipeline operating guidelines.« less

Dynamic contrast-enhanced MRI: Study of inter-software accuracy and reproducibility using simulated and clinical data.

PubMed

Beuzit, Luc; Eliat, Pierre-Antoine; Brun, Vanessa; Ferré, Jean-Christophe; Gandon, Yves; Bannier, Elise; Saint-Jalmes, Hervé

2016-06-01

To test the reproducibility and accuracy of pharmacokinetic parameter measurements on five analysis software packages (SPs) for dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), using simulated and clinical data. This retrospective study was Institutional Review Board-approved. Simulated tissues consisted of pixel clusters of calculated dynamic signal changes for combinations of Tofts model pharmacokinetic parameters (volume transfer constant [K(trans) ], extravascular extracellular volume fraction [ve ]), longitudinal relaxation time (T1 ). The clinical group comprised 27 patients treated for rectal cancer, with 36 3T DCE-MR scans performed between November 2012 and February 2014, including dual-flip-angle T1 mapping and a dynamic postcontrast T1 -weighted, 3D spoiled gradient-echo sequence. The clinical and simulated images were postprocessed with five SPs to measure K(trans) , ve , and the initial area under the gadolinium curve (iAUGC). Modified Bland-Altman analysis was conducted, intraclass correlation coefficients (ICCs) and within-subject coefficients of variation were calculated. Thirty-one examinations from 23 patients were of sufficient technical quality and postprocessed. Measurement errors were observed on the simulated data for all the pharmacokinetic parameters and SPs, with a bias ranging from -0.19 min(-1) to 0.09 min(-1) for K(trans) , -0.15 to 0.01 for ve , and -0.65 to 1.66 mmol.L(-1) .min for iAUGC. The ICC between SPs revealed moderate agreement for the simulated data (K(trans) : 0.50; ve : 0.67; iAUGC: 0.77) and very poor agreement for the clinical data (K(trans) : 0.10; ve : 0.16; iAUGC: 0.21). Significant errors were found in the calculated DCE-MRI pharmacokinetic parameters for the perfusion analysis SPs, resulting in poor inter-software reproducibility. J. Magn. Reson. Imaging 2016;43:1288-1300. © 2015 Wiley Periodicals, Inc.

Design and reliability analysis of DP-3 dynamic positioning control architecture

NASA Astrophysics Data System (ADS)

Wang, Fang; Wan, Lei; Jiang, Da-Peng; Xu, Yu-Ru

2011-12-01

As the exploration and exploitation of oil and gas proliferate throughout deepwater area, the requirements on the reliability of dynamic positioning system become increasingly stringent. The control objective ensuring safety operation at deep water will not be met by a single controller for dynamic positioning. In order to increase the availability and reliability of dynamic positioning control system, the triple redundancy hardware and software control architectures were designed and developed according to the safe specifications of DP-3 classification notation for dynamically positioned ships and rigs. The hardware redundant configuration takes the form of triple-redundant hot standby configuration including three identical operator stations and three real-time control computers which connect each other through dual networks. The function of motion control and redundancy management of control computers were implemented by software on the real-time operating system VxWorks. The software realization of task loose synchronization, majority voting and fault detection were presented in details. A hierarchical software architecture was planed during the development of software, consisting of application layer, real-time layer and physical layer. The behavior of the DP-3 dynamic positioning control system was modeled by a Markov model to analyze its reliability. The effects of variation in parameters on the reliability measures were investigated. The time domain dynamic simulation was carried out on a deepwater drilling rig to prove the feasibility of the proposed control architecture.

Lewis hybrid computing system, users manual

NASA Technical Reports Server (NTRS)

Bruton, W. M.; Cwynar, D. S.

1979-01-01

The Lewis Research Center's Hybrid Simulation Lab contains a collection of analog, digital, and hybrid (combined analog and digital) computing equipment suitable for the dynamic simulation and analysis of complex systems. This report is intended as a guide to users of these computing systems. The report describes the available equipment' and outlines procedures for its use. Particular is given to the operation of the PACER 100 digital processor. System software to accomplish the usual digital tasks such as compiling, editing, etc. and Lewis-developed special purpose software are described.

Numerical modeling tools for chemical vapor deposition

NASA Technical Reports Server (NTRS)

Jasinski, Thomas J.; Childs, Edward P.

1992-01-01

Development of general numerical simulation tools for chemical vapor deposition (CVD) was the objective of this study. Physical models of important CVD phenomena were developed and implemented into the commercial computational fluid dynamics software FLUENT. The resulting software can address general geometries as well as the most important phenomena occurring with CVD reactors: fluid flow patterns, temperature and chemical species distribution, gas phase and surface deposition. The physical models are documented which are available and examples are provided of CVD simulation capabilities.

Development of a Gas Dynamic and Thermodynamic Simulation Model of the Lontra Blade Compressor™

NASA Astrophysics Data System (ADS)

Karlovsky, Jerome

2015-08-01

The Lontra Blade Compressor™ is a patented double acting, internally compressing, positive displacement rotary compressor of innovative design. The Blade Compressor is in production for waste-water treatment, and will soon be launched for a range of applications at higher pressure ratios. In order to aid the design and development process, a thermodynamic and gas dynamic simulation program has been written in house. The software has been successfully used to optimise geometries and running conditions of current designs, and is also being used to evaluate future designs for different applications and markets. The simulation code has three main elements. A positive displacement chamber model, a leakage model and a gas dynamic model to simulate gas flow through ports and to track pressure waves in the inlet and outlet pipes. All three of these models are interlinked in order to track mass and energy flows within the system. A correlation study has been carried out to verify the software. The main correlation markers used were mass flow, chamber pressure, pressure wave tracking in the outlet pipe, and volumetric efficiency. It will be shown that excellent correlation has been achieved between measured and simulated data. Mass flow predictions were to within 2% of measured data, and the timings and magnitudes of all major gas dynamic effects were well replicated. The simulation will be further developed in the near future to help with the optimisation of exhaust and inlet silencers.

A Visual Basic simulation software tool for performance analysis of a membrane-based advanced water treatment plant.

PubMed

Pal, P; Kumar, R; Srivastava, N; Chaudhuri, J

2014-02-01

A Visual Basic simulation software (WATTPPA) has been developed to analyse the performance of an advanced wastewater treatment plant. This user-friendly and menu-driven software is based on the dynamic mathematical model for an industrial wastewater treatment scheme that integrates chemical, biological and membrane-based unit operations. The software-predicted results corroborate very well with the experimental findings as indicated in the overall correlation coefficient of the order of 0.99. The software permits pre-analysis and manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. It allows quick performance analysis of the whole system as well as the individual units. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for hazardous wastewater.

Onyx-Advanced Aeropropulsion Simulation Framework Created

NASA Technical Reports Server (NTRS)

Reed, John A.

2001-01-01

The Numerical Propulsion System Simulation (NPSS) project at the NASA Glenn Research Center is developing a new software environment for analyzing and designing aircraft engines and, eventually, space transportation systems. Its purpose is to dramatically reduce the time, effort, and expense necessary to design and test jet engines by creating sophisticated computer simulations of an aerospace object or system (refs. 1 and 2). Through a university grant as part of that effort, researchers at the University of Toledo have developed Onyx, an extensible Java-based (Sun Micro-systems, Inc.), objectoriented simulation framework, to investigate how advanced software design techniques can be successfully applied to aeropropulsion system simulation (refs. 3 and 4). The design of Onyx's architecture enables users to customize and extend the framework to add new functionality or adapt simulation behavior as required. It exploits object-oriented technologies, such as design patterns, domain frameworks, and software components, to develop a modular system in which users can dynamically replace components with others having different functionality.

A parameters optimization method for planar joint clearance model and its application for dynamics simulation of reciprocating compressor

NASA Astrophysics Data System (ADS)

Hai-yang, Zhao; Min-qiang, Xu; Jin-dong, Wang; Yong-bo, Li

2015-05-01

In order to improve the accuracy of dynamics response simulation for mechanism with joint clearance, a parameter optimization method for planar joint clearance contact force model was presented in this paper, and the optimized parameters were applied to the dynamics response simulation for mechanism with oversized joint clearance fault. By studying the effect of increased clearance on the parameters of joint clearance contact force model, the relation of model parameters between different clearances was concluded. Then the dynamic equation of a two-stage reciprocating compressor with four joint clearances was developed using Lagrange method, and a multi-body dynamic model built in ADAMS software was used to solve this equation. To obtain a simulated dynamic response much closer to that of experimental tests, the parameters of joint clearance model, instead of using the designed values, were optimized by genetic algorithms approach. Finally, the optimized parameters were applied to simulate the dynamics response of model with oversized joint clearance fault according to the concluded parameter relation. The dynamics response of experimental test verified the effectiveness of this application.

Transitioning NWChem to the Next Generation of Manycore Machines

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

Bylaska, Eric J.; Apra, Edoardo; Kowalski, Karol

The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM,more » AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.« less

Assessment of the Draft AIAA S-119 Flight Dynamic Model Exchange Standard

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Murri, Daniel G.; Hill, Melissa A.; Jessick, Matthew V.; Penn, John M.; Hasan, David A.; Crues, Edwin Z.; Falck, Robert D.; McCarthy, Thomas G.; Vuong, Nghia;

Development and Implementation of Software for Visualizing and Editing Multidimensional Flight Simulation Input Data

NASA Technical Reports Server (NTRS)

Whelan, Todd Michael

1996-01-01

In a real-time or batch mode simulation that is designed to model aircraft dynamics over a wide range of flight conditions, a table look- up scheme is implemented to determine the forces and moments on the vehicle based upon the values of parameters such as angle of attack, altitude, Mach number, and control surface deflections. Simulation Aerodynamic Variable Interface (SAVI) is a graphical user interface to the flight simulation input data, designed to operate on workstations that support X Windows. The purpose of the application is to provide two and three dimensional visualization of the data, to allow an intuitive sense of the data set. SAVI also allows the user to manipulate the data, either to conduct an interactive study of the influence of changes on the vehicle dynamics, or to make revisions to data set based on new information such as flight test. This paper discusses the reasons for developing the application, provides an overview of its capabilities, and outlines the software architecture and operating environment.

Why should biochemistry students be introduced to molecular dynamics simulations--and how can we introduce them?

PubMed

Elmore, Donald E

2016-01-01

Molecular dynamics (MD) simulations play an increasingly important role in many aspects of biochemical research but are often not part of the biochemistry curricula at the undergraduate level. This article discusses the pedagogical value of exposing students to MD simulations and provides information to help instructors consider what software and hardware resources are necessary to successfully introduce these simulations into their courses. In addition, a brief review of the MD-based activities in this issue and other sources are provided. © 2016 The International Union of Biochemistry and Molecular Biology.

Dynamic modelling and experimental study of cantilever beam with clearance

NASA Astrophysics Data System (ADS)

Li, B.; Jin, W.; Han, L.; He, Z.

2012-05-01

Clearances occur in almost all mechanical systems, typically such as the clearance between slide plate of gun barrel and guide. Therefore, to study the clearances of mechanisms can be very important to increase the working performance and lifetime of mechanisms. In this paper, rigid dynamic modelling of cantilever with clearance was done according to the subject investigated. In the rigid dynamic modelling, clearance is equivalent to the spring-dashpot model, the impact of beam and boundary face was also taken into consideration. In ADAMS software, the dynamic simulation was carried out according to the model above. The software simulated the movement of cantilever with clearance under external excitation. Research found: When the clearance is larger, the force of impact will become larger. In order to study how the stiffness of the cantilever's supporting part influences natural frequency of the system, A Euler beam which is restricted by a draught spring and a torsion spring at its end was raised. Through numerical calculation, the relationship between natural frequency and stiffness was found. When the value of the stiffness is close to the limit value, the corresponding boundary condition is illustrated. An ADAMS experiment was carried out to check the theory and the simulation.

Improving the Aircraft Design Process Using Web-Based Modeling and Simulation

NASA Technical Reports Server (NTRS)

Reed, John A.; Follen, Gregory J.; Afjeh, Abdollah A.; Follen, Gregory J. (Technical Monitor)

2000-01-01

Designing and developing new aircraft systems is time-consuming and expensive. Computational simulation is a promising means for reducing design cycle times, but requires a flexible software environment capable of integrating advanced multidisciplinary and multifidelity analysis methods, dynamically managing data across heterogeneous computing platforms, and distributing computationally complex tasks. Web-based simulation, with its emphasis on collaborative composition of simulation models, distributed heterogeneous execution, and dynamic multimedia documentation, has the potential to meet these requirements. This paper outlines the current aircraft design process, highlighting its problems and complexities, and presents our vision of an aircraft design process using Web-based modeling and simulation.

Improving the Aircraft Design Process Using Web-based Modeling and Simulation

NASA Technical Reports Server (NTRS)

Reed, John A.; Follen, Gregory J.; Afjeh, Abdollah A.

2003-01-01

Designing and developing new aircraft systems is time-consuming and expensive. Computational simulation is a promising means for reducing design cycle times, but requires a flexible software environment capable of integrating advanced multidisciplinary and muitifidelity analysis methods, dynamically managing data across heterogeneous computing platforms, and distributing computationally complex tasks. Web-based simulation, with its emphasis on collaborative composition of simulation models, distributed heterogeneous execution, and dynamic multimedia documentation, has the potential to meet these requirements. This paper outlines the current aircraft design process, highlighting its problems and complexities, and presents our vision of an aircraft design process using Web-based modeling and simulation.

Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation

PubMed Central

Tambunan, Usman Sumo Friend; Nasution, Mochammad Arfin Fardiansyah; Azhima, Fauziah; Parikesit, Arli Aditya; Toepak, Erwin Prasetya; Idrus, Syarifuddin; Kerami, Djati

2017-01-01

Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world’s population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S-adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2′OH, resulting in S-adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔGbinding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever. PMID:28469408

VEDA: a web-based virtual environment for dynamic atomic force microscopy.

PubMed

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy

NASA Astrophysics Data System (ADS)

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Simulating star clusters with the AMUSE software framework. I. Dependence of cluster lifetimes on model assumptions and cluster dissolution modes

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

Whitehead, Alfred J.; McMillan, Stephen L. W.; Vesperini, Enrico

2013-12-01

We perform a series of simulations of evolving star clusters using the Astrophysical Multipurpose Software Environment (AMUSE), a new community-based multi-physics simulation package, and compare our results to existing work. These simulations model a star cluster beginning with a King model distribution and a selection of power-law initial mass functions and contain a tidal cutoff. They are evolved using collisional stellar dynamics and include mass loss due to stellar evolution. After studying and understanding that the differences between AMUSE results and results from previous studies are understood, we explored the variation in cluster lifetimes due to the random realization noisemore » introduced by transforming a King model to specific initial conditions. This random realization noise can affect the lifetime of a simulated star cluster by up to 30%. Two modes of star cluster dissolution were identified: a mass evolution curve that contains a runaway cluster dissolution with a sudden loss of mass, and a dissolution mode that does not contain this feature. We refer to these dissolution modes as 'dynamical' and 'relaxation' dominated, respectively. For Salpeter-like initial mass functions, we determined the boundary between these two modes in terms of the dynamical and relaxation timescales.« less

An undergraduate laboratory activity on molecular dynamics simulations.

PubMed

Spitznagel, Benjamin; Pritchett, Paige R; Messina, Troy C; Goadrich, Mark; Rodriguez, Juan

2016-01-01

Vision and Change [AAAS, 2011] outlines a blueprint for modernizing biology education by addressing conceptual understanding of key concepts, such as the relationship between structure and function. The document also highlights skills necessary for student success in 21st century Biology, such as the use of modeling and simulation. Here we describe a laboratory activity that allows students to investigate the dynamic nature of protein structure and function through the use of a modeling technique known as molecular dynamics (MD). The activity takes place over two lab periods that are 3 hr each. The first lab period unpacks the basic approach behind MD simulations, beginning with the kinematic equations that all bioscience students learn in an introductory physics course. During this period students are taught rudimentary programming skills in Python while guided through simple modeling exercises that lead up to the simulation of the motion of a single atom. In the second lab period students extend concepts learned in the first period to develop skills in the use of expert MD software. Here students simulate and analyze changes in protein conformation resulting from temperature change, solvation, and phosphorylation. The article will describe how these activities can be carried out using free software packages, including Abalone and VMD/NAMD. © 2016 The International Union of Biochemistry and Molecular Biology.

Approaches to incorporating climate change effects in state and transition simulation models of vegetation

Treesearch

Becky K. Kerns; Miles A. Hemstrom; David Conklin; Gabriel I. Yospin; Bart Johnson; Dominique Bachelet; Scott Bridgham

2012-01-01

Understanding landscape vegetation dynamics often involves the use of scientifically-based modeling tools that are capable of testing alternative management scenarios given complex ecological, management, and social conditions. State-and-transition simulation model (STSM) frameworks and software such as PATH and VDDT are commonly used tools that simulate how landscapes...

Distributed dynamic simulations of networked control and building performance applications.

PubMed

Yahiaoui, Azzedine

2018-02-01

The use of computer-based automation and control systems for smart sustainable buildings, often so-called Automated Buildings (ABs), has become an effective way to automatically control, optimize, and supervise a wide range of building performance applications over a network while achieving the minimum energy consumption possible, and in doing so generally refers to Building Automation and Control Systems (BACS) architecture. Instead of costly and time-consuming experiments, this paper focuses on using distributed dynamic simulations to analyze the real-time performance of network-based building control systems in ABs and improve the functions of the BACS technology. The paper also presents the development and design of a distributed dynamic simulation environment with the capability of representing the BACS architecture in simulation by run-time coupling two or more different software tools over a network. The application and capability of this new dynamic simulation environment are demonstrated by an experimental design in this paper.

Distributed dynamic simulations of networked control and building performance applications

PubMed Central

Yahiaoui, Azzedine

2017-01-01

The use of computer-based automation and control systems for smart sustainable buildings, often so-called Automated Buildings (ABs), has become an effective way to automatically control, optimize, and supervise a wide range of building performance applications over a network while achieving the minimum energy consumption possible, and in doing so generally refers to Building Automation and Control Systems (BACS) architecture. Instead of costly and time-consuming experiments, this paper focuses on using distributed dynamic simulations to analyze the real-time performance of network-based building control systems in ABs and improve the functions of the BACS technology. The paper also presents the development and design of a distributed dynamic simulation environment with the capability of representing the BACS architecture in simulation by run-time coupling two or more different software tools over a network. The application and capability of this new dynamic simulation environment are demonstrated by an experimental design in this paper. PMID:29568135

Modeling Nanocomposites for Molecular Dynamics (MD) Simulations

DTIC Science & Technology

2015-01-01

Parallel Simulator ( LAMMPS ) is used as the MD simulator [9], the coordinates must be formatted for use in LAMMPSs. VMD has a set of tools (TopoTools...that can be used to generate a LAMMPS -readable format [6]. 3 Figure 4. Ethylene Monomer Produced From Coordinates in PDB and Rendered Using...where, i and j are the atom subscripts. Simulations are performed using LAMMPS simulation software. Periodic boundary conditions are

The use of emulator-based simulators for on-board software maintenance

NASA Astrophysics Data System (ADS)

Irvine, M. M.; Dartnell, A.

2002-07-01

Traditionally, onboard software maintenance activities within the space sector are performed using hardware-based facilities. These facilities are developed around the use of hardware emulation or breadboards containing target processors. Some sort of environment is provided around the hardware to support the maintenance actives. However, these environments are not easy to use to set-up the required test scenarios, particularly when the onboard software executes in a dynamic I/O environment, e.g. attitude control software, or data handling software. In addition, the hardware and/or environment may not support the test set-up required during investigations into software anomalies, e.g. raise spurious interrupt, fail memory, etc, and the overall "visibility" of the software executing may be limited. The Software Maintenance Simulator (SOMSIM) is a tool that can support the traditional maintenance facilities. The following list contains some of the main benefits that SOMSIM can provide: Low cost flexible extension to existing product - operational simulator containing software processor emulator; System-level high-fidelity test-bed in which software "executes"; Provides a high degree of control/configuration over the entire "system", including contingency conditions perhaps not possible with real hardware; High visibility and control over execution of emulated software. This paper describes the SOMSIM concept in more detail, and also describes the SOMSIM study being carried out for ESA/ESOC by VEGA IT GmbH.

Visualization of spiral and scroll waves in simulated and experimental cardiac tissue

NASA Astrophysics Data System (ADS)

Cherry, E. M.; Fenton, F. H.

2008-12-01

The heart is a nonlinear biological system that can exhibit complex electrical dynamics, complete with period-doubling bifurcations and spiral and scroll waves that can lead to fibrillatory states that compromise the heart's ability to contract and pump blood efficiently. Despite the importance of understanding the range of cardiac dynamics, studying how spiral and scroll waves can initiate, evolve, and be terminated is challenging because of the complicated electrophysiology and anatomy of the heart. Nevertheless, over the last two decades advances in experimental techniques have improved access to experimental data and have made it possible to visualize the electrical state of the heart in more detail than ever before. During the same time, progress in mathematical modeling and computational techniques has facilitated using simulations as a tool for investigating cardiac dynamics. In this paper, we present data from experimental and simulated cardiac tissue and discuss visualization techniques that facilitate understanding of the behavior of electrical spiral and scroll waves in the context of the heart. The paper contains many interactive media, including movies and interactive two- and three-dimensional Java appletsDisclaimer: IOP Publishing was not involved in the programming of this software and does not accept any responsibility for it. You download and run the software at your own risk. If you experience any problems with the software, please contact the author directly. To the fullest extent permitted by law, IOP Publishing Ltd accepts no responsibility for any loss, damage and/or other adverse effect on your computer system caused by your downloading and running this software. IOP Publishing Ltd accepts no responsibility for consequential loss..

Simulation in a dynamic prototyping environment: Petri nets or rules?

NASA Technical Reports Server (NTRS)

Moore, Loretta A.; Price, Shannon W.; Hale, Joseph P.

1994-01-01

An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are normally delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.

Simulation in a dynamic prototyping environment: Petri nets or rules?

NASA Technical Reports Server (NTRS)

Moore, Loretta A.; Price, Shannon; Hale, Joseph P.

1994-01-01

An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.

Next Generation Simulation Framework for Robotic and Human Space Missions

NASA Technical Reports Server (NTRS)

Cameron, Jonathan M.; Balaram, J.; Jain, Abhinandan; Kuo, Calvin; Lim, Christopher; Myint, Steven

2012-01-01

The Dartslab team at NASA's Jet Propulsion Laboratory (JPL) has a long history of developing physics-based simulations based on the Darts/Dshell simulation framework that have been used to simulate many planetary robotic missions, such as the Cassini spacecraft and the rovers that are currently driving on Mars. Recent collaboration efforts between the Dartslab team at JPL and the Mission Operations Directorate (MOD) at NASA Johnson Space Center (JSC) have led to significant enhancements to the Dartslab DSENDS (Dynamics Simulator for Entry, Descent and Surface landing) software framework. The new version of DSENDS is now being used for new planetary mission simulations at JPL. JSC is using DSENDS as the foundation for a suite of software known as COMPASS (Core Operations, Mission Planning, and Analysis Spacecraft Simulation) that is the basis for their new human space mission simulations and analysis. In this paper, we will describe the collaborative process with the JPL Dartslab and the JSC MOD team that resulted in the redesign and enhancement of the DSENDS software. We will outline the improvements in DSENDS that simplify creation of new high-fidelity robotic/spacecraft simulations. We will illustrate how DSENDS simulations are assembled and show results from several mission simulations.

Efficient and Robust Optimization for Building Energy Simulation

PubMed Central

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-01-01

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell’s Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell’s method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell’s Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell’s Hybrid method presently used in HVACSIM+. PMID:27325907

Efficient and Robust Optimization for Building Energy Simulation.

PubMed

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-06-15

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell's Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell's method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell's Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell's Hybrid method presently used in HVACSIM+.

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure

NASA Astrophysics Data System (ADS)

Lippert, Ross A.; Predescu, Cristian; Ierardi, Douglas J.; Mackenzie, Kenneth M.; Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

2013-10-01

In molecular dynamics simulations, control over temperature and pressure is typically achieved by augmenting the original system with additional dynamical variables to create a thermostat and a barostat, respectively. These variables generally evolve on timescales much longer than those of particle motion, but typical integrator implementations update the additional variables along with the particle positions and momenta at each time step. We present a framework that replaces the traditional integration procedure with separate barostat, thermostat, and Newtonian particle motion updates, allowing thermostat and barostat updates to be applied infrequently. Such infrequent updates provide a particularly substantial performance advantage for simulations parallelized across many computer processors, because thermostat and barostat updates typically require communication among all processors. Infrequent updates can also improve accuracy by alleviating certain sources of error associated with limited-precision arithmetic. In addition, separating the barostat, thermostat, and particle motion update steps reduces certain truncation errors, bringing the time-average pressure closer to its target value. Finally, this framework, which we have implemented on both general-purpose and special-purpose hardware, reduces software complexity and improves software modularity.

The use of real-time, hardware-in-the-loop simulation in the design and development of the new Hughes HS601 spacecraft attitude control system

NASA Technical Reports Server (NTRS)

Slafer, Loren I.

1989-01-01

Realtime simulation and hardware-in-the-loop testing is being used extensively in all phases of the design, development, and testing of the attitude control system (ACS) for the new Hughes HS601 satellite bus. Realtime, hardware-in-the-loop simulation, integrated with traditional analysis and pure simulation activities is shown to provide a highly efficient and productive overall development program. Implementation of high fidelity simulations of the satellite dynamics and control system algorithms, capable of real-time execution (using applied Dynamics International's System 100), provides a tool which is capable of being integrated with the critical flight microprocessor to create a mixed simulation test (MST). The MST creates a highly accurate, detailed simulated on-orbit test environment, capable of open and closed loop ACS testing, in which the ACS design can be validated. The MST is shown to provide a valuable extension of traditional test methods. A description of the MST configuration is presented, including the spacecraft dynamics simulation model, sensor and actuator emulators, and the test support system. Overall system performance parameters are presented. MST applications are discussed; supporting ACS design, developing on-orbit system performance predictions, flight software development and qualification testing (augmenting the traditional software-based testing), mission planning, and a cost-effective subsystem-level acceptance test. The MST is shown to provide an ideal tool in which the ACS designer can fly the spacecraft on the ground.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB.

PubMed

Mansouri, Misagh; Reinbolt, Jeffrey A

2012-05-11

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB's variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1s (OpenSim) to 2.9s (MATLAB). For the closed-loop case, a proportional-integral-derivative controller was used to successfully balance a pole on model's hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB

PubMed Central

Mansouri, Misagh; Reinbolt, Jeffrey A.

2013-01-01

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB’s variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1 s (OpenSim) to 2.9 s (MATLAB). For the closed-loop case, a proportional–integral–derivative controller was used to successfully balance a pole on model’s hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. PMID:22464351

An order (n) algorithm for the dynamics simulation of robotic systems

NASA Technical Reports Server (NTRS)

Chun, H. M.; Turner, J. D.; Frisch, Harold P.

1989-01-01

The formulation of an Order (n) algorithm for DISCOS (Dynamics Interaction Simulation of Controls and Structures), which is an industry-standard software package for simulation and analysis of flexible multibody systems is presented. For systems involving many bodies, the new Order (n) version of DISCOS is much faster than the current version. Results of the experimental validation of the dynamics software are also presented. The experiment is carried out on a seven-joint robot arm at NASA's Goddard Space Flight Center. The algorithm used in the current version of DISCOS requires the inverse of a matrix whose dimension is equal to the number of constraints in the system. Generally, the number of constraints in a system is roughly proportional to the number of bodies in the system, and matrix inversion requires O(p exp 3) operations, where p is the dimension of the matrix. The current version of DISCOS is therefore considered an Order (n exp 3) algorithm. In contrast, the Order (n) algorithm requires inversion of matrices which are small, and the number of matrices to be inverted increases only linearly with the number of bodies. The newly-developed Order (n) DISCOS is currently capable of handling chain and tree topologies as well as multiple closed loops. Continuing development will extend the capability of the software to deal with typical robotics applications such as put-and-place, multi-arm hand-off and surface sliding.

LArSoft: toolkit for simulation, reconstruction and analysis of liquid argon TPC neutrino detectors

NASA Astrophysics Data System (ADS)

Snider, E. L.; Petrillo, G.

2017-10-01

LArSoft is a set of detector-independent software tools for the simulation, reconstruction and analysis of data from liquid argon (LAr) neutrino experiments The common features of LAr time projection chambers (TPCs) enable sharing of algorithm code across detectors of very different size and configuration. LArSoft is currently used in production simulation and reconstruction by the ArgoNeuT, DUNE, LArlAT, MicroBooNE, and SBND experiments. The software suite offers a wide selection of algorithms and utilities, including those for associated photo-detectors and the handling of auxiliary detectors outside the TPCs. Available algorithms cover the full range of simulation and reconstruction, from raw waveforms to high-level reconstructed objects, event topologies and classification. The common code within LArSoft is contributed by adopting experiments, which also provide detector-specific geometry descriptions, and code for the treatment of electronic signals. LArSoft is also a collaboration of experiments, Fermilab and associated software projects which cooperate in setting requirements, priorities, and schedules. In this talk, we outline the general architecture of the software and the interaction with external libraries and detector-specific code. We also describe the dynamics of LArSoft software development between the contributing experiments, the projects supporting the software infrastructure LArSoft relies on, and the core LArSoft support project.

Landsat-7 Simulation and Testing Environments

NASA Technical Reports Server (NTRS)

Holmes, E.; Ha, K.; Hawkins, K.; Lombardo, J.; Ram, M.; Sabelhaus, P.; Scott, S.; Phillips, R.

1999-01-01

A spacecraft Attitude Control and Determination Subsystem (ACDS) is heavily dependent upon simulation throughout its entire development, implementation and ground test cycle. Engineering simulation tools are typically developed to design and analyze control systems to validate the design and software simulation tools are required to qualify the flight software. However, the need for simulation does not end here. Operating the ACDS of a spacecraft on the ground requires the simulation of spacecraft dynamics, disturbance modeling and celestial body motion. Sensor data must also be simulated and substituted for actual sensor data on the ground so that the spacecraft will respond by sending commands to the actuators as they will on orbit. And finally, the simulators is the primary training tool and test-bed for the Flight Operations Team. In this paper various ACDS simulation, developed for or used by the Landsat 7 project will be described. The paper will include a description of each tool, its unique attributes, and its role in the overall development and testing of the ACDS. Finally, a section is included which discusses how the coordinated use of these simulation tools can maximize the probability of uncovering software, hardware and operations errors during the ground test process.

Dynamic Modeling Using MCSim and R (SOT 2016 Biological Modeling Webinar Series)

EPA Science Inventory

MCSim is a stand-alone software package for simulating and analyzing dynamic models, with a focus on Bayesian analysis using Markov Chain Monte Carlo. While it is an extremely powerful package, it is somewhat inflexible, and offers only a limited range of analysis options, with n...

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

PubMed Central

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.

2015-01-01

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815

An Internet Protocol-Based Software System for Real-Time, Closed-Loop, Multi-Spacecraft Mission Simulation Applications

NASA Technical Reports Server (NTRS)

Davis, George; Cary, Everett; Higinbotham, John; Burns, Richard; Hogie, Keith; Hallahan, Francis

2003-01-01

The paper will provide an overview of the web-based distributed simulation software system developed for end-to-end, multi-spacecraft mission design, analysis, and test at the NASA Goddard Space Flight Center (GSFC). This software system was developed for an internal research and development (IR&D) activity at GSFC called the Distributed Space Systems (DSS) Distributed Synthesis Environment (DSE). The long-term goal of the DSS-DSE is to integrate existing GSFC stand-alone test beds, models, and simulation systems to create a "hands on", end-to-end simulation environment for mission design, trade studies and simulations. The short-term goal of the DSE was therefore to develop the system architecture, and then to prototype the core software simulation capability based on a distributed computing approach, with demonstrations of some key capabilities by the end of Fiscal Year 2002 (FY02). To achieve the DSS-DSE IR&D objective, the team adopted a reference model and mission upon which FY02 capabilities were developed. The software was prototyped according to the reference model, and demonstrations were conducted for the reference mission to validate interfaces, concepts, etc. The reference model, illustrated in Fig. 1, included both space and ground elements, with functional capabilities such as spacecraft dynamics and control, science data collection, space-to-space and space-to-ground communications, mission operations, science operations, and data processing, archival and distribution addressed.

A Distributed Simulation Software System for Multi-Spacecraft Missions

NASA Technical Reports Server (NTRS)

Burns, Richard; Davis, George; Cary, Everett

2003-01-01

The paper will provide an overview of the web-based distributed simulation software system developed for end-to-end, multi-spacecraft mission design, analysis, and test at the NASA Goddard Space Flight Center (GSFC). This software system was developed for an internal research and development (IR&D) activity at GSFC called the Distributed Space Systems (DSS) Distributed Synthesis Environment (DSE). The long-term goal of the DSS-DSE is to integrate existing GSFC stand-alone test beds, models, and simulation systems to create a "hands on", end-to-end simulation environment for mission design, trade studies and simulations. The short-term goal of the DSE was therefore to develop the system architecture, and then to prototype the core software simulation capability based on a distributed computing approach, with demonstrations of some key capabilities by the end of Fiscal Year 2002 (FY02). To achieve the DSS-DSE IR&D objective, the team adopted a reference model and mission upon which FY02 capabilities were developed. The software was prototyped according to the reference model, and demonstrations were conducted for the reference mission to validate interfaces, concepts, etc. The reference model, illustrated in Fig. 1, included both space and ground elements, with functional capabilities such as spacecraft dynamics and control, science data collection, space-to-space and space-to-ground communications, mission operations, science operations, and data processing, archival and distribution addressed.

Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

PubMed

Roberts, Christopher C; Chang, Chia-En A

2016-08-25

We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering, and enzymology in both predictive and explanatory roles.

Computational Fluid Dynamics (CFD) investigation onto passenger car disk brake design

NASA Astrophysics Data System (ADS)

Munisamy, Kannan M.; Kanasan Moorthy, Shangkari K.

2013-06-01

The aim of this study is to investigate the flow and heat transfer in ventilated disc brakes using Computational Fluid Dynamics (CFD). NACA Series blade is designed for ventilated disc brake and the cooling characteristic is compared to the baseline design. The ventilated disc brakes are simulated using commercial CFD software FLUENTTM using simulation configuration that was obtained from experiment data. The NACA Series blade design shows improvements in Nusselt number compared to baseline design.

Applying Parallel Processing Techniques to Tether Dynamics Simulation

NASA Technical Reports Server (NTRS)

Wells, B. Earl

1996-01-01

The focus of this research has been to determine the effectiveness of applying parallel processing techniques to a sizable real-world problem, the simulation of the dynamics associated with a tether which connects two objects in low earth orbit, and to explore the degree to which the parallelization process can be automated through the creation of new software tools. The goal has been to utilize this specific application problem as a base to develop more generally applicable techniques.

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.

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.

Evaluation of a grid based molecular dynamics approach for polypeptide simulations.

PubMed

Merelli, Ivan; Morra, Giulia; Milanesi, Luciano

2007-09-01

Molecular dynamics is very important for biomedical research because it makes possible simulation of the behavior of a biological macromolecule in silico. However, molecular dynamics is computationally rather expensive: the simulation of some nanoseconds of dynamics for a large macromolecule such as a protein takes very long time, due to the high number of operations that are needed for solving the Newton's equations in the case of a system of thousands of atoms. In order to obtain biologically significant data, it is desirable to use high-performance computation resources to perform these simulations. Recently, a distributed computing approach based on replacing a single long simulation with many independent short trajectories has been introduced, which in many cases provides valuable results. This study concerns the development of an infrastructure to run molecular dynamics simulations on a grid platform in a distributed way. The implemented software allows the parallel submission of different simulations that are singularly short but together bring important biological information. Moreover, each simulation is divided into a chain of jobs to avoid data loss in case of system failure and to contain the dimension of each data transfer from the grid. The results confirm that the distributed approach on grid computing is particularly suitable for molecular dynamics simulations thanks to the elevated scalability.

OpenSatKit Enables Quick Startup for CubeSat Missions

NASA Technical Reports Server (NTRS)

McComas, David; Melton, Ryan

2017-01-01

The software required to develop, integrate, and operate a spacecraft is substantial regardless of whether its a large or small satellite. Even getting started can be a monumental task. To solve this problem, NASAs Core Flight System (cFS), NASA's 42 spacecraft dynamics simulator, and Ball Aerospaces COSMOS ground system have been integrated together into a kit called OpenSatKit that provides a complete and open source software solution for starting a new satellite mission. Users can have a working system with flight software, dynamics simulation, and a ground command and control system up and running within hours.Every satellite mission requires three primary categories of software to function. The first is Flight Software (FSW) which provides the onboard control of the satellites and its payload(s). NASA's cFS provides a great platform for developing this software. Second, while developing a satellite on earth, it is necessary to simulate the satellites orbit, attitude, and actuators, to ensure that the systems that control these aspects will work correctly in the real environment. NASAs 42 simulator provides these functionalities. Finally, the ground has to be able to communicate with the satellite, monitor its performance and health, and display its data. Additionally, test scripts have to be written to verify the system on the ground. Ball Aerospace's COSMOS command and control system provides this functionality. Once the OpenSatKit is up and running, the next step is to customize the platform and get it running on the end target. Starting from a fully working system makes porting the cFS from Linux to a users platform much easier. An example Raspberry Pi target is included in the kit so users can gain experience working with a low cost hardware target. All users can benefit from OpenSatKit but the greatest impact and benefits will be to SmallSat missions with constrained budgets and small software teams. This paper describes OpenSatKits system design, the steps necessary to run the system to target the Raspberry Pi, and future plans. OpenSatKit is a free fully functional spacecraft software system that we hope will greatly benefit the SmallSat community.

Ship electric propulsion simulator based on networking technology

NASA Astrophysics Data System (ADS)

Zheng, Huayao; Huang, Xuewu; Chen, Jutao; Lu, Binquan

2006-11-01

According the new ship building tense, a novel electric propulsion simulator (EPS) had been developed in Marine Simulation Center of SMU. The architecture, software function and FCS network technology of EPS and integrated power system (IPS) were described. In allusion to the POD propeller in ship, a special physical model was built. The POD power was supplied from the simulative 6.6 kV Medium Voltage Main Switchboard, its control could be realized in local or remote mode. Through LAN, the simulated feature information of EPS will pass to the physical POD model, which would reflect the real thruster working status in different sea conditions. The software includes vessel-propeller math module, thruster control system, distribution and emergency integrated management, double closed loop control system, vessel static water resistance and dynamic software; instructor main control software. The monitor and control system is realized by real time data collection system and CAN bus technology. During the construction, most devices such as monitor panels and intelligent meters, are developed in lab which were based on embedded microcomputer system with CAN interface to link the network. They had also successfully used in practice and would be suitable for the future demands of digitalization ship.

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

PubMed Central

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

2017-01-01

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms. PMID:29202130

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

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

Gygi, Francois; Galli, Giulia; Schwegler, Eric

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solarmore » energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems relevant to energy conversion devices.« less

Modular, Autonomous Command and Data Handling Software with Built-In Simulation and Test

NASA Technical Reports Server (NTRS)

Cuseo, John

2012-01-01

The spacecraft system that plays the greatest role throughout the program lifecycle is the Command and Data Handling System (C&DH), along with the associated algorithms and software. The C&DH takes on this role as cost driver because it is the brains of the spacecraft and is the element of the system that is primarily responsible for the integration and interoperability of all spacecraft subsystems. During design and development, many activities associated with mission design, system engineering, and subsystem development result in products that are directly supported by the C&DH, such as interfaces, algorithms, flight software (FSW), and parameter sets. A modular system architecture has been developed that provides a means for rapid spacecraft assembly, test, and integration. This modular C&DH software architecture, which can be targeted and adapted to a wide variety of spacecraft architectures, payloads, and mission requirements, eliminates the current practice of rewriting the spacecraft software and test environment for every mission. This software allows missionspecific software and algorithms to be rapidly integrated and tested, significantly decreasing time involved in the software development cycle. Additionally, the FSW includes an Onboard Dynamic Simulation System (ODySSy) that allows the C&DH software to support rapid integration and test. With this solution, the C&DH software capabilities will encompass all phases of the spacecraft lifecycle. ODySSy is an on-board simulation capability built directly into the FSW that provides dynamic built-in test capabilities as soon as the FSW image is loaded onto the processor. It includes a six-degrees- of-freedom, high-fidelity simulation that allows complete closed-loop and hardware-in-the-loop testing of a spacecraft in a ground processing environment without any additional external stimuli. ODySSy can intercept and modify sensor inputs using mathematical sensor models, and can intercept and respond to actuator commands. ODySSy integration is unique in that it allows testing of actual mission sequences on the flight vehicle while the spacecraft is in various stages of assembly, test, and launch operations all without any external support equipment or simulators. The ODySSy component of the FSW significantly decreases the time required for integration and test by providing an automated, standardized, and modular approach to integrated avionics and component interface and functional verification. ODySSy further provides the capability for on-orbit support in the form of autonomous mission planning and fault protection.

An overview of the utility of population simulation software in molecular ecology.

PubMed

Hoban, Sean

2014-05-01

Stochastic simulation software that simultaneously model genetic, population and environmental processes can inform many topics in molecular ecology. These include forecasting species and community response to environmental change, inferring dispersal ecology, revealing cryptic mating, quantifying past population dynamics, assessing in situ management options and monitoring neutral and adaptive biodiversity change. Advances in population demographic-genetic simulation software, especially with respect to individual life history, landscapes and genetic processes, are transforming and expanding the ways that molecular data can be used. The aim of this review is to explain the roles that such software can play in molecular ecology studies (whether as a principal component or a supporting function) so that researchers can decide whether, when and precisely how simulations can be incorporated into their work. First, I use seven case studies to demonstrate how simulations are employed, their specific advantage/necessity and what alternative or complementary (nonsimulation) approaches are available. I also explain how simulations can be integrated with existing spatial, environmental, historical and genetic data sets. I next describe simulation features that may be of interest to molecular ecologists, such as spatial and behavioural considerations and species' interactions, to provide guidance on how particular simulation capabilities can serve particular needs. Lastly, I discuss the prospect of simulation software in emerging challenges (climate change, biodiversity monitoring, population exploitation) and opportunities (genomics, ancient DNA), in order to emphasize that the scope of simulation-based work is expanding. I also suggest practical considerations, priorities and elements of best practice. This should accelerate the uptake of simulation approaches and firmly embed them as a versatile tool in the molecular ecologist's toolbox. © 2014 John Wiley & Sons Ltd.

Shock-driven fluid-structure interaction for civil design

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

Wood, Stephen L; Deiterding, Ralf

The multiphysics fluid-structure interaction simulation of shock-loaded structures requires the dynamic coupling of a shock-capturing flow solver to a solid mechanics solver for large deformations. The Virtual Test Facility combines a Cartesian embedded boundary approach with dynamic mesh adaptation in a generic software framework of flow solvers using hydrodynamic finite volume upwind schemes that are coupled to various explicit finite element solid dynamics solvers (Deiterding et al., 2006). This paper gives a brief overview of the computational approach and presents first simulations that utilize the general purpose solid dynamics code DYNA3D for complex 3D structures of interest in civil engineering.more » Results from simulations of a reinforced column, highway bridge, multistory building, and nuclear reactor building are presented.« less

Development of the functional simulator for the Galileo attitude and articulation control system

NASA Technical Reports Server (NTRS)

Namiri, M. K.

1983-01-01

A simulation program for verifying and checking the performance of the Galileo Spacecraft's Attitude and Articulation Control Subsystem's (AACS) flight software is discussed. The program, which is called Functional Simulator (FUNSIM), provides a simple method of interfacing user-supplied mathematical models coded in FORTRAN which describes spacecraft dynamics, sensors, and actuators; this is done with the AACS flight software, coded in HAL/S (High-level Advanced Language/Shuttle). It is thus able to simulate the AACS flight software accurately to the HAL/S statement level in the environment of a mainframe computer system. FUNSIM also has a command and data subsystem (CDS) simulator. It is noted that the input/output data and timing are simulated with the same precision as the flight microprocessor. FUNSIM uses a variable stepsize numerical integration algorithm complete with individual error bound control on the state variable to solve the equations of motion. The program has been designed to provide both line printer and matrix dot plotting of the variables requested in the run section and to provide error diagnostics.

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

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

Felberg, Lisa E.; Brookes, David H.; Yap, Eng-Hui

2016-11-02

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmannmore » Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.« less

On finding the analytic dependencies of the external field potential on the control function when optimizing the beam dynamics

NASA Astrophysics Data System (ADS)

Ovsyannikov, A. D.; Kozynchenko, S. A.; Kozynchenko, V. A.

2017-12-01

When developing a particle accelerator for generating the high-precision beams, the injection system design is of importance, because it largely determines the output characteristics of the beam. At the present paper we consider the injection systems consisting of electrodes with given potentials. The design of such systems requires carrying out simulation of beam dynamics in the electrostatic fields. For external field simulation we use the new approach, proposed by A.D. Ovsyannikov, which is based on analytical approximations, or finite difference method, taking into account the real geometry of the injection system. The software designed for solving the problems of beam dynamics simulation and optimization in the injection system for non-relativistic beams has been developed. Both beam dynamics and electric field simulations in the injection system which use analytical approach and finite difference method have been made and the results presented in this paper.

D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits.

PubMed

Baig, Hasan; Madsen, Jan

2017-01-15

Simulation and behavioral analysis of genetic circuits is a standard approach of functional verification prior to their physical implementation. Many software tools have been developed to perform in silico analysis for this purpose, but none of them allow users to interact with the model during runtime. The runtime interaction gives the user a feeling of being in the lab performing a real world experiment. In this work, we present a user-friendly software tool named D-VASim (Dynamic Virtual Analyzer and Simulator), which provides a virtual laboratory environment to simulate and analyze the behavior of genetic logic circuit models represented in an SBML (Systems Biology Markup Language). Hence, SBML models developed in other software environments can be analyzed and simulated in D-VASim. D-VASim offers deterministic as well as stochastic simulation; and differs from other software tools by being able to extract and validate the Boolean logic from the SBML model. D-VASim is also capable of analyzing the threshold value and propagation delay of a genetic circuit model. D-VASim is available for Windows and Mac OS and can be downloaded from bda.compute.dtu.dk/downloads/. haba@dtu.dk, jama@dtu.dk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Numerical simulation analysis of four-stage mutation of solid-liquid two-phase grinding

NASA Astrophysics Data System (ADS)

Li, Junye; Liu, Yang; Hou, Jikun; Hu, Jinglei; Zhang, Hengfu; Wu, Guiling

2018-03-01

In order to explore the numerical simulation of solid-liquid two-phase abrasive grain polishing and abrupt change tube, in this paper, the fourth order abrupt change tube was selected as the research object, using the fluid mechanics software to simulate,based on the theory of solid-liquid two-phase flow dynamics, study on the mechanism of AFM micromachining a workpiece during polishing.Analysis at different inlet pressures, the dynamic pressure distribution pipe mutant fourth order abrasive flow field, turbulence intensity, discuss the influence of the inlet pressure of different abrasive flow polishing effect.

Beam Dynamics Simulation Platform and Studies of Beam Breakup in Dielectric Wakefield Structures

NASA Astrophysics Data System (ADS)

Schoessow, P.; Kanareykin, A.; Jing, C.; Kustov, A.; Altmark, A.; Gai, W.

2010-11-01

A particle-Green's function beam dynamics code (BBU-3000) to study beam breakup effects is incorporated into a parallel computing framework based on the Boinc software environment, and supports both task farming on a heterogeneous cluster and local grid computing. User access to the platform is through a web browser.

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.

PubMed

Brackley, C A; Morozov, A N; Marenduzzo, D

2014-04-07

An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Finally, two possible implementations of the discretised model in the multi-purpose molecular dynamics software package LAMMPS are described.

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

Biyikli, Emre; To, Albert C., E-mail: albertto@pitt.edu

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with themore » associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3–8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.« less

Multiresolution molecular mechanics: Implementation and efficiency

NASA Astrophysics Data System (ADS)

Biyikli, Emre; To, Albert C.

2017-01-01

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3-8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

Analyzing Dynamics of Cooperating Spacecraft

NASA Technical Reports Server (NTRS)

Hughes, Stephen P.; Folta, David C.; Conway, Darrel J.

2004-01-01

A software library has been developed to enable high-fidelity computational simulation of the dynamics of multiple spacecraft distributed over a region of outer space and acting with a common purpose. All of the modeling capabilities afforded by this software are available independently in other, separate software systems, but have not previously been brought together in a single system. A user can choose among several dynamical models, many high-fidelity environment models, and several numerical-integration schemes. The user can select whether to use models that assume weak coupling between spacecraft, or strong coupling in the case of feedback control or tethering of spacecraft to each other. For weak coupling, spacecraft orbits are propagated independently, and are synchronized in time by controlling the step size of the integration. For strong coupling, the orbits are integrated simultaneously. Among the integration schemes that the user can choose are Runge-Kutta Verner, Prince-Dormand, Adams-Bashforth-Moulton, and Bulirsh- Stoer. Comparisons of performance are included for both the weak- and strongcoupling dynamical models for all of the numerical integrators.

The Application of SNiPER to the JUNO Simulation

NASA Astrophysics Data System (ADS)

Lin, Tao; Zou, Jiaheng; Li, Weidong; Deng, Ziyan; Fang, Xiao; Cao, Guofu; Huang, Xingtao; You, Zhengyun; JUNO Collaboration

2017-10-01

The JUNO (Jiangmen Underground Neutrino Observatory) is a multipurpose neutrino experiment which is designed to determine neutrino mass hierarchy and precisely measure oscillation parameters. As one of the important systems, the JUNO offline software is being developed using the SNiPER software. In this proceeding, we focus on the requirements of JUNO simulation and present the working solution based on the SNiPER. The JUNO simulation framework is in charge of managing event data, detector geometries and materials, physics processes, simulation truth information etc. It glues physics generator, detector simulation and electronics simulation modules together to achieve a full simulation chain. In the implementation of the framework, many attractive characteristics of the SNiPER have been used, such as dynamic loading, flexible flow control, multiple event management and Python binding. Furthermore, additional efforts have been made to make both detector and electronics simulation flexible enough to accommodate and optimize different detector designs. For the Geant4-based detector simulation, each sub-detector component is implemented as a SNiPER tool which is a dynamically loadable and configurable plugin. So it is possible to select the detector configuration at runtime. The framework provides the event loop to drive the detector simulation and interacts with the Geant4 which is implemented as a passive service. All levels of user actions are wrapped into different customizable tools, so that user functions can be easily extended by just adding new tools. The electronics simulation has been implemented by following an event driven scheme. The SNiPER task component is used to simulate data processing steps in the electronics modules. The electronics and trigger are synchronized by triggered events containing possible physics signals. The JUNO simulation software has been released and is being used by the JUNO collaboration to do detector design optimization, event reconstruction algorithm development and physics sensitivity studies.

Cross-Paradigm Simulation Modeling: Challenges and Successes

DTIC Science & Technology

2011-12-01

is also highlighted. 2.1 Discrete-Event Simulation Discrete-event simulation ( DES ) is a modeling method for stochastic, dynamic models where...which almost anything can be coded; models can be incredibly detailed. Most commercial DES software has a graphical interface which allows the user to...results. Although the above definition is the commonly accepted definition of DES , there are two different worldviews that dominate DES modeling today: a

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

2015-08-01

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

Adjustable Autonomy Testbed

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Schrenkenghost, Debra K.

2001-01-01

The Adjustable Autonomy Testbed (AAT) is a simulation-based testbed located in the Intelligent Systems Laboratory in the Automation, Robotics and Simulation Division at NASA Johnson Space Center. The purpose of the testbed is to support evaluation and validation of prototypes of adjustable autonomous agent software for control and fault management for complex systems. The AA T project has developed prototype adjustable autonomous agent software and human interfaces for cooperative fault management. This software builds on current autonomous agent technology by altering the architecture, components and interfaces for effective teamwork between autonomous systems and human experts. Autonomous agents include a planner, flexible executive, low level control and deductive model-based fault isolation. Adjustable autonomy is intended to increase the flexibility and effectiveness of fault management with an autonomous system. The test domain for this work is control of advanced life support systems for habitats for planetary exploration. The CONFIG hybrid discrete event simulation environment provides flexible and dynamically reconfigurable models of the behavior of components and fluids in the life support systems. Both discrete event and continuous (discrete time) simulation are supported, and flows and pressures are computed globally. This provides fast dynamic simulations of interacting hardware systems in closed loops that can be reconfigured during operations scenarios, producing complex cascading effects of operations and failures. Current object-oriented model libraries support modeling of fluid systems, and models have been developed of physico-chemical and biological subsystems for processing advanced life support gases. In FY01, water recovery system models will be developed.

Numerical simulation of water hammer in low pressurized pipe: comparison of SimHydraulics and Lax-Wendroff method with experiment

NASA Astrophysics Data System (ADS)

Himr, D.

2013-04-01

Article describes simulation of unsteady flow during water hammer with two programs, which use different numerical approaches to solve ordinary one dimensional differential equations describing the dynamics of hydraulic elements and pipes. First one is Matlab-Simulink-SimHydraulics, which is a commercial software developed to solve the dynamics of general hydraulic systems. It defines them with block elements. The other software is called HYDRA and it is based on the Lax-Wendrff numerical method, which serves as a tool to solve the momentum and continuity equations. This program was developed in Matlab by Brno University of Technology. Experimental measurements were performed on a simple test rig, which consists of an elastic pipe with strong damping connecting two reservoirs. Water hammer is induced with fast closing the valve. Physical properties of liquid and pipe elasticity parameters were considered in both simulations, which are in very good agreement and differences in comparison with experimental data are minimal.

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

Space life support engineering program

NASA Technical Reports Server (NTRS)

Seagrave, Richard C.

1992-01-01

A comprehensive study to develop software to simulate the dynamic operation of water reclamation systems in long-term closed-loop life support systems is being carried out as part of an overall program for the design of systems for a moon station or a Mars voyage. This project is being done in parallel with a similar effort in the Department of Chemistry to develop durable accurate low-cost sensors for monitoring of trace chemical and biological species in recycled water supplies. Aspen-Plus software is being used on a group of high-performance work stations to develop the steady state descriptions for a number of existing technologies. Following completion, a dynamic simulation package will be developed for determining the response of such systems to changes in the metabolic needs of the crew and to upsets in system hardware performance.

Design of Measure and Control System for Precision Pesticide Deploying Dynamic Simulating Device

NASA Astrophysics Data System (ADS)

Liang, Yong; Liu, Pingzeng; Wang, Lu; Liu, Jiping; Wang, Lang; Han, Lei; Yang, Xinxin

A measure and control system for precision deploying pesticide simulating equipment is designed in order to study pesticide deployment technology. The system can simulate every state of practical pesticide deployment, and carry through precise, simultaneous measure to every factor affecting pesticide deployment effects. The hardware and software incorporates a structural design of modularization. The system is divided into many different function modules of hardware and software, and exploder corresponding modules. The modules’ interfaces are uniformly defined, which is convenient for module connection, enhancement of system’s universality, explodes efficiency and systemic reliability, and make the program’s characteristics easily extended and easy maintained. Some relevant hardware and software modules can be adapted to other measures and control systems easily. The paper introduces the design of special numeric control system, the main module of information acquisition system and the speed acquisition module in order to explain the design process of the module.

Real-Time Simulation

NASA Technical Reports Server (NTRS)

1997-01-01

Coryphaeus Software, founded in 1989 by former NASA electronic engineer Steve Lakowske, creates real-time 3D software. Designer's Workbench, the company flagship product, is a modeling and simulation tool for the development of both static and dynamic 3D databases. Other products soon followed. Activation, specifically designed for game developers, allows developers to play and test the 3D games before they commit to a target platform. Game publishers can shorten development time and prove the "playability" of the title, maximizing their chances of introducing a smash hit. Another product, EasyT, lets users create massive, realistic representation of Earth terrains that can be viewed and traversed in real time. Finally, EasyScene software control the actions among interactive objects within a virtual world. Coryphaeus products are used on Silican Graphics workstation and supercomputers to simulate real-world performance in synthetic environments. Customers include aerospace, aviation, architectural and engineering firms, game developers, and the entertainment industry.

Software systems for modeling articulated figures

NASA Technical Reports Server (NTRS)

Phillips, Cary B.

1989-01-01

Research in computer animation and simulation of human task performance requires sophisticated geometric modeling and user interface tools. The software for a research environment should present the programmer with a powerful but flexible substrate of facilities for displaying and manipulating geometric objects, yet insure that future tools have a consistent and friendly user interface. Jack is a system which provides a flexible and extensible programmer and user interface for displaying and manipulating complex geometric figures, particularly human figures in a 3D working environment. It is a basic software framework for high-performance Silicon Graphics IRIS workstations for modeling and manipulating geometric objects in a general but powerful way. It provides a consistent and user-friendly interface across various applications in computer animation and simulation of human task performance. Currently, Jack provides input and control for applications including lighting specification and image rendering, anthropometric modeling, figure positioning, inverse kinematics, dynamic simulation, and keyframe animation.

Molecular modeling, simulation and virtual screening of MurD ligase protein from Salmonella typhimurium LT2.

PubMed

Samal, Himanshu Bhusan; Das, Jugal Kishore; Mahapatra, Rajani Kanta; Suar, Mrutyunjay

2015-01-01

The Mur enzymes of the peptidoglycan biosynthesis pathway constitute ideal targets for the design of new classes of antimicrobial inhibitors in Gram-negative bacteria. We built a homology model of MurD of Salmonella typhimurium LT2 using MODELLER (9v12) software. 'The homology model was subjected to energy minimization by molecular dynamics (MD) simulation study with GROMACS software for a simulation time of 20 ns in water environment. The model was subjected for virtual screening study from the Zinc Database using Dockblaster software. Inhibition assay for the best inhibitor, 3-(amino methyl)-n-(4-methoxyphenyl) aniline, by flow cytometric analysis revealed the effective inhibition of peptidoglycan biosynthesis. Results from this study provide new insights for the molecular understanding and development of new antibacterial drugs against the pathogen. Copyright © 2015 Elsevier Inc. All rights reserved.

Team Software Development for Aerothermodynamic and Aerodynamic Analysis and Design

NASA Technical Reports Server (NTRS)

Alexandrov, N.; Atkins, H. L.; Bibb, K. L.; Biedron, R. T.; Carpenter, M. H.; Gnoffo, P. A.; Hammond, D. P.; Jones, W. T.; Kleb, W. L.; Lee-Rausch, E. M.

2003-01-01

A collaborative approach to software development is described. The approach employs the agile development techniques: project retrospectives, Scrum status meetings, and elements of Extreme Programming to efficiently develop a cohesive and extensible software suite. The software product under development is a fluid dynamics simulator for performing aerodynamic and aerothermodynamic analysis and design. The functionality of the software product is achieved both through the merging, with substantial rewrite, of separate legacy codes and the authorship of new routines. Examples of rapid implementation of new functionality demonstrate the benefits obtained with this agile software development process. The appendix contains a discussion of coding issues encountered while porting legacy Fortran 77 code to Fortran 95, software design principles, and a Fortran 95 coding standard.

Software sensors for bioprocesses.

PubMed

Bogaerts, Ph; Vande Wouwer, A

2003-10-01

State estimation is a significant problem in biotechnological processes, due to the general lack of hardware sensor measurements of the variables describing the process dynamics. The objective of this paper is to review a number of software sensor design methods, including extended Kalman filters, receding-horizon observers, asymptotic observers, and hybrid observers, which can be efficiently applied to bioprocesses. These several methods are illustrated with simulation and real-life case studies.

A Collaborative Approach to Bridging the Research-Policy Gap through the Development of Policy Advice Software

ERIC Educational Resources Information Center

Milne, Barry John; Lay-Yee, Roy; McLay, Jessica; Tobias, Martin; Tuohy, Pat; Armstrong, Ann; Lynn, Robert; Pearson, Janet; Mannion, Oliver; Davis, Peter

2014-01-01

We have developed a software-based tool to support a dynamic micro-simulation model of life-course development (to age 13) as an aid to policy makers assessing the impact of policies affecting children. We demonstrate how this approach bridges the research-policy gap by creating: (1) an easy transfer of evidence in a form that policymakers can use…

Total Cost of Ownership, System Acceptance and Perceived Success of Enterprise Resource Planning Software: Simulating a Dynamic Feedback Perspective of ERP in the Higher Education Environment

ERIC Educational Resources Information Center

Fryling, Meg

2010-01-01

Enterprise Research Planning (ERP) software is advertised as the product that will "run the enterprise", improving data access and accuracy as well as enhancing business process efficiency. Unfortunately, organizations often make implementation decisions with little consideration for the maintenance phase of an ERP, resulting in significant…

Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

PubMed

Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

2018-02-01

Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.

New Automotive Air Conditioning System Simulation Tool Developed in MATLAB/Simulink

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

Kiss, T.; Chaney, L.; Meyer, J.

Further improvements in vehicle fuel efficiency require accurate evaluation of the vehicle's transient total power requirement. When operated, the air conditioning (A/C) system is the largest auxiliary load on a vehicle; therefore, accurate evaluation of the load it places on the vehicle's engine and/or energy storage system is especially important. Vehicle simulation software, such as 'Autonomie,' has been used by OEMs to evaluate vehicles' energy performance. A transient A/C simulation tool incorporated into vehicle simulation models would also provide a tool for developing more efficient A/C systems through a thorough consideration of the transient A/C system performance. The dynamic systemmore » simulation software Matlab/Simulink was used to develop new and more efficient vehicle energy system controls. The various modeling methods used for the new simulation tool are described in detail. Comparison with measured data is provided to demonstrate the validity of the model.« less

Simulation Model for Scenario Optimization of the Ready-Mix Concrete Delivery Problem

NASA Astrophysics Data System (ADS)

Galić, Mario; Kraus, Ivan

2016-12-01

This paper introduces a discrete simulation model for solving routing and network material flow problems in construction projects. Before the description of the model a detailed literature review is provided. The model is verified using a case study of solving the ready-mix concrete network flow and routing problem in metropolitan area in Croatia. Within this study real-time input parameters were taken into account. Simulation model is structured in Enterprise Dynamics simulation software and Microsoft Excel linked with Google Maps. The model is dynamic, easily managed and adjustable, but also provides good estimation for minimization of costs and realization time in solving discrete routing and material network flow problems.

ALI: A CSSL/multiprocessor software interface

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

Makoui, A.; Karplus, W.J.

ALI (A Language Interface) is a software package which translates simulation models expressed in one of the higher-level languages, CSSL-IV or ACSL, into sequences of instructions for each processor of a network of microprocessors. The partitioning of the source program among the processors is automatically accomplished. The code is converted into a data flow graph, analyzed and divided among the processors to minimize the overall execution time in the presence of interprocessor communication delays. This paper describes ALI from the user's point of view and includes a detailed example of the application of ALI to a specific dynamic system simulation.

Simulation of salt production process

NASA Astrophysics Data System (ADS)

Muraveva, E. A.

2017-10-01

In this paper an approach to the use of simulation software iThink to simulate the salt production system has been proposed. The dynamic processes of the original system are substituted by processes simulated in the abstract model, but in compliance with the basic rules of the original system, which allows one to accelerate and reduce the cost of the research. As a result, a stable workable simulation model was obtained that can display the rate of the salt exhaustion and many other parameters which are important for business planning.

Integration of GIS and Bim for Indoor Geovisual Analytics

NASA Astrophysics Data System (ADS)

Wu, B.; Zhang, S.

2016-06-01

This paper presents an endeavour of integration of GIS (Geographical Information System) and BIM (Building Information Modelling) for indoor geovisual analytics. The merits of two types of technologies, GIS and BIM are firstly analysed in the context of indoor environment. GIS has well-developed capabilities of spatial analysis such as network analysis, while BIM has the advantages for indoor 3D modelling and dynamic simulation. This paper firstly investigates the important aspects for integrating GIS and BIM. Different data standards and formats such as the IFC (Industry Foundation Classes) and GML (Geography Markup Language) are discussed. Their merits and limitations in data transformation between GIS and BIM are analysed in terms of semantic and geometric information. An optimized approach for data exchange between GIS and BIM datasets is then proposed. After that, a strategy of using BIM for 3D indoor modelling, GIS for spatial analysis, and BIM again for visualization and dynamic simulation of the analysis results is presented. Based on the developments, this paper selects a typical problem, optimized indoor emergency evacuation, to demonstrate the integration of GIS and BIM for indoor geovisual analytics. The block Z of the Hong Kong Polytechnic University is selected as a test site. Detailed indoor and outdoor 3D models of the block Z are created using a BIM software Revit. The 3D models are transferred to a GIS software ArcGIS to carry out spatial analysis. Optimized evacuation plans considering dynamic constraints are generated based on network analysis in ArcGIS assuming there is a fire accident inside the building. The analysis results are then transferred back to BIM software for visualization and dynamic simulation. The developed methods and results are of significance to facilitate future development of GIS and BIM integrated solutions in various applications.

Active synchronization between two different chaotic dynamical system

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

Maheri, M.; Arifin, N. Md; Ismail, F.

2015-05-15

In this paper we investigate on the synchronization problem between two different chaotic dynamical system based on the Lyapunov stability theorem by using nonlinear control functions. Active control schemes are used for synchronization Liu system as drive and Rossler system as response. Numerical simulation by using Maple software are used to show effectiveness of the proposed schemes.

Consider a non-spherical elephant: computational fluid dynamics simulations of heat transfer coefficients and drag verified using wind tunnel experiments.

PubMed

Dudley, Peter N; Bonazza, Riccardo; Porter, Warren P

2013-07-01

Animal momentum and heat transfer analysis has historically used direct animal measurements or approximations to calculate drag and heat transfer coefficients. Research can now use modern 3D rendering and computational fluid dynamics software to simulate animal-fluid interactions. Key questions are the level of agreement between simulations and experiments and how superior they are to classical approximations. In this paper we compared experimental and simulated heat transfer and drag calculations on a scale model solid aluminum African elephant casting. We found good agreement between experimental and simulated data and large differences from classical approximations. We used the simulation results to calculate coefficients for heat transfer and drag of the elephant geometry. Copyright © 2013 Wiley Periodicals, Inc.

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

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

Grama, Ananth

2013-12-18

A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability.more » • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.« less

Visualization for Molecular Dynamics Simulation of Gas and Metal Surface Interaction

NASA Astrophysics Data System (ADS)

Puzyrkov, D.; Polyakov, S.; Podryga, V.

2016-02-01

The development of methods, algorithms and applications for visualization of molecular dynamics simulation outputs is discussed. The visual analysis of the results of such calculations is a complex and actual problem especially in case of the large scale simulations. To solve this challenging task it is necessary to decide on: 1) what data parameters to render, 2) what type of visualization to choose, 3) what development tools to use. In the present work an attempt to answer these questions was made. For visualization it was offered to draw particles in the corresponding 3D coordinates and also their velocity vectors, trajectories and volume density in the form of isosurfaces or fog. We tested the way of post-processing and visualization based on the Python language with use of additional libraries. Also parallel software was developed that allows processing large volumes of data in the 3D regions of the examined system. This software gives the opportunity to achieve desired results that are obtained in parallel with the calculations, and at the end to collect discrete received frames into a video file. The software package "Enthought Mayavi2" was used as the tool for visualization. This visualization application gave us the opportunity to study the interaction of a gas with a metal surface and to closely observe the adsorption effect.

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.

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.

Performance analysis and optimization of an advanced pharmaceutical wastewater treatment plant through a visual basic software tool (PWWT.VB).

PubMed

Pal, Parimal; Thakura, Ritwik; Chakrabortty, Sankha

2016-05-01

A user-friendly, menu-driven simulation software tool has been developed for the first time to optimize and analyze the system performance of an advanced continuous membrane-integrated pharmaceutical wastewater treatment plant. The software allows pre-analysis and manipulation of input data which helps in optimization and shows the software performance visually on a graphical platform. Moreover, the software helps the user to "visualize" the effects of the operating parameters through its model-predicted output profiles. The software is based on a dynamic mathematical model, developed for a systematically integrated forward osmosis-nanofiltration process for removal of toxic organic compounds from pharmaceutical wastewater. The model-predicted values have been observed to corroborate well with the extensive experimental investigations which were found to be consistent under varying operating conditions like operating pressure, operating flow rate, and draw solute concentration. Low values of the relative error (RE = 0.09) and high values of Willmott-d-index (d will = 0.981) reflected a high degree of accuracy and reliability of the software. This software is likely to be a very efficient tool for system design or simulation of an advanced membrane-integrated treatment plant for hazardous wastewater.

A Process for the Creation of T-MATS Propulsion System Models from NPSS data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink (Math Works, Inc.) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

A Process for the Creation of T-MATS Propulsion System Models from NPSS Data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink(Trademark) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

A Process for the Creation of T-MATS Propulsion System Models from NPSS Data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink(Registered TradeMark) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

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 Generic Multibody Parachute Simulation Model

NASA Technical Reports Server (NTRS)

Neuhaus, Jason Richard; Kenney, Patrick Sean

2006-01-01

Flight simulation of dynamic atmospheric vehicles with parachute systems is a complex task that is not easily modeled in many simulation frameworks. In the past, the performance of vehicles with parachutes was analyzed by simulations dedicated to parachute operations and were generally not used for any other portion of the vehicle flight trajectory. This approach required multiple simulation resources to completely analyze the performance of the vehicle. Recently, improved software engineering practices and increased computational power have allowed a single simulation to model the entire flight profile of a vehicle employing a parachute.

Thermal dynamic simulation of wall for building energy efficiency under varied climate environment

NASA Astrophysics Data System (ADS)

Wang, Xuejin; Zhang, Yujin; Hong, Jing

2017-08-01

Aiming at different kind of walls in five cities of different zoning for thermal design, using thermal instantaneous response factors method, the author develops software to calculation air conditioning cooling load temperature, thermal response factors, and periodic response factors. On the basis of the data, the author gives the net work analysis about the influence of dynamic thermal of wall on air-conditioning load and thermal environment in building of different zoning for thermal design regional, and put forward the strategy how to design thermal insulation and heat preservation wall base on dynamic thermal characteristic of wall under different zoning for thermal design regional. And then provide the theory basis and the technical references for the further study on the heat preservation with the insulation are in the service of energy saving wall design. All-year thermal dynamic load simulating and energy consumption analysis for new energy-saving building is very important in building environment. This software will provide the referable scientific foundation for all-year new thermal dynamic load simulation, energy consumption analysis, building environment systems control, carrying through farther research on thermal particularity and general particularity evaluation for new energy -saving walls building. Based on which, we will not only expediently design system of building energy, but also analyze building energy consumption and carry through scientific energy management. The study will provide the referable scientific foundation for carrying through farther research on thermal particularity and general particularity evaluation for new energy saving walls building.

Influence of wheel-rail contact modelling on vehicle dynamic simulation

NASA Astrophysics Data System (ADS)

Burgelman, Nico; Sichani, Matin Sh.; Enblom, Roger; Berg, Mats; Li, Zili; Dollevoet, Rolf

2015-08-01

This paper presents a comparison of four models of rolling contact used for online contact force evaluation in rail vehicle dynamics. Until now only a few wheel-rail contact models have been used for online simulation in multibody software (MBS). Many more models exist and their behaviour has been studied offline, but a comparative study of the mutual influence between the calculation of the creep forces and the simulated vehicle dynamics seems to be missing. Such a comparison would help researchers with the assessment of accuracy and calculation time. The contact methods investigated in this paper are FASTSIM, Linder, Kik-Piotrowski and Stripes. They are compared through a coupling between an MBS for the vehicle simulation and Matlab for the contact models. This way the influence of the creep force calculation on the vehicle simulation is investigated. More specifically this study focuses on the influence of the contact model on the simulation of the hunting motion and on the curving behaviour.

Improved Load Alleviation Capability for the KC-135

DTIC Science & Technology

1997-09-01

software, such as Matlab, Mathematica, Simulink, and Robotica Front End for Mathematica available in the simulation laboratory Overview This thesis report is...outlined in Spong’s text in order to utilize the Robotica system development software which automates the process of calculating the kinematic and...kinematic and dynamic equations can be accomplished using a computer tool called Robotica Front End (RFE) [ 15], developed by Doctor Spong. Boom Root d3

Investigating the Utility of Coupling Cocomo with a System Dynamics Simulation of Software Development

DTIC Science & Technology

1991-09-01

SOFTWARE DEVELOPMENT by Richard W. Smith September, 1991 Thesis Advisor: Tarek K. Abdel-Hamid Approved for public release; distribution is unlimited...REPORT Approved for public release; distribution is unlimited. 2b DECLASSIFICATION/DOWNGRADING SCHEDULE 4 PERFORMING ORGANIZATION REPORT NUMBER(S) S...exhausted SECURITY CLASSIFICATION OF THIS P (it All other edttiois are obsotete U NCLASSIFIE) Approved for public release; distribution is unlimited

Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

PubMed

Gallicchio, Emilio; Xia, Junchao; Flynn, William F; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M

2015-11-01

Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.

Study on installation of the submersible mixer

NASA Astrophysics Data System (ADS)

Tian, F.; Shi, W. D.; He, X. H.; Jiang, H.; Xu, Y. H.

2013-12-01

Study on installation of the submersible mixer for sewage treatment has been limited. In this article, large-scale computational fluid dynamics software FLUENT6.3 was adopted. ICEM software was used to build an unstructured grid of sewage treatment pool. After that, the sewage treatment pool was numerically simulated by dynamic coordinate system technology and RNG k-ε turbulent model and PIOS algorithm. Agitation pools on four different installation location cases were simulated respectively, and the external characteristic of the submersible mixer and the velocity cloud of the axial section were respectively comparatively analyzed. The best stirring effect can be reached by the installation location of case C, which is near the bottom of the pool 600 mm and blade distance the bottom at least for 200 mm wide and wide edge and narrow edge distance by 4:3. The conclusion can guide the engineering practice.

Dynamic Modeling and Simulation of an Underactuated System

NASA Astrophysics Data System (ADS)

Libardo Duarte Madrid, Juan; Ospina Henao, P. A.; González Querubín, E.

2017-06-01

In this paper, is used the Lagrangian classical mechanics for modeling the dynamics of an underactuated system, specifically a rotary inverted pendulum that will have two equations of motion. A basic design of the system is proposed in SOLIDWORKS 3D CAD software, which based on the material and dimensions of the model provides some physical variables necessary for modeling. In order to verify the results obtained, a comparison the CAD model simulated in the environment SimMechanics of MATLAB software with the mathematical model who was consisting of Euler-Lagrange’s equations implemented in Simulink MATLAB, solved with the ODE23tb method, included in the MATLAB libraries for the solution of systems of equations of the type and order obtained. This article also has a topological analysis of pendulum trajectories through a phase space diagram, which allows the identification of stable and unstable regions of the system.

Development of computer-aided design system of elastic sensitive elements of automatic metering devices

NASA Astrophysics Data System (ADS)

Kalinkina, M. E.; Kozlov, A. S.; Labkovskaia, R. I.; Pirozhnikova, O. I.; Tkalich, V. L.; Shmakov, N. A.

2018-05-01

The object of research is the element base of devices of control and automation systems, including in its composition annular elastic sensitive elements, methods of their modeling, calculation algorithms and software complexes for automation of their design processes. The article is devoted to the development of the computer-aided design system of elastic sensitive elements used in weight- and force-measuring automation devices. Based on the mathematical modeling of deformation processes in a solid, as well as the results of static and dynamic analysis, the calculation of elastic elements is given using the capabilities of modern software systems based on numerical simulation. In the course of the simulation, the model was a divided hexagonal grid of finite elements with a maximum size not exceeding 2.5 mm. The results of modal and dynamic analysis are presented in this article.

Cerebral aneurysms: relations between geometry, hemodynamics and aneurysm location in the cerebral vasculature

NASA Astrophysics Data System (ADS)

Passerini, Tiziano; Veneziani, Alessandro; Sangalli, Laura; Secchi, Piercesare; Vantini, Simone

2010-11-01

In cerebral blood circulation, the interplay of arterial geometrical features and flow dynamics is thought to play a significant role in the development of aneurysms. In the framework of the Aneurisk project, patient-specific morphology reconstructions were conducted with the open-source software VMTK (www.vmtk.org) on a set of computational angiography images provided by Ospedale Niguarda (Milano, Italy). Computational fluid dynamics (CFD) simulations were performed with a software based on the library LifeV (www.lifev.org). The joint statistical analysis of geometries and simulations highlights the possible association of certain spatial patterns of radius, curvature and shear load along the Internal Carotid Artery (ICA) with the presence, position and previous event of rupture of an aneurysm in the entire cerebral vasculature. Moreover, some possible landmarks are identified to be monitored for the assessment of a Potential Rupture Risk Index.

MONALISA for stochastic simulations of Petri net models of biochemical systems.

PubMed

Balazki, Pavel; Lindauer, Klaus; Einloft, Jens; Ackermann, Jörg; Koch, Ina

2015-07-10

The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In particular, PN allows the topological analysis based on structural properties, which is important and useful when quantitative (kinetic) data are incomplete or unknown. Knowing the kinetic parameters, the simulation of time evolution of such models can help to study the dynamic behavior of the underlying system. If the number of involved entities (molecules) is low, a stochastic simulation should be preferred against the classical deterministic approach of solving ordinary differential equations. The Stochastic Simulation Algorithm (SSA) is a common method for such simulations. The combination of the qualitative and semi-quantitative PN modeling and stochastic analysis techniques provides a valuable approach in the field of systems biology. Here, we describe the implementation of stochastic analysis in a PN environment. We extended MONALISA - an open-source software for creation, visualization and analysis of PN - by several stochastic simulation methods. The simulation module offers four simulation modes, among them the stochastic mode with constant firing rates and Gillespie's algorithm as exact and approximate versions. The simulator is operated by a user-friendly graphical interface and accepts input data such as concentrations and reaction rate constants that are common parameters in the biological context. The key features of the simulation module are visualization of simulation, interactive plotting, export of results into a text file, mathematical expressions for describing simulation parameters, and up to 500 parallel simulations of the same parameter sets. To illustrate the method we discuss a model for insulin receptor recycling as case study. We present a software that combines the modeling power of Petri nets with stochastic simulation of dynamic processes in a user-friendly environment supported by an intuitive graphical interface. The program offers a valuable alternative to modeling, using ordinary differential equations, especially when simulating single-cell experiments with low molecule counts. The ability to use mathematical expressions provides an additional flexibility in describing the simulation parameters. The open-source distribution allows further extensions by third-party developers. The software is cross-platform and is licensed under the Artistic License 2.0.

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

A Strategy for Autogeneration of Space Shuttle Ground Processing Simulation Models for Project Makespan Estimations

NASA Technical Reports Server (NTRS)

Madden, Michael G.; Wyrick, Roberta; O'Neill, Dale E.

2005-01-01

Space Shuttle Processing is a complicated and highly variable project. The planning and scheduling problem, categorized as a Resource Constrained - Stochastic Project Scheduling Problem (RC-SPSP), has a great deal of variability in the Orbiter Processing Facility (OPF) process flow from one flight to the next. Simulation Modeling is a useful tool in estimation of the makespan of the overall process. However, simulation requires a model to be developed, which itself is a labor and time consuming effort. With such a dynamic process, often the model would potentially be out of synchronization with the actual process, limiting the applicability of the simulation answers in solving the actual estimation problem. Integration of TEAMS model enabling software with our existing schedule program software is the basis of our solution. This paper explains the approach used to develop an auto-generated simulation model from planning and schedule efforts and available data.

Modeling of Semiconductor Optical Amplifier Gain Characteristics for Amplification and Switching

NASA Astrophysics Data System (ADS)

Mahad, Farah Diana; Sahmah, Abu; Supa'at, M.; Idrus, Sevia Mahdaliza; Forsyth, David

2011-05-01

The Semiconductor Optical Amplifier (SOA) is presently commonly used as a booster or pre-amplifier in some communication networks. However, SOAs are also a strong candidate for utilization as multi-functional elements in future all-optical switching, regeneration and also wavelength conversion schemes. With this in mind, the purpose of this paper is to simulate the performance of the SOA for improved amplification and switching functions. The SOA is modeled and simulated using OptSim software. In order to verify the simulated results, a MATLAB mathematical model is also used to aid the design of the SOA. Using the model, the gain difference between simulated and mathematical results in the unsaturated region is <1dB. The mathematical analysis is in good agreement with the simulation result, with only a small offset due to inherent software limitations in matching the gain dynamics of the SOA.

MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations.

PubMed

Goret, G; Aoun, B; Pellegrini, E

2017-01-23

The MDANSE software-Molecular Dynamics Analysis of Neutron Scattering Experiments-is presented. It is an interactive application for postprocessing molecular dynamics (MD) simulations. Given the widespread use of MD simulations in material and biomolecular sciences to get a better insight for experimental techniques such as thermal neutron scattering (TNS), the development of MDANSE has focused on providing a user-friendly, interactive, graphical user interface for analyzing many trajectories in the same session and running several analyses simultaneously independently of the interface. This first version of MDANSE already proposes a broad range of analyses, and the application has been designed to facilitate the introduction of new analyses in the framework. All this makes MDANSE a valuable tool for extracting useful information from trajectories resulting from a wide range of MD codes.

Intelligent Launch and Range Operations Virtual Test Bed (ILRO-VTB)

NASA Technical Reports Server (NTRS)

Bardina, Jorge; Rajkumar, T.

2003-01-01

Intelligent Launch and Range Operations Virtual Test Bed (ILRO-VTB) is a real-time web-based command and control, communication, and intelligent simulation environment of ground-vehicle, launch and range operation activities. ILRO-VTB consists of a variety of simulation models combined with commercial and indigenous software developments (NASA Ames). It creates a hybrid software/hardware environment suitable for testing various integrated control system components of launch and range. The dynamic interactions of the integrated simulated control systems are not well understood. Insight into such systems can only be achieved through simulation/emulation. For that reason, NASA has established a VTB where we can learn the actual control and dynamics of designs for future space programs, including testing and performance evaluation. The current implementation of the VTB simulates the operations of a sub-orbital vehicle of mission, control, ground-vehicle engineering, launch and range operations. The present development of the test bed simulates the operations of Space Shuttle Vehicle (SSV) at NASA Kennedy Space Center. The test bed supports a wide variety of shuttle missions with ancillary modeling capabilities like weather forecasting, lightning tracker, toxic gas dispersion model, debris dispersion model, telemetry, trajectory modeling, ground operations, payload models and etc. To achieve the simulations, all models are linked using Common Object Request Broker Architecture (CORBA). The test bed provides opportunities for government, universities, researchers and industries to do a real time of shuttle launch in cyber space.

Intelligent launch and range operations virtual testbed (ILRO-VTB)

NASA Astrophysics Data System (ADS)

Bardina, Jorge; Rajkumar, Thirumalainambi

2003-09-01

Intelligent Launch and Range Operations Virtual Test Bed (ILRO-VTB) is a real-time web-based command and control, communication, and intelligent simulation environment of ground-vehicle, launch and range operation activities. ILRO-VTB consists of a variety of simulation models combined with commercial and indigenous software developments (NASA Ames). It creates a hybrid software/hardware environment suitable for testing various integrated control system components of launch and range. The dynamic interactions of the integrated simulated control systems are not well understood. Insight into such systems can only be achieved through simulation/emulation. For that reason, NASA has established a VTB where we can learn the actual control and dynamics of designs for future space programs, including testing and performance evaluation. The current implementation of the VTB simulates the operations of a sub-orbital vehicle of mission, control, ground-vehicle engineering, launch and range operations. The present development of the test bed simulates the operations of Space Shuttle Vehicle (SSV) at NASA Kennedy Space Center. The test bed supports a wide variety of shuttle missions with ancillary modeling capabilities like weather forecasting, lightning tracker, toxic gas dispersion model, debris dispersion model, telemetry, trajectory modeling, ground operations, payload models and etc. To achieve the simulations, all models are linked using Common Object Request Broker Architecture (CORBA). The test bed provides opportunities for government, universities, researchers and industries to do a real time of shuttle launch in cyber space.

The Propulsive Small Expendable Deployer System (ProSEDS)

NASA Technical Reports Server (NTRS)

Lorenzini, Enrico C.; Cosmo, Mario L.; Estes, Robert D.; Sanmartin, Juan; Pelaez, Jesus; Ruiz, Manuel

2003-01-01

This Final Report covers the following main topics: 1) Brief Description of ProSEDS; 2) Mission Analysis; 3) Dynamics Reference Mission; 4) Dynamics Stability; 5) Deployment Control; 6) Updated System Performance; 7) Updated Mission Analysis; 8) Updated Dynamics Reference Mission; 9) Updated Deployment Control Profiles and Simulations; 10) Updated Reference Mission; 11) Evaluation of Power Delivered by the Tether; 12) Deployment Control Profile Ref. #78 and Simulations; 13) Kalman Filters for Mission Estimation; 14) Analysis/Estimation of Deployment Flight Data; 15) Comparison of ED Tethers and Electrical Thrusters; 16) Dynamics Analysis for Mission Starting at a Lower Altitude; 17) Deployment Performance at a Lower Altitude; 18) Satellite Orbit after a Tether Cut; 19) Deployment with Shorter Dyneema Tether Length; 20) Interactive Software for ED Tethers.

Design of penicillin fermentation process simulation system

NASA Astrophysics Data System (ADS)

Qi, Xiaoyu; Yuan, Zhonghu; Qi, Xiaoxuan; Zhang, Wenqi

2011-10-01

Real-time monitoring for batch process attracts increasing attention. It can ensure safety and provide products with consistent quality. The design of simulation system of batch process fault diagnosis is of great significance. In this paper, penicillin fermentation, a typical non-linear, dynamic, multi-stage batch production process, is taken as the research object. A visual human-machine interactive simulation software system based on Windows operation system is developed. The simulation system can provide an effective platform for the research of batch process fault diagnosis.

Facilitating Students' Interaction with Real Gas Properties Using a Discovery-Based Approach and Molecular Dynamics Simulations

ERIC Educational Resources Information Center

Sweet, Chelsea; Akinfenwa, Oyewumi; Foley, Jonathan J., IV

2018-01-01

We present an interactive discovery-based approach to studying the properties of real gases using simple, yet realistic, molecular dynamics software. Use of this approach opens up a variety of opportunities for students to interact with the behaviors and underlying theories of real gases. Students can visualize gas behavior under a variety of…

Analysis of helicopter flight dynamics through modeling and simulation of primary flight control actuation system

NASA Astrophysics Data System (ADS)

Nelson, Hunter Barton

A simplified second-order transfer function actuator model used in most flight dynamics applications cannot easily capture the effects of different actuator parameters. The present work integrates a nonlinear actuator model into a nonlinear state space rotorcraft model to determine the effect of actuator parameters on key flight dynamics. The completed actuator model was integrated with a swashplate kinematics where step responses were generated over a range of key hydraulic parameters. The actuator-swashplate system was then introduced into a nonlinear state space rotorcraft simulation where flight dynamics quantities such as bandwidth and phase delay analyzed. Frequency sweeps were simulated for unique actuator configurations using the coupled nonlinear actuator-rotorcraft system. The software package CIFER was used for system identification and compared directly to the linearized models. As the actuator became rate saturated, the effects on bandwidth and phase delay were apparent on the predicted handling qualities specifications.

High effective inverse dynamics modelling for dual-arm robot

NASA Astrophysics Data System (ADS)

Shen, Haoyu; Liu, Yanli; Wu, Hongtao

2018-05-01

To deal with the problem of inverse dynamics modelling for dual arm robot, a recursive inverse dynamics modelling method based on decoupled natural orthogonal complement is presented. In this model, the concepts and methods of Decoupled Natural Orthogonal Complement matrices are used to eliminate the constraint forces in the Newton-Euler kinematic equations, and the screws is used to express the kinematic and dynamics variables. On this basis, the paper has developed a special simulation program with symbol software of Mathematica and conducted a simulation research on the a dual-arm robot. Simulation results show that the proposed method based on decoupled natural orthogonal complement can save an enormous amount of CPU time that was spent in computing compared with the recursive Newton-Euler kinematic equations and the results is correct and reasonable, which can verify the reliability and efficiency of the method.

Estimation of light commercial vehicles dynamics by means of HIL-testbench simulation

NASA Astrophysics Data System (ADS)

Groshev, A.; Tumasov, A.; Toropov, E.; Sereda, P.

2018-02-01

The high level of active safety of vehicles is impossible without driver assistance electronic systems. Electronic stability control (ESC) system is one of them. Nowadays such systems are obligatory for installation on vehicles of different categories. The approval of active safety level of vehicles with ESC is possible by means of high speed road tests. The most frequently implemented tests are “fish hook” and “sine with dwell” tests. Such kind of tests provided by The Global technical regulation No. 8 are published by the United Nations Economic Commission for Europe as well as by ECE 13-11. At the same time, not only road tests could be used for estimation of vehicles dynamics. Modern software and hardware technologies allow imitating real tests with acceptable reliability and good convergence between real test data and simulation results. ECE 13-11 Annex 21 - Appendix 1 “Use Of The Dynamic Stability Simulation” regulates demands for special Simulation Test bench that could be used not only for preliminary estimation of vehicles dynamics, but also for official vehicles homologation. This paper describes the approach, proposed by the researchers from Nizhny Novgorod State Technical University n.a. R.E. Alekseev (NNSTU, Russia) with support of engineers of United Engineering Center GAZ Group, as well as specialists of Gorky Automobile Plant. The idea of approach is to use the special HIL (hardware in the loop) -test bench, that consists of Real Time PC with Real Time Software and braking system components including electronic control unit (ECU) of ESC system. The HIL-test bench allows imitating vehicle dynamics in condition of “fish hook” and “sine with dwell” tests. The paper describes the scheme and structure of HIL-test bench and some peculiarities that should be taken into account during HIL-simulation.

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.

Validated simulator for space debris removal with nets and other flexible tethers applications

NASA Astrophysics Data System (ADS)

Gołębiowski, Wojciech; Michalczyk, Rafał; Dyrek, Michał; Battista, Umberto; Wormnes, Kjetil

2016-12-01

In the context of active debris removal technologies and preparation activities for the e.Deorbit mission, a simulator for net-shaped elastic bodies dynamics and their interactions with rigid bodies, has been developed. Its main application is to aid net design and test scenarios for space debris deorbitation. The simulator can model all the phases of the debris capturing process: net launch, flight and wrapping around the target. It handles coupled simulation of rigid and flexible bodies dynamics. Flexible bodies were implemented using Cosserat rods model. It allows to simulate flexible threads or wires with elasticity and damping for stretching, bending and torsion. Threads may be combined into structures of any topology, so the software is able to simulate nets, pure tethers, tether bundles, cages, trusses, etc. Full contact dynamics was implemented. Programmatic interaction with simulation is possible - i.e. for control implementation. The underlying model has been experimentally validated and due to significant gravity influence, experiment had to be performed in microgravity conditions. Validation experiment for parabolic flight was a downscaled process of Envisat capturing. The prepacked net was launched towards the satellite model, it expanded, hit the model and wrapped around it. The whole process was recorded with 2 fast stereographic camera sets for full 3D trajectory reconstruction. The trajectories were used to compare net dynamics to respective simulations and then to validate the simulation tool. The experiments were performed on board of a Falcon-20 aircraft, operated by National Research Council in Ottawa, Canada. Validation results show that model reflects phenomenon physics accurately enough, so it may be used for scenario evaluation and mission design purposes. The functionalities of the simulator are described in detail in the paper, as well as its underlying model, sample cases and methodology behind validation. Results are presented and typical use cases are discussed showing that the software may be used to design throw nets for space debris capturing, but also to simulate deorbitation process, chaser control system or general interactions between rigid and elastic bodies - all in convenient and efficient way. The presented work was led by SKA Polska under the ESA contract, within the CleanSpace initiative.

Design and Performance Evaluation of an Electro-Hydraulic Camless Engine Valve Actuator for Future Vehicle Applications

PubMed Central

Nam, Kanghyun; Cho, Kwanghyun; Park, Sang-Shin; Choi, Seibum B.

2017-01-01

This paper details the new design and dynamic simulation of an electro-hydraulic camless engine valve actuator (EH-CEVA) and experimental verification with lift position sensors. In general, camless engine technologies have been known for improving fuel efficiency, enhancing power output, and reducing emissions of internal combustion engines. Electro-hydraulic valve actuators are used to eliminate the camshaft of an existing internal combustion engines and used to control the valve timing and valve duration independently. This paper presents novel electro-hydraulic actuator design, dynamic simulations, and analysis based on design specifications required to satisfy the operation performances. An EH-CEVA has initially been designed and modeled by means of a powerful hydraulic simulation software, AMESim, which is useful for the dynamic simulations and analysis of hydraulic systems. Fundamental functions and performances of the EH-CEVA have been validated through comparisons with experimental results obtained in a prototype test bench. PMID:29258270

Design and Performance Evaluation of an Electro-Hydraulic Camless Engine Valve Actuator for Future Vehicle Applications.

PubMed

Nam, Kanghyun; Cho, Kwanghyun; Park, Sang-Shin; Choi, Seibum B

2017-12-18

This paper details the new design and dynamic simulation of an electro-hydraulic camless engine valve actuator (EH-CEVA) and experimental verification with lift position sensors. In general, camless engine technologies have been known for improving fuel efficiency, enhancing power output, and reducing emissions of internal combustion engines. Electro-hydraulic valve actuators are used to eliminate the camshaft of an existing internal combustion engines and used to control the valve timing and valve duration independently. This paper presents novel electro-hydraulic actuator design, dynamic simulations, and analysis based on design specifications required to satisfy the operation performances. An EH-CEVA has initially been designed and modeled by means of a powerful hydraulic simulation software, AMESim, which is useful for the dynamic simulations and analysis of hydraulic systems. Fundamental functions and performances of the EH-CEVA have been validated through comparisons with experimental results obtained in a prototype test bench.

Modeling and performance improvement of the constant power regulator systems in variable displacement axial piston pump.

PubMed

Park, Sung Hwan; Lee, Ji Min; Kim, Jong Shik

2013-01-01

An irregular performance of a mechanical-type constant power regulator is considered. In order to find the cause of an irregular discharge flow at the cut-off pressure area, modeling and numerical simulations are performed to observe dynamic behavior of internal parts of the constant power regulator system for a swashplate-type axial piston pump. The commercial numerical simulation software AMESim is applied to model the mechanical-type regulator with hydraulic pump and simulate the performance of it. The validity of the simulation model of the constant power regulator system is verified by comparing simulation results with experiments. In order to find the cause of the irregular performance of the mechanical-type constant power regulator system, the behavior of main components such as the spool, sleeve, and counterbalance piston is investigated using computer simulation. The shape modification of the counterbalance piston is proposed to improve the undesirable performance of the mechanical-type constant power regulator. The performance improvement is verified by computer simulation using AMESim software.

Largenet2: an object-oriented programming library for simulating large adaptive networks.

PubMed

Zschaler, Gerd; Gross, Thilo

2013-01-15

The largenet2 C++ library provides an infrastructure for the simulation of large dynamic and adaptive networks with discrete node and link states. The library is released as free software. It is available at http://biond.github.com/largenet2. Largenet2 is licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported License. gerd@biond.org

An Integrated Crustal Dynamics Simulator

NASA Astrophysics Data System (ADS)

Xing, H. L.; Mora, P.

2007-12-01

Numerical modelling offers an outstanding opportunity to gain an understanding of the crustal dynamics and complex crustal system behaviour. This presentation provides our long-term and ongoing effort on finite element based computational model and software development to simulate the interacting fault system for earthquake forecasting. A R-minimum strategy based finite-element computational model and software tool, PANDAS, for modelling 3-dimensional nonlinear frictional contact behaviour between multiple deformable bodies with the arbitrarily-shaped contact element strategy has been developed by the authors, which builds up a virtual laboratory to simulate interacting fault systems including crustal boundary conditions and various nonlinearities (e.g. from frictional contact, materials, geometry and thermal coupling). It has been successfully applied to large scale computing of the complex nonlinear phenomena in the non-continuum media involving the nonlinear frictional instability, multiple material properties and complex geometries on supercomputers, such as the South Australia (SA) interacting fault system, South California fault model and Sumatra subduction model. It has been also extended and to simulate the hot fractured rock (HFR) geothermal reservoir system in collaboration of Geodynamics Ltd which is constructing the first geothermal reservoir system in Australia and to model the tsunami generation induced by earthquakes. Both are supported by Australian Research Council.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System T-MATS

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

Meeting the memory challenges of brain-scale network simulation.

PubMed

Kunkel, Susanne; Potjans, Tobias C; Eppler, Jochen M; Plesser, Hans Ekkehard; Morrison, Abigail; Diesmann, Markus

2011-01-01

The development of high-performance simulation software is crucial for studying the brain connectome. Using connectome data to generate neurocomputational models requires software capable of coping with models on a variety of scales: from the microscale, investigating plasticity, and dynamics of circuits in local networks, to the macroscale, investigating the interactions between distinct brain regions. Prior to any serious dynamical investigation, the first task of network simulations is to check the consistency of data integrated in the connectome and constrain ranges for yet unknown parameters. Thanks to distributed computing techniques, it is possible today to routinely simulate local cortical networks of around 10(5) neurons with up to 10(9) synapses on clusters and multi-processor shared-memory machines. However, brain-scale networks are orders of magnitude larger than such local networks, in terms of numbers of neurons and synapses as well as in terms of computational load. Such networks have been investigated in individual studies, but the underlying simulation technologies have neither been described in sufficient detail to be reproducible nor made publicly available. Here, we discover that as the network model sizes approach the regime of meso- and macroscale simulations, memory consumption on individual compute nodes becomes a critical bottleneck. This is especially relevant on modern supercomputers such as the Blue Gene/P architecture where the available working memory per CPU core is rather limited. We develop a simple linear model to analyze the memory consumption of the constituent components of neuronal simulators as a function of network size and the number of cores used. This approach has multiple benefits. The model enables identification of key contributing components to memory saturation and prediction of the effects of potential improvements to code before any implementation takes place. As a consequence, development cycles can be shorter and less expensive. Applying the model to our freely available Neural Simulation Tool (NEST), we identify the software components dominant at different scales, and develop general strategies for reducing the memory consumption, in particular by using data structures that exploit the sparseness of the local representation of the network. We show that these adaptations enable our simulation software to scale up to the order of 10,000 processors and beyond. As memory consumption issues are likely to be relevant for any software dealing with complex connectome data on such architectures, our approach and our findings should be useful for researchers developing novel neuroinformatics solutions to the challenges posed by the connectome project.

Dynamic optimization case studies in DYNOPT tool

NASA Astrophysics Data System (ADS)

Ozana, Stepan; Pies, Martin; Docekal, Tomas

2016-06-01

Dynamic programming is typically applied to optimization problems. As the analytical solutions are generally very difficult, chosen software tools are used widely. These software packages are often third-party products bound for standard simulation software tools on the market. As typical examples of such tools, TOMLAB and DYNOPT could be effectively applied for solution of problems of dynamic programming. DYNOPT will be presented in this paper due to its licensing policy (free product under GPL) and simplicity of use. DYNOPT is a set of MATLAB functions for determination of optimal control trajectory by given description of the process, the cost to be minimized, subject to equality and inequality constraints, using orthogonal collocation on finite elements method. The actual optimal control problem is solved by complete parameterization both the control and the state profile vector. It is assumed, that the optimized dynamic model may be described by a set of ordinary differential equations (ODEs) or differential-algebraic equations (DAEs). This collection of functions extends the capability of the MATLAB Optimization Tool-box. The paper will introduce use of DYNOPT in the field of dynamic optimization problems by means of case studies regarding chosen laboratory physical educational models.

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.

Transitioning NWChem to the Next Generation of Manycore Machines

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

Bylaska, Eric J.; Apra, E; Kowalski, Karol

The NorthWest chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers [1-3]. It contains an umbrella of modules that today includes self-consistent eld (SCF), second order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), multiconguration self-consistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real-time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (MD), classical MD, hybrid quantum mechanicsmore » molecular mechanics (QM/MM), hybrid ab initio molecular dynamics molecular mechanics (AIMD/MM), gauge independent atomic orbital nuclear magnetic resonance (GIAO NMR), conductor like screening solvation model (COSMO), conductor-like screening solvation model based on density (COSMO-SMD), and reference interaction site model (RISM) solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities [4]. Moreover, new capabilities continue to be added with each new release.« less

TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

DOE PAGES

Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.; ...

2015-04-16

Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family ofmore » molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.« less

Integration agent-based models and GIS as a virtual urban dynamic laboratory

NASA Astrophysics Data System (ADS)

Chen, Peng; Liu, Miaolong

2007-06-01

Based on the Agent-based Model and spatial data model, a tight-coupling integrating method of GIS and Agent-based Model (ABM) is to be discussed in this paper. The use of object-orientation for both spatial data and spatial process models facilitates their integration, which can allow exploration and explanation of spatial-temporal phenomena such as urban dynamic. In order to better understand how tight coupling might proceed and to evaluate the possible functional and efficiency gains from such a tight coupling, the agent-based model and spatial data model are discussed, and then the relationships affecting spatial data model and agent-based process models interaction. After that, a realistic crowd flow simulation experiment is presented. Using some tools provided by general GIS systems and a few specific programming languages, a new software system integrating GIS and MAS as a virtual laboratory applicable for simulating pedestrian flows in a crowd activity centre has been developed successfully. Under the environment supported by the software system, as an applicable case, a dynamic evolution process of the pedestrian's flows (dispersed process for the spectators) in a crowds' activity center - The Shanghai Stadium has been simulated successfully. At the end of the paper, some new research problems have been pointed out for the future.

A portable structural analysis library for reaction networks.

PubMed

Bedaso, Yosef; Bergmann, Frank T; Choi, Kiri; Medley, Kyle; Sauro, Herbert M

2018-07-01

The topology of a reaction network can have a significant influence on the network's dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the network configuration and are important considerations before any dynamical analysis is made. Most established simulation software tools usually carry out some kind of structural analysis of a network before any attempt is made at dynamic simulation. In this paper, we describe a portable software library, libStructural, that can carry out a variety of popular structural analyses that includes conservation analysis, flux dependency analysis and enumerating elementary modes. The library employs robust algorithms that allow it to be used on large networks with more than a two thousand nodes. The library accepts either a raw or fully labeled stoichiometry matrix or models written in SBML format. The software is written in standard C/C++ and comes with extensive on-line documentation and a test suite. The software is available for Windows, Mac OS X, and can be compiled easily on any Linux operating system. A language binding for Python is also available through the pip package manager making it simple to install on any standard Python distribution. The bulk of the source code is licensed under the open source BSD license with other parts using as either the MIT license or more simply public domain. All source is available on GitHub (https://github.com/sys-bio/Libstructural). Copyright © 2018 Elsevier B.V. All rights reserved.

A Facility and Architecture for Autonomy Research

NASA Technical Reports Server (NTRS)

Pisanich, Greg; Clancy, Daniel (Technical Monitor)

2002-01-01

Autonomy is a key enabling factor in the advancement of the remote robotic exploration. There is currently a large gap between autonomy software at the research level and software that is ready for insertion into near-term space missions. The Mission Simulation Facility (MST) will bridge this gap by providing a simulation framework and suite of simulation tools to support research in autonomy for remote exploration. This system will allow developers of autonomy software to test their models in a high-fidelity simulation and evaluate their system's performance against a set of integrated, standardized simulations. The Mission Simulation ToolKit (MST) uses a distributed architecture with a communication layer that is built on top of the standardized High Level Architecture (HLA). This architecture enables the use of existing high fidelity models, allows mixing simulation components from various computing platforms and enforces the use of a standardized high-level interface among components. The components needed to achieve a realistic simulation can be grouped into four categories: environment generation (terrain, environmental features), robotic platform behavior (robot dynamics), instrument models (camera/spectrometer/etc.), and data analysis. The MST will provide basic components in these areas but allows users to plug-in easily any refined model by means of a communication protocol. Finally, a description file defines the robot and environment parameters for easy configuration and ensures that all the simulation models share the same information.

A Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices

PubMed Central

Hall, Benjamin A; Halim, Khairul Abd; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S P

2016-01-01

The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analysed via coarse-grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. To facilitate the running and analysis of such ensembles of simulations we have developed Sidekick, an automated pipeline software for performing high throughput CGMD simulations of α-helical peptides in lipid bilayer membranes. Through an end-to-end approach, which takes as input a helix sequence and outputs analytical metrics derived from CGMD simulations, we are able to predict the orientation and likelihood of insertion into a lipid bilayer of a given helix of family of helix sequences. We illustrate this software via analysis of insertion into a membrane of short hydrophobic TM helices containing a single cationic arginine residue positioned at different positions along the length of the helix. From analysis of these ensembles of simulations we estimate apparent energy barriers to insertion which are comparable to experimentally determined values. In a second application we use CGMD simulations to examine self-assembly of dimers of TM helices from the ErbB1 receptor tyrosine kinase, and analyse the numbers of simulation repeats necessary to obtain convergence of simple descriptors of the mode of packing of the two helices within a dimer. Our approach offers proof-of-principle platform for the further employment of automation in large ensemble CGMD simulations of membrane proteins. PMID:26580541

Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices.

PubMed

Hall, Benjamin A; Halim, Khairul Bariyyah Abd; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S P

2014-05-13

The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analyzed via coarse grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. To facilitate the running and analysis of such ensembles of simulations, we have developed Sidekick, an automated pipeline software for performing high throughput CGMD simulations of α-helical peptides in lipid bilayer membranes. Through an end-to-end approach, which takes as input a helix sequence and outputs analytical metrics derived from CGMD simulations, we are able to predict the orientation and likelihood of insertion into a lipid bilayer of a given helix of a family of helix sequences. We illustrate this software via analyses of insertion into a membrane of short hydrophobic TM helices containing a single cationic arginine residue positioned at different positions along the length of the helix. From analyses of these ensembles of simulations, we estimate apparent energy barriers to insertion which are comparable to experimentally determined values. In a second application, we use CGMD simulations to examine the self-assembly of dimers of TM helices from the ErbB1 receptor tyrosine kinase and analyze the numbers of simulation repeats necessary to obtain convergence of simple descriptors of the mode of packing of the two helices within a dimer. Our approach offers a proof-of-principle platform for the further employment of automation in large ensemble CGMD simulations of membrane proteins.

Finite Element Analysis of Folded Airbag in Frontal Impact of Adapted Vehicles for Disabled Drivers

NASA Astrophysics Data System (ADS)

Masiá, J.; Eixerés, B.; Dols, J. F.; Esquerdo, T. V.

2009-11-01

The car control adaptations are used in vehicles in order to facilitate the driving to persons with physical handicaps. This does not have to suppose a decrease of the passive safety that is required to the vehicles. In order to analyze this relation there will be characterized the different control adaptations that are in use together with the different devices of passive safety that can be mounted in the vehicles in diverse cases of impact in order to generate models of simulation. The methodology used to generate this simulation consists of the first phase in which there develops the three-dimensional model of the driving place. For it, there has been used a commercial software of three-dimensional design. Once realized this one divides, the model is imported to the finite elements software in which meshing is generated. Finally, dynamic simulation software is used to assign the most important characteristics like material properties, contact interfaces, gas expansion models, airbag fold types, etc.

Development of the ARISTOTLE webware for cloud-based rarefied gas flow modeling

NASA Astrophysics Data System (ADS)

Deschenes, Timothy R.; Grot, Jonathan; Cline, Jason A.

2016-11-01

Rarefied gas dynamics are important for a wide variety of applications. An improvement in the ability of general users to predict these gas flows will enable optimization of current, and discovery of future processes. Despite this potential, most rarefied simulation software is designed by and for experts in the community. This has resulted in low adoption of the methods outside of the immediate RGD community. This paper outlines an ongoing effort to create a rarefied gas dynamics simulation tool that can be used by a general audience. The tool leverages a direct simulation Monte Carlo (DSMC) library that is available to the entire community and a web-based simulation process that will enable all users to take advantage of high performance computing capabilities. First, the DSMC library and simulation architecture are described. Then the DSMC library is used to predict a number of representative transient gas flows that are applicable to the rarefied gas dynamics community. The paper closes with a summary and future direction.

Flow analysis of new type propulsion system for UV’s

NASA Astrophysics Data System (ADS)

Eimanis, M.; Auzins, J.

2017-10-01

This paper presents an original design of an autonomous underwater vehicle where thrust force is created by the helicoidal shape of the hull rather than screw propellers. Propulsion force is created by counter-rotating bow and stern parts. The middle part of the vehicle has the function of a cargo compartment containing all control mechanisms and communications. It’s made of elastic material, containing a Cardan-joint mechanism, which allows changing the direction of vehicle, actuated by bending drives. A bending drive velocity control algorithm for the automatic control of vehicle movement direction is proposed. The dynamics of AUV are simulated using multibody simulation software MSC Adams. For the simulation of water resistance forces and torques the surrogate polynomial metamodels are created on the basis of computer experiments with CFD software. For flow interaction with model geometry the simplified vehicle model is submerged in fluid medium using special CFD software, with the same idea used in wind tunnel experiments. The simulation results are compared with measurements of the AUV prototype, created at Institute of Mechanics of Riga Technical University. Experiments with the prototype showed good agreement with simulation results and confirmed the effectiveness and the future potential of the proposed principle.

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation.

PubMed

Kamberaj, Hiqmet

2018-05-01

In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method. In addition, we applied SPMD simulation to calculate the time correlation functions of the transitions in a two dimensional surface to demonstrate the enhancement of transition path sampling. Our results showed that folded structure can be obtained in a shorter simulation time using the new method when compared with non-augmented dynamical system. Typically, in less than 0.5 ns using replica exchange runs assuming that native folded structure is known and within simulation time scale of 40 ns in the case of blind structure prediction. Furthermore, the root mean square deviations from the reference structures were less than 2Å. To demonstrate the performance of new method, we also implemented three simulation protocols using CHARMM software. Comparisons are also performed with standard targeted molecular dynamics simulation method. Copyright © 2018 Elsevier Inc. All rights reserved.

Design, Fabrication, and Testing of a Hopper Spacecraft Simulator

NASA Astrophysics Data System (ADS)

Mucasey, Evan Phillip Krell

A robust test bed is needed to facilitate future development of guidance, navigation, and control software for future vehicles capable of vertical takeoff and landings. Specifically, this work aims to develop both a hardware and software simulator that can be used for future flight software development for extra-planetary vehicles. To achieve the program requirements of a high thrust to weight ratio with large payload capability, the vehicle is designed to have a novel combination of electric motors and a micro jet engine is used to act as the propulsion elements. The spacecraft simulator underwent several iterations of hardware development using different materials and fabrication methods. The final design used a combination of carbon fiber and fiberglass that was cured under vacuum to serve as the frame of the vehicle which provided a strong, lightweight platform for all flight components and future payloads. The vehicle also uses an open source software development platform, Arduino, to serve as the initial flight computer and has onboard accelerometers, gyroscopes, and magnetometers to sense the vehicles attitude. To prevent instability due to noise, a polynomial kalman filter was designed and this fed the sensed angles and rates into a robust attitude controller which autonomously control the vehicle' s yaw, pitch, and roll angles. In addition to the hardware development of the vehicle itself, both a software simulation and a real time data acquisition interface was written in MATLAB/SIMULINK so that real flight data could be taken and then correlated to the simulation to prove the accuracy of the analytical model. In result, the full scale vehicle was designed and own outside of the lab environment and data showed that the software model accurately predicted the flight dynamics of the vehicle.

Finite Element Simulations of Kaikoura, NZ Earthquake using DInSAR and High-Resolution DSMs

NASA Astrophysics Data System (ADS)

Barba, M.; Willis, M. J.; Tiampo, K. F.; Glasscoe, M. T.; Clark, M. K.; Zekkos, D.; Stahl, T. A.; Massey, C. I.

2017-12-01

Three-dimensional displacements from the Kaikoura, NZ, earthquake in November 2016 are imaged here using Differential Interferometric Synthetic Aperture Radar (DInSAR) and high-resolution Digital Surface Model (DSM) differencing and optical pixel tracking. Full-resolution co- and post-seismic interferograms of Sentinel-1A/B images are constructed using the JPL ISCE software. The OSU SETSM software is used to produce repeat 0.5 m posting DSMs from commercial satellite imagery, which are supplemented with UAV derived DSMs over the Kaikoura fault rupture on the eastern South Island, NZ. DInSAR provides long-wavelength motions while DSM differencing and optical pixel tracking provides both horizontal and vertical near fault motions, improving the modeling of shallow rupture dynamics. JPL GeoFEST software is used to perform finite element modeling of the fault segments and slip distributions and, in turn, the associated asperity distribution. The asperity profile is then used to simulate event rupture, the spatial distribution of stress drop, and the associated stress changes. Finite element modeling of slope stability is accomplished using the ultra high-resolution UAV derived DSMs to examine the evolution of post-earthquake topography, landslide dynamics and volumes. Results include new insights into shallow dynamics of fault slip and partitioning, estimates of stress change, and improved understanding of its relationship with the associated seismicity, deformation, and triggered cascading hazards.

MULTIMEDIA ENVIRONMENTAL DISTRIBUTION OF TOXICS (MEND-TOX): PART II, SOFTWARE IMPLEMENTATION AND CASE STUDIES

EPA Science Inventory

An integrated hybrid spatial-compartmental simulator is presented for analyzing the dynamic distribution of chemicals in the multimedia environment. Information obtained from such analysis, which includes temporal chemical concentration profiles in various media, mass distribu...

Moving Target Techniques: Leveraging Uncertainty for CyberDefense

DTIC Science & Technology

2015-12-15

cyberattacks is a continual struggle for system managers. Attackers often need only find one vulnerability (a flaw or bug that an attacker can exploit...additional parsing code itself could have security-relevant software bugs . Dynamic  Network   Techniques in the dynamic network domain change the...evaluation of MT techniques can benefit from a variety of evaluation approaches, including abstract analysis, modeling and simulation, test bed

Dynamic bandwidth allocation based on multiservice in software-defined wavelength-division multiplexing time-division multiplexing passive optical network

NASA Astrophysics Data System (ADS)

Wang, Fu; Liu, Bo; Zhang, Lijia; Jin, Feifei; Zhang, Qi; Tian, Qinghua; Tian, Feng; Rao, Lan; Xin, Xiangjun

2017-03-01

The wavelength-division multiplexing passive optical network (WDM-PON) is a potential technology to carry multiple services in an optical access network. However, it has the disadvantages of high cost and an immature technique for users. A software-defined WDM/time-division multiplexing PON was proposed to meet the requirements of high bandwidth, high performance, and multiple services. A reasonable and effective uplink dynamic bandwidth allocation algorithm was proposed. A controller with dynamic wavelength and slot assignment was introduced, and a different optical dynamic bandwidth management strategy was formulated flexibly for services of different priorities according to the network loading. The simulation compares the proposed algorithm with the interleaved polling with adaptive cycle time algorithm. The algorithm shows better performance in average delay, throughput, and bandwidth utilization. The results show that the delay is reduced to 62% and the throughput is improved by 35%.

Advanced Methodology for Simulation of Complex Flows Using Structured Grid Systems

NASA Technical Reports Server (NTRS)

Steinthorsson, Erlendur; Modiano, David

1995-01-01

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

SILHIL Replication of Electric Aircraft Powertrain Dynamics and Inner-Loop Control for V&V of System Health Management Routines

NASA Technical Reports Server (NTRS)

Bole, Brian; Teubert, Christopher Allen; Cuong Chi, Quach; Hogge, Edward; Vazquez, Sixto; Goebel, Kai; George, Vachtsevanos

2013-01-01

Software-in-the-loop and Hardware-in-the-loop testing of failure prognostics and decision making tools for aircraft systems will facilitate more comprehensive and cost-effective testing than what is practical to conduct with flight tests. A framework is described for the offline recreation of dynamic loads on simulated or physical aircraft powertrain components based on a real-time simulation of airframe dynamics running on a flight simulator, an inner-loop flight control policy executed by either an autopilot routine or a human pilot, and a supervisory fault management control policy. The creation of an offline framework for verifying and validating supervisory failure prognostics and decision making routines is described for the example of battery charge depletion failure scenarios onboard a prototype electric unmanned aerial vehicle.

Dynamic Simulation on the Installation Process of HGIS in Transformer Substation

NASA Astrophysics Data System (ADS)

Lin, Tao; Li, Shaohua; Wang, Hu; Che, Deyong; Qi, Guangcai; Yao, Jianfeng; Zhang, Qingzhe

The technological requirements of Hypid Gas Insulated Switchgear (HGIS) installation in transformer substation is high and the control points of quality is excessive. Most of the engineers and technicians in the construction enterprises are not familiar with equipments of HGIS. In order to solve these problem, equipments of HGIS is modeled on the computer by SolidWorks software. Installation process of civil foundation and closed-type equipments is optimized dynamically with virtual assemble technology. Announcements and application work are composited into animation file. Skills of modeling and simulation is tidied classify as well. The result of the visual dynamic simulation can instruct the actual construction process of HGIS to a certain degree and can promote reasonable construction planning and management. It can also improve the method and quality of staff training for electric power construction enterprises.

The Effect of a Computerized Simulation on Middle School Students' Understanding of the Kinetic Molecular Theory

ERIC Educational Resources Information Center

Stern, Luli; Barnea, Nitza; Shauli, Sofia

2008-01-01

The objective of this study was to evaluate the effect of a dynamic software simulation on the understanding of the kinetic molecular theory by 7th graders. Students in the control group (n = 62) studied a curricular unit that addressed the differences in arrangement and motion of molecules in the three phases of matter. The experimental group (n…

The use of Virtual Analogy Simulation (VAS) in physics learning

NASA Astrophysics Data System (ADS)

Faizin, M. Noor; Samsudin, A.

2018-05-01

The purpose of this research is to explore the use of VAS software in electrical dynamic learning in junior high student, so as to obtain an overview of this software consistency in help students build a scientific conception. This research was administered via research and Development (R & D) with the design of embedded experimental models. The respondents which were involved in this research were 60 students of ninth grade in one of junior high schools in Kudus central java. The improving process of students’ concept is examined based on normalized gain analysis from pretest and posttest scores. The result of this research shows that there was difference between learning using conventional learning (power point software) with VAS software. VAS is more effective to assist students in understanding the electrical dynamic concept shown with N-gain of 0.36, or 36 % were included in the medium category, whereas the conventional learning with N-gain of 0.28, or 28%.

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

PubMed Central

Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

2012-01-01

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz. PMID:23093919

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

PubMed

Chovancova, Eva; Pavelka, Antonin; Benes, Petr; Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

2012-01-01

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.

Extreme scale multi-physics simulations of the tsunamigenic 2004 Sumatra megathrust earthquake

NASA Astrophysics Data System (ADS)

Ulrich, T.; Gabriel, A. A.; Madden, E. H.; Wollherr, S.; Uphoff, C.; Rettenberger, S.; Bader, M.

2017-12-01

SeisSol (www.seissol.org) is an open-source software package based on an arbitrary high-order derivative Discontinuous Galerkin method (ADER-DG). It solves spontaneous dynamic rupture propagation on pre-existing fault interfaces according to non-linear friction laws, coupled to seismic wave propagation with high-order accuracy in space and time (minimal dispersion errors). SeisSol exploits unstructured meshes to account for complex geometries, e.g. high resolution topography and bathymetry, 3D subsurface structure, and fault networks. We present the up-to-date largest (1500 km of faults) and longest (500 s) dynamic rupture simulation modeling the 2004 Sumatra-Andaman earthquake. We demonstrate the need for end-to-end-optimization and petascale performance of scientific software to realize realistic simulations on the extreme scales of subduction zone earthquakes: Considering the full complexity of subduction zone geometries leads inevitably to huge differences in element sizes. The main code improvements include a cache-aware wave propagation scheme and optimizations of the dynamic rupture kernels using code generation. In addition, a novel clustered local-time-stepping scheme for dynamic rupture has been established. Finally, asynchronous output has been implemented to overlap I/O and compute time. We resolve the frictional sliding process on the curved mega-thrust and a system of splay faults, as well as the seismic wave field and seafloor displacement with frequency content up to 2.2 Hz. We validate the scenario by geodetic, seismological and tsunami observations. The resulting rupture dynamics shed new light on the activation and importance of splay faults.

The fabrication of a customized occlusal splint based on the merging of dynamic jaw tracking records, cone beam computed tomography, and CAD-CAM digital impression.

PubMed

Aslanidou, Katerina; Kau, Chung How; Vlachos, Christos; Saleh, Tayem Abou

2017-01-01

The aim of this case report was to present the procedure of fabricating a customized occlusal splint, through a revolutionary software that combines cone beam computed tomography (CBCT) with jaw motion tracking (JMT) data and superimposes a digital impression. The case report was conducted on a 46-year-old female patient diagnosed with the temporomandibular disorder. A CBCT scan and an optical impression were obtained. The range of the patient's mandibular movements was captured with a JMT device. The data were combined in the SICAT software (SICAT, Sirona, Bonn, Germany). The software enabled the visualization of patient-specific mandibular movements and provided a real dynamic anatomical evaluation of the condylar position in the glenoid fossa. After the assessment of the range of movements during opening, protrusion, and lateral movements all the data were sent to SICAT and a customized occlusal splint was manufactured. The SICAT software provides a three-dimensional real-dynamic simulation of mandibular movements relative to the patient-specific anatomy of the jaw; thus, it opens new possibilities and potentials for the management of temporomandibular disorders.

Research on dynamic balancing simulation of rotary shaft based on ADAMS

NASA Astrophysics Data System (ADS)

Zheng, Weiqiang; Rui, Chengjie; Yang, Jie; Liu, Pingyi

2018-02-01

Due to the design and processing technology of rotary shaft, the mass center of it does not coincide with the rotating axis of the rotary shaft and there is an unbalanced mass. The unbalanced mass can have some disadvantages, such as the centrifugal force, the vibration and so on. Those disadvantages could reduce the accuracy and service life of the equipment.In this paper, the dynamic balance of the rotary shaft is analysed by the theory analysis combined with the dynamic simulation software. This method ensures that the rotary shaft meets the dynamic balancing requirements during the design stage. It effectively supports the structural design of the rotary shift, and provides a way of thinking and method for the design and development of the same type of products.

Adaptation and development of software simulation methodologies for cardiovascular engineering: present and future challenges from an end-user perspective

PubMed Central

Díaz-Zuccarini, V.; Narracott, A.J.; Burriesci, G.; Zervides, C.; Rafiroiu, D.; Jones, D.; Hose, D.R.; Lawford, P.V.

2009-01-01

This paper describes the use of diverse software tools in cardiovascular applications. These tools were primarily developed in the field of engineering and the applications presented push the boundaries of the software to address events related to venous and arterial valve closure, exploration of dynamic boundary conditions or the inclusion of multi-scale boundary conditions from protein to organ levels. The future of cardiovascular research and the challenges that modellers and clinicians face from validation to clinical uptake are discussed from an end-user perspective. PMID:19487202

Adaptation and development of software simulation methodologies for cardiovascular engineering: present and future challenges from an end-user perspective.

PubMed

Díaz-Zuccarini, V; Narracott, A J; Burriesci, G; Zervides, C; Rafiroiu, D; Jones, D; Hose, D R; Lawford, P V

2009-07-13

This paper describes the use of diverse software tools in cardiovascular applications. These tools were primarily developed in the field of engineering and the applications presented push the boundaries of the software to address events related to venous and arterial valve closure, exploration of dynamic boundary conditions or the inclusion of multi-scale boundary conditions from protein to organ levels. The future of cardiovascular research and the challenges that modellers and clinicians face from validation to clinical uptake are discussed from an end-user perspective.

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

PubMed

Saho, Tatsunori; Onishi, Hideo

2015-07-01

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

Microcomputer based software for biodynamic simulation

NASA Technical Reports Server (NTRS)

Rangarajan, N.; Shams, T.

1993-01-01

This paper presents a description of a microcomputer based software package, called DYNAMAN, which has been developed to allow an analyst to simulate the dynamics of a system consisting of a number of mass segments linked by joints. One primary application is in predicting the motion of a human occupant in a vehicle under the influence of a variety of external forces, specially those generated during a crash event. Extensive use of a graphical user interface has been made to aid the user in setting up the input data for the simulation and in viewing the results from the simulation. Among its many applications, it has been successfully used in the prototype design of a moving seat that aids in occupant protection during a crash, by aircraft designers in evaluating occupant injury in airplane crashes, and by users in accident reconstruction for reconstructing the motion of the occupant and correlating the impacts with observed injuries.

Hybrid Modeling for Testing Intelligent Software for Lunar-Mars Closed Life Support

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Nicholson, Leonard S. (Technical Monitor)

1999-01-01

Intelligent software is being developed for closed life support systems with biological components, for human exploration of the Moon and Mars. The intelligent software functions include planning/scheduling, reactive discrete control and sequencing, management of continuous control, and fault detection, diagnosis, and management of failures and errors. Four types of modeling information have been essential to system modeling and simulation to develop and test the software and to provide operational model-based what-if analyses: discrete component operational and failure modes; continuous dynamic performance within component modes, modeled qualitatively or quantitatively; configuration of flows and power among components in the system; and operations activities and scenarios. CONFIG, a multi-purpose discrete event simulation tool that integrates all four types of models for use throughout the engineering and operations life cycle, has been used to model components and systems involved in the production and transfer of oxygen and carbon dioxide in a plant-growth chamber and between that chamber and a habitation chamber with physicochemical systems for gas processing.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics.

PubMed

de Buyl, Pierre; Nies, Erik

2015-04-07

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics

NASA Astrophysics Data System (ADS)

de Buyl, Pierre; Nies, Erik

2015-04-01

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

Real-time computing platform for spiking neurons (RT-spike).

PubMed

Ros, Eduardo; Ortigosa, Eva M; Agís, Rodrigo; Carrillo, Richard; Arnold, Michael

2006-07-01

A computing platform is described for simulating arbitrary networks of spiking neurons in real time. A hybrid computing scheme is adopted that uses both software and hardware components to manage the tradeoff between flexibility and computational power; the neuron model is implemented in hardware and the network model and the learning are implemented in software. The incremental transition of the software components into hardware is supported. We focus on a spike response model (SRM) for a neuron where the synapses are modeled as input-driven conductances. The temporal dynamics of the synaptic integration process are modeled with a synaptic time constant that results in a gradual injection of charge. This type of model is computationally expensive and is not easily amenable to existing software-based event-driven approaches. As an alternative we have designed an efficient time-based computing architecture in hardware, where the different stages of the neuron model are processed in parallel. Further improvements occur by computing multiple neurons in parallel using multiple processing units. This design is tested using reconfigurable hardware and its scalability and performance evaluated. Our overall goal is to investigate biologically realistic models for the real-time control of robots operating within closed action-perception loops, and so we evaluate the performance of the system on simulating a model of the cerebellum where the emulation of the temporal dynamics of the synaptic integration process is important.

Matriarch: A Python Library for Materials Architecture.

PubMed

Giesa, Tristan; Jagadeesan, Ravi; Spivak, David I; Buehler, Markus J

2015-10-12

Biological materials, such as proteins, often have a hierarchical structure ranging from basic building blocks at the nanoscale (e.g., amino acids) to assembled structures at the macroscale (e.g., fibers). Current software for materials engineering allows the user to specify polypeptide chains and simple secondary structures prior to molecular dynamics simulation, but is not flexible in terms of the geometric arrangement of unequilibrated structures. Given some knowledge of a larger-scale structure, instructing the software to create it can be very difficult and time-intensive. To this end, the present paper reports a mathematical language, using category theory, to describe the architecture of a material, i.e., its set of building blocks and instructions for combining them. While this framework applies to any hierarchical material, here we concentrate on proteins. We implement this mathematical language as an open-source Python library called Matriarch. It is a domain-specific language that gives the user the ability to create almost arbitrary structures with arbitrary amino acid sequences and, from them, generate Protein Data Bank (PDB) files. In this way, Matriarch is more powerful than commercial software now available. Matriarch can be used in tandem with molecular dynamics simulations and helps engineers design and modify biologically inspired materials based on their desired functionality. As a case study, we use our software to alter both building blocks and building instructions for tropocollagen, and determine their effect on its structure and mechanical properties.

Thrust vector control algorithm design for the Cassini spacecraft

NASA Technical Reports Server (NTRS)

Enright, Paul J.

1993-01-01

This paper describes a preliminary design of the thrust vector control algorithm for the interplanetary spacecraft, Cassini. Topics of discussion include flight software architecture, modeling of sensors, actuators, and vehicle dynamics, and controller design and analysis via classical methods. Special attention is paid to potential interactions with structural flexibilities and propellant dynamics. Controller performance is evaluated in a simulation environment built around a multi-body dynamics model, which contains nonlinear models of the relevant hardware and preliminary versions of supporting attitude determination and control functions.

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.

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors.

PubMed

Glowacki, David R; O'Connor, Michael; Calabró, Gaetano; Price, James; Tew, Philip; Mitchell, Thomas; Hyde, Joseph; Tew, David P; Coughtrie, David J; McIntosh-Smith, Simon

2014-01-01

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude.

Fast and Precise Emulation of Stochastic Biochemical Reaction Networks With Amplified Thermal Noise in Silicon Chips.

PubMed

Kim, Jaewook; Woo, Sung Sik; Sarpeshkar, Rahul

2018-04-01

The analysis and simulation of complex interacting biochemical reaction pathways in cells is important in all of systems biology and medicine. Yet, the dynamics of even a modest number of noisy or stochastic coupled biochemical reactions is extremely time consuming to simulate. In large part, this is because of the expensive cost of random number and Poisson process generation and the presence of stiff, coupled, nonlinear differential equations. Here, we demonstrate that we can amplify inherent thermal noise in chips to emulate randomness physically, thus alleviating these costs significantly. Concurrently, molecular flux in thermodynamic biochemical reactions maps to thermodynamic electronic current in a transistor such that stiff nonlinear biochemical differential equations are emulated exactly in compact, digitally programmable, highly parallel analog "cytomorphic" transistor circuits. For even small-scale systems involving just 80 stochastic reactions, our 0.35-μm BiCMOS chips yield a 311× speedup in the simulation time of Gillespie's stochastic algorithm over COPASI, a fast biochemical-reaction software simulator that is widely used in computational biology; they yield a 15 500× speedup over equivalent MATLAB stochastic simulations. The chip emulation results are consistent with these software simulations over a large range of signal-to-noise ratios. Most importantly, our physical emulation of Poisson chemical dynamics does not involve any inherently sequential processes and updates such that, unlike prior exact simulation approaches, they are parallelizable, asynchronous, and enable even more speedup for larger-size networks.

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

PubMed

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

2015-07-01

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

Current capabilities for simulating the extreme distortion of thin structures subjected to severe impacts

NASA Technical Reports Server (NTRS)

Key, Samuel W.

1993-01-01

The explicit transient dynamics technology in use today for simulating the impact and subsequent transient dynamic response of a structure has its origins in the 'hydrocodes' dating back to the late 1940's. The growth in capability in explicit transient dynamics technology parallels the growth in speed and size of digital computers. Computer software for simulating the explicit transient dynamic response of a structure is characterized by algorithms that use a large number of small steps. In explicit transient dynamics software there is a significant emphasis on speed and simplicity. The finite element technology used to generate the spatial discretization of a structure is based on a compromise between completeness of the representation for the physical processes modelled and speed in execution. That is, since it is expected in every calculation that the deformation will be finite and the material will be strained beyond the elastic range, the geometry and the associated gradient operators must be reconstructed, as well as complex stress-strain models evaluated at every time step. As a result, finite elements derived for explicit transient dynamics software use the simplest and barest constructions possible for computational efficiency while retaining an essential representation of the physical behavior. The best example of this technology is the four-node bending quadrilateral derived by Belytschko, Lin and Tsay. Today, the speed, memory capacity and availability of computer hardware allows a number of the previously used algorithms to be 'improved.' That is, it is possible with today's computing hardware to modify many of the standard algorithms to improve their representation of the physical process at the expense of added complexity and computational effort. The purpose is to review a number of these algorithms and identify the improvements possible. In many instances, both the older, faster version of the algorithm and the improved and somewhat slower version of the algorithm are found implemented together in software. Specifically, the following seven algorithmic items are examined: the invariant time derivatives of stress used in material models expressed in rate form; incremental objectivity and strain used in the numerical integration of the material models; the use of one-point element integration versus mean quadrature; shell elements used to represent the behavior of thin structural components; beam elements based on stress-resultant plasticity versus cross-section integration; the fidelity of elastic-plastic material models in their representation of ductile metals; and the use of Courant subcycling to reduce computational effort.

Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

PubMed

Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

2011-11-24

The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

Protein Simulation Data in the Relational Model.

PubMed

Simms, Andrew M; Daggett, Valerie

2012-10-01

High performance computing is leading to unprecedented volumes of data. Relational databases offer a robust and scalable model for storing and analyzing scientific data. However, these features do not come without a cost-significant design effort is required to build a functional and efficient repository. Modeling protein simulation data in a relational database presents several challenges: the data captured from individual simulations are large, multi-dimensional, and must integrate with both simulation software and external data sites. Here we present the dimensional design and relational implementation of a comprehensive data warehouse for storing and analyzing molecular dynamics simulations using SQL Server.

Protein Simulation Data in the Relational Model

PubMed Central

Simms, Andrew M.; Daggett, Valerie

2011-01-01

High performance computing is leading to unprecedented volumes of data. Relational databases offer a robust and scalable model for storing and analyzing scientific data. However, these features do not come without a cost—significant design effort is required to build a functional and efficient repository. Modeling protein simulation data in a relational database presents several challenges: the data captured from individual simulations are large, multi-dimensional, and must integrate with both simulation software and external data sites. Here we present the dimensional design and relational implementation of a comprehensive data warehouse for storing and analyzing molecular dynamics simulations using SQL Server. PMID:23204646

Applications of CFD and visualization techniques

NASA Technical Reports Server (NTRS)

Saunders, James H.; Brown, Susan T.; Crisafulli, Jeffrey J.; Southern, Leslie A.

1992-01-01

In this paper, three applications are presented to illustrate current techniques for flow calculation and visualization. The first two applications use a commercial computational fluid dynamics (CFD) code, FLUENT, performed on a Cray Y-MP. The results are animated with the aid of data visualization software, apE. The third application simulates a particulate deposition pattern using techniques inspired by developments in nonlinear dynamical systems. These computations were performed on personal computers.

Python as a federation tool for GENESIS 3.0.

PubMed

Cornelis, Hugo; Rodriguez, Armando L; Coop, Allan D; Bower, James M

2012-01-01

The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be 'glued' together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience.

Python as a Federation Tool for GENESIS 3.0

PubMed Central

Cornelis, Hugo; Rodriguez, Armando L.; Coop, Allan D.; Bower, James M.

2012-01-01

The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be ‘glued’ together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience. PMID:22276101

Control system software, simulation, and robotic applications

NASA Technical Reports Server (NTRS)

Frisch, Harold P.

1991-01-01

All essential existing capabilities needed to create a man-machine interaction dynamics and performance (MMIDAP) capability are reviewed. The multibody system dynamics software program Order N DISCOS will be used for machine and musculo-skeletal dynamics modeling. The program JACK will be used for estimating and animating whole body human response to given loading situations and motion constraints. The basic elements of performance (BEP) task decomposition methodologies associated with the Human Performance Institute database will be used for performance assessment. Techniques for resolving the statically indeterminant muscular load sharing problem will be used for a detailed understanding of potential musculotendon or ligamentous fatigue, pain, discomfort, and trauma. The envisioned capacity is to be used for mechanical system design, human performance assessment, extrapolation of man/machine interaction test data, biomedical engineering, and soft prototyping within a concurrent engineering (CE) system.

Architectures and Evaluation for Adjustable Control Autonomy for Space-Based Life Support Systems

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Schreckenghost, Debra K.

2001-01-01

In the past five years, a number of automation applications for control of crew life support systems have been developed and evaluated in the Adjustable Autonomy Testbed at NASA's Johnson Space Center. This paper surveys progress on an adjustable autonomous control architecture for situations where software and human operators work together to manage anomalies and other system problems. When problems occur, the level of control autonomy can be adjusted, so that operators and software agents can work together on diagnosis and recovery. In 1997 adjustable autonomy software was developed to manage gas transfer and storage in a closed life support test. Four crewmembers lived and worked in a chamber for 91 days, with both air and water recycling. CO2 was converted to O2 by gas processing systems and wheat crops. With the automation software, significantly fewer hours were spent monitoring operations. System-level validation testing of the software by interactive hybrid simulation revealed problems both in software requirements and implementation. Since that time, we have been developing multi-agent approaches for automation software and human operators, to cooperatively control systems and manage problems. Each new capability has been tested and demonstrated in realistic dynamic anomaly scenarios, using the hybrid simulation tool.

Mission Simulation Toolkit

NASA Technical Reports Server (NTRS)

Pisaich, Gregory; Flueckiger, Lorenzo; Neukom, Christian; Wagner, Mike; Buchanan, Eric; Plice, Laura

2007-01-01

The Mission Simulation Toolkit (MST) is a flexible software system for autonomy research. It was developed as part of the Mission Simulation Facility (MSF) project that was started in 2001 to facilitate the development of autonomous planetary robotic missions. Autonomy is a key enabling factor for robotic exploration. There has been a large gap between autonomy software (at the research level), and software that is ready for insertion into near-term space missions. The MST bridges this gap by providing a simulation framework and a suite of tools for supporting research and maturation of autonomy. MST uses a distributed framework based on the High Level Architecture (HLA) standard. A key feature of the MST framework is the ability to plug in new models to replace existing ones with the same services. This enables significant simulation flexibility, particularly the mixing and control of fidelity level. In addition, the MST provides automatic code generation from robot interfaces defined with the Unified Modeling Language (UML), methods for maintaining synchronization across distributed simulation systems, XML-based robot description, and an environment server. Finally, the MSF supports a number of third-party products including dynamic models and terrain databases. Although the communication objects and some of the simulation components that are provided with this toolkit are specifically designed for terrestrial surface rovers, the MST can be applied to any other domain, such as aerial, aquatic, or space.

A discrete event simulation model for evaluating the performances of an m/g/c/c state dependent queuing system.

PubMed

Khalid, Ruzelan; Nawawi, Mohd Kamal M; Kawsar, Luthful A; Ghani, Noraida A; Kamil, Anton A; Mustafa, Adli

2013-01-01

M/G/C/C state dependent queuing networks consider service rates as a function of the number of residing entities (e.g., pedestrians, vehicles, and products). However, modeling such dynamic rates is not supported in modern Discrete Simulation System (DES) software. We designed an approach to cater this limitation and used it to construct the M/G/C/C state-dependent queuing model in Arena software. Using the model, we have evaluated and analyzed the impacts of various arrival rates to the throughput, the blocking probability, the expected service time and the expected number of entities in a complex network topology. Results indicated that there is a range of arrival rates for each network where the simulation results fluctuate drastically across replications and this causes the simulation results and analytical results exhibit discrepancies. Detail results that show how tally the simulation results and the analytical results in both abstract and graphical forms and some scientific justifications for these have been documented and discussed.

Benchmark tests for a Formula SAE Student car prototyping

NASA Astrophysics Data System (ADS)

Mariasiu, Florin

2011-12-01

Aerodynamic characteristics of a vehicle are important elements in its design and construction. A low drag coefficient brings significant fuel savings and increased engine power efficiency. In designing and developing vehicles trough computer simulation process to determine the vehicles aerodynamic characteristics are using dedicated CFD (Computer Fluid Dynamics) software packages. However, the results obtained by this faster and cheaper method, are validated by experiments in wind tunnels tests, which are expensive and were complex testing equipment are used in relatively high costs. Therefore, the emergence and development of new low-cost testing methods to validate CFD simulation results would bring great economic benefits for auto vehicles prototyping process. This paper presents the initial development process of a Formula SAE Student race-car prototype using CFD simulation and also present a measurement system based on low-cost sensors through which CFD simulation results were experimentally validated. CFD software package used for simulation was Solid Works with the FloXpress add-on and experimental measurement system was built using four piezoresistive force sensors FlexiForce type.

Pilot-in-the-Loop CFD Method Development

DTIC Science & Technology

2017-02-01

Penn State University. All software supporting piloted simulations must run at real time speeds or faster. This requirement drives the number of...dynamics of interacting blade tip vortices with a ground plane,” American Helicopter Society 64 th Annual Forum Proceedings, 2008. [2] Johnson, W

Time Warp Operating System, Version 2.5.1

NASA Technical Reports Server (NTRS)

Bellenot, Steven F.; Gieselman, John S.; Hawley, Lawrence R.; Peterson, Judy; Presley, Matthew T.; Reiher, Peter L.; Springer, Paul L.; Tupman, John R.; Wedel, John J., Jr.; Wieland, Frederick P.;

Space life support engineering program

NASA Technical Reports Server (NTRS)

Seagrave, Richard C.

1991-01-01

This report covers the first six months of work performed under the NASA University Grant awarded to Iowa State University to perform research on two topics relating to the development of closed-loop long-term life support systems. A comprehensive study to develop software to simulate the dynamic operation of water reclamation systems in long-term closed-loop life support systems is being carried out as part of an overall program for the design of systems for a Mars voyage. This project is being done in parallel with a similar effort in the Department of Chemistry to develop durable accurate low-cost sensors for monitoring of trace chemical and biological species in recycled water supplies. Aspen-Plus software is being used on a group of high-performance workstations to develop the steady state descriptions for a number of existing technologies. Following completion, a dynamic simulation package will be developed for determining the response of such systems to changes in the metabolic needs of the crew and to upsets in system hardware performance.

Direct-coupled microcomputer-based building emulator for building energy management and control systems

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

Lam, H.N.

1999-07-01

In this paper, the development and implementation of a direct-coupled building emulator for a building energy management and control system (EMCS) is presented. The building emulator consists of a microcomputer and a computer model of an air-conditioning system implemented in a modular dynamic simulation software package for direct-coupling to an EMCS, without using analog-to-digital and digital-to-analog converters. The building emulator can be used to simulate in real time the behavior of the air-conditioning system under a given operating environment and subject to a given usage pattern. Software modules for data communication, graphical display, dynamic data exchange, and synchronization of simulationmore » outputs with real time have been developed to achieve direct digital data transfer between the building emulator and a commercial EMCS. Based on the tests conducted, the validity of the building emulator has been established and the proportional-plus-integral control function of the EMCS assessed.« less

Modelling and Control of Robotic Leg as Assistive Device

NASA Astrophysics Data System (ADS)

Jingye, Yee; Zain, Badrul Aisham bin Md

2017-10-01

The ageing population (people older than 60 years old) is expected to constitute 21.8% of global population by year 2050. When human ages, bodily function including locomotors will deteriorate. Besides, there are hundreds of thousands of victims who suffer from multiple health conditions worldwide that leads to gait impairment. A promising solution will be the lower limb powered-exoskeleton. This study is to be a start-up platform to design a lower limb powered-exoskeleton for a normal Malaysian male, by designing and simulating the dynamic model of a 2-link robotic leg to observe its behaviour under different input conditions with and without a PID controller. Simulink in MATLAB software is used as the dynamic modelling and simulation software for this study. It is observed that the 2-links robotic leg behaved differently under different input conditions, and perform the best when it is constrained and controlled by PID controller. Simulink model is formed as a foundation for the upcoming researches and can be modified and utilised by the future researchers.

Modeling and Performance Improvement of the Constant Power Regulator Systems in Variable Displacement Axial Piston Pump

PubMed Central

Park, Sung Hwan; Lee, Ji Min; Kim, Jong Shik

2013-01-01

An irregular performance of a mechanical-type constant power regulator is considered. In order to find the cause of an irregular discharge flow at the cut-off pressure area, modeling and numerical simulations are performed to observe dynamic behavior of internal parts of the constant power regulator system for a swashplate-type axial piston pump. The commercial numerical simulation software AMESim is applied to model the mechanical-type regulator with hydraulic pump and simulate the performance of it. The validity of the simulation model of the constant power regulator system is verified by comparing simulation results with experiments. In order to find the cause of the irregular performance of the mechanical-type constant power regulator system, the behavior of main components such as the spool, sleeve, and counterbalance piston is investigated using computer simulation. The shape modification of the counterbalance piston is proposed to improve the undesirable performance of the mechanical-type constant power regulator. The performance improvement is verified by computer simulation using AMESim software. PMID:24282389

MOlecular MAterials Property Prediction Package (MOMAP) 1.0: a software package for predicting the luminescent properties and mobility of organic functional materials

NASA Astrophysics Data System (ADS)

Niu, Yingli; Li, Wenqiang; Peng, Qian; Geng, Hua; Yi, Yuanping; Wang, Linjun; Nan, Guangjun; Wang, Dong; Shuai, Zhigang

2018-04-01

MOlecular MAterials Property Prediction Package (MOMAP) is a software toolkit for molecular materials property prediction. It focuses on luminescent properties and charge mobility properties. This article contains a brief descriptive introduction of key features, theoretical models and algorithms of the software, together with examples that illustrate the performance. First, we present the theoretical models and algorithms for molecular luminescent properties calculation, which includes the excited-state radiative/non-radiative decay rate constant and the optical spectra. Then, a multi-scale simulation approach and its algorithm for the molecular charge mobility are described. This approach is based on hopping model and combines with Kinetic Monte Carlo and molecular dynamics simulations, and it is especially applicable for describing a large category of organic semiconductors, whose inter-molecular electronic coupling is much smaller than intra-molecular charge reorganisation energy.

Ship Air Wake Detection Using a Small Fixed Wing Unmanned Aerial Vehicle

NASA Astrophysics Data System (ADS)

Phelps, David M.

A ship's air wake is dynamically detected using an airborne inertial measurement unit (IMU) and global positioning system (GPS) attached to a fixed wing unmanned aerial system. A fixed wing unmanned aerial system (UAS) was flown through the air wake created by an underway 108 ft (32.9m) long research vessel in pre designated flight paths. The instrumented aircraft was used to validate computational fluid dynamic (CFD) simulations of naval ship air wakes. Computer models of the research ship and the fixed wing UAS were generated and gridded using NASA's TetrUSS software. Simulations were run using Kestrel, a Department of Defense CFD software to validate the physical experimental data collection method. Air wake simulations were run at various relative wind angles and speeds. The fixed wing UAS was subjected to extensive wind tunnel testing to generate a table of aerodynamic coefficients as a function of control surface deflections, angle of attack and sideslip. The wind tunnel experimental data was compared against similarly structured CFD experiments to validate the grid and model of fixed wing UAS. Finally, a CFD simulation of the fixed wing UAV flying through the generated wake was completed. Forces on the instrumented aircraft were calculated from the data collected by the IMU. Comparison of experimental and simulation data showed that the fixed wing UAS could detect interactions with the ship air wake.

Estimating the impact of enterprise resource planning project management decisions on post-implementation maintenance costs: a case study using simulation modelling

NASA Astrophysics Data System (ADS)

Fryling, Meg

2010-11-01

Organisations often make implementation decisions with little consideration for the maintenance phase of an enterprise resource planning (ERP) system, resulting in significant recurring maintenance costs. Poor cost estimations are likely related to the lack of an appropriate framework for enterprise-wide pre-packaged software maintenance, which requires an ongoing relationship with the software vendor (Markus, M.L., Tanis, C., and Fenema, P.C., 2000. Multisite ERP implementation. CACM, 43 (4), 42-46). The end result is that critical project decisions are made with little empirical data, resulting in substantial long-term cost impacts. The product of this research is a formal dynamic simulation model that enables theory testing, scenario exploration and policy analysis. The simulation model ERPMAINT1 was developed by combining and extending existing frameworks in several research domains, and by incorporating quantitative and qualitative case study data. The ERPMAINT1 model evaluates tradeoffs between different ERP project management decisions and their impact on post-implementation total cost of ownership (TCO). Through model simulations a variety of dynamic insights were revealed that could assist ERP project managers. Major findings from the simulation show that upfront investments in mentoring and system exposure translate to long-term cost savings. The findings also indicate that in addition to customisations, add-ons have a significant impact on TCO.

How to improve the equity of health financial sources? - Simulation and analysis of total health expenditure of one Chinese province on system dynamics.

PubMed

Wang, Xin; Sun, Yuanling; Mu, Xin; Guan, Li; Li, Jingjie

2015-08-27

We simulate and analyze Total Health Expenditure (THE) in financial sources and other economic indicators (such as THE per capita, GDP, etc.) in a province of China from 2002 to 2012 on System Dynamics. Based on actual data and certain mathematical methods, we use system dynamic software to construct a logic model for THE and changing proportions, and thus simulate the actual conditions of development and changes in THE. According to the simulation results, the government possess the largest investment in the average annual growth rate of THE, which was 25.16% in 2012. Social investment comprises the majority of the possession ratio, which was up to 41.20%. The personal investment growth rate decreased by almost 21%, but the total amount of personal investment increased by 28075 million yuan, which is far higher than the increase in government investment. Individuals are still the main carriers of health care expenses. The equity of health financial sources is still poor. The System Dynamics method used in this paper identifies a dynamic measurement process, provides a scientific basis for simulation and analysis of the changes in THE and its key constraining factors, as well as put forward suggestions for the improvement of equity of health financial sources.

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

PubMed

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang

2010-12-01

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. © 2010 Wiley Periodicals, Inc.

Study of Effect of Impacting Direction on Abrasive Nanometric Cutting Process with Molecular Dynamics

NASA Astrophysics Data System (ADS)

Li, Junye; Meng, Wenqing; Dong, Kun; Zhang, Xinming; Zhao, Weihong

2018-01-01

Abrasive flow polishing plays an important part in modern ultra-precision machining. Ultrafine particles suspended in the medium of abrasive flow removes the material in nanoscale. In this paper, three-dimensional molecular dynamics (MD) simulations are performed to investigate the effect of impacting direction on abrasive cutting process during abrasive flow polishing. The molecular dynamics simulation software Lammps was used to simulate the cutting of single crystal copper with SiC abrasive grains at different cutting angles (0o-45o). At a constant friction coefficient, we found a direct relation between cutting angle and cutting force, which ultimately increases the number of dislocation during abrasive flow machining. Our theoretical study reveal that a small cutting angle is beneficial for improving surface quality and reducing internal defects in the workpiece. However, there is no obvious relationship between cutting angle and friction coefficient.

The research of hourglass worm dynamic balancing simulation based on SolidWorks motion

NASA Astrophysics Data System (ADS)

Wang, Zhuangzhuang; Yang, Jie; Liu, Pingyi; Zhao, Junpeng

2018-02-01

Hourglass worm is extensively used in industry due to its characteristic of heavy-load and a large reduction ratio. Varying sizes of unbalanced mass distribution appeared in the design of a single head worm. With machines developing towards higher speed and precision, the vibration and shock caused by the unbalanced mass distribution of rotating parts must be considered. Therefore, the balance grade of these parts must meet higher requirements. A method based on theoretical analysis and SolidWorks motion software simulation is presented in this paper; the virtual dynamic balance simulation test of the hourglass worm was carried out during the design of the product, so as to ensure that the hourglass worm meet the requirements of dynamic balance in the design process. This can effectively support the structural design of the hourglass worm and provide a way of thinking and designing the same type of products.

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.

Study of Effect of Impacting Direction on Abrasive Nanometric Cutting Process with Molecular Dynamics.

PubMed

Li, Junye; Meng, Wenqing; Dong, Kun; Zhang, Xinming; Zhao, Weihong

2018-01-11

Abrasive flow polishing plays an important part in modern ultra-precision machining. Ultrafine particles suspended in the medium of abrasive flow removes the material in nanoscale. In this paper, three-dimensional molecular dynamics (MD) simulations are performed to investigate the effect of impacting direction on abrasive cutting process during abrasive flow polishing. The molecular dynamics simulation software Lammps was used to simulate the cutting of single crystal copper with SiC abrasive grains at different cutting angles (0 o -45 o ). At a constant friction coefficient, we found a direct relation between cutting angle and cutting force, which ultimately increases the number of dislocation during abrasive flow machining. Our theoretical study reveal that a small cutting angle is beneficial for improving surface quality and reducing internal defects in the workpiece. However, there is no obvious relationship between cutting angle and friction coefficient.

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.

GiPSi:a framework for open source/open architecture software development for organ-level surgical simulation.

PubMed

Cavuşoğlu, M Cenk; Göktekin, Tolga G; Tendick, Frank

2006-04-01

This paper presents the architectural details of an evolving open source/open architecture software framework for developing organ-level surgical simulations. Our goal is to facilitate shared development of reusable models, to accommodate heterogeneous models of computation, and to provide a framework for interfacing multiple heterogeneous models. The framework provides an application programming interface for interfacing dynamic models defined over spatial domains. It is specifically designed to be independent of the specifics of the modeling methods used, and therefore facilitates seamless integration of heterogeneous models and processes. Furthermore, each model has separate geometries for visualization, simulation, and interfacing, allowing the model developer to choose the most natural geometric representation for each case. Input/output interfaces for visualization and haptics for real-time interactive applications have also been provided.

Scalable Molecular Dynamics with NAMD

PubMed Central

Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus

2008-01-01

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654

Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications

PubMed Central

Miao, Yinglong; McCammon, J. Andrew

2018-01-01

A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of biomolecules. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of the biomolecules. Furthermore, by constructing a boost potential that follows a Gaussian distribution, accurate reweighting of GaMD simulations is achieved via cumulant expansion to the second order. The free energy profiles obtained from GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize biomolecular structural dynamics quantitatively. In this chapter, we present the theory of GaMD, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model system, protein folding, biomolecular large-scale conformational transitions and biomolecular recognition. PMID:29720925

Virtual Habitat -a dynamic simulation of closed life support systems -human model status

NASA Astrophysics Data System (ADS)

Markus Czupalla, M. Sc.; Zhukov, Anton; Hwang, Su-Au; Schnaitmann, Jonas

In order to optimize Life Support Systems on a system level, stability questions must be in-vestigated. To do so the exploration group of the Technical University of Munich (TUM) is developing the "Virtual Habitat" (V-HAB) dynamic LSS simulation software. V-HAB shall provide the possibility to conduct dynamic simulations of entire mission scenarios for any given LSS configuration. The Virtual Habitat simulation tool consists of four main modules: • Closed Environment Module (CEM) -monitoring of compounds in a closed environment • Crew Module (CM) -dynamic human simulation • P/C Systems Module (PCSM) -dynamic P/C subsystems • Plant Module (PM) -dynamic plant simulation The core module of the simulation is the dynamic and environment sensitive human module. Introduced in its basic version in 2008, the human module has been significantly updated since, increasing its capabilities and maturity significantly. In this paper three newly added human model subsystems (thermal regulation, digestion and schedule controller) are introduced touching also on the human stress subsystem which is cur-rently under development. Upon the introduction of these new subsystems, the integration of these into the overall V-HAB human model is discussed, highlighting the impact on the most important I/F. The overall human model capabilities shall further be summarized and presented based on meaningful test cases. In addition to the presentation of the results, the correlation strategy for the Virtual Habitat human model shall be introduced assessing the models current confidence level and giving an outlook on the future correlation strategy. Last but not least, the remaining V-HAB mod-ules shall be introduced shortly showing how the human model is integrated into the overall simulation.

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.

STAR-CCM+ Verification and Validation Plan

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

Pointer, William David

2016-09-30

The commercial Computational Fluid Dynamics (CFD) code STAR-CCM+ provides general purpose finite volume method solutions for fluid dynamics and energy transport. This document defines plans for verification and validation (V&V) of the base code and models implemented within the code by the Consortium for Advanced Simulation of Light water reactors (CASL). The software quality assurance activities described herein are port of the overall software life cycle defined in the CASL Software Quality Assurance (SQA) Plan [Sieger, 2015]. STAR-CCM+ serves as the principal foundation for development of an advanced predictive multi-phase boiling simulation capability within CASL. The CASL Thermal Hydraulics Methodsmore » (THM) team develops advanced closure models required to describe the subgrid-resolution behavior of secondary fluids or fluid phases in multiphase boiling flows within the Eulerian-Eulerian framework of the code. These include wall heat partitioning models that describe the formation of vapor on the surface and the forces the define bubble/droplet dynamic motion. The CASL models are implemented as user coding or field functions within the general framework of the code. This report defines procedures and requirements for V&V of the multi-phase CFD capability developed by CASL THM. Results of V&V evaluations will be documented in a separate STAR-CCM+ V&V assessment report. This report is expected to be a living document and will be updated as additional validation cases are identified and adopted as part of the CASL THM V&V suite.« less

PLATSIM: An efficient linear simulation and analysis package for large-order flexible systems

NASA Technical Reports Server (NTRS)

Maghami, Periman; Kenny, Sean P.; Giesy, Daniel P.

1995-01-01

PLATSIM is a software package designed to provide efficient time and frequency domain analysis of large-order generic space platforms implemented with any linear time-invariant control system. Time domain analysis provides simulations of the overall spacecraft response levels due to either onboard or external disturbances. The time domain results can then be processed by the jitter analysis module to assess the spacecraft's pointing performance in a computationally efficient manner. The resulting jitter analysis algorithms have produced an increase in speed of several orders of magnitude over the brute force approach of sweeping minima and maxima. Frequency domain analysis produces frequency response functions for uncontrolled and controlled platform configurations. The latter represents an enabling technology for large-order flexible systems. PLATSIM uses a sparse matrix formulation for the spacecraft dynamics model which makes both the time and frequency domain operations quite efficient, particularly when a large number of modes are required to capture the true dynamics of the spacecraft. The package is written in MATLAB script language. A graphical user interface (GUI) is included in the PLATSIM software package. This GUI uses MATLAB's Handle graphics to provide a convenient way for setting simulation and analysis parameters.

Tracking Debris Shed by a Space-Shuttle Launch Vehicle

NASA Technical Reports Server (NTRS)

Stuart, Phillip C.; Rogers, Stuart E.

2009-01-01

The DEBRIS software predicts the trajectories of debris particles shed by a space-shuttle launch vehicle during ascent, to aid in assessing potential harm to the space-shuttle orbiter and crew. The user specifies the location of release and other initial conditions for a debris particle. DEBRIS tracks the particle within an overset grid system by means of a computational fluid dynamics (CFD) simulation of the local flow field and a ballistic simulation that takes account of the mass of the particle and its aerodynamic properties in the flow field. The computed particle trajectory is stored in a file to be post-processed by other software for viewing and analyzing the trajectory. DEBRIS supplants a prior debris tracking code that took .15 minutes to calculate a single particle trajectory: DEBRIS can calculate 1,000 trajectories in .20 seconds on a desktop computer. Other improvements over the prior code include adaptive time-stepping to ensure accuracy, forcing at least one step per grid cell to ensure resolution of all CFD-resolved flow features, ability to simulate rebound of debris from surfaces, extensive error checking, a builtin suite of test cases, and dynamic allocation of memory.

Arsenic removal from contaminated groundwater by membrane-integrated hybrid plant: optimization and control using Visual Basic platform.

PubMed

Chakrabortty, S; Sen, M; Pal, P

2014-03-01

A simulation software (ARRPA) has been developed in Microsoft Visual Basic platform for optimization and control of a novel membrane-integrated arsenic separation plant in the backdrop of absence of such software. The user-friendly, menu-driven software is based on a dynamic linearized mathematical model, developed for the hybrid treatment scheme. The model captures the chemical kinetics in the pre-treating chemical reactor and the separation and transport phenomena involved in nanofiltration. The software has been validated through extensive experimental investigations. The agreement between the outputs from computer simulation program and the experimental findings are excellent and consistent under varying operating conditions reflecting high degree of accuracy and reliability of the software. High values of the overall correlation coefficient (R (2) = 0.989) and Willmott d-index (0.989) are indicators of the capability of the software in analyzing performance of the plant. The software permits pre-analysis, manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. Performance analysis of the whole system as well as the individual units is possible using the tool. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for removal of arsenic from contaminated groundwater.

Multi-Purpose Crew Vehicle Camera Asset Planning: Imagery Previsualization

NASA Technical Reports Server (NTRS)

Beaulieu, K.

2014-01-01

Using JSC-developed and other industry-standard off-the-shelf 3D modeling, animation, and rendering software packages, the Image Science Analysis Group (ISAG) supports Orion Project imagery planning efforts through dynamic 3D simulation and realistic previsualization of ground-, vehicle-, and air-based camera output.

Teaching Model Building to High School Students: Theory and Reality.

ERIC Educational Resources Information Center

Roberts, Nancy; Barclay, Tim

1988-01-01

Builds on a National Science Foundation (NSF) microcomputer based laboratory project to introduce system dynamics into the precollege setting. Focuses on providing students with powerful and investigatory theory building tools. Discusses developed hardware, software, and curriculum materials used to introduce model building and simulations into…

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.

Optimizing legacy molecular dynamics software with directive-based offload

NASA Astrophysics Data System (ADS)

Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

2015-10-01

Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.

Avionics System Architecture Tool

NASA Technical Reports Server (NTRS)

Chau, Savio; Hall, Ronald; Traylor, marcus; Whitfield, Adrian

2005-01-01

Avionics System Architecture Tool (ASAT) is a computer program intended for use during the avionics-system-architecture- design phase of the process of designing a spacecraft for a specific mission. ASAT enables simulation of the dynamics of the command-and-data-handling functions of the spacecraft avionics in the scenarios in which the spacecraft is expected to operate. ASAT is built upon I-Logix Statemate MAGNUM, providing a complement of dynamic system modeling tools, including a graphical user interface (GUI), modeling checking capabilities, and a simulation engine. ASAT augments this with a library of predefined avionics components and additional software to support building and analyzing avionics hardware architectures using these components.

Nonlinear dynamic macromodeling techniques for audio systems

NASA Astrophysics Data System (ADS)

Ogrodzki, Jan; Bieńkowski, Piotr

2015-09-01

This paper develops a modelling method and a models identification technique for the nonlinear dynamic audio systems. Identification is performed by means of a behavioral approach based on a polynomial approximation. This approach makes use of Discrete Fourier Transform and Harmonic Balance Method. A model of an audio system is first created and identified and then it is simulated in real time using an algorithm of low computational complexity. The algorithm consists in real time emulation of the system response rather than in simulation of the system itself. The proposed software is written in Python language using object oriented programming techniques. The code is optimized for a multithreads environment.

Dynamical mechanical characteristic simulation and analysis of the low voltage switch under vibration and shock conditions

NASA Astrophysics Data System (ADS)

Miao, Xiaodan; Han, Feng

2017-04-01

The low voltage switch has widely application especially in the hostile environment such as large vibration and shock conditions. In order to ensure the validity of the switch in the hostile environment, it is necessary to predict its mechanical characteristic. In traditional method, the complex and expensive testing system is build up to verify its validity. This paper presented a method based on finite element analysis to predict the dynamic mechanical characteristic of the switch by using ANSYS software. This simulation could provide the basis for the design and optimization of the switch to shorten the design process to improve the product efficiency.

NCAR global model topography generation software for unstructured grids

NASA Astrophysics Data System (ADS)

Lauritzen, P. H.; Bacmeister, J. T.; Callaghan, P. F.; Taylor, M. A.

2015-06-01

It is the purpose of this paper to document the NCAR global model topography generation software for unstructured grids. Given a model grid, the software computes the fraction of the grid box covered by land, the gridbox mean elevation, and associated sub-grid scale variances commonly used for gravity wave and turbulent mountain stress parameterizations. The software supports regular latitude-longitude grids as well as unstructured grids; e.g. icosahedral, Voronoi, cubed-sphere and variable resolution grids. As an example application and in the spirit of documenting model development, exploratory simulations illustrating the impacts of topographic smoothing with the NCAR-DOE CESM (Community Earth System Model) CAM5.2-SE (Community Atmosphere Model version 5.2 - Spectral Elements dynamical core) are shown.

Co-simulation coupling spectral/finite elements for 3D soil/structure interaction problems

NASA Astrophysics Data System (ADS)

Zuchowski, Loïc; Brun, Michael; De Martin, Florent

2018-05-01

The coupling between an implicit finite elements (FE) code and an explicit spectral elements (SE) code has been explored for solving the elastic wave propagation in the case of soil/structure interaction problem. The coupling approach is based on domain decomposition methods in transient dynamics. The spatial coupling at the interface is managed by a standard coupling mortar approach, whereas the time integration is dealt with an hybrid asynchronous time integrator. An external coupling software, handling the interface problem, has been set up in order to couple the FE software Code_Aster with the SE software EFISPEC3D.

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.

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.

Computer-based simulation of the Bielschowsky head-tilt test using the SEE++ software system.

PubMed

Kaltofen, Thomas; Buchberger, Michael; Priglinger, Siegfried

2008-01-01

Latest measurements of the vestibulo-ocular reflex (VOR) allowed the integration of the simulation of the Bielschowsky head-tilt test (BHTT) into the SEE++ software system. SEE++ realizes a biomechanical model of the human eye in order to simulate eye motility disorders and strabismus surgeries. With the addition of the BHTT it can now also be used for differential-diagnostic simulations of complex disorders (e.g., superior oblique palsies). In order to simulate the BHTT in SEE++, the user can freely choose the desired head-tilt angle from -45 degrees to +45 degrees. The chosen angle is shown in the 3D view with a human body model and is also used in the calculation of the Hess-Lancaster test. The integration of the BHTT offers an additional improvement of the possibilities for simulating eye motility disorders. Moreover, SEE++ allows the creation of a video of the "virtual patient" while tilting the head from one side to the other, which shows dynamic changes in the simulated Hess-diagrams. Comparisons of simulation results with patient-measured data showed a good correlation between the simulated and the measured data. Further comparisons with patient data are planned.

Controls/CFD Interdisciplinary Research Software Generates Low-Order Linear Models for Control Design From Steady-State CFD Results

NASA Technical Reports Server (NTRS)

Melcher, Kevin J.

1997-01-01

The NASA Lewis Research Center is developing analytical methods and software tools to create a bridge between the controls and computational fluid dynamics (CFD) disciplines. Traditionally, control design engineers have used coarse nonlinear simulations to generate information for the design of new propulsion system controls. However, such traditional methods are not adequate for modeling the propulsion systems of complex, high-speed vehicles like the High Speed Civil Transport. To properly model the relevant flow physics of high-speed propulsion systems, one must use simulations based on CFD methods. Such CFD simulations have become useful tools for engineers that are designing propulsion system components. The analysis techniques and software being developed as part of this effort are an attempt to evolve CFD into a useful tool for control design as well. One major aspect of this research is the generation of linear models from steady-state CFD results. CFD simulations, often used during the design of high-speed inlets, yield high resolution operating point data. Under a NASA grant, the University of Akron has developed analytical techniques and software tools that use these data to generate linear models for control design. The resulting linear models have the same number of states as the original CFD simulation, so they are still very large and computationally cumbersome. Model reduction techniques have been successfully applied to reduce these large linear models by several orders of magnitude without significantly changing the dynamic response. The result is an accurate, easy to use, low-order linear model that takes less time to generate than those generated by traditional means. The development of methods for generating low-order linear models from steady-state CFD is most complete at the one-dimensional level, where software is available to generate models with different kinds of input and output variables. One-dimensional methods have been extended somewhat so that linear models can also be generated from two- and three-dimensional steady-state results. Standard techniques are adequate for reducing the order of one-dimensional CFD-based linear models. However, reduction of linear models based on two- and three-dimensional CFD results is complicated by very sparse, ill-conditioned matrices. Some novel approaches are being investigated to solve this problem.

GFEChutes Lo-Fi

NASA Technical Reports Server (NTRS)

Gist, Emily; Turner, Gary; Shelton, Robert; Vautier, Mana; Shaikh, Ashraf

2013-01-01

NASA needed to provide a software model of a parachute system for a manned re-entry vehicle. NASA has parachute codes, e.g., the Descent Simulation System (DSS), that date back to the Apollo Program. Since the space shuttle did not rely on parachutes as its primary descent control mechanism, DSS has not been maintained or incorporated into modern simulation architectures such as Osiris and Antares, which are used for new mission simulations. GFEChutes Lo-Fi is an object-oriented implementation of conventional parachute codes designed for use in modern simulation environments. The GFE (Government Furnished Equipment), low-fidelity (Lo-Fi) parachute model (GFEChutes Lo-Fi) is a software package capable of modeling the effects of multiple parachutes, deployed concurrently and/or sequentially, on a vehicle during the subsonic phase of reentry into planetary atmosphere. The term "low-fidelity" distinguishes models that represent the parachutes as simple forces acting on the vehicle, as opposed to independent aerodynamic bodies. GFEChutes Lo-Fi was created from these existing models to be clean, modular, certified as NASA Class C software, and portable, or "plug and play." The GFE Lo-Fi Chutes Model provides basic modeling capability of a sequential series of parachute activities. Actions include deploying the parachute, changing the reefing on the parachute, and cutting away the parachute. Multiple chutes can be deployed at any given time, but all chutes in that case are assumed to behave as individually isolated chutes; there is no modeling of any interactions between deployed chutes. Drag characteristics of a deployed chute are based on a coefficient of drag, the face area of the chute, and the local dynamic pressure only. The orientation of the chute is approximately modeled for purposes of obtaining torques on the vehicle, but the dynamic state of the chute as a separate entity is not integrated - the treatment is simply an approximation. The innovation in GFEChutes Lo-Fi is to use an object design that closely followed the mechanical characteristics and structure of a physical system of parachutes and their deployment mechanisms. Software objects represent the components of the system, and use of an object hierarchy allows a progression from general component outlines to specific implementations. These extra chutes were not part of the baseline deceleration sequence of drogues and mains, but still had to be simulated. The major innovation in GFEChutes Lo-Fi is the software design and architecture.

Excavator Design Validation

NASA Technical Reports Server (NTRS)

Pholsiri, Chalongrath; English, James; Seberino, Charles; Lim, Yi-Je

2010-01-01

The Excavator Design Validation tool verifies excavator designs by automatically generating control systems and modeling their performance in an accurate simulation of their expected environment. Part of this software design includes interfacing with human operations that can be included in simulation-based studies and validation. This is essential for assessing productivity, versatility, and reliability. This software combines automatic control system generation from CAD (computer-aided design) models, rapid validation of complex mechanism designs, and detailed models of the environment including soil, dust, temperature, remote supervision, and communication latency to create a system of high value. Unique algorithms have been created for controlling and simulating complex robotic mechanisms automatically from just a CAD description. These algorithms are implemented as a commercial cross-platform C++ software toolkit that is configurable using the Extensible Markup Language (XML). The algorithms work with virtually any mobile robotic mechanisms using module descriptions that adhere to the XML standard. In addition, high-fidelity, real-time physics-based simulation algorithms have also been developed that include models of internal forces and the forces produced when a mechanism interacts with the outside world. This capability is combined with an innovative organization for simulation algorithms, new regolith simulation methods, and a unique control and study architecture to make powerful tools with the potential to transform the way NASA verifies and compares excavator designs. Energid's Actin software has been leveraged for this design validation. The architecture includes parametric and Monte Carlo studies tailored for validation of excavator designs and their control by remote human operators. It also includes the ability to interface with third-party software and human-input devices. Two types of simulation models have been adapted: high-fidelity discrete element models and fast analytical models. By using the first to establish parameters for the second, a system has been created that can be executed in real time, or faster than real time, on a desktop PC. This allows Monte Carlo simulations to be performed on a computer platform available to all researchers, and it allows human interaction to be included in a real-time simulation process. Metrics on excavator performance are established that work with the simulation architecture. Both static and dynamic metrics are included.

Simulating Freak Waves in the Ocean with CFD Modeling

NASA Astrophysics Data System (ADS)

Manolidis, M.; Orzech, M.; Simeonov, J.

2017-12-01

Rogue, or freak, waves constitute an active topic of research within the world scientific community, as various maritime authorities around the globe seek to better understand and more accurately assess the risks that the occurrence of such phenomena entail. Several experimental studies have shed some light on the mechanics of rogue wave formation. In our work we numerically simulate the formation of such waves in oceanic conditions by means of Computational Fluid Dynamics (CFD) software. For this purpose we implement the NHWAVE and OpenFOAM software packages. Both are non-hydrostatic, turbulent flow solvers, but NHWAVE implements a shock-capturing scheme at the free surface-interface, while OpenFOAM utilizes the Volume Of Fluid (VOF) method. NHWAVE has been shown to accurately reproduce highly nonlinear surface wave phenomena, such as soliton propagation and wave shoaling. We conducted a range of tests simulating rogue wave formation and horizontally varying currents to evaluate and compare the capabilities of the two software packages. Then we used each model to investigate the effect of ocean currents and current gradients on the formation of rogue waves. We present preliminary results.

A molecular dynamics study on sI hydrogen hydrate.

PubMed

Mondal, S; Ghosh, S; Chattaraj, P K

2013-07-01

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

An Object Model for a Rocket Engine Numerical Simulator

NASA Technical Reports Server (NTRS)

Mitra, D.; Bhalla, P. N.; Pratap, V.; Reddy, P.

1998-01-01

Rocket Engine Numerical Simulator (RENS) is a packet of software which numerically simulates the behavior of a rocket engine. Different parameters of the components of an engine is the input to these programs. Depending on these given parameters the programs output the behaviors of those components. These behavioral values are then used to guide the design of or to diagnose a model of a rocket engine "built" by a composition of these programs simulating different components of the engine system. In order to use this software package effectively one needs to have a flexible model of a rocket engine. These programs simulating different components then should be plugged into this modular representation. Our project is to develop an object based model of such an engine system. We are following an iterative and incremental approach in developing the model, as is the standard practice in the area of object oriented design and analysis of softwares. This process involves three stages: object modeling to represent the components and sub-components of a rocket engine, dynamic modeling to capture the temporal and behavioral aspects of the system, and functional modeling to represent the transformational aspects. This article reports on the first phase of our activity under a grant (RENS) from the NASA Lewis Research center. We have utilized Rambaugh's object modeling technique and the tool UML for this purpose. The classes of a rocket engine propulsion system are developed and some of them are presented in this report. The next step, developing a dynamic model for RENS, is also touched upon here. In this paper we will also discuss the advantages of using object-based modeling for developing this type of an integrated simulator over other tools like an expert systems shell or a procedural language, e.g., FORTRAN. Attempts have been made in the past to use such techniques.

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.

RuleMonkey: software for stochastic simulation of rule-based models

PubMed Central

2010-01-01

Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now needed for the simulation and analysis of rule-based models of biochemical systems. Results Here, we present a software tool called RuleMonkey, which implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant tool for network-free simulation of rule-based models. We also compare RuleMonkey against problem-specific codes implementing network-free simulation methods. Conclusions RuleMonkey enables the simulation of rule-based models for which the underlying reaction networks are large. It is typically faster than DYNSTOC for benchmark problems that we have examined. RuleMonkey is freely available as a stand-alone application http://public.tgen.org/rulemonkey. It is also available as a simulation engine within GetBonNie, a web-based environment for building, analyzing and sharing rule-based models. PMID:20673321

SSAGES: Software Suite for Advanced General Ensemble Simulations

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

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniquesmore » as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.« less

SSAGES: Software Suite for Advanced General Ensemble Simulations.

PubMed

Sidky, Hythem; Colón, Yamil J; Helfferich, Julian; Sikora, Benjamin J; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S; Reid, Daniel R; Sevgen, Emre; Thapar, Vikram; Webb, Michael A; Whitmer, Jonathan K; de Pablo, Juan J

2018-01-28

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

The predictive power of SIMION/SDS simulation software for modeling ion mobility spectrometry instruments

NASA Astrophysics Data System (ADS)

Lai, Hanh; McJunkin, Timothy R.; Miller, Carla J.; Scott, Jill R.; Almirall, José R.

2008-09-01

The combined use of SIMION 7.0 and the statistical diffusion simulation (SDS) user program in conjunction with SolidWorks® with COSMSOSFloWorks® fluid dynamics software to model a complete, commercial ion mobility spectrometer (IMS) was demonstrated for the first time and compared to experimental results for tests using compounds of immediate interest in the security industry (e.g., 2,4,6-trinitrotoluene, 2,7-dinitrofluorene, and cocaine). The effort of this research was to evaluate the predictive power of SIMION/SDS for application to IMS instruments. The simulation was evaluated against experimental results in three studies: (1) a drift:carrier gas flow rates study assesses the ability of SIMION/SDS to correctly predict the ion drift times; (2) a drift gas composition study evaluates the accuracy in predicting the resolution; (3) a gate width study compares the simulated peak shape and peak intensity with the experimental values. SIMION/SDS successfully predicted the correct drift time, intensity, and resolution trends for the operating parameters studied. Despite the need for estimations and assumptions in the construction of the simulated instrument, SIMION/SDS was able to predict the resolution between two ion species in air within 3% accuracy. The preliminary success of IMS simulations using SIMION/SDS software holds great promise for the design of future instruments with enhanced performance.

SSAGES: Software Suite for Advanced General Ensemble Simulations

NASA Astrophysics Data System (ADS)

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; Webb, Michael A.; Whitmer, Jonathan K.; de Pablo, Juan J.

2018-01-01

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

The Predictive Power of SIMION/SDS Simulation Software for Modeling Ion Mobility Spectrometry Instruments

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

Hanh Lai; Timothy R. McJunkin; Carla J. Miller

2008-09-01

The combined use of SIMION 7.0 and the statistical diffusion simulation (SDS) user program in conjunction with SolidWorks® with COSMSOFloWorks® fluid dynamics software to model a complete, commercial ion mobility spectrometer (IMS) was demonstrated for the first time and compared to experimental results for tests using compounds of immediate interest in the security industry (e.g., 2,4,6-trinitrotoluene and cocaine). The effort of this research was to evaluate the predictive power of SIMION/SDS for application to IMS instruments. The simulation was evaluated against experimental results in three studies: 1) a drift:carrier gas flow rates study assesses the ability of SIMION/SDS to correctlymore » predict the ion drift times; 2) a drift gas composition study evaluates the accuracy in predicting the resolution; and 3) a gate width study compares the simulated peak shape and peak intensity with the experimental values. SIMION/SDS successfully predicted the correct drift time, intensity, and resolution trends for the operating parameters studied. Despite the need for estimations and assumptions in the construction of the simulated instrument, SIMION/SDS was able to predict the resolution between two ion species in air within 3% accuracy. The preliminary success of IMS simulations using SIMION/SDS software holds great promise for the design of future instruments with enhanced performance.« less

ShinyGPAS: interactive genomic prediction accuracy simulator based on deterministic formulas.

PubMed

Morota, Gota

2017-12-20

Deterministic formulas for the accuracy of genomic predictions highlight the relationships among prediction accuracy and potential factors influencing prediction accuracy prior to performing computationally intensive cross-validation. Visualizing such deterministic formulas in an interactive manner may lead to a better understanding of how genetic factors control prediction accuracy. The software to simulate deterministic formulas for genomic prediction accuracy was implemented in R and encapsulated as a web-based Shiny application. Shiny genomic prediction accuracy simulator (ShinyGPAS) simulates various deterministic formulas and delivers dynamic scatter plots of prediction accuracy versus genetic factors impacting prediction accuracy, while requiring only mouse navigation in a web browser. ShinyGPAS is available at: https://chikudaisei.shinyapps.io/shinygpas/ . ShinyGPAS is a shiny-based interactive genomic prediction accuracy simulator using deterministic formulas. It can be used for interactively exploring potential factors that influence prediction accuracy in genome-enabled prediction, simulating achievable prediction accuracy prior to genotyping individuals, or supporting in-class teaching. ShinyGPAS is open source software and it is hosted online as a freely available web-based resource with an intuitive graphical user interface.

A Comparison of Three Approaches to Model Human Behavior

NASA Astrophysics Data System (ADS)

Palmius, Joel; Persson-Slumpi, Thomas

2010-11-01

One way of studying social processes is through the use of simulations. The use of simulations for this purpose has been established as its own field, social simulations, and has been used for studying a variety of phenomena. A simulation of a social setting can serve as an aid for thinking about that social setting, and for experimenting with different parameters and studying the outcomes caused by them. When using the simulation as an aid for thinking and experimenting, the chosen simulation approach will implicitly steer the simulationist towards thinking in a certain fashion in order to fit the model. To study the implications of model choice on the understanding of a setting where human anticipation comes into play, a simulation scenario of a coffee room was constructed using three different simulation approaches: Cellular Automata, Systems Dynamics and Agent-based modeling. The practical implementations of the models were done in three different simulation packages: Stella for Systems Dynamic, CaFun for Cellular automata and SesAM for Agent-based modeling. The models were evaluated both using Randers' criteria for model evaluation, and through introspection where the authors reflected upon how their understanding of the scenario was steered through the model choice. Further the software used for implementing the simulation models was evaluated, and practical considerations for the choice of software package are listed. It is concluded that the models have very different strengths. The Agent-based modeling approach offers the most intuitive support for thinking about and modeling a social setting where the behavior of the individual is in focus. The Systems Dynamics model would be preferable in situations where populations and large groups would be studied as wholes, but where individual behavior is of less concern. The Cellular Automata models would be preferable where processes need to be studied from the basis of a small set of very simple rules. It is further concluded that in most social simulation settings the Agent-based modeling approach would be the probable choice. This since the other models does not offer much in the way of supporting the modeling of the anticipatory behavior of humans acting in an organization.

Molecular modeling of lipase binding to a substrate-water interface.

PubMed

Gruber, Christian C; Pleiss, Jürgen

2012-01-01

Interactions of lipases with hydrophobic substrate-water interfaces are of great interest to design improved lipase variants and engineer reaction conditions. This chapter describes the necessary steps to carry out molecular dynamics simulations of Candida antarctica lipase B at tributyrin-water interface using the GROMACS simulation software. Special attention is drawn to the preparation of the protein and the substrate-water interface and to the analysis of the obtained trajectory.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System (T-MATS)

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei (OA)

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This presentation describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this presentation is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture.

Mechanisms test bed math model modification and simulation support

NASA Technical Reports Server (NTRS)

Gilchrist, Andrea C.; Tobbe, Patrick A.

1995-01-01

This report summarizes the work performed under contract NAS8-38771 in support of the Marshall Space Flight Center Six Degree of Freedom Motion Facility and Flight Robotics Laboratory. The contract activities included the development of the two flexible body and Remote Manipulator System simulations, Dynamic Overhead Target Simulator control system and operating software, Global Positioning System simulation, and Manipulator Coupled Spacecraft Controls Testbed. Technical support was also provided for the Lightning Imaging Sensor and Solar X-Ray Imaging programs. The cover sheets and introductory sections for the documentation written under this contract are provided as an appendix.

A simulation of the instrument pointing system for the Astro-1 mission

NASA Technical Reports Server (NTRS)

Whorton, M.; West, M.; Rakoczy, J.

1991-01-01

NASA has recently completed a shuttle-borne stellar ultraviolet astronomy mission known as Astro-1. A three axis instrument pointing system (IPS) was employed to accurately point the science instruments. In order to analyze the pointing control system and verify pointing performance, a simulation of the IPS was developed using the multibody dynamics software TREETOPS. The TREETOPS IPS simulation is capable of accurately modeling the multibody IPS system undergoing large angle, nonlinear motion. The simulation is documented and example cases are presented demonstrating disturbance rejection, fine pointing operations, and multiple target pointing and slewing of the IPS.

GPAW - massively parallel electronic structure calculations with Python-based software.

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

Enkovaara, J.; Romero, N.; Shende, S.

2011-01-01

Electronic structure calculations are a widely used tool in materials science and large consumer of supercomputing resources. Traditionally, the software packages for these kind of simulations have been implemented in compiled languages, where Fortran in its different versions has been the most popular choice. While dynamic, interpreted languages, such as Python, can increase the effciency of programmer, they cannot compete directly with the raw performance of compiled languages. However, by using an interpreted language together with a compiled language, it is possible to have most of the productivity enhancing features together with a good numerical performance. We have used thismore » approach in implementing an electronic structure simulation software GPAW using the combination of Python and C programming languages. While the chosen approach works well in standard workstations and Unix environments, massively parallel supercomputing systems can present some challenges in porting, debugging and profiling the software. In this paper we describe some details of the implementation and discuss the advantages and challenges of the combined Python/C approach. We show that despite the challenges it is possible to obtain good numerical performance and good parallel scalability with Python based software.« less

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

PubMed Central

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

2015-01-01

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

DEVELOPMENT AND APPLICATIONS OF CFD SIMULATIONS SUPPORTING URBAN AIR QUALITY AND HOMELAND SECURITY

EPA Science Inventory

Prior to September 11, 2001 developments of Computational Fluid Dynamics (CFD) were begun to support air quality applications. CFD models are emerging as a promising technology for such assessments, in part due to the advancing power of computational hardware and software. CFD si...

Real-time application of advanced three-dimensional graphic techniques for research aircraft simulation

NASA Technical Reports Server (NTRS)

Davis, Steven B.

1990-01-01

Visual aids are valuable assets to engineers for design, demonstration, and evaluation. Discussed here are a variety of advanced three-dimensional graphic techniques used to enhance the displays of test aircraft dynamics. The new software's capabilities are examined and possible future uses are considered.

Computing and data processing

NASA Technical Reports Server (NTRS)

Smarr, Larry; Press, William; Arnett, David W.; Cameron, Alastair G. W.; Crutcher, Richard M.; Helfand, David J.; Horowitz, Paul; Kleinmann, Susan G.; Linsky, Jeffrey L.; Madore, Barry F.

1991-01-01

The applications of computers and data processing to astronomy are discussed. Among the topics covered are the emerging national information infrastructure, workstations and supercomputers, supertelescopes, digital astronomy, astrophysics in a numerical laboratory, community software, archiving of ground-based observations, dynamical simulations of complex systems, plasma astrophysics, and the remote control of fourth dimension supercomputers.

How Does Technology-Enabled Active Learning Affect Undergraduate Students' Understanding of Electromagnetism Concepts?

ERIC Educational Resources Information Center

Dori, Yehudit Judy; Belcher, John

2005-01-01

Educational technology supports meaningful learning and enables the presentation of spatial and dynamic images, which portray relationships among complex concepts. The Technology-Enabled Active Learning (TEAL) Project at the Massachusetts Institute of Technology (MIT) involves media-rich software for simulation and visualization in freshman…

Dynamic Staffing and Rescheduling in Software Project Management: A Hybrid Approach.

PubMed

Ge, Yujia; Xu, Bin

2016-01-01

Resource allocation could be influenced by various dynamic elements, such as the skills of engineers and the growth of skills, which requires managers to find an effective and efficient tool to support their staffing decision-making processes. Rescheduling happens commonly and frequently during the project execution. Control options have to be made when new resources are added or tasks are changed. In this paper we propose a software project staffing model considering dynamic elements of staff productivity with a Genetic Algorithm (GA) and Hill Climbing (HC) based optimizer. Since a newly generated reschedule dramatically different from the initial schedule could cause an obvious shifting cost increase, our rescheduling strategies consider both efficiency and stability. The results of real world case studies and extensive simulation experiments show that our proposed method is effective and could achieve comparable performance to other heuristic algorithms in most cases.

Dynamic Staffing and Rescheduling in Software Project Management: A Hybrid Approach

PubMed Central

Ge, Yujia; Xu, Bin

2016-01-01

Resource allocation could be influenced by various dynamic elements, such as the skills of engineers and the growth of skills, which requires managers to find an effective and efficient tool to support their staffing decision-making processes. Rescheduling happens commonly and frequently during the project execution. Control options have to be made when new resources are added or tasks are changed. In this paper we propose a software project staffing model considering dynamic elements of staff productivity with a Genetic Algorithm (GA) and Hill Climbing (HC) based optimizer. Since a newly generated reschedule dramatically different from the initial schedule could cause an obvious shifting cost increase, our rescheduling strategies consider both efficiency and stability. The results of real world case studies and extensive simulation experiments show that our proposed method is effective and could achieve comparable performance to other heuristic algorithms in most cases. PMID:27285420

A microkernel design for component-based parallel numerical software systems.

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

Balay, S.

1999-01-13

What is the minimal software infrastructure and what type of conventions are needed to simplify development of sophisticated parallel numerical application codes using a variety of software components that are not necessarily available as source code? We propose an opaque object-based model where the objects are dynamically loadable from the file system or network. The microkernel required to manage such a system needs to include, at most: (1) a few basic services, namely--a mechanism for loading objects at run time via dynamic link libraries, and consistent schemes for error handling and memory management; and (2) selected methods that all objectsmore » share, to deal with object life (destruction, reference counting, relationships), and object observation (viewing, profiling, tracing). We are experimenting with these ideas in the context of extensible numerical software within the ALICE (Advanced Large-scale Integrated Computational Environment) project, where we are building the microkernel to manage the interoperability among various tools for large-scale scientific simulations. This paper presents some preliminary observations and conclusions from our work with microkernel design.« less

Open-Source Software in Computational Research: A Case Study

DOE PAGES

Syamlal, Madhava; O'Brien, Thomas J.; Benyahia, Sofiane; ...

2008-01-01

A case study of open-source (OS) development of the computational research software MFIX, used for multiphase computational fluid dynamics simulations, is presented here. The verification and validation steps required for constructing modern computational software and the advantages of OS development in those steps are discussed. The infrastructure used for enabling the OS development of MFIX is described. The impact of OS development on computational research and education in gas-solids flow, as well as the dissemination of information to other areas such as geophysical and volcanology research, is demonstrated. This study shows that the advantages of OS development were realized inmore » the case of MFIX: verification by many users, which enhances software quality; the use of software as a means for accumulating and exchanging information; the facilitation of peer review of the results of computational research.« less

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

PubMed

Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal

2018-01-01

Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.

ICEG2D (v2.0) - An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils With Ice Accretion

NASA Technical Reports Server (NTRS)

Thompson David S.; Soni, Bharat K.

2001-01-01

An integrated geometry/grid/simulation software package, ICEG2D, is being developed to automate computational fluid dynamics (CFD) simulations for single- and multi-element airfoils with ice accretions. The current version, ICEG213 (v2.0), was designed to automatically perform four primary functions: (1) generate a grid-ready surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generate high-quality structured and generalized grids starting from a defined surface definition, (3) generate the input and restart files needed to run the structured grid CFD solver NPARC or the generalized grid CFD solver HYBFL2D, and (4) using the flow solutions, generate solution-adaptive grids. ICEG2D (v2.0) can be operated in either a batch mode using a script file or in an interactive mode by entering directives from a command line within a Unix shell. This report summarizes activities completed in the first two years of a three-year research and development program to address automation issues related to CFD simulations for airfoils with ice accretions. As well as describing the technology employed in the software, this document serves as a users manual providing installation and operating instructions. An evaluation of the software is also presented.

The Virtual Mouse Brain: A Computational Neuroinformatics Platform to Study Whole Mouse Brain Dynamics.

PubMed

Melozzi, Francesca; Woodman, Marmaduke M; Jirsa, Viktor K; Bernard, Christophe

2017-01-01

Connectome-based modeling of large-scale brain network dynamics enables causal in silico interrogation of the brain's structure-function relationship, necessitating the close integration of diverse neuroinformatics fields. Here we extend the open-source simulation software The Virtual Brain (TVB) to whole mouse brain network modeling based on individual diffusion magnetic resonance imaging (dMRI)-based or tracer-based detailed mouse connectomes. We provide practical examples on how to use The Virtual Mouse Brain (TVMB) to simulate brain activity, such as seizure propagation and the switching behavior of the resting state dynamics in health and disease. TVMB enables theoretically driven experimental planning and ways to test predictions in the numerous strains of mice available to study brain function in normal and pathological conditions.

Development and testing of a numerical simulation method for thermally nonequilibrium dissociating flows in ANSYS Fluent

NASA Astrophysics Data System (ADS)

Shoev, G. V.; Bondar, Ye. A.; Oblapenko, G. P.; Kustova, E. V.

2016-03-01

Various issues of numerical simulation of supersonic gas flows with allowance for thermochemical nonequilibrium on the basis of fluid dynamic equations in the two-temperature approximation are discussed. The computational tool for modeling flows with thermochemical nonequilibrium is the commercial software package ANSYS Fluent with an additional userdefined open-code module. A comparative analysis of results obtained by various models of vibration-dissociation coupling in binary gas mixtures of nitrogen and oxygen is performed. Results of numerical simulations are compared with available experimental data.

Recent Developments in Hardware-in-the-Loop Formation Navigation and Control

NASA Technical Reports Server (NTRS)

Mitchell, Jason W.; Luquette, Richard J.

2005-01-01

The Formation Flying Test-Bed (FFTB) at NASA Goddard Space Flight Center (GSFC) provides a hardware-in-the-loop test environment for formation navigation and control. The facility is evolving as a modular, hybrid, dynamic simulation facility for end-tc-end guidance, navigation, and control (GN&C) design and analysis of formation flying spacecraft. The core capabilities of the FFTB, as a platform for testing critical hardware and software algorithms in-the-loop, are reviewed with a focus on many recent improvements. Two significant upgrades to the FFTB are a message-oriented middleware (MOM) architecture, and a software crosslink for inter-spacecraft ranging. The MOM architecture provides a common messaging bus for software agents, easing integration, arid supporting the GSFC Mission Services Evolution Center (GMSEC) architecture via software bridge. Additionally, the FFTB s hardware capabilities are expanding. Recently, two Low-Power Transceivers (LPTs) with ranging capability have been introduced into the FFTB. The LPT crosslinks will be connected to a modified Crosslink Channel Simulator (CCS), which applies realistic space-environment effects to the Radio Frequency (RF) signals produced by the LPTs.

ICEG2D: An Integrated Software Package for Automated Prediction of Flow Fields for Single-Element Airfoils with Ice Accretion

NASA Technical Reports Server (NTRS)

Thompson, David S.; Soni, Bharat K.

2000-01-01

An integrated software package, ICEG2D, was developed to automate computational fluid dynamics (CFD) simulations for single-element airfoils with ice accretion. ICEG2D is designed to automatically perform three primary functions: (1) generating a grid-ready, surface definition based on the geometrical characteristics of the iced airfoil surface, (2) generating a high-quality grid using the generated surface point distribution, and (3) generating the input and restart files needed to run the general purpose CFD solver NPARC. ICEG2D can be executed in batch mode using a script file or in an interactive mode by entering directives from a command line. This report summarizes activities completed in the first year of a three-year research and development program to address issues related to CFD simulations for aircraft components with ice accretion. Specifically, this document describes the technology employed in the software, the installation procedure, and a description of the operation of the software package. Validation of the geometry and grid generation modules of ICEG2D is also discussed.

Simulation study on dynamics model of two kinds of on-orbit soft-contact mechanism

NASA Astrophysics Data System (ADS)

Ye, X.; Dong, Z. H.; Yang, F.

2018-05-01

Aiming at the problem that the operating conditions of the space manipulator is harsh and the space manipulator could not bear the large collision momentum, this paper presents a new concept and technical method, namely soft contact technology. Based on ADAMS dynamics software, this paper compares and simulates the mechanism model of on-orbit soft-contact mechanism based on the bionic model and the integrated double joint model. The main purpose is to verify the path planning ability and the momentum buffering ability based on the different design concept mechanism. The simulation results show that both the two mechanism models have the path planning function before the space target contact, and also has the momentum buffer and controllability during the space target contact process.

Orbits: Computer simulation

NASA Technical Reports Server (NTRS)

Muszynska, A.

1985-01-01

In rotating machinery dynamics an orbit (Lissajous curve) represents the dynamic path of the shaft centerline motion during shaft rotation and resulting precession. The orbit can be observed with an oscilloscope connected to XY promixity probes. The orbits can also be simulated by a computer. The software for HP computer simulates orbits for two cases: (1) Symmetric orbit with four frequency components with different radial amplitudes and relative phase angles; and (2) Nonsymmetric orbit with two frequency components with two different vertical/horizontal amplitudes and two different relative phase angles. Each orbit carries a Keyphasor mark (one-per-turn reference). The frequencies, amplitudes, and phase angles, as well as number of time steps for orbit computation, have to be chosen and introduced to the computer by the user. The orbit graphs can be observed on the computer screen.

Autonomous Integrated Receive System (AIRS) requirements definition. Volume 3: Performance and simulation

NASA Technical Reports Server (NTRS)

Chie, C. M.; Su, Y. T.; Lindsey, W. C.; Koukos, J.

1984-01-01

The autonomous and integrated aspects of the operation of the AIRS (Autonomous Integrated Receive System) are discussed from a system operation point of view. The advantages of AIRS compared to the existing SSA receive chain equipment are highlighted. The three modes of AIRS operation are addressed in detail. The configurations of the AIRS are defined as a function of the operating modes and the user signal characteristics. Each AIRS configuration selection is made up of three components: the hardware, the software algorithms and the parameters used by these algorithms. A comparison between AIRS and the wide dynamics demodulation (WDD) is provided. The organization of the AIRS analytical/simulation software is described. The modeling and analysis is for simulating the performance of the PN subsystem is documented. The frequence acquisition technique using a frequency-locked loop is also documented. Doppler compensation implementation is described. The technological aspects of employing CCD's for PN acquisition are addressed.

Modelling the effect of changing design fineness ratio of an airship on its aerodynamic lift and drag performance

NASA Astrophysics Data System (ADS)

Jalasabri, J.; Romli, F. I.; Harmin, M. Y.

2017-12-01

In developing successful airship designs, it is important to fully understand the effect of the design on the performance of the airship. The aim of this research work is to establish the trend for effects of design fineness ratio of an airship towards its aerodynamic performance. An approximate computer-aided design (CAD) model of the Atlant-100 airship is constructed using CATIA software and it is applied in the computational fluid dynamics (CFD) simulation analysis using Star-CCM+ software. In total, 36 simulation runs are executed with different combinations of values for design fineness ratio, altitude and velocity. The obtained simulation results are analyzed using MINITAB to capture the effects relationship on lift and drag coefficients. Based on the results, it is concluded that the design fineness ratio does have a significant impact on the generated aerodynamic lift and drag forces on the airship.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

PubMed

Parton, Daniel L; Grinaway, Patrick B; Hanson, Sonya M; Beauchamp, Kyle A; Chodera, John D

2016-06-01

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences-from a single sequence to an entire superfamily-and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics-such as Markov state models (MSMs)-which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates. Ensembler is free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded from https://github.com/choderalab/ensembler.

Simulating the dynamic interaction of a robotic arm and the Space Shuttle remote manipulator system. M.S. Thesis - George Washington Univ., Dec. 1994

NASA Technical Reports Server (NTRS)

Garrahan, Steven L.; Tolson, Robert H.; Williams, Robert L., II

1995-01-01

Industrial robots are usually attached to a rigid base. Placing the robot on a compliant base introduces dynamic coupling between the two systems. The Vehicle Emulation System (VES) is a six DOF platform that is capable of modeling this interaction. The VES employs a force-torque sensor as the interface between robot and base. A computer simulation of the VES is presented. Each of the hardware and software components is described and Simulink is used as the programming environment. The simulation performance is compared with experimental results to validate accuracy. A second simulation which models the dynamic interaction of a robot and a flexible base acts as a comparison to the simulated motion of the VES. Results are presented that compare the simulated VES motion with the motion of the VES hardware using the same admittance model. The two computer simulations are compared to determine how well the VES is expected to emulate the desired motion. Simulation results are given for robots mounted to the end effector of the Space Shuttle Remote Manipulator System (SRMS). It is shown that for fast motions of the two robots studied, the SRMS experiences disturbances on the order of centimeters. Larger disturbances are possible if different manipulators are used.

Dynamic prediction in functional concurrent regression with an application to child growth.

PubMed

Leroux, Andrew; Xiao, Luo; Crainiceanu, Ciprian; Checkley, William

2018-04-15

In many studies, it is of interest to predict the future trajectory of subjects based on their historical data, referred to as dynamic prediction. Mixed effects models have traditionally been used for dynamic prediction. However, the commonly used random intercept and slope model is often not sufficiently flexible for modeling subject-specific trajectories. In addition, there may be useful exposures/predictors of interest that are measured concurrently with the outcome, complicating dynamic prediction. To address these problems, we propose a dynamic functional concurrent regression model to handle the case where both the functional response and the functional predictors are irregularly measured. Currently, such a model cannot be fit by existing software. We apply the model to dynamically predict children's length conditional on prior length, weight, and baseline covariates. Inference on model parameters and subject-specific trajectories is conducted using the mixed effects representation of the proposed model. An extensive simulation study shows that the dynamic functional regression model provides more accurate estimation and inference than existing methods. Methods are supported by fast, flexible, open source software that uses heavily tested smoothing techniques. © 2017 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

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

Experimental, Numerical, and Analytical Slosh Dynamics of Water and Liquid Nitrogen in a Spherical Tank

NASA Technical Reports Server (NTRS)

Storey, Jedediah Morse

2016-01-01

Understanding, predicting, and controlling fluid slosh dynamics is critical to safety and improving performance of space missions when a significant percentage of the spacecraft's mass is a liquid. Computational fluid dynamics simulations can be used to predict the dynamics of slosh, but these programs require extensive validation. Many experimental and numerical studies of water slosh have been conducted. However, slosh data for cryogenic liquids is lacking. Water and cryogenic liquid nitrogen are used in various ground-based tests with a spherical tank to characterize damping, slosh mode frequencies, and slosh forces. A single ring baffle is installed in the tank for some of the tests. Analytical models for slosh modes, slosh forces, and baffle damping are constructed based on prior work. Select experiments are simulated using a commercial CFD software, and the numerical results are compared to the analytical and experimental results for the purposes of validation and methodology-improvement.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

PubMed Central

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

PubMed

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Analysis of Decomposition for Structure I Methane Hydrate by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Wei, Na; Sun, Wan-Tong; Meng, Ying-Feng; Liu, An-Qi; Zhou, Shou-Wei; Guo, Ping; Fu, Qiang; Lv, Xin

2018-05-01

Under multi-nodes of temperatures and pressures, microscopic decomposition mechanisms of structure I methane hydrate in contact with bulk water molecules have been studied through LAMMPS software by molecular dynamics simulation. Simulation system consists of 482 methane molecules in hydrate and 3027 randomly distributed bulk water molecules. Through analyses of simulation results, decomposition number of hydrate cages, density of methane molecules, radial distribution function for oxygen atoms, mean square displacement and coefficient of diffusion of methane molecules have been studied. A significant result shows that structure I methane hydrate decomposes from hydrate-bulk water interface to hydrate interior. As temperature rises and pressure drops, the stabilization of hydrate will weaken, decomposition extent will go deep, and mean square displacement and coefficient of diffusion of methane molecules will increase. The studies can provide important meanings for the microscopic decomposition mechanisms analyses of methane hydrate.

Motion Law Analysis and Structural Optimization of the Ejection Device of Tray Seeder

NASA Astrophysics Data System (ADS)

Luo, Xin; Hu, Bin; Dong, Chunwang; Huang, Lili

An ejection mechanism consisting four reset springs, an electromagnet and a seed disk was designed for tray seeder. The motion conditions of seeds in the seed disk were theoretical analyzed and intensity and height of seed ejection were calculated. The motions of the seeds and seed disk were multi-body dynamic simulated using Cosmos modules plug-in SolidWorks software package. The simulation results showed the consistence with the theoretical analysis.

The flight robotics laboratory

NASA Technical Reports Server (NTRS)

Tobbe, Patrick A.; Williamson, Marlin J.; Glaese, John R.

1988-01-01

The Flight Robotics Laboratory of the Marshall Space Flight Center is described in detail. This facility, containing an eight degree of freedom manipulator, precision air bearing floor, teleoperated motion base, reconfigurable operator's console, and VAX 11/750 computer system, provides simulation capability to study human/system interactions of remote systems. The facility hardware, software and subsequent integration of these components into a real time man-in-the-loop simulation for the evaluation of spacecraft contact proximity and dynamics are described.

Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

PubMed

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

PubMed

Vermaas, Josh V; Hardy, David J; Stone, John E; Tajkhorshid, Emad; Kohlmeyer, Axel

2016-06-27

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.

Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

PubMed Central

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit PMID:25816325

Exploring the limits of knowledge on boreal peatland development using a new model: the Holocene Peatland Model

NASA Astrophysics Data System (ADS)

Quillet, Anne; Garneau, Michelle; Frolking, Steve; Roulet, Nigel; Peng, Changhui

2010-05-01

The Holocene Peatland Model (HPM) (Frolking et al. 2009, Frolking et al. in prep.) is a recently developed tool integrating up-to-date knowledge on peatland dynamics that explores peatland development and carbon dynamics on a millennial timescale. HPM combines the water and carbon cycles with net primary production and peat decomposition and takes the multiple feedbacks into account. The model remains simple and few site-specific inputs are needed. HPM simulates the transient development of the peatland and delivers peat age, peat depth, peat composition, carbon accumulation and water table depth for each simulated year. Evaluating the ability of the model to reproduce peatland development can be achieved in several manners. Commonly one could choose to compare simulations results with observations from field data. However, we argue that the overall response of the model does not give much information about the value of the model design. Modelling of peatlands dynamics requires a lot of information regarding the behaviour of a peatland system within its environment (including allogenic changes in climate, hydrological conditions, nutrient availability or autogenic processes such as microtopographical effects). The actual state of knowledge does not cover all processes, interactions or feedbacks and a lot of peatland properties are neither well defined nor measured yet, so that estimates have been needed to build the model. The work presented here aims at analyzing the role of the model parameterization on the simulation results. To do so, a sensitivity analysis is performed with a Monte-Carlo analysis and with help of the GUI-HDMR software (Ziehn and Tomlin, 2009). This method ranks the parameters and combinations of them according to their influence on simulation results. The results will emphasize how the simulation is sensitive to the parameter values. First, the distribution of outputs gives insight into the possible responses of the simulation to HPM's assemblage of current knowledge. Second, the importance of some parameters on simulation results points out certain gaps in the current understanding of peatland dynamics. Thus, this study helps determine some avenues that should be explored in future in order to improve peatlands dynamics understanding. Frolking S, NT Roulet, A Quillet, E Tuittila, JL Bubier. 2009. Simulating long-term carbon and water dynamics in northern peatlands Eos Trans. AGU, 90(52), Fall Meet. Suppl., Abstract PP12B-05. Frolking S, NT Roulet, E Tuittila, JL Bubier, A Quillet. XXXX. A new model of Holocene peatland net primary production, decomposition, and peat accumulation. in prep. Ziehn T, AS Tomlin. 2009. GUI-HDMR - A solftware tool for global sensitivity analysis of complex models. Environmental Modelling & Software, 24, 775-785.

Antiterrorist Software

NASA Technical Reports Server (NTRS)

Clark, David A.

1998-01-01

In light of the escalation of terrorism, the Department of Defense spearheaded the development of new antiterrorist software for all Government agencies by issuing a Broad Agency Announcement to solicit proposals. This Government-wide competition resulted in a team that includes NASA Lewis Research Center's Computer Services Division, who will develop the graphical user interface (GUI) and test it in their usability lab. The team launched a program entitled Joint Sphere of Security (JSOS), crafted a design architecture (see the following figure), and is testing the interface. This software system has a state-ofthe- art, object-oriented architecture, with a main kernel composed of the Dynamic Information Architecture System (DIAS) developed by Argonne National Laboratory. DIAS will be used as the software "breadboard" for assembling the components of explosions, such as blast and collapse simulations.

Dynamic Brazilian Test of Rock Under Intermediate Strain Rate: Pendulum Hammer-Driven SHPB Test and Numerical Simulation

NASA Astrophysics Data System (ADS)

Zhu, W. C.; Niu, L. L.; Li, S. H.; Xu, Z. H.

2015-09-01

The tensile strength of rock subjected to dynamic loading constitutes many engineering applications such as rock drilling and blasting. The dynamic Brazilian test of rock specimens was conducted with the split Hopkinson pressure bar (SHPB) driven by pendulum hammer, in order to determine the indirect tensile strength of rock under an intermediate strain rate ranging from 5.2 to 12.9 s-1, which is achieved when the incident bar is impacted by pendulum hammer with different velocities. The incident wave excited by pendulum hammer is triangular in shape, featuring a long rising time, and it is considered to be helpful for achieving a constant strain rate in the rock specimen. The dynamic indirect tensile strength of rock increases with strain rate. Then, the numerical simulator RFPA-Dynamics, a well-recognized software for simulating the rock failure under dynamic loading, is validated by reproducing the Brazilian test of rock when the incident stress wave retrieved at the incident bar is input as the boundary condition, and then it is employed to study the Brazilian test of rock under the higher strain rate. Based on the numerical simulation, the strain-rate dependency of tensile strength and failure pattern of the Brazilian disc specimen under the intermediate strain rate are numerically simulated, and the associated failure mechanism is clarified. It is deemed that the material heterogeneity should be a reason for the strain-rate dependency of rock.

SEDS1 mission software verification using a signal simulator

NASA Technical Reports Server (NTRS)

Pierson, William E.

1992-01-01

The first flight of the Small Expendable Deployer System (SEDS1) is schedule to fly as the secondary payload of a Delta 2 in March, 1993. The objective of the SEDS1 mission is to collect data to validate the concept of tethered satellite systems and to verify computer simulations used to predict their behavior. SEDS1 will deploy a 50 lb. instrumented satellite as an end mass using a 20 km tether. Langley Research Center is providing the end mass instrumentation, while the Marshall Space Flight Center is designing and building the deployer. The objective of the experiment is to test the SEDS design concept by demonstrating that the system will satisfactorily deploy the full 20 km tether without stopping prematurely, come to a smooth stop on the application of a brake, and cut the tether at the proper time after it swings to the local vertical. Also, SEDS1 will collect data which will be used to test the accuracy of tether dynamics models used to stimulate this type of deployment. The experiment will last about 1.5 hours and complete approximately 1.5 orbits. Radar tracking of the Delta II and end mass is planned. In addition, the SEDS1 on-board computer will continuously record, store, and transmit mission data over the Delta II S-band telemetry system. The Data System will count tether windings as the tether unwinds, log the times of each turn and other mission events, monitor tether tension, and record the temperature of system components. A summary of the measurements taken during the SEDS1 are shown. The Data System will also control the tether brake and cutter mechanisms. Preliminary versions of two major sections of the flight software, the data telemetry modules and the data collection modules, were developed and tested under the 1990 NASA/ASEE Summer Faculty Fellowship Program. To facilitate the debugging of these software modules, a prototype SEDS Data System was programmed to simulate turn count signals. During the 1991 summer program, the concept of simulating signals produced by the SEDS electronics systems and circuits was expanded and more precisely defined. During the 1992 summer program, the SEDS signal simulator was programmed to test the requirements of the SEDS Mission software, and this simulator will be used in the formal verification of the SEDS Mission Software. The formal test procedures specification was written which incorporates the use of the signal simulator to test the SEDS Mission Software and which incorporates procedures for testing the other major component of the SEDS software, the Monitor Software.

MaMiCo: Software design for parallel molecular-continuum flow simulations

NASA Astrophysics Data System (ADS)

Neumann, Philipp; Flohr, Hanno; Arora, Rahul; Jarmatz, Piet; Tchipev, Nikola; Bungartz, Hans-Joachim

2016-03-01

The macro-micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementation SimpleMD, the node-level optimized software ls1 mardyn, and the community codes ESPResSo and LAMMPS. We detail interface implementations to connect each solver with MaMiCo. The coupling for each waLBerla-MD setup is validated in three-dimensional channel flow simulations which are solved by means of a state-based coupling method. We provide sequential and strong scaling measurements for the four molecular-continuum simulations. The overhead of MaMiCo is found to come at 10%-20% of the total (MD) runtime. The measurements further show that scalability of the hybrid simulations is reached on up to 500 Intel SandyBridge, and more than 1000 AMD Bulldozer compute cores.

A Discrete Event Simulation Model for Evaluating the Performances of an M/G/C/C State Dependent Queuing System

PubMed Central

Khalid, Ruzelan; M. Nawawi, Mohd Kamal; Kawsar, Luthful A.; Ghani, Noraida A.; Kamil, Anton A.; Mustafa, Adli

2013-01-01

M/G/C/C state dependent queuing networks consider service rates as a function of the number of residing entities (e.g., pedestrians, vehicles, and products). However, modeling such dynamic rates is not supported in modern Discrete Simulation System (DES) software. We designed an approach to cater this limitation and used it to construct the M/G/C/C state-dependent queuing model in Arena software. Using the model, we have evaluated and analyzed the impacts of various arrival rates to the throughput, the blocking probability, the expected service time and the expected number of entities in a complex network topology. Results indicated that there is a range of arrival rates for each network where the simulation results fluctuate drastically across replications and this causes the simulation results and analytical results exhibit discrepancies. Detail results that show how tally the simulation results and the analytical results in both abstract and graphical forms and some scientific justifications for these have been documented and discussed. PMID:23560037

Final Project Report: Data Locality Enhancement of Dynamic Simulations for Exascale Computing

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

Shen, Xipeng

The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future manycore systems, alleviating the memory performance issues for exascale computing. In the first three years, the PI and his group have achieves some significant progress towards the goal, producing a set of novel techniques for improving the memory performance and data locality in manycore systems, yielding 18 conference and workshop papers and 4 journal papers and graduating 6 Ph.Ds. This report summarizes the research results of thismore » project through that period.« less

Simulator of Space Communication Networks

NASA Technical Reports Server (NTRS)

Clare, Loren; Jennings, Esther; Gao, Jay; Segui, John; Kwong, Winston

2005-01-01

Multimission Advanced Communications Hybrid Environment for Test and Evaluation (MACHETE) is a suite of software tools that simulates the behaviors of communication networks to be used in space exploration, and predict the performance of established and emerging space communication protocols and services. MACHETE consists of four general software systems: (1) a system for kinematic modeling of planetary and spacecraft motions; (2) a system for characterizing the engineering impact on the bandwidth and reliability of deep-space and in-situ communication links; (3) a system for generating traffic loads and modeling of protocol behaviors and state machines; and (4) a system of user-interface for performance metric visualizations. The kinematic-modeling system makes it possible to characterize space link connectivity effects, including occultations and signal losses arising from dynamic slant-range changes and antenna radiation patterns. The link-engineering system also accounts for antenna radiation patterns and other phenomena, including modulations, data rates, coding, noise, and multipath fading. The protocol system utilizes information from the kinematic-modeling and link-engineering systems to simulate operational scenarios of space missions and evaluate overall network performance. In addition, a Communications Effect Server (CES) interface for MACHETE has been developed to facilitate hybrid simulation of space communication networks with actual flight/ground software/hardware embedded in the overall system.

FATSLiM: a fast and robust software to analyze MD simulations of membranes.

PubMed

Buchoux, Sébastien

2017-01-01

When studying biological membranes, Molecular Dynamics (MD) simulations reveal to be quite complementary to experimental techniques. Because the simulated systems keep increasing both in size and complexity, the analysis of MD trajectories need to be computationally efficient while being robust enough to perform analysis on membranes that may be curved or deformed due to their size and/or protein-lipid interactions. This work presents a new software named FATSLiM ('Fast Analysis Toolbox for Simulations of Lipid Membranes') that can extract physical properties from MD simulations of membranes (with or without interacting proteins). Because it relies on the calculation of local normals, FATSLiM does not depend of the bilayer morphology and thus can handle with the same accuracy vesicles for instance. Thanks to an efficiency-driven development, it is also fast and consumes a rather low amount of memory. FATSLiM (http://fatslim.github.io) is a stand-alone software written in Python. Source code is released under the GNU GPLv3 and is freely available at https://github.com/FATSLiM/fatslim A complete online documentation including instructions for platform-independent installation is available at http://pythonhosted.org/fatslim CONTACT: sebastien.buchoux@u-picardie.frSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Simulation of a tethered microgravity robot pair and validation on a planar air bearing

NASA Astrophysics Data System (ADS)

Mantellato, R.; Lorenzini, E. C.; Sternberg, D.; Roascio, D.; Saenz-Otero, A.; Zachrau, H. J.

2017-09-01

A software model has been developed to simulate the on-orbit dynamics of a dual-mass tethered system where one or both of the tethered spacecraft are able to produce propulsive thrust. The software simulates translations and rotations of both spacecraft, with the visco-elastic tether being simulated as a lumped-mass model. Thanks to this last feature, tether longitudinal and lateral modes of vibration and tether tension can be accurately assessed. Also, the way the spacecraft motion responds to sudden tether tension spikes can be studied in detail. The code enables the simulation of different scenarios, including space tug missions for deorbit maneuvers in a debris mitigation context and general-purpose tethered formation flight missions. This study aims to validate the software through a representative test campaign performed with the MIT Synchronized Position Hold Engage and Reorient Experimental Satellites (SPHERES) planar air bearing system. Results obtained with the numerical simulator are compared with data from direct measurements in different testing setups. The studied cases take into account different initial conditions of the spacecraft velocities and relative attitudes, and thrust forces. Data analysis is presented comparing the results of the simulations with direct measurements of acceleration and Azimuth rate of the two bodies in the planar air bearing test facility using a Nylon tether. Plans for conducting a microgravity test campaign using the SPHERES satellites aboard the International Space Station are also being scheduled in the near future in order to further validate the simulation using data from the relevant operational environment of extended microgravity with full six degree of freedom (per body) motion.

Pilot interaction with automated airborne decision making systems

NASA Technical Reports Server (NTRS)

Rouse, W. B.; Hammer, J. M.; Morris, N. M.; Brown, E. N.; Yoon, W. C.

1983-01-01

The use of advanced software engineering methods (e.g., from artificial intelligence) to aid aircraft crews in procedure selection and execution is investigated. Human problem solving in dynamic environments as effected by the human's level of knowledge of system operations is examined. Progress on the development of full scale simulation facilities is also discussed.

Simulation of Dual Firing of Hydrogen and JP-8 in a Swirling Combustor

DTIC Science & Technology

2012-06-14

completed using the Ansys CFX computational fluid dynamics software. The total Lower Heating Value of the fuel mixture is maintained at a constant 6 kW...PERSON a. REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18

KETCindy--Collaboration of Cinderella and KETpic Reports on CADGME 2014 Conference Working Group

ERIC Educational Resources Information Center

Kaneko, Masataka; Yamashita, Satoshi; Kitahara, Kiyoshi; Maeda, Yoshifumi; Nakamura, Yasuyuki; Kortenkamp, Ulrich; Takato, Setsuo

2015-01-01

Dynamic Geometry Software (DGS) is a powerful tool which enables students to move geometric objects interactively. Through experimental simulations with DGS, mathematical facts and background mechanisms are accessible to students. However, especially when those facts and mechanisms are complicated, it is not so easy for some students to record and…

Design and Analysis of Turbomachinery for Space Applications

NASA Technical Reports Server (NTRS)

Dorney, D.; Garcia, Roberto (Technical Monitor)

2002-01-01

This presentation provides an overview of CORSAIR, a three dimensional computational fluid dynamics software code for the analysis of turbomachinery components available from NASA, and discusses its potential use in the design of these parts. Topics covered include: time-dependent equations of motion, grid topology, turbulence models, boundary conditions, parallel simulations and miscellaneous capabilities.

Use of Data Visualisation in the Teaching of Statistics: A New Zealand Perspective

ERIC Educational Resources Information Center

Forbes, Sharleen; Chapman, Jeanette; Harraway, John; Stirling, Doug; Wild, Chris

2014-01-01

For many years, students have been taught to visualise data by drawing graphs. Recently, there has been a growing trend to teach statistics, particularly statistical concepts, using interactive and dynamic visualisation tools. Free down-loadable teaching and simulation software designed specifically for schools, and more general data visualisation…

Design and performance characterization strategy using modeling for biofiltration control of odorous hydrogen sulfide.

PubMed

Martin, Ronald W; Mihelcic, James R; Crittenden, John C

2004-07-01

Biofilter, dynamic modeling software characterizing contaminant removal via biofiltration, was used in the preliminary design of a biofilter to treat odorous hydrogen sulfide (H2S). Steady-state model simulations were run to generate performance plots for various influent concentrations, loadings, residence times, media sizes, and temperatures. Although elimination capacity and removal efficiency frequently are used to characterize biofilter performance, effluent concentration can be used to characterize performance when treating to a target effluent concentration. Model simulations illustrate that, at a given temperature, a biofilter cannot reduce H2S emissions below a minimum value, no matter how large the biofilter or how long the residence time. However, a higher biofilter temperature results in lower effluent H2S concentrations. Because dynamic model simulations show that shock loading can significantly increase the effluent concentration above values predicted by the steady-state model simulations, it is recommended that, to consistently meet treatment objectives, dynamic feed conditions should be considered. This study illustrates that modeling can serve as a valuable tool in the design and performance optimization of biofilters.

On Parallelizing Single Dynamic Simulation Using HPC Techniques and APIs of Commercial Software

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

Diao, Ruisheng; Jin, Shuangshuang; Howell, Frederic

Time-domain simulations are heavily used in today’s planning and operation practices to assess power system transient stability and post-transient voltage/frequency profiles following severe contingencies to comply with industry standards. Because of the increased modeling complexity, it is several times slower than real time for state-of-the-art commercial packages to complete a dynamic simulation for a large-scale model. With the growing stochastic behavior introduced by emerging technologies, power industry has seen a growing need for performing security assessment in real time. This paper presents a parallel implementation framework to speed up a single dynamic simulation by leveraging the existing stability model librarymore » in commercial tools through their application programming interfaces (APIs). Several high performance computing (HPC) techniques are explored such as parallelizing the calculation of generator current injection, identifying fast linear solvers for network solution, and parallelizing data outputs when interacting with APIs in the commercial package, TSAT. The proposed method has been tested on a WECC planning base case with detailed synchronous generator models and exhibits outstanding scalable performance with sufficient accuracy.« less

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.

Research on Chinese characters display of airborne MFD based on GL studio

NASA Astrophysics Data System (ADS)

Wang, Zhile; Dong, Junyu; Hu, Wenting; Cui, Yipeng

2018-04-01

GL Studio cannot display Chinese characters during developing the airborne MFD, this paper propose a method of establishing a Chinese character font with GB2312 encoding, establish the font table and the display unit of Chinese characters based on GL Studio. Abstract the storage and display data model of Chinese characters, parse the GB encoding of the corresponding Chinese characters that MFD received, find the coordinates of the Chinese characters in the font table, establish the dynamic control model and the dynamic display model of Chinese characters based on the display unit of Chinese characters. In GL Studio and VC ++.NET environment, this model has been successfully applied to develop the airborne MFD in a variety of mission simulators. This method has successfully solved the problem that GL Studio software cannot develop MFD software of Chinese domestic aircraft and can also be used for other professional airborne MFD development tools such as IDATA. It has been proved by experiments that this is a fast effective scalable and reconfigurable method of developing both actual equipment and simulators.

Pre Service Teachers' Usage of Dynamic Mathematics Software

ERIC Educational Resources Information Center

Bulut, Mehmet; Bulut, Neslihan

2011-01-01

Aim of this study is about mathematics education and dynamic mathematics software. Dynamic mathematics software provides new opportunities for using both computer algebra system and dynamic geometry software. GeoGebra selected as dynamic mathematics software in this research. In this study, it is investigated that what is the usage of pre service…

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).

Integrated optomechanical analysis and testing software development at MIT Lincoln Laboratory

NASA Astrophysics Data System (ADS)

Stoeckel, Gerhard P.; Doyle, Keith B.

2013-09-01

Advanced analytical software capabilities are being developed to advance the design of prototypical hardware in the Engineering Division at MIT Lincoln Laboratory. The current effort is focused on the integration of analysis tools tailored to the work flow, organizational structure, and current technology demands. These tools are being designed to provide superior insight into the interdisciplinary behavior of optical systems and enable rapid assessment and execution of design trades to optimize the design of optomechanical systems. The custom software architecture is designed to exploit and enhance the functionality of existing industry standard commercial software, provide a framework for centralizing internally developed tools, and deliver greater efficiency, productivity, and accuracy through standardization, automation, and integration. Specific efforts have included the development of a feature-rich software package for Structural-Thermal-Optical Performance (STOP) modeling, advanced Line Of Sight (LOS) jitter simulations, and improved integration of dynamic testing and structural modeling.

[Quality assurance of the renal applications software].

PubMed

del Real Núñez, R; Contreras Puertas, P I; Moreno Ortega, E; Mena Bares, L M; Maza Muret, F R; Latre Romero, J M

2007-01-01

The need for quality assurance of all technical aspects of nuclear medicine studies is widely recognised. However, little attention has been paid to the quality assurance of the applications software. Our work reported here aims at verifying the analysis software for processing of renal nuclear medicine studies (renograms). The software tools were used to build a synthetic dynamic model of renal system. The model consists of two phases: perfusion and function. The organs of interest (kidneys, bladder and aortic artery) were simple geometric forms. The uptake of the renal structures was described by mathematic functions. Curves corresponding to normal or pathological conditions were simulated for kidneys, bladder and aortic artery by appropriate selection of parameters. There was no difference between the parameters of the mathematic curves and the quantitative data produced by the renal analysis program. Our test procedure is simple to apply, reliable, reproducible and rapid to verify the renal applications software.

Steamer II: Steamer prototype component inventory and user interface commands. Technical report, 1988-1989

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

Dickieson, J.L.; Thode, W.F.; Newbury, K.

1988-12-01

Over the last several years, Navy Personnel Research and Development has produced a prototype simulation of a 1200-psi steam plant. This simulation, called Steamer, is installed on an expensive Symbolics minicomputer at the Surface Warfare Officers School, Pacific Coronado, California. The fundamental research goal of the Steamer prototype system was to evaluate the potential of, what was then, new artificial intelligence (AI) hardware and software technology for supporting the construction of computer-based training systems using graphic representations of complex, dynamic systems. The area of propulsion engineering was chosen for a number of reasons. This document describes the Steamer prototype systemmore » components and user interface commands and establishes a starting point for designing, developing, and implementing Steamer II. Careful examination of the actual program code produced an inventory that describes the hardware, system software, application software, and documentation for the Steamer prototype system. Exercising all menu options systematically produced an inventory of all Steamer prototype user interface commands.« less

Fe/starch nanoparticle - Pseudomonas aeruginosa: Bio-physiochemical and MD studies.

PubMed

Mofradnia, Soheil Rezazadeh; Tavakoli, Zahra; Yazdian, Fatemeh; Rashedi, Hamid; Rasekh, Behnam

2018-05-03

In this research, we attempt to study biosurfactant production by Pseudomonas aeruginosa using Fe/starch nanoparticles. Fe/starch showed no bacterial toxicity at 1 mg/ml and increased the growth rate and biosurfactant production up to 23.21 and 20.73%, respectively. Surface tension, dry weight cell, and emulsification indexes (E24) were measured. Biosurfactant production was considered via computational techniques and molecular dynamic (MD) simulation through flexible and periodic conditions (by material studio software) as well. The results of software predictions demonstrate by radial distribution function (RDF), density, energy and temperature graphs. According to the present experimental results, increased 30% growth of the bacterium has been observed and the subsequent production of biosurfactant. The difference between the experimental results and simulation data were achieved up to 0.17 g/cm 3 , which confirms the prediction of data by the software due to a difference of <14.5% (ideal error value is 20%). Copyright © 2017. Published by Elsevier B.V.

DEPEND - A design environment for prediction and evaluation of system dependability

NASA Technical Reports Server (NTRS)

Goswami, Kumar K.; Iyer, Ravishankar K.

1990-01-01

The development of DEPEND, an integrated simulation environment for the design and dependability analysis of fault-tolerant systems, is described. DEPEND models both hardware and software components at a functional level, and allows automatic failure injection to assess system performance and reliability. It relieves the user of the work needed to inject failures, maintain statistics, and output reports. The automatic failure injection scheme is geared toward evaluating a system under high stress (workload) conditions. The failures that are injected can affect both hardware and software components. To illustrate the capability of the simulator, a distributed system which employs a prediction-based, dynamic load-balancing heuristic is evaluated. Experiments were conducted to determine the impact of failures on system performance and to identify the failures to which the system is especially susceptible.

An Object Oriented Extensible Architecture for Affordable Aerospace Propulsion Systems

NASA Technical Reports Server (NTRS)

Follen, Gregory J.

2003-01-01

Driven by a need to explore and develop propulsion systems that exceeded current computing capabilities, NASA Glenn embarked on a novel strategy leading to the development of an architecture that enables propulsion simulations never thought possible before. Full engine 3 Dimensional Computational Fluid Dynamic propulsion system simulations were deemed impossible due to the impracticality of the hardware and software computing systems required. However, with a software paradigm shift and an embracing of parallel and distributed processing, an architecture was designed to meet the needs of future propulsion system modeling. The author suggests that the architecture designed at the NASA Glenn Research Center for propulsion system modeling has potential for impacting the direction of development of affordable weapons systems currently under consideration by the Applied Vehicle Technology Panel (AVT).

Optimizing legacy molecular dynamics software with directive-based offload

DOE PAGES

Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; ...

2015-05-14

The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less

Dynamic Performance Comparison for MPPT-PV Systems using Hybrid Pspice/Matlab Simulation

NASA Astrophysics Data System (ADS)

Aouchiche, N.; Becherif, M.; HadjArab, A.; Aitcheikh, M. S.; Ramadan, H. S.; Cheknane, A.

2016-10-01

The power generated by solar photovoltaic (PV) module depends on the surrounding irradiance and temperature. This paper presents a hybrid Matlab™/Pspice™ simulation model of PV system, combined with Cadence software SLPS. The hybridization is performed in order to gain the advantages of both simulation tools such as accuracy and efficiency in both Pspice electronic circuit and Matlab™ mathematical modelling respectively. For this purpose, the PV panel and the boost converter are developed using Pspice™ and hybridized with the mathematical Matlab™ model of maximum power point method controller (MPPT) through SLPS. The main objective is verify the significance of using the proposed hybrid simulation techniques in comparing the different MPPT algorithms such as the perturbation and observation (P&O), incremental of conductance (Inc-Cond) and counter reaction voltage using pilot cell (Pilot-Cell). Various simulations are performed under different atmospheric conditions in order to evaluate the dynamic behaviour for the system under study in terms of stability, efficiency and rapidity.

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

PubMed Central

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

2011-01-01

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

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

PubMed

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

2017-09-30

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

Shear test on viscoelastic granular material using Contact Dynamics simulations

NASA Astrophysics Data System (ADS)

Quezada, Juan Carlos; Sagnol, Loba; Chazallon, Cyrille

2017-06-01

By means of 3D contact dynamic simulations, the behavior of a viscoelastic granular material under shear loading is investigated. A viscoelastic fluid phase surrounding the solid particles is simulated by a contact model acting between them. This contact law was implemented in the LMGC90 software, based on the Burgers model. This model is able to simulate also the effect of creep relaxation. To validate the proposed contact model, several direct shear tests were performed, experimentally and numerically using the Leutner device. The numerical samples were created using spheres with two particle size distribution, each one identified for two layers from a road structure. Our results show a reasonable agreement between experimental and numerical data regarding the strain-stress evolution curves and the stress levels measured at failure. The proposed model can be used to simulate the mechanical behavior of multi-layer road structure and to study the influence of traffic on road deformation, cracking and particles pull-out induced by traffic loading.

Voxel based parallel post processor for void nucleation and growth analysis of atomistic simulations of material fracture.

PubMed

Hemani, H; Warrier, M; Sakthivel, N; Chaturvedi, S

2014-05-01

Molecular dynamics (MD) simulations are used in the study of void nucleation and growth in crystals that are subjected to tensile deformation. These simulations are run for typically several hundred thousand time steps depending on the problem. We output the atom positions at a required frequency for post processing to determine the void nucleation, growth and coalescence due to tensile deformation. The simulation volume is broken up into voxels of size equal to the unit cell size of crystal. In this paper, we present the algorithm to identify the empty unit cells (voids), their connections (void size) and dynamic changes (growth and coalescence of voids) for MD simulations of large atomic systems (multi-million atoms). We discuss the parallel algorithms that were implemented and discuss their relative applicability in terms of their speedup and scalability. We also present the results on scalability of our algorithm when it is incorporated into MD software LAMMPS. Copyright © 2014 Elsevier Inc. All rights reserved.

Virtual reality in radiology: virtual intervention

NASA Astrophysics Data System (ADS)

Harreld, Michael R.; Valentino, Daniel J.; Duckwiler, Gary R.; Lufkin, Robert B.; Karplus, Walter J.

1995-04-01

Intracranial aneurysms are the primary cause of non-traumatic subarachnoid hemorrhage. Morbidity and mortality remain high even with current endovascular intervention techniques. It is presently impossible to identify which aneurysms will grow and rupture, however hemodynamics are thought to play an important role in aneurysm development. With this in mind, we have simulated blood flow in laboratory animals using three dimensional computational fluid dynamics software. The data output from these simulations is three dimensional, complex and transient. Visualization of 3D flow structures with standard 2D display is cumbersome, and may be better performed using a virtual reality system. We are developing a VR-based system for visualization of the computed blood flow and stress fields. This paper presents the progress to date and future plans for our clinical VR-based intervention simulator. The ultimate goal is to develop a software system that will be able to accurately model an aneurysm detected on clinical angiography, visualize this model in virtual reality, predict its future behavior, and give insight into the type of treatment necessary. An associated database will give historical and outcome information on prior aneurysms (including dynamic, structural, and categorical data) that will be matched to any current case, and assist in treatment planning (e.g., natural history vs. treatment risk, surgical vs. endovascular treatment risks, cure prediction, complication rates).

Generative technique for dynamic infrared image sequences

NASA Astrophysics Data System (ADS)

Zhang, Qian; Cao, Zhiguo; Zhang, Tianxu

2001-09-01

The generative technique of the dynamic infrared image was discussed in this paper. Because infrared sensor differs from CCD camera in imaging mechanism, it generates the infrared image by incepting the infrared radiation of scene (including target and background). The infrared imaging sensor is affected deeply by the atmospheric radiation, the environmental radiation and the attenuation of atmospheric radiation transfers. Therefore at first in this paper the imaging influence of all kinds of the radiations was analyzed and the calculation formula of radiation was provided, in addition, the passive scene and the active scene were analyzed separately. Then the methods of calculation in the passive scene were provided, and the functions of the scene model, the atmospheric transmission model and the material physical attribute databases were explained. Secondly based on the infrared imaging model, the design idea, the achievable way and the software frame for the simulation software of the infrared image sequence were introduced in SGI workstation. Under the guidance of the idea above, in the third segment of the paper an example of simulative infrared image sequences was presented, which used the sea and sky as background and used the warship as target and used the aircraft as eye point. At last the simulation synthetically was evaluated and the betterment scheme was presented.

Computational Modeling Approaches to Multiscale Design of Icephobic Surfaces

NASA Technical Reports Server (NTRS)

Tallman, Aaron; Wang, Yan; Vargas, Mario

2017-01-01

To aid in the design of surfaces that prevent icing, a model and computational simulation of impact ice formation at the single droplet scale was implemented. The nucleation of a single supercooled droplet impacting on a substrate, in rime ice conditions, was simulated. Open source computational fluid dynamics (CFD) software was used for the simulation. To aid in the design of surfaces that prevent icing, a model of impact ice formation at the single droplet scale was proposed•No existing model simulates simultaneous impact and freezing of a single super-cooled water droplet•For the 10-week project, a low-fidelity feasibility study was the goal.

User's Guide for the Commercial Modular Aero-Propulsion System Simulation (C-MAPSS): Version 2

NASA Technical Reports Server (NTRS)

Liu, Yuan; Frederick, Dean K.; DeCastro, Jonathan A.; Litt, Jonathan S.; Chan, William W.

2012-01-01

This report is a Users Guide for version 2 of the NASA-developed Commercial Modular Aero-Propulsion System Simulation (C-MAPSS) software, which is a transient simulation of a large commercial turbofan engine (up to 90,000-lb thrust) with a realistic engine control system. The software supports easy access to health, control, and engine parameters through a graphical user interface (GUI). C-MAPSS v.2 has some enhancements over the original, including three actuators rather than one, the addition of actuator and sensor dynamics, and an improved controller, while retaining or improving on the convenience and user-friendliness of the original. C-MAPSS v.2 provides the user with a graphical turbofan engine simulation environment in which advanced algorithms can be implemented and tested. C-MAPSS can run user-specified transient simulations, and it can generate state-space linear models of the nonlinear engine model at an operating point. The code has a number of GUI screens that allow point-and-click operation, and have editable fields for user-specified input. The software includes an atmospheric model which allows simulation of engine operation at altitudes from sea level to 40,000 ft, Mach numbers from 0 to 0.90, and ambient temperatures from -60 to 103 F. The package also includes a power-management system that allows the engine to be operated over a wide range of thrust levels throughout the full range of flight conditions.

Computational Infrastructure for Geodynamics (CIG)

NASA Astrophysics Data System (ADS)

Gurnis, M.; Kellogg, L. H.; Bloxham, J.; Hager, B. H.; Spiegelman, M.; Willett, S.; Wysession, M. E.; Aivazis, M.

2004-12-01

Solid earth geophysicists have a long tradition of writing scientific software to address a wide range of problems. In particular, computer simulations came into wide use in geophysics during the decade after the plate tectonic revolution. Solution schemes and numerical algorithms that developed in other areas of science, most notably engineering, fluid mechanics, and physics, were adapted with considerable success to geophysics. This software has largely been the product of individual efforts and although this approach has proven successful, its strength for solving problems of interest is now starting to show its limitations as we try to share codes and algorithms or when we want to recombine codes in novel ways to produce new science. With funding from the NSF, the US community has embarked on a Computational Infrastructure for Geodynamics (CIG) that will develop, support, and disseminate community-accessible software for the greater geodynamics community from model developers to end-users. The software is being developed for problems involving mantle and core dynamics, crustal and earthquake dynamics, magma migration, seismology, and other related topics. With a high level of community participation, CIG is leveraging state-of-the-art scientific computing into a suite of open-source tools and codes. The infrastructure that we are now starting to develop will consist of: (a) a coordinated effort to develop reusable, well-documented and open-source geodynamics software; (b) the basic building blocks - an infrastructure layer - of software by which state-of-the-art modeling codes can be quickly assembled; (c) extension of existing software frameworks to interlink multiple codes and data through a superstructure layer; (d) strategic partnerships with the larger world of computational science and geoinformatics; and (e) specialized training and workshops for both the geodynamics and broader Earth science communities. The CIG initiative has already started to leverage and develop long-term strategic partnerships with open source development efforts within the larger thrusts of scientific computing and geoinformatics. These strategic partnerships are essential as the frontier has moved into multi-scale and multi-physics problems in which many investigators now want to use simulation software for data interpretation, data assimilation, and hypothesis testing.

Development and Integration of Control System Models

NASA Technical Reports Server (NTRS)

Kim, Young K.

1998-01-01

The computer simulation tool, TREETOPS, has been upgraded and used at NASA/MSFC to model various complicated mechanical systems and to perform their dynamics and control analysis with pointing control systems. A TREETOPS model of Advanced X-ray Astrophysics Facility - Imaging (AXAF-1) dynamics and control system was developed to evaluate the AXAF-I pointing performance for Normal Pointing Mode. An optical model of Shooting Star Experiment (SSE) was also developed and its optical performance analysis was done using the MACOS software.

Influence of model order reduction methods on dynamical-optical simulations

NASA Astrophysics Data System (ADS)

Störkle, Johannes; Eberhard, Peter

2017-04-01

In this work, the influence of model order reduction (MOR) methods on optical aberrations is analyzed within a dynamical-optical simulation of a high precision optomechanical system. Therefore, an integrated modeling process and new methods have to be introduced for the computation and investigation of the overall dynamical-optical behavior. For instance, this optical system can be a telescope optic or a lithographic objective. In order to derive a simplified mechanical model for transient time simulations with low computational cost, the method of elastic multibody systems in combination with MOR methods can be used. For this, software tools and interfaces are defined and created. Furthermore, mechanical and optical simulation models are derived and implemented. With these, on the one hand, the mechanical sensitivity can be investigated for arbitrary external excitations and on the other hand, the related optical behavior can be predicted. In order to clarify these methods, academic examples are chosen and the influences of the MOR methods and simulation strategies are analyzed. Finally, the systems are investigated with respect to the mechanical-optical frequency responses, and in conclusion, some recommendations for the application of reduction methods are given.

Tetramethylpyrazine-Loaded Hydrogels: Preparation, Penetration Through a Subcutaneous-Mucous-Membrane Model, and a Molecular Dynamics Simulation.

PubMed

Xia, Hongmei; Xu, Yinxiang; Cheng, Zhiqing; Cheng, Yongfeng

2017-07-01

Tetramethylpyrazine (TMP) was extracted from Ligusticum chuanxiong hort. The compound is known to have a variety of medicinal functions; in particular, it is used for the treatment of cerebral ischemic diseases. TMP-loaded hydrogels offer an excellent preparation with the capacity to bypass the blood-brain barrier, allowing treatment of the brain through intranasal administration. We prepared TMP-loaded hydrogels using carbomer 940 and evaluated the release of TMP from the hydrogel. We determined the release rate using Franz-type diffusion cell experiments with a subcutaneous-mucous-membrane model and also by a molecular dynamics (MD) simulation. In general, the former method was more complicated than the latter was. The dynamic behavior of TMP release from the hydrogel was revealed by analysis of the mean square displacement of the trajectory in the MD simulation. The coefficient of TMP diffusion from the hydrogel was calculated at different temperatures (277, 298, and 310 K) by using MD software. The results showed that the coefficient of diffusion increased with an increase in temperature. This trend was observed both experimentally and in the MD simulation. Therefore, the MD simulation was a complementary method to verify the experimental data.

Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions.

PubMed

Krajniak, Jakub; Zhang, Zidan; Pandiyan, Sudharsan; Nies, Eric; Samaey, Giovanni

2018-06-11

We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non-bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse-grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain-specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

A Nonlinear Dynamic Model and Free Vibration Analysis of Deployable Mesh Reflectors

NASA Technical Reports Server (NTRS)

Shi, H.; Yang, B.; Thomson, M.; Fang, H.

2011-01-01

This paper presents a dynamic model of deployable mesh reflectors, in which geometric and material nonlinearities of such a space structure are fully described. Then, by linearization around an equilibrium configuration of the reflector structure, a linearized model is obtained. With this linearized model, the natural frequencies and mode shapes of a reflector can be computed. The nonlinear dynamic model of deployable mesh reflectors is verified by using commercial finite element software in numerical simulation. As shall be seen, the proposed nonlinear model is useful for shape (surface) control of deployable mesh reflectors under thermal loads.

Exhibit D modular design attitude control system study

NASA Technical Reports Server (NTRS)

Chichester, F.

1984-01-01

A dynamically equivalent four body approximation of the NASTRAN finite element model supplied for hybrid deployable truss to support the digital computer simulation of the ten body model of the flexible space platform that incorporates the four body truss model were investigated. Coefficients for sensitivity of state variables of the linearized model of the three axes rotational dynamics of the prototype flexible spacecraft were generated with respect to the model's parameters. Software changes required to accommodate addition of another rigid body to the five body model of the rotational dynamics of the prototype flexible spacecraft were evaluated.

Analysis of Bioprocesses. Dynamic Modeling is a Must.

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

Ramkrishna, Doraiswami; Song, Hyun-Seob

2016-01-01

The goal of this paper is to report on the performance of a promising dynamic framework based on the cybernetic concepts which have evolved over three decades. We present case studies of successful dynamic simulations of wild-type strains as well as specific KO mutants on bacteria and yeast. An extensive metabolic engineering effort, including genome scale networks, is called for to secure the methodology and realize its full potential. Towards this end, the software AUMIC is under active further development to enable speedy applications. Its wide use will be enabled by a publication that is shortly due.

Developing a Telescope Simulator Towards a Global Autonomous Robotic Telescope Network

NASA Astrophysics Data System (ADS)

Giakoumidis, N.; Ioannou, Z.; Dong, H.; Mavridis, N.

2013-05-01

A robotic telescope network is a system that integrates a number of telescopes to observe a variety of astronomical targets without being operated by a human. This system autonomously selects and observes targets in accordance to an optimized target. It dynamically allocates telescope resources depending on the observation requests, specifications of the telescopes, target visibility, meteorological conditions, daylight, location restrictions and availability and many other factors. In this paper, we introduce a telescope simulator, which can control a telescope to a desired position in order to observe a specific object. The system includes a Client Module, a Server Module, and a Dynamic Scheduler module. We make use and integrate a number of open source software to simulate the movement of a robotic telescope, the telescope characteristics, the observational data and weather conditions in order to test and optimize our system.

Plane-Wave DFT Methods for Chemistry

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

Bylaska, Eric J.

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

Numerical simulation of deformation and failure processes of a complex technical object under impact loading

NASA Astrophysics Data System (ADS)

Kraus, E. I.; Shabalin, I. I.; Shabalin, T. I.

2018-04-01

The main points of development of numerical tools for simulation of deformation and failure of complex technical objects under nonstationary conditions of extreme loading are presented. The possibility of extending the dynamic method for construction of difference grids to the 3D case is shown. A 3D realization of discrete-continuum approach to the deformation and failure of complex technical objects is carried out. The efficiency of the existing software package for 3D modelling is shown.

THYME: Toolkit for Hybrid Modeling of Electric Power Systems

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

Nutaro Kalyan Perumalla, James Joseph

2011-01-01

THYME is an object oriented library for building models of wide area control and communications in electric power systems. This software is designed as a module to be used with existing open source simulators for discrete event systems in general and communication systems in particular. THYME consists of a typical model for simulating electro-mechanical transients (e.g., as are used in dynamic stability studies), data handling objects to work with CDF and PTI formatted power flow data, and sample models of discrete sensors and controllers.

MITHRA 1.0: A full-wave simulation tool for free electron lasers

NASA Astrophysics Data System (ADS)

Fallahi, Arya; Yahaghi, Alireza; Kärtner, Franz X.

2018-07-01

Free Electron Lasers (FELs) are a solution for providing intense, coherent and bright radiation in the hard X-ray regime. Due to the low wall-plug efficiency of FEL facilities, it is crucial and additionally very useful to develop complete and accurate simulation tools for better optimizing a FEL interaction. The highly sophisticated dynamics involved in a FEL process was the main obstacle hindering the development of general simulation tools for this problem. We present a numerical algorithm based on finite difference time domain/Particle in cell (FDTD/PIC) in a Lorentz boosted coordinate system which is able to fulfill a full-wave simulation of a FEL process. The developed software offers a suitable tool for the analysis of FEL interactions without considering any of the usual approximations. A coordinate transformation to bunch rest frame makes the very different length scales of bunch size, optical wavelengths and the undulator period transform to values with the same order. Consequently, FDTD/PIC simulations in conjunction with efficient parallelization techniques make the full-wave simulation feasible using the available computational resources. Several examples of free electron lasers are analyzed using the developed software, the results are benchmarked based on standard FEL codes and discussed in detail.

Software Aids Visualization of Computed Unsteady Flow

NASA Technical Reports Server (NTRS)

Kao, David; Kenwright, David

2003-01-01

Unsteady Flow Analysis Toolkit (UFAT) is a computer program that synthesizes motions of time-dependent flows represented by very large sets of data generated in computational fluid dynamics simulations. Prior to the development of UFAT, it was necessary to rely on static, single-snapshot depictions of time-dependent flows generated by flow-visualization software designed for steady flows. Whereas it typically takes weeks to analyze the results of a largescale unsteady-flow simulation by use of steady-flow visualization software, the analysis time is reduced to hours when UFAT is used. UFAT can be used to generate graphical objects of flow visualization results using multi-block curvilinear grids in the format of a previously developed NASA data-visualization program, PLOT3D. These graphical objects can be rendered using FAST, another popular flow visualization software developed at NASA. Flow-visualization techniques that can be exploited by use of UFAT include time-dependent tracking of particles, detection of vortex cores, extractions of stream ribbons and surfaces, and tetrahedral decomposition for optimal particle tracking. Unique computational features of UFAT include capabilities for automatic (batch) processing, restart, memory mapping, and parallel processing. These capabilities significantly reduce analysis time and storage requirements, relative to those of prior flow-visualization software. UFAT can be executed on a variety of supercomputers.

Virtual reality simulation of fuzzy-logic control during underwater dynamic positioning

NASA Astrophysics Data System (ADS)

Thekkedan, Midhin Das; Chin, Cheng Siong; Woo, Wai Lok

2015-03-01

In this paper, graphical-user-interface (GUI) software for simulation and fuzzy-logic control of a remotely operated vehicle (ROV) using MATLAB™ GUI Designing Environment is proposed. The proposed ROV's GUI platform allows the controller such as fuzzy-logic control systems design to be compared with other controllers such as proportional-integral-derivative (PID) and sliding-mode controller (SMC) systematically and interactively. External disturbance such as sea current can be added to improve the modelling in actual underwater environment. The simulated results showed the position responses of the fuzzy-logic control exhibit reasonable performance under the sea current disturbance.

Preliminary Computational Fluid Dynamics (CFD) Simulation of EIIB Push Barge in Shallow Water

NASA Astrophysics Data System (ADS)

Beneš, Petr; Kollárik, Róbert

2011-12-01

This study presents preliminary CFD simulation of EIIb push barge in inland conditions using CFD software Ansys Fluent. The RANSE (Reynolds Averaged Navier-Stokes Equation) methods are used for the viscosity solution of turbulent flow around the ship hull. Different RANSE methods are used for the comparison of their results in ship resistance calculations, for selecting the appropriate and removing inappropriate methods. This study further familiarizes on the creation of geometrical model which considers exact water depth to vessel draft ratio in shallow water conditions, grid generation, setting mathematical model in Fluent and evaluation of the simulations results.

Hierarchical analytical and simulation modelling of human-machine systems with interference

NASA Astrophysics Data System (ADS)

Braginsky, M. Ya; Tarakanov, D. V.; Tsapko, S. G.; Tsapko, I. V.; Baglaeva, E. A.

2017-01-01

The article considers the principles of building the analytical and simulation model of the human operator and the industrial control system hardware and software. E-networks as the extension of Petri nets are used as the mathematical apparatus. This approach allows simulating complex parallel distributed processes in human-machine systems. The structural and hierarchical approach is used as the building method for the mathematical model of the human operator. The upper level of the human operator is represented by the logical dynamic model of decision making based on E-networks. The lower level reflects psychophysiological characteristics of the human-operator.

An expert system for municipal solid waste management simulation analysis

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

Hsieh, M.C.; Chang, N.B.

1996-12-31

Optimization techniques were usually used to model the complicated metropolitan solid waste management system to search for the best dynamic combination of waste recycling, facility siting, and system operation, where sophisticated and well-defined interrelationship are required in the modeling process. But this paper applied the Concurrent Object-Oriented Simulation (COOS), a new simulation software construction method, to bridge the gap between the physical system and its computer representation. The case study of Kaohsiung solid waste management system in Taiwan is prepared for the illustration of the analytical methodology of COOS and its implementation in the creation of an expert system.

Simulating 3D Spacecraft Constellations for Low Frequency Radio Imaging

NASA Astrophysics Data System (ADS)

Hegedus, A. M.; Amiri, N.; Lazio, J.; Belov, K.; Kasper, J. C.

2016-12-01

Constellations of small spacecraft could be used to realize a low-frequency phased array for either heliophysics or astrophysics observations. However, there are issues that arise with an orbiting array that do not occur on the ground, thus rendering much of the existing radio astronomy software inadequate for data analysis and simulation. In this work we address these issues and consider the performance of two constellation concepts. The first is a 32-spacecraft constellation for astrophysical observations, and the second is a 5-element concept for pointing to the location of radio emission from coronal mass ejections (CMEs). For the first, we fill the software gap by extending the APSYNSIM software to simulate the aperture synthesis for a radio interferometer in orbit. This involves using the dynamic baselines from the relative motion of the individual spacecraft as well as the capability to add galactic noise. The ability to simulate phase errors corresponding to positional uncertainty of the antennas was also added. The upgraded software was then used to model the imaging of a 32 spacecraft constellation that would orbit the moon to image radio galaxies like Cygnus A at .3-30 MHz. Animated images showing the improvement of the dirty image as the orbits progressed were made. RMSE plots that show how well the dirty image matches the input image as a function of integration time were made. For the second concept we performed radio interferometric simulations of the Sun Radio Interferometer Space Experiment (SunRISE) using the Common Astronomy Software Applications (CASA) package. SunRISE is a five spacecraft phased array that would orbit Earth to localize the low frequency radio emission from CMEs. This involved simulating the array in CASA, creating truth images for the CMEs over the entire frequency band of SunRISE, and observing them with the simulated array to see how well it could localize the true position of the CME. The results of our analysis show that we can localize the radio emission originating from the head or flanks of the CMEs in spite of the phase errors introduced by uncertainties in orbit and clock estimation.

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.

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

PubMed Central

Ribeiro, João V.; Bernardi, Rafael C.; Rudack, Till; Stone, John E.; Phillips, James C.; Freddolino, Peter L.; Schulten, Klaus

2016-01-01

The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services. PMID:27216779

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

NASA Astrophysics Data System (ADS)

Ribeiro, João V.; Bernardi, Rafael C.; Rudack, Till; Stone, John E.; Phillips, James C.; Freddolino, Peter L.; Schulten, Klaus

2016-05-01

The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

PubMed

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.

NASA Operational Simulator for Small Satellites: Tools for Software Based Validation and Verification of Small Satellites

NASA Technical Reports Server (NTRS)

Grubb, Matt

2016-01-01

The NASA Operational Simulator for Small Satellites (NOS3) is a suite of tools to aid in areas such as software development, integration test (IT), mission operations training, verification and validation (VV), and software systems check-out. NOS3 provides a software development environment, a multi-target build system, an operator interface-ground station, dynamics and environment simulations, and software-based hardware models. NOS3 enables the development of flight software (FSW) early in the project life cycle, when access to hardware is typically not available. For small satellites there are extensive lead times on many of the commercial-off-the-shelf (COTS) components as well as limited funding for engineering test units (ETU). Considering the difficulty of providing a hardware test-bed to each developer tester, hardware models are modeled based upon characteristic data or manufacturers data sheets for each individual component. The fidelity of each hardware models is such that FSW executes unaware that physical hardware is not present. This allows binaries to be compiled for both the simulation environment, and the flight computer, without changing the FSW source code. For hardware models that provide data dependent on the environment, such as a GPS receiver or magnetometer, an open-source tool from NASA GSFC (42 Spacecraft Simulation) is used to provide the necessary data. The underlying infrastructure used to transfer messages between FSW and the hardware models can also be used to monitor, intercept, and inject messages, which has proven to be beneficial for VV of larger missions such as James Webb Space Telescope (JWST). As hardware is procured, drivers can be added to the environment to enable hardware-in-the-loop (HWIL) testing. When strict time synchronization is not vital, any number of combinations of hardware components and software-based models can be tested. The open-source operator interface used in NOS3 is COSMOS from Ball Aerospace. For testing, plug-ins are implemented in COSMOS to control the NOS3 simulations, while the command and telemetry tools available in COSMOS are used to communicate with FSW. NOS3 is actively being used for FSW development and component testing of the Simulation-to-Flight 1 (STF-1) CubeSat. As NOS3 matures, hardware models have been added for common CubeSat components such as Novatel GPS receivers, ClydeSpace electrical power systems and batteries, ISISpace antenna systems, etc. In the future, NASA IVV plans to distribute NOS3 to other CubeSat developers and release the suite to the open-source community.

A Case Study of Dynamic Response Analysis and Safety Assessment for a Suspended Monorail System.

PubMed

Bao, Yulong; Li, Yongle; Ding, Jiajie

2016-11-10

A suspended monorail transit system is a category of urban rail transit, which is effective in alleviating traffic pressure and injury prevention. Meanwhile, with the advantages of low cost and short construction time, suspended monorail transit systems show vast potential for future development. However, the suspended monorail has not been systematically studied in China, and there is a lack of relevant knowledge and analytical methods. To ensure the health and reliability of a suspended monorail transit system, the driving safety of vehicles and structure dynamic behaviors when vehicles are running on the bridge should be analyzed and evaluated. Based on the method of vehicle-bridge coupling vibration theory, the finite element method (FEM) software ANSYS and multi-body dynamics software SIMPACK are adopted respectively to establish the finite element model for bridge and the multi-body vehicle. A co-simulation method is employed to investigate the vehicle-bridge coupling vibration for the transit system. The traffic operation factors, including train formation, track irregularity and tire stiffness, are incorporated into the models separately to analyze the bridge and vehicle responses. The results show that the coupling of dynamic effects of the suspended monorail system between vehicle and bridge are significant in the case studied, and it is strongly suggested to take necessary measures for vibration suppression. The simulation of track irregularity is a critical factor for its vibration safety, and the track irregularity of A-level road roughness negatively influences the system vibration safety.

A Case Study of Dynamic Response Analysis and Safety Assessment for a Suspended Monorail System

PubMed Central

Bao, Yulong; Li, Yongle; Ding, Jiajie

2016-01-01

A suspended monorail transit system is a category of urban rail transit, which is effective in alleviating traffic pressure and injury prevention. Meanwhile, with the advantages of low cost and short construction time, suspended monorail transit systems show vast potential for future development. However, the suspended monorail has not been systematically studied in China, and there is a lack of relevant knowledge and analytical methods. To ensure the health and reliability of a suspended monorail transit system, the driving safety of vehicles and structure dynamic behaviors when vehicles are running on the bridge should be analyzed and evaluated. Based on the method of vehicle-bridge coupling vibration theory, the finite element method (FEM) software ANSYS and multi-body dynamics software SIMPACK are adopted respectively to establish the finite element model for bridge and the multi-body vehicle. A co-simulation method is employed to investigate the vehicle-bridge coupling vibration for the transit system. The traffic operation factors, including train formation, track irregularity and tire stiffness, are incorporated into the models separately to analyze the bridge and vehicle responses. The results show that the coupling of dynamic effects of the suspended monorail system between vehicle and bridge are significant in the case studied, and it is strongly suggested to take necessary measures for vibration suppression. The simulation of track irregularity is a critical factor for its vibration safety, and the track irregularity of A-level road roughness negatively influences the system vibration safety. PMID:27834923

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.

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.

CFD Fuel Slosh Modeling of Fluid-Structure Interaction in Spacecraft Propellant Tanks with Diaphragms

NASA Technical Reports Server (NTRS)

Sances, Dillon J.; Gangadharan, Sathya N.; Sudermann, James E.; Marsell, Brandon

2010-01-01

Liquid sloshing within spacecraft propellant tanks causes rapid energy dissipation at resonant modes, which can result in attitude destabilization of the vehicle. Identifying resonant slosh modes currently requires experimental testing and mechanical pendulum analogs to characterize the slosh dynamics. Computational Fluid Dynamics (CFD) techniques have recently been validated as an effective tool for simulating fuel slosh within free-surface propellant tanks. Propellant tanks often incorporate an internal flexible diaphragm to separate ullage and propellant which increases modeling complexity. A coupled fluid-structure CFD model is required to capture the damping effects of a flexible diaphragm on the propellant. ANSYS multidisciplinary engineering software employs a coupled solver for analyzing two-way Fluid Structure Interaction (FSI) cases such as the diaphragm propellant tank system. Slosh models generated by ANSYS software are validated by experimental lateral slosh test results. Accurate data correlation would produce an innovative technique for modeling fuel slosh within diaphragm tanks and provide an accurate and efficient tool for identifying resonant modes and the slosh dynamic response.

Resource Economics

NASA Astrophysics Data System (ADS)

Conrad, Jon M.

2000-01-01

Resource Economics is a text for students with a background in calculus, intermediate microeconomics, and a familiarity with the spreadsheet software Excel. The book covers basic concepts, shows how to set up spreadsheets to solve dynamic allocation problems, and presents economic models for fisheries, forestry, nonrenewable resources, stock pollutants, option value, and sustainable development. Within the text, numerical examples are posed and solved using Excel's Solver. These problems help make concepts operational, develop economic intuition, and serve as a bridge to the study of real-world problems of resource management. Through these examples and additional exercises at the end of Chapters 1 to 8, students can make dynamic models operational, develop their economic intuition, and learn how to set up spreadsheets for the simulation of optimization of resource and environmental systems. Book is unique in its use of spreadsheet software (Excel) to solve dynamic allocation problems Conrad is co-author of a previous book for the Press on the subject for graduate students Approach is extremely student-friendly; gives students the tools to apply research results to actual environmental issues

Simulating Effects of High Angle of Attack on Turbofan Engine Performance

NASA Technical Reports Server (NTRS)

Liu, Yuan; Claus, Russell W.; Litt, Jonathan S.; Guo, Ten-Huei

2013-01-01

A method of investigating the effects of high angle of attack (AOA) flight on turbofan engine performance is presented. The methodology involves combining a suite of diverse simulation tools. Three-dimensional, steady-state computational fluid dynamics (CFD) software is used to model the change in performance of a commercial aircraft-type inlet and fan geometry due to various levels of AOA. Parallel compressor theory is then applied to assimilate the CFD data with a zero-dimensional, nonlinear, dynamic turbofan engine model. The combined model shows that high AOA operation degrades fan performance and, thus, negatively impacts compressor stability margins and engine thrust. In addition, the engine response to high AOA conditions is shown to be highly dependent upon the type of control system employed.

A Systems Dynamic Model for Drug Abuse and Drug-Related Crime in the Western Cape Province of South Africa

PubMed Central

Coetzee, Lezanie

2017-01-01

The complex problem of drug abuse and drug-related crimes in communities in the Western Cape province cannot be studied in isolation but through the system they are embedded in. In this paper, a theoretical model to evaluate the syndemic of substance abuse and drug-related crimes within the Western Cape province of South Africa is constructed and explored. The dynamics of drug abuse and drug-related crimes within the Western Cape are simulated using STELLA software. The simulation results are consistent with the data from SACENDU and CrimeStats SA, highlighting the usefulness of such a model in designing and planning interventions to combat substance abuse and its related problems. PMID:28555161

Sampling the isothermal-isobaric ensemble by Langevin dynamics

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

Gao, Xingyu; Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094; CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, Beijing 100088

2016-03-28

We present a new method of conducting fully flexible-cell molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way, in the sense that the stationary configurational distribution is proved to be consistent with that of the isothermal-isobaric ensemble. In order to apply the proposed method in computer simulations, a second order symmetric numerical integration scheme is developed by Trotter’s splitting of the single-step propagator. Moreover, a practical guide of choosing working parameters is suggested for user specified thermo- and baro-coupling timemore » scales. The method and software implementation are carefully validated by a numerical example.« less

Study of percolation behavior depending on molecular structure design

NASA Astrophysics Data System (ADS)

Yu, Ji Woong; Lee, Won Bo

Each differently designed anisotropic nano-crystals(ANCs) are studied using Langevin dynamic simulation and their percolation behaviors are presented. Popular molecular dynamics software LAMMPS was used to design the system and perform the simulation. We calculated the minimum number density at which percolation occurs(i.e. percolation threshold), radial distribution function, and the average number of ANCs for a cluster. Electrical conductivity is improved when the number of transfers of electrons between ANCs, so called ''inter-hopping process'', which has the considerable contribution to resistance decreases and the number of inter-hopping process is directly related with the concentration of ANCs. Therefore, with the investigation of relationship between molecular architecture and percolation behavior, optimal design of ANC can be achieved.

Numerical Simulation on the Dynamic Splitting Tensile Test of reinforced concrete

NASA Astrophysics Data System (ADS)

Zhao, Zhuan; Jia, Haokai; Jing, Lin

2018-03-01

The research for crack resistance was of RC was based on the split Hopkinson bar and numerical simulate software LS-DYNA3D. In the research, the difference of dynamic splitting failure modes between plane concrete and reinforced concrete were completed, and the change rule of tensile stress distribution with reinforcement ratio was studied; also the effect rule with the strain rate and the crack resistance was also discussed by the radial tensile stress time history curve of RC specimen under different loading speeds. The results shows that the reinforcement in the concrete can impede the crack extension, defer the failure time of concrete, increase the tension intensity of concrete; with strain rate of concrete increased, the crack resistance of RC increased.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

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

2012-01-01

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

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.

Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

PubMed

Medley, J Kyle; Choi, Kiri; König, Matthias; Smith, Lucian; Gu, Stanley; Hellerstein, Joseph; Sealfon, Stuart C; Sauro, Herbert M

2018-06-01

The considerable difficulty encountered in reproducing the results of published dynamical models limits validation, exploration and reuse of this increasingly large biomedical research resource. To address this problem, we have developed Tellurium Notebook, a software system for model authoring, simulation, and teaching that facilitates building reproducible dynamical models and reusing models by 1) providing a notebook environment which allows models, Python code, and narrative to be intermixed, 2) supporting the COMBINE archive format during model development for capturing model information in an exchangeable format and 3) enabling users to easily simulate and edit public COMBINE-compliant models from public repositories to facilitate studying model dynamics, variants and test cases. Tellurium Notebook, a Python-based Jupyter-like environment, is designed to seamlessly inter-operate with these community standards by automating conversion between COMBINE standards formulations and corresponding in-line, human-readable representations. Thus, Tellurium brings to systems biology the strategy used by other literate notebook systems such as Mathematica. These capabilities allow users to edit every aspect of the standards-compliant models and simulations, run the simulations in-line, and re-export to standard formats. We provide several use cases illustrating the advantages of our approach and how it allows development and reuse of models without requiring technical knowledge of standards. Adoption of Tellurium should accelerate model development, reproducibility and reuse.

Molecular-dynamic simulations of the thermophysical properties of hexanitrohexaazaisowurtzitane single crystal at high pressures and temperatures

NASA Astrophysics Data System (ADS)

Kozlova, S. A.; Gubin, S. A.; Maklashova, I. V.; Selezenev, A. A.

2017-11-01

Molecular dynamic simulations of isothermal compression parameters are performed for a hexanitrohexaazaisowurtzitane single crystal (C6H6O12N12) using a modified ReaxFF-log reactive force field. It is shown that the pressure-compression ratio curve for a single C6H6O12N12 crystal at constant temperature T = 300 K in pressure range P = 0.05-40 GPa is in satisfactory agreement with experimental compression isotherms obtained for a single C6H6O12N12 crystal. Hugoniot molecular-dynamic simulations of the shock-wave hydrostatic compression of a single C6H6O12N12 crystal are performed. Along with Hugoniot temperature-pressure curves, calculated shock-wave pressure-compression ratios for a single C6H6O12N12 crystal are obtained for a wide pressure range of P = 1-40 GPa. It is established that the percussive adiabat obtained for a single C6H6O12N12 crystal is in a good agreement with the experimental data. All calculations are performed using a LAMMPS molecular dynamics simulation software package that provides a ReaxFF-lg reactive force field to support the approach.

The SPORT-NMR Software: A Tool for Determining Relaxation Times in Unresolved NMR Spectra

NASA Astrophysics Data System (ADS)

Geppi, Marco; Forte, Claudia

1999-03-01

A software package which allows the correct determination of individual relaxation times for all the nonequivalent nuclei in poorly resolved NMR spectra is described. The procedure used, based on the fitting of each spectrum in the series recorded in the relaxation experiment, should improve the analysis of relaxation data in terms of quantitative dynamic information, especially in anisotropic phases. Tests on simulated data and experimental examples concerning1H and13CT1ρmeasurement in a solid copolymer and2HT1ZandT1Qmeasurement in a liquid crystal are shown and discussed.

Investigation of the Aerodynamic Performance of a DG808s UAS in Propeller Slipstream Using Computational Fluid Dynamics

NASA Astrophysics Data System (ADS)

Chandra, Yatish

Unmanned Aerial Systems (UASs) are relatively affordable and immediately available compared to commercial aircraft. Hence, their aerodynamics and design accuracies are often based on extrapolating from design standards and procedures widely used in the aerospace industry for commercial aircraft with most often, acceptable results. Engineering level software such as Advanced Aircraft Analysis (AAA) use general aviation aircraft data and later extrapolate them onto UASs for aerodynamic and flight dynamics modeling but are limited by their platform repository and relatively high Reynolds number evaluations. UASs however, are aircraft which fly at comparatively low speeds and low Reynolds number with close proximities between the components wherein such standards may not hold good. This thesis focuses on evaluating the accuracy and impact of such industry standards on the aerodynamics and flight dynamics of UASs. A DG808s UAS is chosen for the study which was previously modeled using the AAA software at The University of Kansas by the Flight Systems Team. Using the STAR-CCM+ code, performance data were compared and assessed with AAA. Aerodynamic simulations were carried out for two different configurations viz., aircraft with and without propeller slipstream effects. Data obtained for the non-powered simulations were found to be in good agreement with the AAA model. For the powered flight however, discrepancies between the AAA model and CFD data were observed with large values for the vertical tail side-force coefficient. A comparison with the system identification data from the flight tests was made to confirm and validate this vertical tail behavior with the help of rudder deflection inputs. A relationship between the propeller RPM and the aerodynamic model was established by simulating two different propeller speeds. Based on the STAR-CCM+ data and the resulting comparisons with AAA, updates necessary to the UAS aerodynamic and flight dynamics models currently used in the industry were discussed and concluded with a stress on dependency on higher fidelity methods such as Computational Fluid Dynamics.

POLARIS: Agent-based modeling framework development and implementation for integrated travel demand and network and operations simulations

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

Auld, Joshua; Hope, Michael; Ley, Hubert

This paper discusses the development of an agent-based modelling software development kit, and the implementation and validation of a model using it that integrates dynamic simulation of travel demand, network supply and network operations. A description is given of the core utilities in the kit: a parallel discrete event engine, interprocess exchange engine, and memory allocator, as well as a number of ancillary utilities: visualization library, database IO library, and scenario manager. The overall framework emphasizes the design goals of: generality, code agility, and high performance. This framework allows the modeling of several aspects of transportation system that are typicallymore » done with separate stand-alone software applications, in a high-performance and extensible manner. The issue of integrating such models as dynamic traffic assignment and disaggregate demand models has been a long standing issue for transportation modelers. The integrated approach shows a possible way to resolve this difficulty. The simulation model built from the POLARIS framework is a single, shared-memory process for handling all aspects of the integrated urban simulation. The resulting gains in computational efficiency and performance allow planning models to be extended to include previously separate aspects of the urban system, enhancing the utility of such models from the planning perspective. Initial tests with case studies involving traffic management center impacts on various network events such as accidents, congestion and weather events, show the potential of the system.« less

Mobility analysis, simulation, and scale model testing for the design of wheeled planetary rovers

NASA Technical Reports Server (NTRS)

Lindemann, Randel A.; Eisen, Howard J.

1993-01-01

The use of computer based techniques to model and simulate wheeled rovers on rough natural terrains is considered. Physical models of a prototype vehicle can be used to test the correlation of the simulations in scaled testing. The computer approaches include a quasi-static planar or two dimensional analysis and design tool based on the traction necessary for the vehicle to have imminent mobility. The computer program modeled a six by six wheel drive vehicle of original kinematic configuration, called the Rocker Bogie. The Rocker Bogie was optimized using the quasi-static software with respect to its articulation parameters prior to fabrication of a prototype. In another approach used, the dynamics of the Rocker Bogie vehicle in 3-D space was modeled on an engineering workstation using commercial software. The model included the complex and nonlinear interaction of the tire and terrain. The results of the investigation yielded numerical and graphical results of the rover traversing rough terrain on the earth, moon, and Mars. In addition, animations of the rover excursions were also generated. A prototype vehicle was then used in a series of testbed and field experiments. Correspondence was then established between the computer models and the physical model. The results indicated the utility of the quasi-static tool for configurational design, as well as the predictive ability of the 3-D simulation to model the dynamic behavior of the vehicle over short traverses.

A Low Cost Simulation System to Demonstrate Pilot Induced Oscillation Phenomenon

NASA Technical Reports Server (NTRS)

Ali, Syed Firasat

1997-01-01

A flight simulation system with graphics and software on Silicon Graphics computer workstations has been installed in the Flight Vehicle Design Laboratory at Tuskegee University. The system has F-15E flight simulation software from NASA Dryden which uses the graphics of SGI flight simulation demos. On the system, thus installed, a study of pilot induced oscillations is planned for future work. Preliminary research is conducted by obtaining two sets of straight level flights with pilot in the loop. In one set of flights no additional delay is used between the stick input and the appearance of airplane response on the computer monitor. In another set of flights, a 500 ms additional delay is used. The flight data is analyzed to find cross correlations between deflections of control surfaces and response of the airplane. The pilot dynamics features depicted from cross correlations of straight level flights are discussed in this report. The correlations presented here will serve as reference material for the corresponding correlations in a future study of pitch attitude tracking tasks involving pilot induced oscillations.

Fluid dynamics simulation for design on sludge drying equipment

NASA Astrophysics Data System (ADS)

Li, Shuiping; Liang, Wang; Kai, Zhang

2017-10-01

Sludge drying equipment is a key component in the sludge drying disposal, the structure of drying equipment directly affects the drying disposal of the sludge, so it is necessary to analyse the performance of the drying equipment with different structure. Fluent software can be very convenient to get the distribution of the flow field and temperature field inside the drying equipment which reflects the performance of the structure. In this paper, the outlet position of the sludge and the shape of the sludge inlet are designed. The geometrical model of the drying equipment is established by using pre-processing software Gambit, and the meshing of the model is carried out. The Eulerian model is used to simulate the flow of each phase and the interaction between them, and the realizable turbulence model is used to simulate the turbulence of each phase. Finally, the simulation results of the scheme are compared and the optimal structure scheme is obtained, the operational requirement is proposed. The CFD theory provides a reliable basis for the drying equipment research and reduces the time and costs of the research.

A virtual simulator designed for collision prevention in proton therapy.

PubMed

Jung, Hyunuk; Kum, Oyeon; Han, Youngyih; Park, Hee Chul; Kim, Jin Sung; Choi, Doo Ho

2015-10-01

In proton therapy, collisions between the patient and nozzle potentially occur because of the large nozzle structure and efforts to minimize the air gap. Thus, software was developed to predict such collisions between the nozzle and patient using treatment virtual simulation. Three-dimensional (3D) modeling of a gantry inner-floor, nozzle, and robotic-couch was performed using SolidWorks based on the manufacturer's machine data. To obtain patient body information, a 3D-scanner was utilized right before CT scanning. Using the acquired images, a 3D-image of the patient's body contour was reconstructed. The accuracy of the image was confirmed against the CT image of a humanoid phantom. The machine components and the virtual patient were combined on the treatment-room coordinate system, resulting in a virtual simulator. The simulator simulated the motion of its components such as rotation and translation of the gantry, nozzle, and couch in real scale. A collision, if any, was examined both in static and dynamic modes. The static mode assessed collisions only at fixed positions of the machine's components, while the dynamic mode operated any time a component was in motion. A collision was identified if any voxels of two components, e.g., the nozzle and the patient or couch, overlapped when calculating volume locations. The event and collision point were visualized, and collision volumes were reported. All components were successfully assembled, and the motions were accurately controlled. The 3D-shape of the phantom agreed with CT images within a deviation of 2 mm. Collision situations were simulated within minutes, and the results were displayed and reported. The developed software will be useful in improving patient safety and clinical efficiency of proton therapy.

PlanetPack: A radial-velocity time-series analysis tool facilitating exoplanets detection, characterization, and dynamical simulations

NASA Astrophysics Data System (ADS)

Baluev, Roman V.

2013-08-01

We present PlanetPack, a new software tool that we developed to facilitate and standardize the advanced analysis of radial velocity (RV) data for the goal of exoplanets detection, characterization, and basic dynamical N-body simulations. PlanetPack is a command-line interpreter, that can run either in an interactive mode or in a batch mode of automatic script interpretation. Its major abilities include: (i) advanced RV curve fitting with the proper maximum-likelihood treatment of unknown RV jitter; (ii) user-friendly multi-Keplerian as well as Newtonian N-body RV fits; (iii) use of more efficient maximum-likelihood periodograms that involve the full multi-planet fitting (sometimes called as “residual” or “recursive” periodograms); (iv) easily calculatable parametric 2D likelihood function level contours, reflecting the asymptotic confidence regions; (v) fitting under some useful functional constraints is user-friendly; (vi) basic tasks of short- and long-term planetary dynamical simulation using a fast Everhart-type integrator based on Gauss-Legendre spacings; (vii) fitting the data with red noise (auto-correlated errors); (viii) various analytical and numerical methods for the tasks of determining the statistical significance. It is planned that further functionality may be added to PlanetPack in the future. During the development of this software, a lot of effort was made to improve the calculational speed, especially for CPU-demanding tasks. PlanetPack was written in pure C++ (standard of 1998/2003), and is expected to be compilable and useable on a wide range of platforms.

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.

The change in critical technologies for computational physics

NASA Technical Reports Server (NTRS)

Watson, Val

1990-01-01

It is noted that the types of technology required for computational physics are changing as the field matures. Emphasis has shifted from computer technology to algorithm technology and, finally, to visual analysis technology as areas of critical research for this field. High-performance graphical workstations tied to a supercommunicator with high-speed communications along with the development of especially tailored visualization software has enabled analysis of highly complex fluid-dynamics simulations. Particular reference is made here to the development of visual analysis tools at NASA's Numerical Aerodynamics Simulation Facility. The next technology which this field requires is one that would eliminate visual clutter by extracting key features of simulations of physics and technology in order to create displays that clearly portray these key features. Research in the tuning of visual displays to human cognitive abilities is proposed. The immediate transfer of technology to all levels of computers, specifically the inclusion of visualization primitives in basic software developments for all work stations and PCs, is recommended.

Cybersim: geographic, temporal, and organizational dynamics of malware propagation

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

Santhi, Nandakishore; Yan, Guanhua; Eidenbenz, Stephan

2010-01-01

Cyber-infractions into a nation's strategic security envelope pose a constant and daunting challenge. We present the modular CyberSim tool which has been developed in response to the need to realistically simulate at a national level, software vulnerabilities and resulting mal ware propagation in online social networks. CyberSim suite (a) can generate realistic scale-free networks from a database of geocoordinated computers to closely model social networks arising from personal and business email contacts and online communities; (b) maintains for each,bost a list of installed software, along with the latest published vulnerabilities; (d) allows designated initial nodes where malware gets introduced; (e)more » simulates, using distributed discrete event-driven technology, the spread of malware exploiting a specific vulnerability, with packet delay and user online behavior models; (f) provides a graphical visualization of spread of infection, its severity, businesses affected etc to the analyst. We present sample simulations on a national level network with millions of computers.« less

Autonomous Cryogenics Loading Operations Simulation Software: Knowledgebase Autonomous Test Engineer

NASA Technical Reports Server (NTRS)

Wehner, Walter S., Jr.

2013-01-01

Working on the ACLO (Autonomous Cryogenics Loading Operations) project I have had the opportunity to add functionality to the physics simulation software known as KATE (Knowledgebase Autonomous Test Engineer), create a new application allowing WYSIWYG (what-you-see-is-what-you-get) creation of KATE schematic files and begin a preliminary design and implementation of a new subsystem that will provide vision services on the IHM (Integrated Health Management) bus. The functionality I added to KATE over the past few months includes a dynamic visual representation of the fluid height in a pipe based on number of gallons of fluid in the pipe and implementing the IHM bus connection within KATE. I also fixed a broken feature in the system called the Browser Display, implemented many bug fixes and made changes to the GUI (Graphical User Interface).

Designing and encoding models for synthetic biology.

PubMed

Endler, Lukas; Rodriguez, Nicolas; Juty, Nick; Chelliah, Vijayalakshmi; Laibe, Camille; Li, Chen; Le Novère, Nicolas

2009-08-06

A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology 'loop'.